Get a list of variant groups

Retrieve all variant groups from the CIViC DB

getAllVariantGroups(page = 1, count = 25)

Arguments

page	the page number to retrieve
count	the number of variant groups to retrieve

Value

An S3 Object of type civic_api containing the content, url, and response

Examples

getAllVariantGroups(count = 10)
#> $content
#> $content$`_meta`
#> $content$`_meta`$current_page
#> [1] 1
#> 
#> $content$`_meta`$per_page
#> [1] "10"
#> 
#> $content$`_meta`$total_pages
#> [1] 3
#> 
#> $content$`_meta`$total_count
#> [1] 24
#> 
#> $content$`_meta`$links
#> $content$`_meta`$links$`next`
#> [1] "https://civicdb.org/api/variant_groups?count=10&page=2"
#> 
#> $content$`_meta`$links$previous
#> NULL
#> 
#> 
#> 
#> $content$records
#> $content$records[[1]]
#> $content$records[[1]]$id
#> [1] 1
#> 
#> $content$records[[1]]$name
#> [1] "Imatinib Resistance"
#> 
#> $content$records[[1]]$description
#> [1] "While imatinib has shown to be incredibly successful in treating philadelphia chromosome positive CML, patients that have shown primary or secondary resistance to the drug have been observed to harbor T315I and E255K ABL kinase domain mutations. These mutations, among others, have been observed both in primary refractory disease and acquired resistance. In gastrointestinal stromal tumors (GIST), PDGFRA 842 mutations have also been shown to confer resistance to imatinib. "
#> 
#> $content$records[[1]]$variants
#> $content$records[[1]]$variants[[1]]
#> $content$records[[1]]$variants[[1]]$id
#> [1] 2
#> 
#> $content$records[[1]]$variants[[1]]$entrez_name
#> [1] "ABL1"
#> 
#> $content$records[[1]]$variants[[1]]$entrez_id
#> [1] 25
#> 
#> $content$records[[1]]$variants[[1]]$name
#> [1] "BCR-ABL T315I"
#> 
#> $content$records[[1]]$variants[[1]]$description
#> [1] "While the efficacy of imatinib has revolutionized chronic myelogenous leukemia (CML) treatment, it is still not a cure-all. Both initial resistance and acquired resistance as a result of selection have been seen in a small subset of CML patients. The ABL kinase domain mutation T315I (aka T334I) has been shown to be one such mutation that confers resistance to imatinib. Second generation TKI's (dasatinib and ponatinib) specific to BCR-ABL have shown efficacy in treating resistant cases."
#> 
#> $content$records[[1]]$variants[[1]]$gene_id
#> [1] 4
#> 
#> $content$records[[1]]$variants[[1]]$type
#> [1] "variant"
#> 
#> $content$records[[1]]$variants[[1]]$variant_types
#> $content$records[[1]]$variants[[1]]$variant_types[[1]]
#> $content$records[[1]]$variants[[1]]$variant_types[[1]]$id
#> [1] 120
#> 
#> $content$records[[1]]$variants[[1]]$variant_types[[1]]$name
#> [1] "transcript_fusion"
#> 
#> $content$records[[1]]$variants[[1]]$variant_types[[1]]$display_name
#> [1] "Transcript Fusion"
#> 
#> $content$records[[1]]$variants[[1]]$variant_types[[1]]$so_id
#> [1] "SO:0001886"
#> 
#> $content$records[[1]]$variants[[1]]$variant_types[[1]]$description
#> [1] "A feature fusion where the deletion brings together transcript regions."
#> 
#> $content$records[[1]]$variants[[1]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001886"
#> 
#> 
#> $content$records[[1]]$variants[[1]]$variant_types[[2]]
#> $content$records[[1]]$variants[[1]]$variant_types[[2]]$id
#> [1] 47
#> 
#> $content$records[[1]]$variants[[1]]$variant_types[[2]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[1]]$variants[[1]]$variant_types[[2]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[1]]$variants[[1]]$variant_types[[2]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[1]]$variants[[1]]$variant_types[[2]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[1]]$variants[[1]]$variant_types[[2]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[1]]$variants[[1]]$civic_actionability_score
#> [1] 105
#> 
#> $content$records[[1]]$variants[[1]]$coordinates
#> $content$records[[1]]$variants[[1]]$coordinates$chromosome
#> [1] "9"
#> 
#> $content$records[[1]]$variants[[1]]$coordinates$start
#> [1] 133748283
#> 
#> $content$records[[1]]$variants[[1]]$coordinates$stop
#> [1] 133748283
#> 
#> $content$records[[1]]$variants[[1]]$coordinates$reference_bases
#> [1] "C"
#> 
#> $content$records[[1]]$variants[[1]]$coordinates$variant_bases
#> [1] "T"
#> 
#> $content$records[[1]]$variants[[1]]$coordinates$representative_transcript
#> [1] "ENST00000318560.5"
#> 
#> $content$records[[1]]$variants[[1]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[1]]$variants[[1]]$coordinates$start2
#> NULL
#> 
#> $content$records[[1]]$variants[[1]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[1]]$variants[[1]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[1]]$variants[[1]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[1]]$variants[[1]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[1]]$variants[[2]]
#> $content$records[[1]]$variants[[2]]$id
#> [1] 102
#> 
#> $content$records[[1]]$variants[[2]]$entrez_name
#> [1] "PDGFRA"
#> 
#> $content$records[[1]]$variants[[2]]$entrez_id
#> [1] 5156
#> 
#> $content$records[[1]]$variants[[2]]$name
#> [1] "DI842-843VM"
#> 
#> $content$records[[1]]$variants[[2]]$description
#> [1] "PDGFRA D842 mutations are characterized broadly as imatinib resistance mutations. The DI842-843VM variant is the result of a double point mutation. This is most well characterized in gastrointestinal stromal tumors, but other cell lines containing these mutations have been shown to be resistant as well. In imatinib resistant cell lines, a number of other therapeutics have demonstrated efficacy. These include; crenolanib, sirolimus, and midostaurin (PKC412)."
#> 
#> $content$records[[1]]$variants[[2]]$gene_id
#> [1] 38
#> 
#> $content$records[[1]]$variants[[2]]$type
#> [1] "variant"
#> 
#> $content$records[[1]]$variants[[2]]$variant_types
#> $content$records[[1]]$variants[[2]]$variant_types[[1]]
#> $content$records[[1]]$variants[[2]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[1]]$variants[[2]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[1]]$variants[[2]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[1]]$variants[[2]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[1]]$variants[[2]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[1]]$variants[[2]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[1]]$variants[[2]]$civic_actionability_score
#> [1] 4
#> 
#> $content$records[[1]]$variants[[2]]$coordinates
#> $content$records[[1]]$variants[[2]]$coordinates$chromosome
#> [1] "4"
#> 
#> $content$records[[1]]$variants[[2]]$coordinates$start
#> [1] 55152093
#> 
#> $content$records[[1]]$variants[[2]]$coordinates$stop
#> [1] 55152097
#> 
#> $content$records[[1]]$variants[[2]]$coordinates$reference_bases
#> [1] "ACATC"
#> 
#> $content$records[[1]]$variants[[2]]$coordinates$variant_bases
#> [1] "TCATG"
#> 
#> $content$records[[1]]$variants[[2]]$coordinates$representative_transcript
#> [1] "ENST00000257290.5"
#> 
#> $content$records[[1]]$variants[[2]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[1]]$variants[[2]]$coordinates$start2
#> NULL
#> 
#> $content$records[[1]]$variants[[2]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[1]]$variants[[2]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[1]]$variants[[2]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[1]]$variants[[2]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[1]]$variants[[3]]
#> $content$records[[1]]$variants[[3]]$id
#> [1] 98
#> 
#> $content$records[[1]]$variants[[3]]$entrez_name
#> [1] "PDGFRA"
#> 
#> $content$records[[1]]$variants[[3]]$entrez_id
#> [1] 5156
#> 
#> $content$records[[1]]$variants[[3]]$name
#> [1] "D842I"
#> 
#> $content$records[[1]]$variants[[3]]$description
#> [1] "PDGFRA D842 mutations are characterized broadly as imatinib resistance mutations. This is most well characterized in gastrointestinal stromal tumors, but other cell lines containing these mutations have been shown to be resistant as well. In imatinib resistant cell lines, a number of other therapeutics have demonstrated efficacy. These include; crenolanib, sirolimus, and midostaurin (PKC412)."
#> 
#> $content$records[[1]]$variants[[3]]$gene_id
#> [1] 38
#> 
#> $content$records[[1]]$variants[[3]]$type
#> [1] "variant"
#> 
#> $content$records[[1]]$variants[[3]]$variant_types
#> $content$records[[1]]$variants[[3]]$variant_types[[1]]
#> $content$records[[1]]$variants[[3]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[1]]$variants[[3]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[1]]$variants[[3]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[1]]$variants[[3]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[1]]$variants[[3]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[1]]$variants[[3]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[1]]$variants[[3]]$civic_actionability_score
#> [1] 4
#> 
#> $content$records[[1]]$variants[[3]]$coordinates
#> $content$records[[1]]$variants[[3]]$coordinates$chromosome
#> [1] "4"
#> 
#> $content$records[[1]]$variants[[3]]$coordinates$start
#> [1] 55152092
#> 
#> $content$records[[1]]$variants[[3]]$coordinates$stop
#> [1] 55152093
#> 
#> $content$records[[1]]$variants[[3]]$coordinates$reference_bases
#> [1] "GA"
#> 
#> $content$records[[1]]$variants[[3]]$coordinates$variant_bases
#> [1] "AT"
#> 
#> $content$records[[1]]$variants[[3]]$coordinates$representative_transcript
#> [1] "ENST00000257290.5"
#> 
#> $content$records[[1]]$variants[[3]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[1]]$variants[[3]]$coordinates$start2
#> NULL
#> 
#> $content$records[[1]]$variants[[3]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[1]]$variants[[3]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[1]]$variants[[3]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[1]]$variants[[3]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[1]]$variants[[4]]
#> $content$records[[1]]$variants[[4]]$id
#> [1] 100
#> 
#> $content$records[[1]]$variants[[4]]$entrez_name
#> [1] "PDGFRA"
#> 
#> $content$records[[1]]$variants[[4]]$entrez_id
#> [1] 5156
#> 
#> $content$records[[1]]$variants[[4]]$name
#> [1] "D842Y"
#> 
#> $content$records[[1]]$variants[[4]]$description
#> [1] "PDGFRA D842 mutations are characterized broadly as imatinib resistance mutations. This is most well characterized in gastrointestinal stromal tumors, but other cell lines containing these mutations have been shown to be resistant as well. In imatinib resistant cell lines, a number of other therapeutics have demonstrated efficacy. These include; crenolanib, sirolimus, and midostaurin (PKC412)."
#> 
#> $content$records[[1]]$variants[[4]]$gene_id
#> [1] 38
#> 
#> $content$records[[1]]$variants[[4]]$type
#> [1] "variant"
#> 
#> $content$records[[1]]$variants[[4]]$variant_types
#> $content$records[[1]]$variants[[4]]$variant_types[[1]]
#> $content$records[[1]]$variants[[4]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[1]]$variants[[4]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[1]]$variants[[4]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[1]]$variants[[4]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[1]]$variants[[4]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[1]]$variants[[4]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[1]]$variants[[4]]$civic_actionability_score
#> [1] 4
#> 
#> $content$records[[1]]$variants[[4]]$coordinates
#> $content$records[[1]]$variants[[4]]$coordinates$chromosome
#> [1] "4"
#> 
#> $content$records[[1]]$variants[[4]]$coordinates$start
#> [1] 55152092
#> 
#> $content$records[[1]]$variants[[4]]$coordinates$stop
#> [1] 55152092
#> 
#> $content$records[[1]]$variants[[4]]$coordinates$reference_bases
#> [1] "G"
#> 
#> $content$records[[1]]$variants[[4]]$coordinates$variant_bases
#> [1] "T"
#> 
#> $content$records[[1]]$variants[[4]]$coordinates$representative_transcript
#> [1] "ENST00000257290.5"
#> 
#> $content$records[[1]]$variants[[4]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[1]]$variants[[4]]$coordinates$start2
#> NULL
#> 
#> $content$records[[1]]$variants[[4]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[1]]$variants[[4]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[1]]$variants[[4]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[1]]$variants[[4]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[1]]$variants[[5]]
#> $content$records[[1]]$variants[[5]]$id
#> [1] 241
#> 
#> $content$records[[1]]$variants[[5]]$entrez_name
#> [1] "ABL1"
#> 
#> $content$records[[1]]$variants[[5]]$entrez_id
#> [1] 25
#> 
#> $content$records[[1]]$variants[[5]]$name
#> [1] "BCR-ABL F317L"
#> 
#> $content$records[[1]]$variants[[5]]$description
#> [1] "BCR-ABL F317L, like the similar BCR-ABL T315I mutation, is becoming a common clinical marker for resistance to front-line therapies in CML. It has been shown to confer resistance to dasatinib, but responds well to ponatinib and other second generation inhibitors."
#> 
#> $content$records[[1]]$variants[[5]]$gene_id
#> [1] 4
#> 
#> $content$records[[1]]$variants[[5]]$type
#> [1] "variant"
#> 
#> $content$records[[1]]$variants[[5]]$variant_types
#> $content$records[[1]]$variants[[5]]$variant_types[[1]]
#> $content$records[[1]]$variants[[5]]$variant_types[[1]]$id
#> [1] 120
#> 
#> $content$records[[1]]$variants[[5]]$variant_types[[1]]$name
#> [1] "transcript_fusion"
#> 
#> $content$records[[1]]$variants[[5]]$variant_types[[1]]$display_name
#> [1] "Transcript Fusion"
#> 
#> $content$records[[1]]$variants[[5]]$variant_types[[1]]$so_id
#> [1] "SO:0001886"
#> 
#> $content$records[[1]]$variants[[5]]$variant_types[[1]]$description
#> [1] "A feature fusion where the deletion brings together transcript regions."
#> 
#> $content$records[[1]]$variants[[5]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001886"
#> 
#> 
#> $content$records[[1]]$variants[[5]]$variant_types[[2]]
#> $content$records[[1]]$variants[[5]]$variant_types[[2]]$id
#> [1] 47
#> 
#> $content$records[[1]]$variants[[5]]$variant_types[[2]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[1]]$variants[[5]]$variant_types[[2]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[1]]$variants[[5]]$variant_types[[2]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[1]]$variants[[5]]$variant_types[[2]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[1]]$variants[[5]]$variant_types[[2]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[1]]$variants[[5]]$civic_actionability_score
#> [1] 99.5
#> 
#> $content$records[[1]]$variants[[5]]$coordinates
#> $content$records[[1]]$variants[[5]]$coordinates$chromosome
#> [1] "9"
#> 
#> $content$records[[1]]$variants[[5]]$coordinates$start
#> [1] 133748288
#> 
#> $content$records[[1]]$variants[[5]]$coordinates$stop
#> [1] 133748288
#> 
#> $content$records[[1]]$variants[[5]]$coordinates$reference_bases
#> [1] "T"
#> 
#> $content$records[[1]]$variants[[5]]$coordinates$variant_bases
#> [1] "C"
#> 
#> $content$records[[1]]$variants[[5]]$coordinates$representative_transcript
#> [1] "ENST00000318560.5"
#> 
#> $content$records[[1]]$variants[[5]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[1]]$variants[[5]]$coordinates$start2
#> NULL
#> 
#> $content$records[[1]]$variants[[5]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[1]]$variants[[5]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[1]]$variants[[5]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[1]]$variants[[5]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[1]]$variants[[6]]
#> $content$records[[1]]$variants[[6]]$id
#> [1] 3
#> 
#> $content$records[[1]]$variants[[6]]$entrez_name
#> [1] "ABL1"
#> 
#> $content$records[[1]]$variants[[6]]$entrez_id
#> [1] 25
#> 
#> $content$records[[1]]$variants[[6]]$name
#> [1] "BCR-ABL E255K"
#> 
#> $content$records[[1]]$variants[[6]]$description
#> [1] "While the efficacy of imatinib has revolutionized chronic myelogenous leukemia (CML) treatment, it is still not a cure-all. Both initial resistance and acquired resistance as a result of selection have been seen in a small subset of CML patients. The ABL kinase domain mutation E255K has been shown to be one such mutation that confers resistance to imatinib. Second generation TKI's (dasatinib and nilotinib) specific to BCR-ABL have shown efficacy in treating resistant cases."
#> 
#> $content$records[[1]]$variants[[6]]$gene_id
#> [1] 4
#> 
#> $content$records[[1]]$variants[[6]]$type
#> [1] "variant"
#> 
#> $content$records[[1]]$variants[[6]]$variant_types
#> $content$records[[1]]$variants[[6]]$variant_types[[1]]
#> $content$records[[1]]$variants[[6]]$variant_types[[1]]$id
#> [1] 120
#> 
#> $content$records[[1]]$variants[[6]]$variant_types[[1]]$name
#> [1] "transcript_fusion"
#> 
#> $content$records[[1]]$variants[[6]]$variant_types[[1]]$display_name
#> [1] "Transcript Fusion"
#> 
#> $content$records[[1]]$variants[[6]]$variant_types[[1]]$so_id
#> [1] "SO:0001886"
#> 
#> $content$records[[1]]$variants[[6]]$variant_types[[1]]$description
#> [1] "A feature fusion where the deletion brings together transcript regions."
#> 
#> $content$records[[1]]$variants[[6]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001886"
#> 
#> 
#> $content$records[[1]]$variants[[6]]$variant_types[[2]]
#> $content$records[[1]]$variants[[6]]$variant_types[[2]]$id
#> [1] 47
#> 
#> $content$records[[1]]$variants[[6]]$variant_types[[2]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[1]]$variants[[6]]$variant_types[[2]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[1]]$variants[[6]]$variant_types[[2]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[1]]$variants[[6]]$variant_types[[2]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[1]]$variants[[6]]$variant_types[[2]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[1]]$variants[[6]]$civic_actionability_score
#> [1] 56
#> 
#> $content$records[[1]]$variants[[6]]$coordinates
#> $content$records[[1]]$variants[[6]]$coordinates$chromosome
#> [1] "9"
#> 
#> $content$records[[1]]$variants[[6]]$coordinates$start
#> [1] 133738363
#> 
#> $content$records[[1]]$variants[[6]]$coordinates$stop
#> [1] 133738363
#> 
#> $content$records[[1]]$variants[[6]]$coordinates$reference_bases
#> [1] "G"
#> 
#> $content$records[[1]]$variants[[6]]$coordinates$variant_bases
#> [1] "A"
#> 
#> $content$records[[1]]$variants[[6]]$coordinates$representative_transcript
#> [1] "ENST00000318560.5"
#> 
#> $content$records[[1]]$variants[[6]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[1]]$variants[[6]]$coordinates$start2
#> NULL
#> 
#> $content$records[[1]]$variants[[6]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[1]]$variants[[6]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[1]]$variants[[6]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[1]]$variants[[6]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[1]]$variants[[7]]
#> $content$records[[1]]$variants[[7]]$id
#> [1] 101
#> 
#> $content$records[[1]]$variants[[7]]$entrez_name
#> [1] "PDGFRA"
#> 
#> $content$records[[1]]$variants[[7]]$entrez_id
#> [1] 5156
#> 
#> $content$records[[1]]$variants[[7]]$name
#> [1] "I843DEL"
#> 
#> $content$records[[1]]$variants[[7]]$description
#> [1] "PDGFRA D842 mutations are characterized broadly as imatinib resistance mutations. This is most well characterized in gastrointestinal stromal tumors, but other cell lines containing these mutations have been shown to be resistant as well. In imatinib resistant cell lines, a number of other therapeutics have demonstrated efficacy. These include; crenolanib, sirolimus, and midostaurin (PKC412)."
#> 
#> $content$records[[1]]$variants[[7]]$gene_id
#> [1] 38
#> 
#> $content$records[[1]]$variants[[7]]$type
#> [1] "variant"
#> 
#> $content$records[[1]]$variants[[7]]$variant_types
#> $content$records[[1]]$variants[[7]]$variant_types[[1]]
#> $content$records[[1]]$variants[[7]]$variant_types[[1]]$id
#> [1] 107
#> 
#> $content$records[[1]]$variants[[7]]$variant_types[[1]]$name
#> [1] "inframe_deletion"
#> 
#> $content$records[[1]]$variants[[7]]$variant_types[[1]]$display_name
#> [1] "Inframe Deletion"
#> 
#> $content$records[[1]]$variants[[7]]$variant_types[[1]]$so_id
#> [1] "SO:0001822"
#> 
#> $content$records[[1]]$variants[[7]]$variant_types[[1]]$description
#> [1] "An inframe non synonymous variant that deletes bases from the coding sequence."
#> 
#> $content$records[[1]]$variants[[7]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001822"
#> 
#> 
#> 
#> $content$records[[1]]$variants[[7]]$civic_actionability_score
#> [1] 5
#> 
#> $content$records[[1]]$variants[[7]]$coordinates
#> $content$records[[1]]$variants[[7]]$coordinates$chromosome
#> [1] "4"
#> 
#> $content$records[[1]]$variants[[7]]$coordinates$start
#> [1] 55152095
#> 
#> $content$records[[1]]$variants[[7]]$coordinates$stop
#> [1] 55152097
#> 
#> $content$records[[1]]$variants[[7]]$coordinates$reference_bases
#> [1] "ATC"
#> 
#> $content$records[[1]]$variants[[7]]$coordinates$variant_bases
#> NULL
#> 
#> $content$records[[1]]$variants[[7]]$coordinates$representative_transcript
#> [1] "ENST00000257290.5"
#> 
#> $content$records[[1]]$variants[[7]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[1]]$variants[[7]]$coordinates$start2
#> NULL
#> 
#> $content$records[[1]]$variants[[7]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[1]]$variants[[7]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[1]]$variants[[7]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[1]]$variants[[7]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[1]]$variants[[8]]
#> $content$records[[1]]$variants[[8]]$id
#> [1] 99
#> 
#> $content$records[[1]]$variants[[8]]$entrez_name
#> [1] "PDGFRA"
#> 
#> $content$records[[1]]$variants[[8]]$entrez_id
#> [1] 5156
#> 
#> $content$records[[1]]$variants[[8]]$name
#> [1] "D842V"
#> 
#> $content$records[[1]]$variants[[8]]$description
#> [1] "PDGFRA D842 mutations are characterized broadly as imatinib resistance mutations. This is most well characterized in gastrointestinal stromal tumors, but other cell lines containing these mutations have been shown to be resistant as well. Exogenous expression of the A842V mutation resulted in constitutive tyrosine phosphorylation of PDGFRA in the absence of ligand in 293T cells and cytokine-independent proliferation of the IL-3-dependent Ba/F3 cell line, both evidence that this is an activating mutation. In imatinib resistant cell lines, a number of other therapeutics have demonstrated efficacy. These include; crenolanib, sirolimus, and midostaurin (PKC412)."
#> 
#> $content$records[[1]]$variants[[8]]$gene_id
#> [1] 38
#> 
#> $content$records[[1]]$variants[[8]]$type
#> [1] "variant"
#> 
#> $content$records[[1]]$variants[[8]]$variant_types
#> $content$records[[1]]$variants[[8]]$variant_types[[1]]
#> $content$records[[1]]$variants[[8]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[1]]$variants[[8]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[1]]$variants[[8]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[1]]$variants[[8]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[1]]$variants[[8]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[1]]$variants[[8]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[1]]$variants[[8]]$civic_actionability_score
#> [1] 100.5
#> 
#> $content$records[[1]]$variants[[8]]$coordinates
#> $content$records[[1]]$variants[[8]]$coordinates$chromosome
#> [1] "4"
#> 
#> $content$records[[1]]$variants[[8]]$coordinates$start
#> [1] 55152093
#> 
#> $content$records[[1]]$variants[[8]]$coordinates$stop
#> [1] 55152093
#> 
#> $content$records[[1]]$variants[[8]]$coordinates$reference_bases
#> [1] "A"
#> 
#> $content$records[[1]]$variants[[8]]$coordinates$variant_bases
#> [1] "T"
#> 
#> $content$records[[1]]$variants[[8]]$coordinates$representative_transcript
#> [1] "ENST00000257290.5"
#> 
#> $content$records[[1]]$variants[[8]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[1]]$variants[[8]]$coordinates$start2
#> NULL
#> 
#> $content$records[[1]]$variants[[8]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[1]]$variants[[8]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[1]]$variants[[8]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[1]]$variants[[8]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> 
#> $content$records[[1]]$type
#> [1] "variant_group"
#> 
#> 
#> $content$records[[2]]
#> $content$records[[2]]$id
#> [1] 2
#> 
#> $content$records[[2]]$name
#> [1] "KIT Exon 17"
#> 
#> $content$records[[2]]$description
#> [1] ""
#> 
#> $content$records[[2]]$variants
#> $content$records[[2]]$variants[[1]]
#> $content$records[[2]]$variants[[1]]$id
#> [1] 1265
#> 
#> $content$records[[2]]$variants[[1]]$entrez_name
#> [1] "KIT"
#> 
#> $content$records[[2]]$variants[[1]]$entrez_id
#> [1] 3815
#> 
#> $content$records[[2]]$variants[[1]]$name
#> [1] "D820A"
#> 
#> $content$records[[2]]$variants[[1]]$description
#> [1] ""
#> 
#> $content$records[[2]]$variants[[1]]$gene_id
#> [1] 29
#> 
#> $content$records[[2]]$variants[[1]]$type
#> [1] "variant"
#> 
#> $content$records[[2]]$variants[[1]]$variant_types
#> $content$records[[2]]$variants[[1]]$variant_types[[1]]
#> $content$records[[2]]$variants[[1]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[2]]$variants[[1]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[2]]$variants[[1]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[2]]$variants[[1]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[2]]$variants[[1]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[2]]$variants[[1]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[2]]$variants[[1]]$civic_actionability_score
#> [1] 7.5
#> 
#> $content$records[[2]]$variants[[1]]$coordinates
#> $content$records[[2]]$variants[[1]]$coordinates$chromosome
#> [1] "4"
#> 
#> $content$records[[2]]$variants[[1]]$coordinates$start
#> [1] 55599333
#> 
#> $content$records[[2]]$variants[[1]]$coordinates$stop
#> [1] 55599333
#> 
#> $content$records[[2]]$variants[[1]]$coordinates$reference_bases
#> [1] "A"
#> 
#> $content$records[[2]]$variants[[1]]$coordinates$variant_bases
#> [1] "C"
#> 
#> $content$records[[2]]$variants[[1]]$coordinates$representative_transcript
#> [1] "ENST00000288135.5"
#> 
#> $content$records[[2]]$variants[[1]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[2]]$variants[[1]]$coordinates$start2
#> NULL
#> 
#> $content$records[[2]]$variants[[1]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[2]]$variants[[1]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[2]]$variants[[1]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[2]]$variants[[1]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[2]]$variants[[2]]
#> $content$records[[2]]$variants[[2]]$id
#> [1] 1263
#> 
#> $content$records[[2]]$variants[[2]]$entrez_name
#> [1] "KIT"
#> 
#> $content$records[[2]]$variants[[2]]$entrez_id
#> [1] 3815
#> 
#> $content$records[[2]]$variants[[2]]$name
#> [1] "N822K"
#> 
#> $content$records[[2]]$variants[[2]]$description
#> [1] ""
#> 
#> $content$records[[2]]$variants[[2]]$gene_id
#> [1] 29
#> 
#> $content$records[[2]]$variants[[2]]$type
#> [1] "variant"
#> 
#> $content$records[[2]]$variants[[2]]$variant_types
#> $content$records[[2]]$variants[[2]]$variant_types[[1]]
#> $content$records[[2]]$variants[[2]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[2]]$variants[[2]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[2]]$variants[[2]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[2]]$variants[[2]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[2]]$variants[[2]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[2]]$variants[[2]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[2]]$variants[[2]]$civic_actionability_score
#> [1] 24.5
#> 
#> $content$records[[2]]$variants[[2]]$coordinates
#> $content$records[[2]]$variants[[2]]$coordinates$chromosome
#> [1] "4"
#> 
#> $content$records[[2]]$variants[[2]]$coordinates$start
#> [1] 55599340
#> 
#> $content$records[[2]]$variants[[2]]$coordinates$stop
#> [1] 55599340
#> 
#> $content$records[[2]]$variants[[2]]$coordinates$reference_bases
#> [1] "T"
#> 
#> $content$records[[2]]$variants[[2]]$coordinates$variant_bases
#> [1] "A"
#> 
#> $content$records[[2]]$variants[[2]]$coordinates$representative_transcript
#> [1] "ENST00000288135.5"
#> 
#> $content$records[[2]]$variants[[2]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[2]]$variants[[2]]$coordinates$start2
#> NULL
#> 
#> $content$records[[2]]$variants[[2]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[2]]$variants[[2]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[2]]$variants[[2]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[2]]$variants[[2]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[2]]$variants[[3]]
#> $content$records[[2]]$variants[[3]]$id
#> [1] 1266
#> 
#> $content$records[[2]]$variants[[3]]$entrez_name
#> [1] "KIT"
#> 
#> $content$records[[2]]$variants[[3]]$entrez_id
#> [1] 3815
#> 
#> $content$records[[2]]$variants[[3]]$name
#> [1] "D820G"
#> 
#> $content$records[[2]]$variants[[3]]$description
#> [1] ""
#> 
#> $content$records[[2]]$variants[[3]]$gene_id
#> [1] 29
#> 
#> $content$records[[2]]$variants[[3]]$type
#> [1] "variant"
#> 
#> $content$records[[2]]$variants[[3]]$variant_types
#> $content$records[[2]]$variants[[3]]$variant_types[[1]]
#> $content$records[[2]]$variants[[3]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[2]]$variants[[3]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[2]]$variants[[3]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[2]]$variants[[3]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[2]]$variants[[3]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[2]]$variants[[3]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[2]]$variants[[3]]$civic_actionability_score
#> [1] 7.5
#> 
#> $content$records[[2]]$variants[[3]]$coordinates
#> $content$records[[2]]$variants[[3]]$coordinates$chromosome
#> [1] "4"
#> 
#> $content$records[[2]]$variants[[3]]$coordinates$start
#> [1] 55599333
#> 
#> $content$records[[2]]$variants[[3]]$coordinates$stop
#> [1] 55599333
#> 
#> $content$records[[2]]$variants[[3]]$coordinates$reference_bases
#> [1] "A"
#> 
#> $content$records[[2]]$variants[[3]]$coordinates$variant_bases
#> [1] "G"
#> 
#> $content$records[[2]]$variants[[3]]$coordinates$representative_transcript
#> [1] "ENST00000288135.5"
#> 
#> $content$records[[2]]$variants[[3]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[2]]$variants[[3]]$coordinates$start2
#> NULL
#> 
#> $content$records[[2]]$variants[[3]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[2]]$variants[[3]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[2]]$variants[[3]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[2]]$variants[[3]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[2]]$variants[[4]]
#> $content$records[[2]]$variants[[4]]$id
#> [1] 983
#> 
#> $content$records[[2]]$variants[[4]]$entrez_name
#> [1] "KIT"
#> 
#> $content$records[[2]]$variants[[4]]$entrez_id
#> [1] 3815
#> 
#> $content$records[[2]]$variants[[4]]$name
#> [1] "D816H"
#> 
#> $content$records[[2]]$variants[[4]]$description
#> [1] ""
#> 
#> $content$records[[2]]$variants[[4]]$gene_id
#> [1] 29
#> 
#> $content$records[[2]]$variants[[4]]$type
#> [1] "variant"
#> 
#> $content$records[[2]]$variants[[4]]$variant_types
#> $content$records[[2]]$variants[[4]]$variant_types[[1]]
#> $content$records[[2]]$variants[[4]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[2]]$variants[[4]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[2]]$variants[[4]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[2]]$variants[[4]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[2]]$variants[[4]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[2]]$variants[[4]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[2]]$variants[[4]]$civic_actionability_score
#> [1] 7.5
#> 
#> $content$records[[2]]$variants[[4]]$coordinates
#> $content$records[[2]]$variants[[4]]$coordinates$chromosome
#> [1] "4"
#> 
#> $content$records[[2]]$variants[[4]]$coordinates$start
#> [1] 55599320
#> 
#> $content$records[[2]]$variants[[4]]$coordinates$stop
#> [1] 55599320
#> 
#> $content$records[[2]]$variants[[4]]$coordinates$reference_bases
#> [1] "G"
#> 
#> $content$records[[2]]$variants[[4]]$coordinates$variant_bases
#> [1] "C"
#> 
#> $content$records[[2]]$variants[[4]]$coordinates$representative_transcript
#> [1] "ENST00000288135.5"
#> 
#> $content$records[[2]]$variants[[4]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[2]]$variants[[4]]$coordinates$start2
#> NULL
#> 
#> $content$records[[2]]$variants[[4]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[2]]$variants[[4]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[2]]$variants[[4]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[2]]$variants[[4]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[2]]$variants[[5]]
#> $content$records[[2]]$variants[[5]]$id
#> [1] 986
#> 
#> $content$records[[2]]$variants[[5]]$entrez_name
#> [1] "KIT"
#> 
#> $content$records[[2]]$variants[[5]]$entrez_id
#> [1] 3815
#> 
#> $content$records[[2]]$variants[[5]]$name
#> [1] "D820Y"
#> 
#> $content$records[[2]]$variants[[5]]$description
#> [1] ""
#> 
#> $content$records[[2]]$variants[[5]]$gene_id
#> [1] 29
#> 
#> $content$records[[2]]$variants[[5]]$type
#> [1] "variant"
#> 
#> $content$records[[2]]$variants[[5]]$variant_types
#> $content$records[[2]]$variants[[5]]$variant_types[[1]]
#> $content$records[[2]]$variants[[5]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[2]]$variants[[5]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[2]]$variants[[5]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[2]]$variants[[5]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[2]]$variants[[5]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[2]]$variants[[5]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[2]]$variants[[5]]$civic_actionability_score
#> [1] 14.5
#> 
#> $content$records[[2]]$variants[[5]]$coordinates
#> $content$records[[2]]$variants[[5]]$coordinates$chromosome
#> [1] "4"
#> 
#> $content$records[[2]]$variants[[5]]$coordinates$start
#> [1] 55599332
#> 
#> $content$records[[2]]$variants[[5]]$coordinates$stop
#> [1] 55599332
#> 
#> $content$records[[2]]$variants[[5]]$coordinates$reference_bases
#> [1] "G"
#> 
#> $content$records[[2]]$variants[[5]]$coordinates$variant_bases
#> [1] "T"
#> 
#> $content$records[[2]]$variants[[5]]$coordinates$representative_transcript
#> [1] "ENST00000288135.5"
#> 
#> $content$records[[2]]$variants[[5]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[2]]$variants[[5]]$coordinates$start2
#> NULL
#> 
#> $content$records[[2]]$variants[[5]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[2]]$variants[[5]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[2]]$variants[[5]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[2]]$variants[[5]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[2]]$variants[[6]]
#> $content$records[[2]]$variants[[6]]$id
#> [1] 1264
#> 
#> $content$records[[2]]$variants[[6]]$entrez_name
#> [1] "KIT"
#> 
#> $content$records[[2]]$variants[[6]]$entrez_id
#> [1] 3815
#> 
#> $content$records[[2]]$variants[[6]]$name
#> [1] "C809G"
#> 
#> $content$records[[2]]$variants[[6]]$description
#> [1] ""
#> 
#> $content$records[[2]]$variants[[6]]$gene_id
#> [1] 29
#> 
#> $content$records[[2]]$variants[[6]]$type
#> [1] "variant"
#> 
#> $content$records[[2]]$variants[[6]]$variant_types
#> $content$records[[2]]$variants[[6]]$variant_types[[1]]
#> $content$records[[2]]$variants[[6]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[2]]$variants[[6]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[2]]$variants[[6]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[2]]$variants[[6]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[2]]$variants[[6]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[2]]$variants[[6]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[2]]$variants[[6]]$civic_actionability_score
#> [1] 7.5
#> 
#> $content$records[[2]]$variants[[6]]$coordinates
#> $content$records[[2]]$variants[[6]]$coordinates$chromosome
#> [1] "4"
#> 
#> $content$records[[2]]$variants[[6]]$coordinates$start
#> [1] 55599299
#> 
#> $content$records[[2]]$variants[[6]]$coordinates$stop
#> [1] 55599299
#> 
#> $content$records[[2]]$variants[[6]]$coordinates$reference_bases
#> [1] "T"
#> 
#> $content$records[[2]]$variants[[6]]$coordinates$variant_bases
#> [1] "G"
#> 
#> $content$records[[2]]$variants[[6]]$coordinates$representative_transcript
#> [1] "ENST00000288135.5"
#> 
#> $content$records[[2]]$variants[[6]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[2]]$variants[[6]]$coordinates$start2
#> NULL
#> 
#> $content$records[[2]]$variants[[6]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[2]]$variants[[6]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[2]]$variants[[6]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[2]]$variants[[6]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[2]]$variants[[7]]
#> $content$records[[2]]$variants[[7]]$id
#> [1] 989
#> 
#> $content$records[[2]]$variants[[7]]$entrez_name
#> [1] "KIT"
#> 
#> $content$records[[2]]$variants[[7]]$entrez_id
#> [1] 3815
#> 
#> $content$records[[2]]$variants[[7]]$name
#> [1] "Y823D"
#> 
#> $content$records[[2]]$variants[[7]]$description
#> [1] ""
#> 
#> $content$records[[2]]$variants[[7]]$gene_id
#> [1] 29
#> 
#> $content$records[[2]]$variants[[7]]$type
#> [1] "variant"
#> 
#> $content$records[[2]]$variants[[7]]$variant_types
#> $content$records[[2]]$variants[[7]]$variant_types[[1]]
#> $content$records[[2]]$variants[[7]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[2]]$variants[[7]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[2]]$variants[[7]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[2]]$variants[[7]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[2]]$variants[[7]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[2]]$variants[[7]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[2]]$variants[[7]]$civic_actionability_score
#> [1] 7.5
#> 
#> $content$records[[2]]$variants[[7]]$coordinates
#> $content$records[[2]]$variants[[7]]$coordinates$chromosome
#> [1] "4"
#> 
#> $content$records[[2]]$variants[[7]]$coordinates$start
#> [1] 55599341
#> 
#> $content$records[[2]]$variants[[7]]$coordinates$stop
#> [1] 55599341
#> 
#> $content$records[[2]]$variants[[7]]$coordinates$reference_bases
#> [1] "T"
#> 
#> $content$records[[2]]$variants[[7]]$coordinates$variant_bases
#> [1] "G"
#> 
#> $content$records[[2]]$variants[[7]]$coordinates$representative_transcript
#> [1] "ENST00000288135.5"
#> 
#> $content$records[[2]]$variants[[7]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[2]]$variants[[7]]$coordinates$start2
#> NULL
#> 
#> $content$records[[2]]$variants[[7]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[2]]$variants[[7]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[2]]$variants[[7]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[2]]$variants[[7]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[2]]$variants[[8]]
#> $content$records[[2]]$variants[[8]]$id
#> [1] 987
#> 
#> $content$records[[2]]$variants[[8]]$entrez_name
#> [1] "KIT"
#> 
#> $content$records[[2]]$variants[[8]]$entrez_id
#> [1] 3815
#> 
#> $content$records[[2]]$variants[[8]]$name
#> [1] "N822H"
#> 
#> $content$records[[2]]$variants[[8]]$description
#> [1] ""
#> 
#> $content$records[[2]]$variants[[8]]$gene_id
#> [1] 29
#> 
#> $content$records[[2]]$variants[[8]]$type
#> [1] "variant"
#> 
#> $content$records[[2]]$variants[[8]]$variant_types
#> $content$records[[2]]$variants[[8]]$variant_types[[1]]
#> $content$records[[2]]$variants[[8]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[2]]$variants[[8]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[2]]$variants[[8]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[2]]$variants[[8]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[2]]$variants[[8]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[2]]$variants[[8]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[2]]$variants[[8]]$civic_actionability_score
#> [1] 0
#> 
#> $content$records[[2]]$variants[[8]]$coordinates
#> $content$records[[2]]$variants[[8]]$coordinates$chromosome
#> [1] "4"
#> 
#> $content$records[[2]]$variants[[8]]$coordinates$start
#> [1] 55599338
#> 
#> $content$records[[2]]$variants[[8]]$coordinates$stop
#> [1] 55599338
#> 
#> $content$records[[2]]$variants[[8]]$coordinates$reference_bases
#> [1] "A"
#> 
#> $content$records[[2]]$variants[[8]]$coordinates$variant_bases
#> [1] "C"
#> 
#> $content$records[[2]]$variants[[8]]$coordinates$representative_transcript
#> NULL
#> 
#> $content$records[[2]]$variants[[8]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[2]]$variants[[8]]$coordinates$start2
#> NULL
#> 
#> $content$records[[2]]$variants[[8]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[2]]$variants[[8]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[2]]$variants[[8]]$coordinates$ensembl_version
#> NULL
#> 
#> $content$records[[2]]$variants[[8]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[2]]$variants[[9]]
#> $content$records[[2]]$variants[[9]]$id
#> [1] 65
#> 
#> $content$records[[2]]$variants[[9]]$entrez_name
#> [1] "KIT"
#> 
#> $content$records[[2]]$variants[[9]]$entrez_id
#> [1] 3815
#> 
#> $content$records[[2]]$variants[[9]]$name
#> [1] "D816V"
#> 
#> $content$records[[2]]$variants[[9]]$description
#> [1] "KIT D816V is a mutation observed in acute myeloid leukemia (AML). This variant has been linked to poorer prognosis and worse outcome in AML patients."
#> 
#> $content$records[[2]]$variants[[9]]$gene_id
#> [1] 29
#> 
#> $content$records[[2]]$variants[[9]]$type
#> [1] "variant"
#> 
#> $content$records[[2]]$variants[[9]]$variant_types
#> $content$records[[2]]$variants[[9]]$variant_types[[1]]
#> $content$records[[2]]$variants[[9]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[2]]$variants[[9]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[2]]$variants[[9]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[2]]$variants[[9]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[2]]$variants[[9]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[2]]$variants[[9]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[2]]$variants[[9]]$civic_actionability_score
#> [1] 67
#> 
#> $content$records[[2]]$variants[[9]]$coordinates
#> $content$records[[2]]$variants[[9]]$coordinates$chromosome
#> [1] "4"
#> 
#> $content$records[[2]]$variants[[9]]$coordinates$start
#> [1] 55599321
#> 
#> $content$records[[2]]$variants[[9]]$coordinates$stop
#> [1] 55599321
#> 
#> $content$records[[2]]$variants[[9]]$coordinates$reference_bases
#> [1] "A"
#> 
#> $content$records[[2]]$variants[[9]]$coordinates$variant_bases
#> [1] "T"
#> 
#> $content$records[[2]]$variants[[9]]$coordinates$representative_transcript
#> [1] "ENST00000288135.5"
#> 
#> $content$records[[2]]$variants[[9]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[2]]$variants[[9]]$coordinates$start2
#> NULL
#> 
#> $content$records[[2]]$variants[[9]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[2]]$variants[[9]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[2]]$variants[[9]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[2]]$variants[[9]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> 
#> $content$records[[2]]$type
#> [1] "variant_group"
#> 
#> 
#> $content$records[[3]]
#> $content$records[[3]]$id
#> [1] 3
#> 
#> $content$records[[3]]$name
#> [1] "Crizotinib Resistance"
#> 
#> $content$records[[3]]$description
#> [1] "The ALK oncogene has long been considered a driving factor in non-small cell lung cancer (NSCLC). The targeted tyrosine kinase inhibitor criztonib has shown to be effective in ALK-mutant NSCLC. However, in patients that have shown acquired resistance to crizotinib, missense mutations in the tyrosine kinase domain have shown to drive this resistance. "
#> 
#> $content$records[[3]]$variants
#> $content$records[[3]]$variants[[1]]
#> $content$records[[3]]$variants[[1]]$id
#> [1] 8
#> 
#> $content$records[[3]]$variants[[1]]$entrez_name
#> [1] "ALK"
#> 
#> $content$records[[3]]$variants[[1]]$entrez_id
#> [1] 238
#> 
#> $content$records[[3]]$variants[[1]]$name
#> [1] "F1174L"
#> 
#> $content$records[[3]]$variants[[1]]$description
#> [1] "ALK F1174L has been observed as recurrent in neuroblastoma, non-small cell lung cancer (NSCLC), and other cancer types. Neuroblastoma cells containing this mutation have shown resistance to low doses of criztonib. However, increased dosage can overcome this resistance in cell lines studies. TAE684 has also proven effective in both NSCLC and neuroblastoma F1174L containing cells."
#> 
#> $content$records[[3]]$variants[[1]]$gene_id
#> [1] 1
#> 
#> $content$records[[3]]$variants[[1]]$type
#> [1] "variant"
#> 
#> $content$records[[3]]$variants[[1]]$variant_types
#> $content$records[[3]]$variants[[1]]$variant_types[[1]]
#> $content$records[[3]]$variants[[1]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[3]]$variants[[1]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[3]]$variants[[1]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[3]]$variants[[1]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[3]]$variants[[1]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[3]]$variants[[1]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[3]]$variants[[1]]$civic_actionability_score
#> [1] 33.5
#> 
#> $content$records[[3]]$variants[[1]]$coordinates
#> $content$records[[3]]$variants[[1]]$coordinates$chromosome
#> [1] "2"
#> 
#> $content$records[[3]]$variants[[1]]$coordinates$start
#> [1] 29443695
#> 
#> $content$records[[3]]$variants[[1]]$coordinates$stop
#> [1] 29443695
#> 
#> $content$records[[3]]$variants[[1]]$coordinates$reference_bases
#> [1] "G"
#> 
#> $content$records[[3]]$variants[[1]]$coordinates$variant_bases
#> [1] "T"
#> 
#> $content$records[[3]]$variants[[1]]$coordinates$representative_transcript
#> [1] "ENST00000389048.3"
#> 
#> $content$records[[3]]$variants[[1]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[3]]$variants[[1]]$coordinates$start2
#> NULL
#> 
#> $content$records[[3]]$variants[[1]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[3]]$variants[[1]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[3]]$variants[[1]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[3]]$variants[[1]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[3]]$variants[[2]]
#> $content$records[[3]]$variants[[2]]$id
#> [1] 6
#> 
#> $content$records[[3]]$variants[[2]]$entrez_name
#> [1] "ALK"
#> 
#> $content$records[[3]]$variants[[2]]$entrez_id
#> [1] 238
#> 
#> $content$records[[3]]$variants[[2]]$name
#> [1] "EML4-ALK C1156Y"
#> 
#> $content$records[[3]]$variants[[2]]$description
#> [1] "In patients with non-small cell lung cancer exhibiting EML4-ALK fusion, C1156Y has been shown to confer resistance to crizotinib. Case reports indicate that secondary mutations can modulate drug sensitivity. EML4-ALK C1156Y/L1196M maintained crizotinib resistance while the lorlatinib resistant combination EML4-ALK C1156Y/L1198F re-sensitized the tumor to crizotinib treatment."
#> 
#> $content$records[[3]]$variants[[2]]$gene_id
#> [1] 1
#> 
#> $content$records[[3]]$variants[[2]]$type
#> [1] "variant"
#> 
#> $content$records[[3]]$variants[[2]]$variant_types
#> $content$records[[3]]$variants[[2]]$variant_types[[1]]
#> $content$records[[3]]$variants[[2]]$variant_types[[1]]$id
#> [1] 120
#> 
#> $content$records[[3]]$variants[[2]]$variant_types[[1]]$name
#> [1] "transcript_fusion"
#> 
#> $content$records[[3]]$variants[[2]]$variant_types[[1]]$display_name
#> [1] "Transcript Fusion"
#> 
#> $content$records[[3]]$variants[[2]]$variant_types[[1]]$so_id
#> [1] "SO:0001886"
#> 
#> $content$records[[3]]$variants[[2]]$variant_types[[1]]$description
#> [1] "A feature fusion where the deletion brings together transcript regions."
#> 
#> $content$records[[3]]$variants[[2]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001886"
#> 
#> 
#> $content$records[[3]]$variants[[2]]$variant_types[[2]]
#> $content$records[[3]]$variants[[2]]$variant_types[[2]]$id
#> [1] 47
#> 
#> $content$records[[3]]$variants[[2]]$variant_types[[2]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[3]]$variants[[2]]$variant_types[[2]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[3]]$variants[[2]]$variant_types[[2]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[3]]$variants[[2]]$variant_types[[2]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[3]]$variants[[2]]$variant_types[[2]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[3]]$variants[[2]]$civic_actionability_score
#> [1] 19
#> 
#> $content$records[[3]]$variants[[2]]$coordinates
#> $content$records[[3]]$variants[[2]]$coordinates$chromosome
#> [1] "2"
#> 
#> $content$records[[3]]$variants[[2]]$coordinates$start
#> [1] 29445258
#> 
#> $content$records[[3]]$variants[[2]]$coordinates$stop
#> [1] 29445258
#> 
#> $content$records[[3]]$variants[[2]]$coordinates$reference_bases
#> [1] "C"
#> 
#> $content$records[[3]]$variants[[2]]$coordinates$variant_bases
#> [1] "T"
#> 
#> $content$records[[3]]$variants[[2]]$coordinates$representative_transcript
#> [1] "ENST00000389048.3"
#> 
#> $content$records[[3]]$variants[[2]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[3]]$variants[[2]]$coordinates$start2
#> NULL
#> 
#> $content$records[[3]]$variants[[2]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[3]]$variants[[2]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[3]]$variants[[2]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[3]]$variants[[2]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[3]]$variants[[3]]
#> $content$records[[3]]$variants[[3]]$id
#> [1] 7
#> 
#> $content$records[[3]]$variants[[3]]$entrez_name
#> [1] "ALK"
#> 
#> $content$records[[3]]$variants[[3]]$entrez_id
#> [1] 238
#> 
#> $content$records[[3]]$variants[[3]]$name
#> [1] "EML4-ALK L1196M"
#> 
#> $content$records[[3]]$variants[[3]]$description
#> [1] "In patients with non-small cell lung cancer exhibiting EML4-ALK fusion, L1196M has been shown to confer resistance to crizotinib. This was also true in a patient with both EML4-ALK C1156Y & L1196M."
#> 
#> $content$records[[3]]$variants[[3]]$gene_id
#> [1] 1
#> 
#> $content$records[[3]]$variants[[3]]$type
#> [1] "variant"
#> 
#> $content$records[[3]]$variants[[3]]$variant_types
#> $content$records[[3]]$variants[[3]]$variant_types[[1]]
#> $content$records[[3]]$variants[[3]]$variant_types[[1]]$id
#> [1] 120
#> 
#> $content$records[[3]]$variants[[3]]$variant_types[[1]]$name
#> [1] "transcript_fusion"
#> 
#> $content$records[[3]]$variants[[3]]$variant_types[[1]]$display_name
#> [1] "Transcript Fusion"
#> 
#> $content$records[[3]]$variants[[3]]$variant_types[[1]]$so_id
#> [1] "SO:0001886"
#> 
#> $content$records[[3]]$variants[[3]]$variant_types[[1]]$description
#> [1] "A feature fusion where the deletion brings together transcript regions."
#> 
#> $content$records[[3]]$variants[[3]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001886"
#> 
#> 
#> $content$records[[3]]$variants[[3]]$variant_types[[2]]
#> $content$records[[3]]$variants[[3]]$variant_types[[2]]$id
#> [1] 47
#> 
#> $content$records[[3]]$variants[[3]]$variant_types[[2]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[3]]$variants[[3]]$variant_types[[2]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[3]]$variants[[3]]$variant_types[[2]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[3]]$variants[[3]]$variant_types[[2]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[3]]$variants[[3]]$variant_types[[2]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[3]]$variants[[3]]$civic_actionability_score
#> [1] 31
#> 
#> $content$records[[3]]$variants[[3]]$coordinates
#> $content$records[[3]]$variants[[3]]$coordinates$chromosome
#> [1] "2"
#> 
#> $content$records[[3]]$variants[[3]]$coordinates$start
#> [1] 29443631
#> 
#> $content$records[[3]]$variants[[3]]$coordinates$stop
#> [1] 29443631
#> 
#> $content$records[[3]]$variants[[3]]$coordinates$reference_bases
#> [1] "G"
#> 
#> $content$records[[3]]$variants[[3]]$coordinates$variant_bases
#> [1] "T"
#> 
#> $content$records[[3]]$variants[[3]]$coordinates$representative_transcript
#> [1] "ENST00000389048.3"
#> 
#> $content$records[[3]]$variants[[3]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[3]]$variants[[3]]$coordinates$start2
#> NULL
#> 
#> $content$records[[3]]$variants[[3]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[3]]$variants[[3]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[3]]$variants[[3]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[3]]$variants[[3]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[3]]$variants[[4]]
#> $content$records[[3]]$variants[[4]]$id
#> [1] 172
#> 
#> $content$records[[3]]$variants[[4]]$entrez_name
#> [1] "ALK"
#> 
#> $content$records[[3]]$variants[[4]]$entrez_id
#> [1] 238
#> 
#> $content$records[[3]]$variants[[4]]$name
#> [1] "EML4-ALK S1206Y"
#> 
#> $content$records[[3]]$variants[[4]]$description
#> [1] ""
#> 
#> $content$records[[3]]$variants[[4]]$gene_id
#> [1] 1
#> 
#> $content$records[[3]]$variants[[4]]$type
#> [1] "variant"
#> 
#> $content$records[[3]]$variants[[4]]$variant_types
#> $content$records[[3]]$variants[[4]]$variant_types[[1]]
#> $content$records[[3]]$variants[[4]]$variant_types[[1]]$id
#> [1] 120
#> 
#> $content$records[[3]]$variants[[4]]$variant_types[[1]]$name
#> [1] "transcript_fusion"
#> 
#> $content$records[[3]]$variants[[4]]$variant_types[[1]]$display_name
#> [1] "Transcript Fusion"
#> 
#> $content$records[[3]]$variants[[4]]$variant_types[[1]]$so_id
#> [1] "SO:0001886"
#> 
#> $content$records[[3]]$variants[[4]]$variant_types[[1]]$description
#> [1] "A feature fusion where the deletion brings together transcript regions."
#> 
#> $content$records[[3]]$variants[[4]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001886"
#> 
#> 
#> $content$records[[3]]$variants[[4]]$variant_types[[2]]
#> $content$records[[3]]$variants[[4]]$variant_types[[2]]$id
#> [1] 47
#> 
#> $content$records[[3]]$variants[[4]]$variant_types[[2]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[3]]$variants[[4]]$variant_types[[2]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[3]]$variants[[4]]$variant_types[[2]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[3]]$variants[[4]]$variant_types[[2]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[3]]$variants[[4]]$variant_types[[2]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[3]]$variants[[4]]$civic_actionability_score
#> [1] 6
#> 
#> $content$records[[3]]$variants[[4]]$coordinates
#> $content$records[[3]]$variants[[4]]$coordinates$chromosome
#> [1] "2"
#> 
#> $content$records[[3]]$variants[[4]]$coordinates$start
#> [1] 29443600
#> 
#> $content$records[[3]]$variants[[4]]$coordinates$stop
#> [1] 29443600
#> 
#> $content$records[[3]]$variants[[4]]$coordinates$reference_bases
#> [1] "G"
#> 
#> $content$records[[3]]$variants[[4]]$coordinates$variant_bases
#> [1] "T"
#> 
#> $content$records[[3]]$variants[[4]]$coordinates$representative_transcript
#> [1] "ENST00000389048.3"
#> 
#> $content$records[[3]]$variants[[4]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[3]]$variants[[4]]$coordinates$start2
#> NULL
#> 
#> $content$records[[3]]$variants[[4]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[3]]$variants[[4]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[3]]$variants[[4]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[3]]$variants[[4]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> 
#> $content$records[[3]]$type
#> [1] "variant_group"
#> 
#> 
#> $content$records[[4]]
#> $content$records[[4]]$id
#> [1] 4
#> 
#> $content$records[[4]]$name
#> [1] "KIT Exon 11"
#> 
#> $content$records[[4]]$description
#> [1] ""
#> 
#> $content$records[[4]]$variants
#> $content$records[[4]]$variants[[1]]
#> $content$records[[4]]$variants[[1]]$id
#> [1] 67
#> 
#> $content$records[[4]]$variants[[1]]$entrez_name
#> [1] "KIT"
#> 
#> $content$records[[4]]$variants[[1]]$entrez_id
#> [1] 3815
#> 
#> $content$records[[4]]$variants[[1]]$name
#> [1] "INTERNAL DUPLICATION"
#> 
#> $content$records[[4]]$variants[[1]]$description
#> [1] "c-KIT internal duplications have been observed in exon 11, within the juxtamembrane domain. In a case study of an anal melanoma patient harboring this event, imatinib confered marked response. Also, cells harboring exon 11 mutations have shown sensitivity to the tyrosine kinase inhibitor imatinib, offering a better prognosis to patients treated with the drug in the first year."
#> 
#> $content$records[[4]]$variants[[1]]$gene_id
#> [1] 29
#> 
#> $content$records[[4]]$variants[[1]]$type
#> [1] "variant"
#> 
#> $content$records[[4]]$variants[[1]]$variant_types
#> $content$records[[4]]$variants[[1]]$variant_types[[1]]
#> $content$records[[4]]$variants[[1]]$variant_types[[1]]$id
#> [1] 106
#> 
#> $content$records[[4]]$variants[[1]]$variant_types[[1]]$name
#> [1] "inframe_insertion"
#> 
#> $content$records[[4]]$variants[[1]]$variant_types[[1]]$display_name
#> [1] "Inframe Insertion"
#> 
#> $content$records[[4]]$variants[[1]]$variant_types[[1]]$so_id
#> [1] "SO:0001821"
#> 
#> $content$records[[4]]$variants[[1]]$variant_types[[1]]$description
#> [1] "An inframe non synonymous variant that inserts bases into in the coding sequence."
#> 
#> $content$records[[4]]$variants[[1]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001821"
#> 
#> 
#> 
#> $content$records[[4]]$variants[[1]]$civic_actionability_score
#> [1] 7.5
#> 
#> $content$records[[4]]$variants[[1]]$coordinates
#> $content$records[[4]]$variants[[1]]$coordinates$chromosome
#> [1] "4"
#> 
#> $content$records[[4]]$variants[[1]]$coordinates$start
#> [1] 55593582
#> 
#> $content$records[[4]]$variants[[1]]$coordinates$stop
#> [1] 55593708
#> 
#> $content$records[[4]]$variants[[1]]$coordinates$reference_bases
#> NULL
#> 
#> $content$records[[4]]$variants[[1]]$coordinates$variant_bases
#> NULL
#> 
#> $content$records[[4]]$variants[[1]]$coordinates$representative_transcript
#> [1] "ENST00000288135.5"
#> 
#> $content$records[[4]]$variants[[1]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[4]]$variants[[1]]$coordinates$start2
#> NULL
#> 
#> $content$records[[4]]$variants[[1]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[4]]$variants[[1]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[4]]$variants[[1]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[4]]$variants[[1]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[4]]$variants[[2]]
#> $content$records[[4]]$variants[[2]]$id
#> [1] 73
#> 
#> $content$records[[4]]$variants[[2]]$entrez_name
#> [1] "KIT"
#> 
#> $content$records[[4]]$variants[[2]]$entrez_id
#> [1] 3815
#> 
#> $content$records[[4]]$variants[[2]]$name
#> [1] "V654A"
#> 
#> $content$records[[4]]$variants[[2]]$description
#> [1] "KIT V654A is an exon 13 mutation that lies within the tyrosine kinase 1 domain of the protein. It has been shown to be an activating mutation by in vitro studies. This mutation is associated with imatinib resistance in melanoma patients. However, second generation TKI's such as sunitinib and midostaurin (PKC 412) have seen success in acheiving tumor response."
#> 
#> $content$records[[4]]$variants[[2]]$gene_id
#> [1] 29
#> 
#> $content$records[[4]]$variants[[2]]$type
#> [1] "variant"
#> 
#> $content$records[[4]]$variants[[2]]$variant_types
#> $content$records[[4]]$variants[[2]]$variant_types[[1]]
#> $content$records[[4]]$variants[[2]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[4]]$variants[[2]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[4]]$variants[[2]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[4]]$variants[[2]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[4]]$variants[[2]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[4]]$variants[[2]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[4]]$variants[[2]]$civic_actionability_score
#> [1] 18
#> 
#> $content$records[[4]]$variants[[2]]$coordinates
#> $content$records[[4]]$variants[[2]]$coordinates$chromosome
#> [1] "4"
#> 
#> $content$records[[4]]$variants[[2]]$coordinates$start
#> [1] 55594258
#> 
#> $content$records[[4]]$variants[[2]]$coordinates$stop
#> [1] 55594258
#> 
#> $content$records[[4]]$variants[[2]]$coordinates$reference_bases
#> [1] "T"
#> 
#> $content$records[[4]]$variants[[2]]$coordinates$variant_bases
#> [1] "C"
#> 
#> $content$records[[4]]$variants[[2]]$coordinates$representative_transcript
#> [1] "ENST00000288135.5"
#> 
#> $content$records[[4]]$variants[[2]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[4]]$variants[[2]]$coordinates$start2
#> NULL
#> 
#> $content$records[[4]]$variants[[2]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[4]]$variants[[2]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[4]]$variants[[2]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[4]]$variants[[2]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[4]]$variants[[3]]
#> $content$records[[4]]$variants[[3]]$id
#> [1] 72
#> 
#> $content$records[[4]]$variants[[3]]$entrez_name
#> [1] "KIT"
#> 
#> $content$records[[4]]$variants[[3]]$entrez_id
#> [1] 3815
#> 
#> $content$records[[4]]$variants[[3]]$name
#> [1] "L576P"
#> 
#> $content$records[[4]]$variants[[3]]$description
#> [1] "KIT L576P is an exon 11 mutation that lies within the juxtamembrane domain. It is one of the most recurrent KIT mutations in melanoma, and both in vitro and in vivo studies have shown sensitivity to imatinib."
#> 
#> $content$records[[4]]$variants[[3]]$gene_id
#> [1] 29
#> 
#> $content$records[[4]]$variants[[3]]$type
#> [1] "variant"
#> 
#> $content$records[[4]]$variants[[3]]$variant_types
#> $content$records[[4]]$variants[[3]]$variant_types[[1]]
#> $content$records[[4]]$variants[[3]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[4]]$variants[[3]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[4]]$variants[[3]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[4]]$variants[[3]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[4]]$variants[[3]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[4]]$variants[[3]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[4]]$variants[[3]]$civic_actionability_score
#> [1] 16
#> 
#> $content$records[[4]]$variants[[3]]$coordinates
#> $content$records[[4]]$variants[[3]]$coordinates$chromosome
#> [1] "4"
#> 
#> $content$records[[4]]$variants[[3]]$coordinates$start
#> [1] 55593661
#> 
#> $content$records[[4]]$variants[[3]]$coordinates$stop
#> [1] 55593661
#> 
#> $content$records[[4]]$variants[[3]]$coordinates$reference_bases
#> [1] "T"
#> 
#> $content$records[[4]]$variants[[3]]$coordinates$variant_bases
#> [1] "C"
#> 
#> $content$records[[4]]$variants[[3]]$coordinates$representative_transcript
#> [1] "ENST00000288135.5"
#> 
#> $content$records[[4]]$variants[[3]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[4]]$variants[[3]]$coordinates$start2
#> NULL
#> 
#> $content$records[[4]]$variants[[3]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[4]]$variants[[3]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[4]]$variants[[3]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[4]]$variants[[3]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[4]]$variants[[4]]
#> $content$records[[4]]$variants[[4]]$id
#> [1] 66
#> 
#> $content$records[[4]]$variants[[4]]$entrez_name
#> [1] "KIT"
#> 
#> $content$records[[4]]$variants[[4]]$entrez_id
#> [1] 3815
#> 
#> $content$records[[4]]$variants[[4]]$name
#> [1] "EXON 11 MUTATION"
#> 
#> $content$records[[4]]$variants[[4]]$description
#> [1] "c-KIT mutations in exon 11 lie within the juxtamembrane domain, and are very recurrent in gastrointestinal stromal tumors, often bearing a poorer prognosis than other KIT mutations. Cells harboring exon 11 mutations have shown sensitivity to the tyrosine kinase inhibitor imatinib, offering a better prognosis to patients treated with the drug in the first year. Small cohorts of melanoma patients harboring exon 11 KIT mutations have shown response to imatinib and sunitinib."
#> 
#> $content$records[[4]]$variants[[4]]$gene_id
#> [1] 29
#> 
#> $content$records[[4]]$variants[[4]]$type
#> [1] "variant"
#> 
#> $content$records[[4]]$variants[[4]]$variant_types
#> $content$records[[4]]$variants[[4]]$variant_types[[1]]
#> $content$records[[4]]$variants[[4]]$variant_types[[1]]$id
#> [1] 45
#> 
#> $content$records[[4]]$variants[[4]]$variant_types[[1]]$name
#> [1] "coding_sequence_variant"
#> 
#> $content$records[[4]]$variants[[4]]$variant_types[[1]]$display_name
#> [1] "Coding Sequence Variant"
#> 
#> $content$records[[4]]$variants[[4]]$variant_types[[1]]$so_id
#> [1] "SO:0001580"
#> 
#> $content$records[[4]]$variants[[4]]$variant_types[[1]]$description
#> [1] "A sequence variant that changes the coding sequence."
#> 
#> $content$records[[4]]$variants[[4]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001580"
#> 
#> 
#> 
#> $content$records[[4]]$variants[[4]]$civic_actionability_score
#> [1] 177.5
#> 
#> $content$records[[4]]$variants[[4]]$coordinates
#> $content$records[[4]]$variants[[4]]$coordinates$chromosome
#> [1] "4"
#> 
#> $content$records[[4]]$variants[[4]]$coordinates$start
#> [1] 55593582
#> 
#> $content$records[[4]]$variants[[4]]$coordinates$stop
#> [1] 55593708
#> 
#> $content$records[[4]]$variants[[4]]$coordinates$reference_bases
#> NULL
#> 
#> $content$records[[4]]$variants[[4]]$coordinates$variant_bases
#> NULL
#> 
#> $content$records[[4]]$variants[[4]]$coordinates$representative_transcript
#> [1] "ENST00000288135.5"
#> 
#> $content$records[[4]]$variants[[4]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[4]]$variants[[4]]$coordinates$start2
#> NULL
#> 
#> $content$records[[4]]$variants[[4]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[4]]$variants[[4]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[4]]$variants[[4]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[4]]$variants[[4]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> 
#> $content$records[[4]]$type
#> [1] "variant_group"
#> 
#> 
#> $content$records[[5]]
#> $content$records[[5]]$id
#> [1] 5
#> 
#> $content$records[[5]]$name
#> [1] "Other V600's"
#> 
#> $content$records[[5]]$description
#> [1] "While BRAF V600E is nearly ubiquitous in many cancer types, other V600 variants have also been observed and studied to a lesser degree. At first approximation, many of these variants seem to behave similarly to V600E, and treatment with dabrafenib has been shown to be effective. "
#> 
#> $content$records[[5]]$variants
#> $content$records[[5]]$variants[[1]]
#> $content$records[[5]]$variants[[1]]$id
#> [1] 13
#> 
#> $content$records[[5]]$variants[[1]]$entrez_name
#> [1] "BRAF"
#> 
#> $content$records[[5]]$variants[[1]]$entrez_id
#> [1] 673
#> 
#> $content$records[[5]]$variants[[1]]$name
#> [1] "V600E+V600M"
#> 
#> $content$records[[5]]$variants[[1]]$description
#> [1] "A case study of a single patient harboring both a V600E and a V600M mutation, dabrafenib was shown to acheive clinical response."
#> 
#> $content$records[[5]]$variants[[1]]$gene_id
#> [1] 5
#> 
#> $content$records[[5]]$variants[[1]]$type
#> [1] "variant"
#> 
#> $content$records[[5]]$variants[[1]]$variant_types
#> $content$records[[5]]$variants[[1]]$variant_types[[1]]
#> $content$records[[5]]$variants[[1]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[5]]$variants[[1]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[5]]$variants[[1]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[5]]$variants[[1]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[5]]$variants[[1]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[5]]$variants[[1]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[5]]$variants[[1]]$civic_actionability_score
#> [1] 7.5
#> 
#> $content$records[[5]]$variants[[1]]$coordinates
#> $content$records[[5]]$variants[[1]]$coordinates$chromosome
#> [1] "7"
#> 
#> $content$records[[5]]$variants[[1]]$coordinates$start
#> [1] 140453135
#> 
#> $content$records[[5]]$variants[[1]]$coordinates$stop
#> [1] 140453137
#> 
#> $content$records[[5]]$variants[[1]]$coordinates$reference_bases
#> NULL
#> 
#> $content$records[[5]]$variants[[1]]$coordinates$variant_bases
#> NULL
#> 
#> $content$records[[5]]$variants[[1]]$coordinates$representative_transcript
#> [1] "ENST00000288602.6"
#> 
#> $content$records[[5]]$variants[[1]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[5]]$variants[[1]]$coordinates$start2
#> NULL
#> 
#> $content$records[[5]]$variants[[1]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[5]]$variants[[1]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[5]]$variants[[1]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[5]]$variants[[1]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[5]]$variants[[2]]
#> $content$records[[5]]$variants[[2]]$id
#> [1] 563
#> 
#> $content$records[[5]]$variants[[2]]$entrez_name
#> [1] "BRAF"
#> 
#> $content$records[[5]]$variants[[2]]$entrez_id
#> [1] 673
#> 
#> $content$records[[5]]$variants[[2]]$name
#> [1] "V600K"
#> 
#> $content$records[[5]]$variants[[2]]$description
#> [1] ""
#> 
#> $content$records[[5]]$variants[[2]]$gene_id
#> [1] 5
#> 
#> $content$records[[5]]$variants[[2]]$type
#> [1] "variant"
#> 
#> $content$records[[5]]$variants[[2]]$variant_types
#> $content$records[[5]]$variants[[2]]$variant_types[[1]]
#> $content$records[[5]]$variants[[2]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[5]]$variants[[2]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[5]]$variants[[2]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[5]]$variants[[2]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[5]]$variants[[2]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[5]]$variants[[2]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[5]]$variants[[2]]$civic_actionability_score
#> [1] 82.5
#> 
#> $content$records[[5]]$variants[[2]]$coordinates
#> $content$records[[5]]$variants[[2]]$coordinates$chromosome
#> [1] "7"
#> 
#> $content$records[[5]]$variants[[2]]$coordinates$start
#> [1] 140453136
#> 
#> $content$records[[5]]$variants[[2]]$coordinates$stop
#> [1] 140453137
#> 
#> $content$records[[5]]$variants[[2]]$coordinates$reference_bases
#> [1] "AC"
#> 
#> $content$records[[5]]$variants[[2]]$coordinates$variant_bases
#> [1] "TT"
#> 
#> $content$records[[5]]$variants[[2]]$coordinates$representative_transcript
#> [1] "ENST00000288602.6"
#> 
#> $content$records[[5]]$variants[[2]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[5]]$variants[[2]]$coordinates$start2
#> NULL
#> 
#> $content$records[[5]]$variants[[2]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[5]]$variants[[2]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[5]]$variants[[2]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[5]]$variants[[2]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[5]]$variants[[3]]
#> $content$records[[5]]$variants[[3]]$id
#> [1] 288
#> 
#> $content$records[[5]]$variants[[3]]$entrez_name
#> [1] "BRAF"
#> 
#> $content$records[[5]]$variants[[3]]$entrez_id
#> [1] 673
#> 
#> $content$records[[5]]$variants[[3]]$name
#> [1] "L597R"
#> 
#> $content$records[[5]]$variants[[3]]$description
#> [1] ""
#> 
#> $content$records[[5]]$variants[[3]]$gene_id
#> [1] 5
#> 
#> $content$records[[5]]$variants[[3]]$type
#> [1] "variant"
#> 
#> $content$records[[5]]$variants[[3]]$variant_types
#> $content$records[[5]]$variants[[3]]$variant_types[[1]]
#> $content$records[[5]]$variants[[3]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[5]]$variants[[3]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[5]]$variants[[3]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[5]]$variants[[3]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[5]]$variants[[3]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[5]]$variants[[3]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[5]]$variants[[3]]$civic_actionability_score
#> [1] 12
#> 
#> $content$records[[5]]$variants[[3]]$coordinates
#> $content$records[[5]]$variants[[3]]$coordinates$chromosome
#> [1] "7"
#> 
#> $content$records[[5]]$variants[[3]]$coordinates$start
#> [1] 140453145
#> 
#> $content$records[[5]]$variants[[3]]$coordinates$stop
#> [1] 140453145
#> 
#> $content$records[[5]]$variants[[3]]$coordinates$reference_bases
#> [1] "A"
#> 
#> $content$records[[5]]$variants[[3]]$coordinates$variant_bases
#> [1] "C"
#> 
#> $content$records[[5]]$variants[[3]]$coordinates$representative_transcript
#> [1] "ENST00000288602.6"
#> 
#> $content$records[[5]]$variants[[3]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[5]]$variants[[3]]$coordinates$start2
#> NULL
#> 
#> $content$records[[5]]$variants[[3]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[5]]$variants[[3]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[5]]$variants[[3]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[5]]$variants[[3]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[5]]$variants[[4]]
#> $content$records[[5]]$variants[[4]]$id
#> [1] 11
#> 
#> $content$records[[5]]$variants[[4]]$entrez_name
#> [1] "BRAF"
#> 
#> $content$records[[5]]$variants[[4]]$entrez_id
#> [1] 673
#> 
#> $content$records[[5]]$variants[[4]]$name
#> [1] "V600D"
#> 
#> $content$records[[5]]$variants[[4]]$description
#> [1] "Patients harboring mutations in valine 600 residue of BRAF have been shown to be sensitive to dabrafenib. For more information on the V600 locus, see the V600E entry."
#> 
#> $content$records[[5]]$variants[[4]]$gene_id
#> [1] 5
#> 
#> $content$records[[5]]$variants[[4]]$type
#> [1] "variant"
#> 
#> $content$records[[5]]$variants[[4]]$variant_types
#> $content$records[[5]]$variants[[4]]$variant_types[[1]]
#> $content$records[[5]]$variants[[4]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[5]]$variants[[4]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[5]]$variants[[4]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[5]]$variants[[4]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[5]]$variants[[4]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[5]]$variants[[4]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[5]]$variants[[4]]$civic_actionability_score
#> [1] 25
#> 
#> $content$records[[5]]$variants[[4]]$coordinates
#> $content$records[[5]]$variants[[4]]$coordinates$chromosome
#> [1] "7"
#> 
#> $content$records[[5]]$variants[[4]]$coordinates$start
#> [1] 140453135
#> 
#> $content$records[[5]]$variants[[4]]$coordinates$stop
#> [1] 140453136
#> 
#> $content$records[[5]]$variants[[4]]$coordinates$reference_bases
#> [1] "CA"
#> 
#> $content$records[[5]]$variants[[4]]$coordinates$variant_bases
#> [1] "AT"
#> 
#> $content$records[[5]]$variants[[4]]$coordinates$representative_transcript
#> [1] "ENST00000288602.6"
#> 
#> $content$records[[5]]$variants[[4]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[5]]$variants[[4]]$coordinates$start2
#> NULL
#> 
#> $content$records[[5]]$variants[[4]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[5]]$variants[[4]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[5]]$variants[[4]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[5]]$variants[[4]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[5]]$variants[[5]]
#> $content$records[[5]]$variants[[5]]$id
#> [1] 17
#> 
#> $content$records[[5]]$variants[[5]]$entrez_name
#> [1] "BRAF"
#> 
#> $content$records[[5]]$variants[[5]]$entrez_id
#> [1] 673
#> 
#> $content$records[[5]]$variants[[5]]$name
#> [1] "V600"
#> 
#> $content$records[[5]]$variants[[5]]$description
#> [1] "BRAF mutations of the valine 600 residue have been shown to be recurrent in many cancer types. Of the V600 mutations, V600E is the most widely researched. V600 mutations as a whole have been correlated to poorer prognosis in colorectal and papilarry thyroid cancers. V600 mutations have also been shown to confer sensitivity to the BRAF inhibitor dabrafenib. For a more detailed summary, click the individual mutations."
#> 
#> $content$records[[5]]$variants[[5]]$gene_id
#> [1] 5
#> 
#> $content$records[[5]]$variants[[5]]$type
#> [1] "variant"
#> 
#> $content$records[[5]]$variants[[5]]$variant_types
#> $content$records[[5]]$variants[[5]]$variant_types[[1]]
#> $content$records[[5]]$variants[[5]]$variant_types[[1]]$id
#> [1] 103
#> 
#> $content$records[[5]]$variants[[5]]$variant_types[[1]]$name
#> [1] "protein_altering_variant"
#> 
#> $content$records[[5]]$variants[[5]]$variant_types[[1]]$display_name
#> [1] "Protein Altering Variant"
#> 
#> $content$records[[5]]$variants[[5]]$variant_types[[1]]$so_id
#> [1] "SO:0001818"
#> 
#> $content$records[[5]]$variants[[5]]$variant_types[[1]]$description
#> [1] "A sequence_variant which is predicted to change the protein encoded in the coding sequence."
#> 
#> $content$records[[5]]$variants[[5]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001818"
#> 
#> 
#> 
#> $content$records[[5]]$variants[[5]]$civic_actionability_score
#> [1] 420
#> 
#> $content$records[[5]]$variants[[5]]$coordinates
#> $content$records[[5]]$variants[[5]]$coordinates$chromosome
#> [1] "7"
#> 
#> $content$records[[5]]$variants[[5]]$coordinates$start
#> [1] 140453136
#> 
#> $content$records[[5]]$variants[[5]]$coordinates$stop
#> [1] 140453137
#> 
#> $content$records[[5]]$variants[[5]]$coordinates$reference_bases
#> NULL
#> 
#> $content$records[[5]]$variants[[5]]$coordinates$variant_bases
#> NULL
#> 
#> $content$records[[5]]$variants[[5]]$coordinates$representative_transcript
#> [1] "ENST00000288602.6"
#> 
#> $content$records[[5]]$variants[[5]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[5]]$variants[[5]]$coordinates$start2
#> NULL
#> 
#> $content$records[[5]]$variants[[5]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[5]]$variants[[5]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[5]]$variants[[5]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[5]]$variants[[5]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> 
#> $content$records[[5]]$type
#> [1] "variant_group"
#> 
#> 
#> $content$records[[6]]
#> $content$records[[6]]$id
#> [1] 6
#> 
#> $content$records[[6]]$name
#> [1] "Motesanib Resistance"
#> 
#> $content$records[[6]]$description
#> [1] "RET activation is a common oncogenic marker of medullary thyroid carcinoma. Treatment of these patients with the targeted therapeutic motesanib has shown to be effective. However, the missense mutations C634W and M918T have shown to confer motesanib resistance in cell lines. "
#> 
#> $content$records[[6]]$variants
#> $content$records[[6]]$variants[[1]]
#> $content$records[[6]]$variants[[1]]$id
#> [1] 113
#> 
#> $content$records[[6]]$variants[[1]]$entrez_name
#> [1] "RET"
#> 
#> $content$records[[6]]$variants[[1]]$entrez_id
#> [1] 5979
#> 
#> $content$records[[6]]$variants[[1]]$name
#> [1] "M918T"
#> 
#> $content$records[[6]]$variants[[1]]$description
#> [1] "RET M819T is the most common somatically acquired mutation in medullary thyroid cancer (MTC). While there currently are no RET-specific inhibiting agents, promiscuous kinase inhibitors have seen some success in treating RET overactivity. Data suggests however, that the M918T mutation may lead to drug resistance, especially against the VEGFR-inhibitor motesanib. It has also been suggested that RET M819T leads to more aggressive MTC with a poorer prognosis."
#> 
#> $content$records[[6]]$variants[[1]]$gene_id
#> [1] 42
#> 
#> $content$records[[6]]$variants[[1]]$type
#> [1] "variant"
#> 
#> $content$records[[6]]$variants[[1]]$variant_types
#> $content$records[[6]]$variants[[1]]$variant_types[[1]]
#> $content$records[[6]]$variants[[1]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[6]]$variants[[1]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[6]]$variants[[1]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[6]]$variants[[1]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[6]]$variants[[1]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[6]]$variants[[1]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[6]]$variants[[1]]$civic_actionability_score
#> [1] 66
#> 
#> $content$records[[6]]$variants[[1]]$coordinates
#> $content$records[[6]]$variants[[1]]$coordinates$chromosome
#> [1] "10"
#> 
#> $content$records[[6]]$variants[[1]]$coordinates$start
#> [1] 43617416
#> 
#> $content$records[[6]]$variants[[1]]$coordinates$stop
#> [1] 43617416
#> 
#> $content$records[[6]]$variants[[1]]$coordinates$reference_bases
#> [1] "T"
#> 
#> $content$records[[6]]$variants[[1]]$coordinates$variant_bases
#> [1] "C"
#> 
#> $content$records[[6]]$variants[[1]]$coordinates$representative_transcript
#> [1] "ENST00000355710.3"
#> 
#> $content$records[[6]]$variants[[1]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[6]]$variants[[1]]$coordinates$start2
#> NULL
#> 
#> $content$records[[6]]$variants[[1]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[6]]$variants[[1]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[6]]$variants[[1]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[6]]$variants[[1]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[6]]$variants[[2]]
#> $content$records[[6]]$variants[[2]]$id
#> [1] 112
#> 
#> $content$records[[6]]$variants[[2]]$entrez_name
#> [1] "RET"
#> 
#> $content$records[[6]]$variants[[2]]$entrez_id
#> [1] 5979
#> 
#> $content$records[[6]]$variants[[2]]$name
#> [1] "C634W"
#> 
#> $content$records[[6]]$variants[[2]]$description
#> [1] "RET C634W has been implicated as an alternate mechanism of activating RET in medullary thyroid cancer. While there currently are no RET-specific inhibiting agents, promiscuous kinase inhibitors have seen some success in treating RET overactivity. Data suggests however, that the C634W mutation may lead to drug resistance, especially against the VEGFR-inhibitor motesanib."
#> 
#> $content$records[[6]]$variants[[2]]$gene_id
#> [1] 42
#> 
#> $content$records[[6]]$variants[[2]]$type
#> [1] "variant"
#> 
#> $content$records[[6]]$variants[[2]]$variant_types
#> $content$records[[6]]$variants[[2]]$variant_types[[1]]
#> $content$records[[6]]$variants[[2]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[6]]$variants[[2]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[6]]$variants[[2]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[6]]$variants[[2]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[6]]$variants[[2]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[6]]$variants[[2]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[6]]$variants[[2]]$civic_actionability_score
#> [1] 3
#> 
#> $content$records[[6]]$variants[[2]]$coordinates
#> $content$records[[6]]$variants[[2]]$coordinates$chromosome
#> [1] "10"
#> 
#> $content$records[[6]]$variants[[2]]$coordinates$start
#> [1] 43609950
#> 
#> $content$records[[6]]$variants[[2]]$coordinates$stop
#> [1] 43609950
#> 
#> $content$records[[6]]$variants[[2]]$coordinates$reference_bases
#> [1] "C"
#> 
#> $content$records[[6]]$variants[[2]]$coordinates$variant_bases
#> [1] "G"
#> 
#> $content$records[[6]]$variants[[2]]$coordinates$representative_transcript
#> [1] "ENST00000355710.3"
#> 
#> $content$records[[6]]$variants[[2]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[6]]$variants[[2]]$coordinates$start2
#> NULL
#> 
#> $content$records[[6]]$variants[[2]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[6]]$variants[[2]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[6]]$variants[[2]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[6]]$variants[[2]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> 
#> $content$records[[6]]$type
#> [1] "variant_group"
#> 
#> 
#> $content$records[[7]]
#> $content$records[[7]]$id
#> [1] 7
#> 
#> $content$records[[7]]$name
#> [1] "NPM1 Exon 12"
#> 
#> $content$records[[7]]$description
#> [1] "NPM1 exon 12 mutations are frequently identified in patients with cytogenetically normal acute myeloid leukemia (AML) and often co-occur with FLT3-ITD. FLT3 status should also be evaluated as co-occurence with FLT3-ITD may impact prognosis. Exon 12 mutations have been identified as a predictor of good prognostic outcomes in the absence of FLT3-ITD. Due to their high frequency, NPM1 mutations have been retrospectively analyzed in the context of a number of therapies including variable results following ATRA treatment as well as improved response to high-dose daunorubicin or valproic acid. Additionally, multiple groups have shown increased surface expression of CD33 associated with NPM1 mutation, suggesting these patients may respond to anti-CD33 therapy. Cytoplasmic sequestration of NPM1 (NPM1c) is associated with a good response to induction therapy."
#> 
#> $content$records[[7]]$variants
#> $content$records[[7]]$variants[[1]]
#> $content$records[[7]]$variants[[1]]$id
#> [1] 86
#> 
#> $content$records[[7]]$variants[[1]]$entrez_name
#> [1] "NPM1"
#> 
#> $content$records[[7]]$variants[[1]]$entrez_id
#> [1] 4869
#> 
#> $content$records[[7]]$variants[[1]]$name
#> [1] "EXON 12 MUTATION"
#> 
#> $content$records[[7]]$variants[[1]]$description
#> [1] "NPM1 exon 12 mutations are frequently identified in patients with cytogenetically normal acute myeloid leukemia (AML) and often co-occur with FLT3-ITD. FLT3 status should also be evaluated as co-occurence with FLT3-ITD may impact prognosis. Exon 12 mutations have been identified as a predictor of good prognostic outcomes in the absence of FLT3-ITD. Due to their high frequency, NPM1 mutations have been retrospectively analyzed in the context of a number of therapies including variable results following ATRA treatment as well as improved response to high-dose daunorubicin or valproic acid. Additionally, multiple groups have shown increased surface expression of CD33 associated with NPM1 mutation, suggesting these patients may respond to anti-CD33 therapy. Cytoplasmic sequestration of NPM1 (NPM1c) is associated with a good response to induction therapy."
#> 
#> $content$records[[7]]$variants[[1]]$gene_id
#> [1] 35
#> 
#> $content$records[[7]]$variants[[1]]$type
#> [1] "variant"
#> 
#> $content$records[[7]]$variants[[1]]$variant_types
#> $content$records[[7]]$variants[[1]]$variant_types[[1]]
#> $content$records[[7]]$variants[[1]]$variant_types[[1]]$id
#> [1] 99
#> 
#> $content$records[[7]]$variants[[1]]$variant_types[[1]]$name
#> [1] "exon_variant"
#> 
#> $content$records[[7]]$variants[[1]]$variant_types[[1]]$display_name
#> [1] "Exon Variant"
#> 
#> $content$records[[7]]$variants[[1]]$variant_types[[1]]$so_id
#> [1] "SO:0001791"
#> 
#> $content$records[[7]]$variants[[1]]$variant_types[[1]]$description
#> [1] "A sequence variant that changes exon sequence."
#> 
#> $content$records[[7]]$variants[[1]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001791"
#> 
#> 
#> 
#> $content$records[[7]]$variants[[1]]$civic_actionability_score
#> [1] 454
#> 
#> $content$records[[7]]$variants[[1]]$coordinates
#> $content$records[[7]]$variants[[1]]$coordinates$chromosome
#> [1] "5"
#> 
#> $content$records[[7]]$variants[[1]]$coordinates$start
#> [1] 170837531
#> 
#> $content$records[[7]]$variants[[1]]$coordinates$stop
#> [1] 170837569
#> 
#> $content$records[[7]]$variants[[1]]$coordinates$reference_bases
#> NULL
#> 
#> $content$records[[7]]$variants[[1]]$coordinates$variant_bases
#> NULL
#> 
#> $content$records[[7]]$variants[[1]]$coordinates$representative_transcript
#> [1] "ENST00000517671.1"
#> 
#> $content$records[[7]]$variants[[1]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[7]]$variants[[1]]$coordinates$start2
#> NULL
#> 
#> $content$records[[7]]$variants[[1]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[7]]$variants[[1]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[7]]$variants[[1]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[7]]$variants[[1]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[7]]$variants[[2]]
#> $content$records[[7]]$variants[[2]]$id
#> [1] 87
#> 
#> $content$records[[7]]$variants[[2]]$entrez_name
#> [1] "NPM1"
#> 
#> $content$records[[7]]$variants[[2]]$entrez_id
#> [1] 4869
#> 
#> $content$records[[7]]$variants[[2]]$name
#> [1] "W288FS"
#> 
#> $content$records[[7]]$variants[[2]]$description
#> [1] "NPM1 W288fs (aka NPM1-A) is located in exon 12 of NPM1 and is the most common NPM1 mutation identified in acute myeloid leukemia. This mutation results in cytoplasmic localization of NPM1 (NPM1c) which is associated with a good response to induction therapy. Although it is the most extensively studied NPM1 exon 12 mutation, it is generally grouped with other exon 12 mutations for patient analysis (see NPM1 Exon 12 variants for more information)."
#> 
#> $content$records[[7]]$variants[[2]]$gene_id
#> [1] 35
#> 
#> $content$records[[7]]$variants[[2]]$type
#> [1] "variant"
#> 
#> $content$records[[7]]$variants[[2]]$variant_types
#> $content$records[[7]]$variants[[2]]$variant_types[[1]]
#> $content$records[[7]]$variants[[2]]$variant_types[[1]]$id
#> [1] 133
#> 
#> $content$records[[7]]$variants[[2]]$variant_types[[1]]$name
#> [1] "frameshift_elongation"
#> 
#> $content$records[[7]]$variants[[2]]$variant_types[[1]]$display_name
#> [1] "Frameshift Elongation"
#> 
#> $content$records[[7]]$variants[[2]]$variant_types[[1]]$so_id
#> [1] "SO:0001909"
#> 
#> $content$records[[7]]$variants[[2]]$variant_types[[1]]$description
#> [1] "A frameshift variant that causes the translational reading frame to be extended relative to the reference feature."
#> 
#> $content$records[[7]]$variants[[2]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001909"
#> 
#> 
#> 
#> $content$records[[7]]$variants[[2]]$civic_actionability_score
#> [1] 43.75
#> 
#> $content$records[[7]]$variants[[2]]$coordinates
#> $content$records[[7]]$variants[[2]]$coordinates$chromosome
#> [1] "5"
#> 
#> $content$records[[7]]$variants[[2]]$coordinates$start
#> [1] 170837547
#> 
#> $content$records[[7]]$variants[[2]]$coordinates$stop
#> [1] 170837548
#> 
#> $content$records[[7]]$variants[[2]]$coordinates$reference_bases
#> [1] ""
#> 
#> $content$records[[7]]$variants[[2]]$coordinates$variant_bases
#> [1] "TCTG"
#> 
#> $content$records[[7]]$variants[[2]]$coordinates$representative_transcript
#> [1] "ENST00000517671.1"
#> 
#> $content$records[[7]]$variants[[2]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[7]]$variants[[2]]$coordinates$start2
#> NULL
#> 
#> $content$records[[7]]$variants[[2]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[7]]$variants[[2]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[7]]$variants[[2]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[7]]$variants[[2]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> 
#> $content$records[[7]]$type
#> [1] "variant_group"
#> 
#> 
#> $content$records[[8]]
#> $content$records[[8]]$id
#> [1] 8
#> 
#> $content$records[[8]]$name
#> [1] "FGFR fusions"
#> 
#> $content$records[[8]]$description
#> [1] "FGFR fusions have been demonstrated across many cancer types to have oncogenic potential. FGFR2 and FGFR3 have been shown to be fused to many 3' partners, which may act as a vehicle for pathway activation. Treatment of cell lines harboring FGFR2 fusions with pazopanib has shown mild \"anti-tumor\" activities, and both ponatinib and pazopanib have shown efficacy in case studies.  "
#> 
#> $content$records[[8]]$variants
#> $content$records[[8]]$variants[[1]]
#> $content$records[[8]]$variants[[1]]$id
#> [1] 53
#> 
#> $content$records[[8]]$variants[[1]]$entrez_name
#> [1] "FGFR3"
#> 
#> $content$records[[8]]$variants[[1]]$entrez_id
#> [1] 2261
#> 
#> $content$records[[8]]$variants[[1]]$name
#> [1] "FGFR3-BAIAP2L1"
#> 
#> $content$records[[8]]$variants[[1]]$description
#> [1] "In a clinical sequencing program for advanced stage cancers, Wu et al (2013, Cancer Discovery) has identified a number of FGFR fusions in patients with many different cancer types. These fusions were also found to retain oligomerization capability, and result in enhanced cell proliferation. These fusions were shown to respond to pazopanib. The authors use these cases to highlight the need for enhanced clinical sequencing efforts."
#> 
#> $content$records[[8]]$variants[[1]]$gene_id
#> [1] 23
#> 
#> $content$records[[8]]$variants[[1]]$type
#> [1] "variant"
#> 
#> $content$records[[8]]$variants[[1]]$variant_types
#> $content$records[[8]]$variants[[1]]$variant_types[[1]]
#> $content$records[[8]]$variants[[1]]$variant_types[[1]]$id
#> [1] 120
#> 
#> $content$records[[8]]$variants[[1]]$variant_types[[1]]$name
#> [1] "transcript_fusion"
#> 
#> $content$records[[8]]$variants[[1]]$variant_types[[1]]$display_name
#> [1] "Transcript Fusion"
#> 
#> $content$records[[8]]$variants[[1]]$variant_types[[1]]$so_id
#> [1] "SO:0001886"
#> 
#> $content$records[[8]]$variants[[1]]$variant_types[[1]]$description
#> [1] "A feature fusion where the deletion brings together transcript regions."
#> 
#> $content$records[[8]]$variants[[1]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001886"
#> 
#> 
#> 
#> $content$records[[8]]$variants[[1]]$civic_actionability_score
#> [1] 3
#> 
#> $content$records[[8]]$variants[[1]]$coordinates
#> $content$records[[8]]$variants[[1]]$coordinates$chromosome
#> [1] "4"
#> 
#> $content$records[[8]]$variants[[1]]$coordinates$start
#> [1] 1795039
#> 
#> $content$records[[8]]$variants[[1]]$coordinates$stop
#> [1] 1810599
#> 
#> $content$records[[8]]$variants[[1]]$coordinates$reference_bases
#> NULL
#> 
#> $content$records[[8]]$variants[[1]]$coordinates$variant_bases
#> NULL
#> 
#> $content$records[[8]]$variants[[1]]$coordinates$representative_transcript
#> [1] "ENST00000340107.4"
#> 
#> $content$records[[8]]$variants[[1]]$coordinates$chromosome2
#> [1] "7"
#> 
#> $content$records[[8]]$variants[[1]]$coordinates$start2
#> [1] 97991744
#> 
#> $content$records[[8]]$variants[[1]]$coordinates$stop2
#> [1] 97920963
#> 
#> $content$records[[8]]$variants[[1]]$coordinates$representative_transcript2
#> [1] "ENST00000005260.8"
#> 
#> $content$records[[8]]$variants[[1]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[8]]$variants[[1]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[8]]$variants[[2]]
#> $content$records[[8]]$variants[[2]]$id
#> [1] 54
#> 
#> $content$records[[8]]$variants[[2]]$entrez_name
#> [1] "FGFR2"
#> 
#> $content$records[[8]]$variants[[2]]$entrez_id
#> [1] 2263
#> 
#> $content$records[[8]]$variants[[2]]$name
#> [1] "FGFR2-TACC3"
#> 
#> $content$records[[8]]$variants[[2]]$description
#> [1] "In a clinical sequencing program for advanced stage cancers, Wu et al has identified a number of FGFR fusions in patients with many different cancer types. These fusions were also found to retain oligomerization capability, and result in enhanced cell proliferation. These fusions were shown to respond to pazopanib. The authors use these cases to highlight the need for enhanced clinical sequencing efforts."
#> 
#> $content$records[[8]]$variants[[2]]$gene_id
#> [1] 22
#> 
#> $content$records[[8]]$variants[[2]]$type
#> [1] "variant"
#> 
#> $content$records[[8]]$variants[[2]]$variant_types
#> $content$records[[8]]$variants[[2]]$variant_types[[1]]
#> $content$records[[8]]$variants[[2]]$variant_types[[1]]$id
#> [1] 120
#> 
#> $content$records[[8]]$variants[[2]]$variant_types[[1]]$name
#> [1] "transcript_fusion"
#> 
#> $content$records[[8]]$variants[[2]]$variant_types[[1]]$display_name
#> [1] "Transcript Fusion"
#> 
#> $content$records[[8]]$variants[[2]]$variant_types[[1]]$so_id
#> [1] "SO:0001886"
#> 
#> $content$records[[8]]$variants[[2]]$variant_types[[1]]$description
#> [1] "A feature fusion where the deletion brings together transcript regions."
#> 
#> $content$records[[8]]$variants[[2]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001886"
#> 
#> 
#> 
#> $content$records[[8]]$variants[[2]]$civic_actionability_score
#> [1] 7.5
#> 
#> $content$records[[8]]$variants[[2]]$coordinates
#> $content$records[[8]]$variants[[2]]$coordinates$chromosome
#> [1] "4"
#> 
#> $content$records[[8]]$variants[[2]]$coordinates$start
#> [1] 123243212
#> 
#> $content$records[[8]]$variants[[2]]$coordinates$stop
#> [1] 123357598
#> 
#> $content$records[[8]]$variants[[2]]$coordinates$reference_bases
#> NULL
#> 
#> $content$records[[8]]$variants[[2]]$coordinates$variant_bases
#> [1] ""
#> 
#> $content$records[[8]]$variants[[2]]$coordinates$representative_transcript
#> [1] "ENST00000358487.5"
#> 
#> $content$records[[8]]$variants[[2]]$coordinates$chromosome2
#> [1] "4"
#> 
#> $content$records[[8]]$variants[[2]]$coordinates$start2
#> [1] 1723266
#> 
#> $content$records[[8]]$variants[[2]]$coordinates$stop2
#> [1] 1741505
#> 
#> $content$records[[8]]$variants[[2]]$coordinates$representative_transcript2
#> [1] "ENST00000313288.4"
#> 
#> $content$records[[8]]$variants[[2]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[8]]$variants[[2]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[8]]$variants[[3]]
#> $content$records[[8]]$variants[[3]]$id
#> [1] 52
#> 
#> $content$records[[8]]$variants[[3]]$entrez_name
#> [1] "FGFR2"
#> 
#> $content$records[[8]]$variants[[3]]$entrez_id
#> [1] 2263
#> 
#> $content$records[[8]]$variants[[3]]$name
#> [1] "FGFR2-MGEA5"
#> 
#> $content$records[[8]]$variants[[3]]$description
#> [1] "In a clinical sequencing program for advanced stage cancers, Wu et al (2013, Cancer Discovery) has idenified a number of FGFR fusions in patients with many different cancer types. These fusions were also found to retain oligomerization capability, and result in enhanced cell proliferation. Cell lines harboring these fusions were shown to respond to pazopanib. Additionally, tumor size reduction was achieved by both ponatinib and pazopanib treatments administered separately in a single patient with intrahepatic cholangiocarcinoma and this fusion. The authors use these cases to highlight the need for enhanced clinical sequencing efforts."
#> 
#> $content$records[[8]]$variants[[3]]$gene_id
#> [1] 22
#> 
#> $content$records[[8]]$variants[[3]]$type
#> [1] "variant"
#> 
#> $content$records[[8]]$variants[[3]]$variant_types
#> $content$records[[8]]$variants[[3]]$variant_types[[1]]
#> $content$records[[8]]$variants[[3]]$variant_types[[1]]$id
#> [1] 120
#> 
#> $content$records[[8]]$variants[[3]]$variant_types[[1]]$name
#> [1] "transcript_fusion"
#> 
#> $content$records[[8]]$variants[[3]]$variant_types[[1]]$display_name
#> [1] "Transcript Fusion"
#> 
#> $content$records[[8]]$variants[[3]]$variant_types[[1]]$so_id
#> [1] "SO:0001886"
#> 
#> $content$records[[8]]$variants[[3]]$variant_types[[1]]$description
#> [1] "A feature fusion where the deletion brings together transcript regions."
#> 
#> $content$records[[8]]$variants[[3]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001886"
#> 
#> 
#> 
#> $content$records[[8]]$variants[[3]]$civic_actionability_score
#> [1] 5
#> 
#> $content$records[[8]]$variants[[3]]$coordinates
#> $content$records[[8]]$variants[[3]]$coordinates$chromosome
#> [1] "10"
#> 
#> $content$records[[8]]$variants[[3]]$coordinates$start
#> [1] 123243212
#> 
#> $content$records[[8]]$variants[[3]]$coordinates$stop
#> [1] 123357917
#> 
#> $content$records[[8]]$variants[[3]]$coordinates$reference_bases
#> NULL
#> 
#> $content$records[[8]]$variants[[3]]$coordinates$variant_bases
#> NULL
#> 
#> $content$records[[8]]$variants[[3]]$coordinates$representative_transcript
#> [1] "ENST00000457416.2"
#> 
#> $content$records[[8]]$variants[[3]]$coordinates$chromosome2
#> [1] "10"
#> 
#> $content$records[[8]]$variants[[3]]$coordinates$start2
#> [1] 103544209
#> 
#> $content$records[[8]]$variants[[3]]$coordinates$stop2
#> [1] 103552700
#> 
#> $content$records[[8]]$variants[[3]]$coordinates$representative_transcript2
#> [1] "ENST00000361464.3"
#> 
#> $content$records[[8]]$variants[[3]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[8]]$variants[[3]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> 
#> $content$records[[8]]$type
#> [1] "variant_group"
#> 
#> 
#> $content$records[[9]]
#> $content$records[[9]]$id
#> [1] 9
#> 
#> $content$records[[9]]$name
#> [1] "TSC Loss"
#> 
#> $content$records[[9]]$description
#> [1] "Inactivating events in TSC1 and TSC2 have been observed in a number of cancer types. Cell lines and case studies have shown that in the loss of TSC, the mTOR inhibitor everolimus has seen significant anti-tumorigenic activity. "
#> 
#> $content$records[[9]]$variants
#> $content$records[[9]]$variants[[1]]
#> $content$records[[9]]$variants[[1]]$id
#> [1] 124
#> 
#> $content$records[[9]]$variants[[1]]$entrez_name
#> [1] "TSC1"
#> 
#> $content$records[[9]]$variants[[1]]$entrez_id
#> [1] 7248
#> 
#> $content$records[[9]]$variants[[1]]$name
#> [1] "FRAMESHIFT TRUNCATION"
#> 
#> $content$records[[9]]$variants[[1]]$description
#> [1] "In a small cohort study of bladder cancer, patients with TSC1 mutations showed better responses to and increased treatment duration tolerance with the mTOR inhibitor everolimus. Additionally, patient-derived bladder cancer cell lines with TSC1 or TSC2 mutations are much more sensitive to everolimus treatment than TSC1/TSC2 wildtype cells."
#> 
#> $content$records[[9]]$variants[[1]]$gene_id
#> [1] 46
#> 
#> $content$records[[9]]$variants[[1]]$type
#> [1] "variant"
#> 
#> $content$records[[9]]$variants[[1]]$variant_types
#> $content$records[[9]]$variants[[1]]$variant_types[[1]]
#> $content$records[[9]]$variants[[1]]$variant_types[[1]]$id
#> [1] 134
#> 
#> $content$records[[9]]$variants[[1]]$variant_types[[1]]$name
#> [1] "frameshift_truncation"
#> 
#> $content$records[[9]]$variants[[1]]$variant_types[[1]]$display_name
#> [1] "Frameshift Truncation"
#> 
#> $content$records[[9]]$variants[[1]]$variant_types[[1]]$so_id
#> [1] "SO:0001910"
#> 
#> $content$records[[9]]$variants[[1]]$variant_types[[1]]$description
#> [1] "A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature."
#> 
#> $content$records[[9]]$variants[[1]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001910"
#> 
#> 
#> 
#> $content$records[[9]]$variants[[1]]$civic_actionability_score
#> [1] 18
#> 
#> $content$records[[9]]$variants[[1]]$coordinates
#> $content$records[[9]]$variants[[1]]$coordinates$chromosome
#> [1] "9"
#> 
#> $content$records[[9]]$variants[[1]]$coordinates$start
#> [1] 135766735
#> 
#> $content$records[[9]]$variants[[1]]$coordinates$stop
#> [1] 135820008
#> 
#> $content$records[[9]]$variants[[1]]$coordinates$reference_bases
#> NULL
#> 
#> $content$records[[9]]$variants[[1]]$coordinates$variant_bases
#> NULL
#> 
#> $content$records[[9]]$variants[[1]]$coordinates$representative_transcript
#> [1] "ENST00000298552.3"
#> 
#> $content$records[[9]]$variants[[1]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[9]]$variants[[1]]$coordinates$start2
#> NULL
#> 
#> $content$records[[9]]$variants[[1]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[9]]$variants[[1]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[9]]$variants[[1]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[9]]$variants[[1]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[9]]$variants[[2]]
#> $content$records[[9]]$variants[[2]]$id
#> [1] 125
#> 
#> $content$records[[9]]$variants[[2]]$entrez_name
#> [1] "TSC1"
#> 
#> $content$records[[9]]$variants[[2]]$entrez_id
#> [1] 7248
#> 
#> $content$records[[9]]$variants[[2]]$name
#> [1] "LOSS-OF-FUNCTION"
#> 
#> $content$records[[9]]$variants[[2]]$description
#> [1] "In a small cohort study of bladder cancer, patients with TSC1 mutations showed better responses to and increased treatment duration tolerance with the mTOR inhibitor everolimus. Additionally, patient-derived bladder cancer cell lines with TSC1 or TSC2 mutations are much more sensitive to everolimus treatment than TSC1/TSC2 wildtype cells."
#> 
#> $content$records[[9]]$variants[[2]]$gene_id
#> [1] 46
#> 
#> $content$records[[9]]$variants[[2]]$type
#> [1] "variant"
#> 
#> $content$records[[9]]$variants[[2]]$variant_types
#> $content$records[[9]]$variants[[2]]$variant_types[[1]]
#> $content$records[[9]]$variants[[2]]$variant_types[[1]]$id
#> [1] 161
#> 
#> $content$records[[9]]$variants[[2]]$variant_types[[1]]$name
#> [1] "loss_of_function_variant"
#> 
#> $content$records[[9]]$variants[[2]]$variant_types[[1]]$display_name
#> [1] "Loss Of Function Variant"
#> 
#> $content$records[[9]]$variants[[2]]$variant_types[[1]]$so_id
#> [1] "SO:0002054"
#> 
#> $content$records[[9]]$variants[[2]]$variant_types[[1]]$description
#> [1] "A sequence variant whereby the gene product has diminished or abolished function."
#> 
#> $content$records[[9]]$variants[[2]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0002054"
#> 
#> 
#> 
#> $content$records[[9]]$variants[[2]]$civic_actionability_score
#> [1] 15
#> 
#> $content$records[[9]]$variants[[2]]$coordinates
#> $content$records[[9]]$variants[[2]]$coordinates$chromosome
#> [1] "9"
#> 
#> $content$records[[9]]$variants[[2]]$coordinates$start
#> [1] 135766735
#> 
#> $content$records[[9]]$variants[[2]]$coordinates$stop
#> [1] 135820008
#> 
#> $content$records[[9]]$variants[[2]]$coordinates$reference_bases
#> NULL
#> 
#> $content$records[[9]]$variants[[2]]$coordinates$variant_bases
#> NULL
#> 
#> $content$records[[9]]$variants[[2]]$coordinates$representative_transcript
#> [1] "ENST00000298552.3"
#> 
#> $content$records[[9]]$variants[[2]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[9]]$variants[[2]]$coordinates$start2
#> NULL
#> 
#> $content$records[[9]]$variants[[2]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[9]]$variants[[2]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[9]]$variants[[2]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[9]]$variants[[2]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> 
#> $content$records[[9]]$type
#> [1] "variant_group"
#> 
#> 
#> $content$records[[10]]
#> $content$records[[10]]$id
#> [1] 10
#> 
#> $content$records[[10]]$name
#> [1] "BRCA Germline Variants"
#> 
#> $content$records[[10]]$description
#> [1] "BRCA germline variants have long been recognized as important potential predictors of breast and ovarian cancer risk. "
#> 
#> $content$records[[10]]$variants
#> $content$records[[10]]$variants[[1]]
#> $content$records[[10]]$variants[[1]]$id
#> [1] 132
#> 
#> $content$records[[10]]$variants[[1]]$entrez_name
#> [1] "BRCA2"
#> 
#> $content$records[[10]]$variants[[1]]$entrez_id
#> [1] 675
#> 
#> $content$records[[10]]$variants[[1]]$name
#> [1] "LOSS-OF-FUNCTION"
#> 
#> $content$records[[10]]$variants[[1]]$description
#> [1] "BRCA2 loss of function mutations have been shown to increase risk of breast and ovarian cancer in those carrying the allele in their germline. Treating BRCA mutant patients with PARP inhibitors such as Olaparib has led to significant response."
#> 
#> $content$records[[10]]$variants[[1]]$gene_id
#> [1] 7
#> 
#> $content$records[[10]]$variants[[1]]$type
#> [1] "variant"
#> 
#> $content$records[[10]]$variants[[1]]$variant_types
#> $content$records[[10]]$variants[[1]]$variant_types[[1]]
#> $content$records[[10]]$variants[[1]]$variant_types[[1]]$id
#> [1] 161
#> 
#> $content$records[[10]]$variants[[1]]$variant_types[[1]]$name
#> [1] "loss_of_function_variant"
#> 
#> $content$records[[10]]$variants[[1]]$variant_types[[1]]$display_name
#> [1] "Loss Of Function Variant"
#> 
#> $content$records[[10]]$variants[[1]]$variant_types[[1]]$so_id
#> [1] "SO:0002054"
#> 
#> $content$records[[10]]$variants[[1]]$variant_types[[1]]$description
#> [1] "A sequence variant whereby the gene product has diminished or abolished function."
#> 
#> $content$records[[10]]$variants[[1]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0002054"
#> 
#> 
#> 
#> $content$records[[10]]$variants[[1]]$civic_actionability_score
#> [1] 126
#> 
#> $content$records[[10]]$variants[[1]]$coordinates
#> $content$records[[10]]$variants[[1]]$coordinates$chromosome
#> [1] "13"
#> 
#> $content$records[[10]]$variants[[1]]$coordinates$start
#> [1] 32889611
#> 
#> $content$records[[10]]$variants[[1]]$coordinates$stop
#> [1] 32973347
#> 
#> $content$records[[10]]$variants[[1]]$coordinates$reference_bases
#> NULL
#> 
#> $content$records[[10]]$variants[[1]]$coordinates$variant_bases
#> NULL
#> 
#> $content$records[[10]]$variants[[1]]$coordinates$representative_transcript
#> [1] "ENST00000380152.3"
#> 
#> $content$records[[10]]$variants[[1]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[10]]$variants[[1]]$coordinates$start2
#> NULL
#> 
#> $content$records[[10]]$variants[[1]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[10]]$variants[[1]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[10]]$variants[[1]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[10]]$variants[[1]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[10]]$variants[[2]]
#> $content$records[[10]]$variants[[2]]$id
#> [1] 131
#> 
#> $content$records[[10]]$variants[[2]]$entrez_name
#> [1] "BRCA1"
#> 
#> $content$records[[10]]$variants[[2]]$entrez_id
#> [1] 672
#> 
#> $content$records[[10]]$variants[[2]]$name
#> [1] "LOSS-OF-FUNCTION"
#> 
#> $content$records[[10]]$variants[[2]]$description
#> [1] "BRCA1 loss of function mutations have been shown to increase risk of breast and ovarian cancer in those carrying the allele in their germline. Treating BRCA mutant patients with PARP inhibitors such as Olaparib has led to significant response."
#> 
#> $content$records[[10]]$variants[[2]]$gene_id
#> [1] 6
#> 
#> $content$records[[10]]$variants[[2]]$type
#> [1] "variant"
#> 
#> $content$records[[10]]$variants[[2]]$variant_types
#> $content$records[[10]]$variants[[2]]$variant_types[[1]]
#> $content$records[[10]]$variants[[2]]$variant_types[[1]]$id
#> [1] 161
#> 
#> $content$records[[10]]$variants[[2]]$variant_types[[1]]$name
#> [1] "loss_of_function_variant"
#> 
#> $content$records[[10]]$variants[[2]]$variant_types[[1]]$display_name
#> [1] "Loss Of Function Variant"
#> 
#> $content$records[[10]]$variants[[2]]$variant_types[[1]]$so_id
#> [1] "SO:0002054"
#> 
#> $content$records[[10]]$variants[[2]]$variant_types[[1]]$description
#> [1] "A sequence variant whereby the gene product has diminished or abolished function."
#> 
#> $content$records[[10]]$variants[[2]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0002054"
#> 
#> 
#> $content$records[[10]]$variants[[2]]$variant_types[[2]]
#> $content$records[[10]]$variants[[2]]$variant_types[[2]]$id
#> [1] 97
#> 
#> $content$records[[10]]$variants[[2]]$variant_types[[2]]$name
#> [1] "loss_of_heterozygosity"
#> 
#> $content$records[[10]]$variants[[2]]$variant_types[[2]]$display_name
#> [1] "Loss Of Heterozygosity"
#> 
#> $content$records[[10]]$variants[[2]]$variant_types[[2]]$so_id
#> [1] "SO:0001786"
#> 
#> $content$records[[10]]$variants[[2]]$variant_types[[2]]$description
#> [1] "A functional variant whereby the sequence alteration causes a loss of function of one allele of a gene."
#> 
#> $content$records[[10]]$variants[[2]]$variant_types[[2]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001786"
#> 
#> 
#> 
#> $content$records[[10]]$variants[[2]]$civic_actionability_score
#> [1] 119
#> 
#> $content$records[[10]]$variants[[2]]$coordinates
#> $content$records[[10]]$variants[[2]]$coordinates$chromosome
#> [1] "17"
#> 
#> $content$records[[10]]$variants[[2]]$coordinates$start
#> [1] 41196312
#> 
#> $content$records[[10]]$variants[[2]]$coordinates$stop
#> [1] 41277387
#> 
#> $content$records[[10]]$variants[[2]]$coordinates$reference_bases
#> NULL
#> 
#> $content$records[[10]]$variants[[2]]$coordinates$variant_bases
#> NULL
#> 
#> $content$records[[10]]$variants[[2]]$coordinates$representative_transcript
#> [1] "ENST00000357654.3"
#> 
#> $content$records[[10]]$variants[[2]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[10]]$variants[[2]]$coordinates$start2
#> NULL
#> 
#> $content$records[[10]]$variants[[2]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[10]]$variants[[2]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[10]]$variants[[2]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[10]]$variants[[2]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> 
#> $content$records[[10]]$type
#> [1] "variant_group"
#> 
#> 
#> 
#> 
#> $url
#> [1] "https://civicdb.org/api/variant_groups"
#> 
#> $response
#> Response [https://civicdb.org/api/variant_groups?page=1&count=10]
#>   Date: 2019-09-03 16:44
#>   Status: 200
#>   Content-Type: application/json; charset=utf-8
#>   Size: 48.3 kB
#> 
#> 
#> attr(,"class")
#> [1] "civic_api"
getAllVariantGroups(page = 2, count = 10)
#> $content
#> $content$`_meta`
#> $content$`_meta`$current_page
#> [1] 2
#> 
#> $content$`_meta`$per_page
#> [1] "10"
#> 
#> $content$`_meta`$total_pages
#> [1] 3
#> 
#> $content$`_meta`$total_count
#> [1] 24
#> 
#> $content$`_meta`$links
#> $content$`_meta`$links$`next`
#> [1] "https://civicdb.org/api/variant_groups?count=10&page=3"
#> 
#> $content$`_meta`$links$previous
#> [1] "https://civicdb.org/api/variant_groups?count=10&page=1"
#> 
#> 
#> 
#> $content$records
#> $content$records[[1]]
#> $content$records[[1]]$id
#> [1] 11
#> 
#> $content$records[[1]]$name
#> [1] "ALK Fusions"
#> 
#> $content$records[[1]]$description
#> [1] "ALK fusion positive non-small cell lung cancer (NSCLC) is treated as its own subset of NSCLC. Many ALK fusions that have been seen as recurrent in cancer serve to increase the activity of the ALK oncogene relative to normal cells. While EML4 is the most common fusion partner, other 5' partners have been observed. The EML4-ALK fusion has shown sensitivity to targeted tyrosine kinase inhibitors such as crizotinib. "
#> 
#> $content$records[[1]]$variants
#> $content$records[[1]]$variants[[1]]
#> $content$records[[1]]$variants[[1]]$id
#> [1] 513
#> 
#> $content$records[[1]]$variants[[1]]$entrez_name
#> [1] "ALK"
#> 
#> $content$records[[1]]$variants[[1]]$entrez_id
#> [1] 238
#> 
#> $content$records[[1]]$variants[[1]]$name
#> [1] "NPM-ALK"
#> 
#> $content$records[[1]]$variants[[1]]$description
#> [1] ""
#> 
#> $content$records[[1]]$variants[[1]]$gene_id
#> [1] 1
#> 
#> $content$records[[1]]$variants[[1]]$type
#> [1] "variant"
#> 
#> $content$records[[1]]$variants[[1]]$variant_types
#> $content$records[[1]]$variants[[1]]$variant_types[[1]]
#> $content$records[[1]]$variants[[1]]$variant_types[[1]]$id
#> [1] 120
#> 
#> $content$records[[1]]$variants[[1]]$variant_types[[1]]$name
#> [1] "transcript_fusion"
#> 
#> $content$records[[1]]$variants[[1]]$variant_types[[1]]$display_name
#> [1] "Transcript Fusion"
#> 
#> $content$records[[1]]$variants[[1]]$variant_types[[1]]$so_id
#> [1] "SO:0001886"
#> 
#> $content$records[[1]]$variants[[1]]$variant_types[[1]]$description
#> [1] "A feature fusion where the deletion brings together transcript regions."
#> 
#> $content$records[[1]]$variants[[1]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001886"
#> 
#> 
#> 
#> $content$records[[1]]$variants[[1]]$civic_actionability_score
#> [1] 27
#> 
#> $content$records[[1]]$variants[[1]]$coordinates
#> $content$records[[1]]$variants[[1]]$coordinates$chromosome
#> [1] "5"
#> 
#> $content$records[[1]]$variants[[1]]$coordinates$start
#> [1] 170814120
#> 
#> $content$records[[1]]$variants[[1]]$coordinates$stop
#> [1] 170818803
#> 
#> $content$records[[1]]$variants[[1]]$coordinates$reference_bases
#> NULL
#> 
#> $content$records[[1]]$variants[[1]]$coordinates$variant_bases
#> NULL
#> 
#> $content$records[[1]]$variants[[1]]$coordinates$representative_transcript
#> [1] "ENST00000517671.1"
#> 
#> $content$records[[1]]$variants[[1]]$coordinates$chromosome2
#> [1] "2"
#> 
#> $content$records[[1]]$variants[[1]]$coordinates$start2
#> [1] 29415640
#> 
#> $content$records[[1]]$variants[[1]]$coordinates$stop2
#> [1] 29446394
#> 
#> $content$records[[1]]$variants[[1]]$coordinates$representative_transcript2
#> [1] "ENST00000389048.3"
#> 
#> $content$records[[1]]$variants[[1]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[1]]$variants[[1]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[1]]$variants[[2]]
#> $content$records[[1]]$variants[[2]]$id
#> [1] 514
#> 
#> $content$records[[1]]$variants[[2]]$entrez_name
#> [1] "ALK"
#> 
#> $content$records[[1]]$variants[[2]]$entrez_id
#> [1] 238
#> 
#> $content$records[[1]]$variants[[2]]$name
#> [1] "RANBP2-ALK"
#> 
#> $content$records[[1]]$variants[[2]]$description
#> [1] ""
#> 
#> $content$records[[1]]$variants[[2]]$gene_id
#> [1] 1
#> 
#> $content$records[[1]]$variants[[2]]$type
#> [1] "variant"
#> 
#> $content$records[[1]]$variants[[2]]$variant_types
#> $content$records[[1]]$variants[[2]]$variant_types[[1]]
#> $content$records[[1]]$variants[[2]]$variant_types[[1]]$id
#> [1] 120
#> 
#> $content$records[[1]]$variants[[2]]$variant_types[[1]]$name
#> [1] "transcript_fusion"
#> 
#> $content$records[[1]]$variants[[2]]$variant_types[[1]]$display_name
#> [1] "Transcript Fusion"
#> 
#> $content$records[[1]]$variants[[2]]$variant_types[[1]]$so_id
#> [1] "SO:0001886"
#> 
#> $content$records[[1]]$variants[[2]]$variant_types[[1]]$description
#> [1] "A feature fusion where the deletion brings together transcript regions."
#> 
#> $content$records[[1]]$variants[[2]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001886"
#> 
#> 
#> 
#> $content$records[[1]]$variants[[2]]$civic_actionability_score
#> [1] 10
#> 
#> $content$records[[1]]$variants[[2]]$coordinates
#> $content$records[[1]]$variants[[2]]$coordinates$chromosome
#> [1] "2"
#> 
#> $content$records[[1]]$variants[[2]]$coordinates$start
#> [1] 109335937
#> 
#> $content$records[[1]]$variants[[2]]$coordinates$stop
#> [1] 109375004
#> 
#> $content$records[[1]]$variants[[2]]$coordinates$reference_bases
#> NULL
#> 
#> $content$records[[1]]$variants[[2]]$coordinates$variant_bases
#> NULL
#> 
#> $content$records[[1]]$variants[[2]]$coordinates$representative_transcript
#> [1] "ENST00000283195.6"
#> 
#> $content$records[[1]]$variants[[2]]$coordinates$chromosome2
#> [1] "2"
#> 
#> $content$records[[1]]$variants[[2]]$coordinates$start2
#> [1] 29415640
#> 
#> $content$records[[1]]$variants[[2]]$coordinates$stop2
#> [1] 29446394
#> 
#> $content$records[[1]]$variants[[2]]$coordinates$representative_transcript2
#> [1] "ENST00000389048.3"
#> 
#> $content$records[[1]]$variants[[2]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[1]]$variants[[2]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[1]]$variants[[3]]
#> $content$records[[1]]$variants[[3]]$id
#> [1] 501
#> 
#> $content$records[[1]]$variants[[3]]$entrez_name
#> [1] "ALK"
#> 
#> $content$records[[1]]$variants[[3]]$entrez_id
#> [1] 238
#> 
#> $content$records[[1]]$variants[[3]]$name
#> [1] "EML4-ALK E2;A20"
#> 
#> $content$records[[1]]$variants[[3]]$description
#> [1] ""
#> 
#> $content$records[[1]]$variants[[3]]$gene_id
#> [1] 1
#> 
#> $content$records[[1]]$variants[[3]]$type
#> [1] "variant"
#> 
#> $content$records[[1]]$variants[[3]]$variant_types
#> $content$records[[1]]$variants[[3]]$variant_types[[1]]
#> $content$records[[1]]$variants[[3]]$variant_types[[1]]$id
#> [1] 120
#> 
#> $content$records[[1]]$variants[[3]]$variant_types[[1]]$name
#> [1] "transcript_fusion"
#> 
#> $content$records[[1]]$variants[[3]]$variant_types[[1]]$display_name
#> [1] "Transcript Fusion"
#> 
#> $content$records[[1]]$variants[[3]]$variant_types[[1]]$so_id
#> [1] "SO:0001886"
#> 
#> $content$records[[1]]$variants[[3]]$variant_types[[1]]$description
#> [1] "A feature fusion where the deletion brings together transcript regions."
#> 
#> $content$records[[1]]$variants[[3]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001886"
#> 
#> 
#> 
#> $content$records[[1]]$variants[[3]]$civic_actionability_score
#> [1] 1.75
#> 
#> $content$records[[1]]$variants[[3]]$coordinates
#> $content$records[[1]]$variants[[3]]$coordinates$chromosome
#> [1] "2"
#> 
#> $content$records[[1]]$variants[[3]]$coordinates$start
#> [1] 42396490
#> 
#> $content$records[[1]]$variants[[3]]$coordinates$stop
#> [1] 42472827
#> 
#> $content$records[[1]]$variants[[3]]$coordinates$reference_bases
#> NULL
#> 
#> $content$records[[1]]$variants[[3]]$coordinates$variant_bases
#> NULL
#> 
#> $content$records[[1]]$variants[[3]]$coordinates$representative_transcript
#> [1] "ENST00000318522.5"
#> 
#> $content$records[[1]]$variants[[3]]$coordinates$chromosome2
#> [1] "2"
#> 
#> $content$records[[1]]$variants[[3]]$coordinates$start2
#> [1] 29415640
#> 
#> $content$records[[1]]$variants[[3]]$coordinates$stop2
#> [1] 29446394
#> 
#> $content$records[[1]]$variants[[3]]$coordinates$representative_transcript2
#> [1] "ENST00000389048.3"
#> 
#> $content$records[[1]]$variants[[3]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[1]]$variants[[3]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[1]]$variants[[4]]
#> $content$records[[1]]$variants[[4]]$id
#> [1] 500
#> 
#> $content$records[[1]]$variants[[4]]$entrez_name
#> [1] "ALK"
#> 
#> $content$records[[1]]$variants[[4]]$entrez_id
#> [1] 238
#> 
#> $content$records[[1]]$variants[[4]]$name
#> [1] "EML4-ALK E20;A20"
#> 
#> $content$records[[1]]$variants[[4]]$description
#> [1] "EML4-ALK variant 2 consists of a fusion of the ALK kinase domain (exons 20-29) with EML4 exons 1-20. Variant 2 has cytoplasmic distribution and makes up ~10% of EML4-ALK fusions found in NSCLC,. Although the specific variant is not consistently reported, single cases demonstrating response to crizotinib treatment in NSCLC and a differentiated malignant neoplasm of unknown origin have been reported. In vitro, this variant has shown greater sensitivity to ALK inhibition with TAE684 and crizotinib than the EML4-ALK variants 1 (E13;A20), 3a (E6;A20) and 3b (E6ins33;A20). The variant was reported to be less stable in cells than other variants, and may be a client protein of Hsp90. Along these lines the variant has shown preclinical sensitivity to Hsp90 inhibition."
#> 
#> $content$records[[1]]$variants[[4]]$gene_id
#> [1] 1
#> 
#> $content$records[[1]]$variants[[4]]$type
#> [1] "variant"
#> 
#> $content$records[[1]]$variants[[4]]$variant_types
#> $content$records[[1]]$variants[[4]]$variant_types[[1]]
#> $content$records[[1]]$variants[[4]]$variant_types[[1]]$id
#> [1] 120
#> 
#> $content$records[[1]]$variants[[4]]$variant_types[[1]]$name
#> [1] "transcript_fusion"
#> 
#> $content$records[[1]]$variants[[4]]$variant_types[[1]]$display_name
#> [1] "Transcript Fusion"
#> 
#> $content$records[[1]]$variants[[4]]$variant_types[[1]]$so_id
#> [1] "SO:0001886"
#> 
#> $content$records[[1]]$variants[[4]]$variant_types[[1]]$description
#> [1] "A feature fusion where the deletion brings together transcript regions."
#> 
#> $content$records[[1]]$variants[[4]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001886"
#> 
#> 
#> 
#> $content$records[[1]]$variants[[4]]$civic_actionability_score
#> [1] 16.5
#> 
#> $content$records[[1]]$variants[[4]]$coordinates
#> $content$records[[1]]$variants[[4]]$coordinates$chromosome
#> [1] "2"
#> 
#> $content$records[[1]]$variants[[4]]$coordinates$start
#> [1] 42396490
#> 
#> $content$records[[1]]$variants[[4]]$coordinates$stop
#> [1] 42552694
#> 
#> $content$records[[1]]$variants[[4]]$coordinates$reference_bases
#> NULL
#> 
#> $content$records[[1]]$variants[[4]]$coordinates$variant_bases
#> NULL
#> 
#> $content$records[[1]]$variants[[4]]$coordinates$representative_transcript
#> [1] "ENST00000318522.5"
#> 
#> $content$records[[1]]$variants[[4]]$coordinates$chromosome2
#> [1] "2"
#> 
#> $content$records[[1]]$variants[[4]]$coordinates$start2
#> [1] 29415640
#> 
#> $content$records[[1]]$variants[[4]]$coordinates$stop2
#> [1] 29446394
#> 
#> $content$records[[1]]$variants[[4]]$coordinates$representative_transcript2
#> [1] "ENST00000389048.3"
#> 
#> $content$records[[1]]$variants[[4]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[1]]$variants[[4]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[1]]$variants[[5]]
#> $content$records[[1]]$variants[[5]]$id
#> [1] 520
#> 
#> $content$records[[1]]$variants[[5]]$entrez_name
#> [1] "ALK"
#> 
#> $content$records[[1]]$variants[[5]]$entrez_id
#> [1] 238
#> 
#> $content$records[[1]]$variants[[5]]$name
#> [1] "CLTC-ALK"
#> 
#> $content$records[[1]]$variants[[5]]$description
#> [1] "The t(2;17)(p23;q23) translocation results in the CLTC-ALK fusion protein, the most common ALK fusion observed in diffuse large B cell lymphoma (DLBCL). ALK-rearranged DLBCL is less responsive to CHOP chemotherapy. Preclinical work indicates that CLTC-ALK DLBCL is responsive to ALK inhibition in cell lines and mouse models, and two case studies show short response followed by progression when heavily pretreated and advanced ALK-positive DLBCL is treated with crizotinib (one case CLTC-ALK, one case an unknown ALK fusion)."
#> 
#> $content$records[[1]]$variants[[5]]$gene_id
#> [1] 1
#> 
#> $content$records[[1]]$variants[[5]]$type
#> [1] "variant"
#> 
#> $content$records[[1]]$variants[[5]]$variant_types
#> $content$records[[1]]$variants[[5]]$variant_types[[1]]
#> $content$records[[1]]$variants[[5]]$variant_types[[1]]$id
#> [1] 120
#> 
#> $content$records[[1]]$variants[[5]]$variant_types[[1]]$name
#> [1] "transcript_fusion"
#> 
#> $content$records[[1]]$variants[[5]]$variant_types[[1]]$display_name
#> [1] "Transcript Fusion"
#> 
#> $content$records[[1]]$variants[[5]]$variant_types[[1]]$so_id
#> [1] "SO:0001886"
#> 
#> $content$records[[1]]$variants[[5]]$variant_types[[1]]$description
#> [1] "A feature fusion where the deletion brings together transcript regions."
#> 
#> $content$records[[1]]$variants[[5]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001886"
#> 
#> 
#> 
#> $content$records[[1]]$variants[[5]]$civic_actionability_score
#> [1] 19
#> 
#> $content$records[[1]]$variants[[5]]$coordinates
#> $content$records[[1]]$variants[[5]]$coordinates$chromosome
#> [1] "17"
#> 
#> $content$records[[1]]$variants[[5]]$coordinates$start
#> [1] 57697219
#> 
#> $content$records[[1]]$variants[[5]]$coordinates$stop
#> [1] 57768072
#> 
#> $content$records[[1]]$variants[[5]]$coordinates$reference_bases
#> NULL
#> 
#> $content$records[[1]]$variants[[5]]$coordinates$variant_bases
#> NULL
#> 
#> $content$records[[1]]$variants[[5]]$coordinates$representative_transcript
#> [1] "ENST00000269122.3"
#> 
#> $content$records[[1]]$variants[[5]]$coordinates$chromosome2
#> [1] "2"
#> 
#> $content$records[[1]]$variants[[5]]$coordinates$start2
#> [1] 29415640
#> 
#> $content$records[[1]]$variants[[5]]$coordinates$stop2
#> [1] 29446394
#> 
#> $content$records[[1]]$variants[[5]]$coordinates$representative_transcript2
#> [1] "ENST00000389048.3"
#> 
#> $content$records[[1]]$variants[[5]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[1]]$variants[[5]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[1]]$variants[[6]]
#> $content$records[[1]]$variants[[6]]$id
#> [1] 5
#> 
#> $content$records[[1]]$variants[[6]]$entrez_name
#> [1] "ALK"
#> 
#> $content$records[[1]]$variants[[6]]$entrez_id
#> [1] 238
#> 
#> $content$records[[1]]$variants[[6]]$name
#> [1] "EML4-ALK"
#> 
#> $content$records[[1]]$variants[[6]]$description
#> [1] "The EML4-ALK fusion variant 1 consisting of ALK kinase domain (exons 20-29) fused to EML4 exons 1-13 is the most common EML4-ALK variant, and was discovered in non-small cell lung cancer. Multiple EML4 breakpoint shave been described with differential sensitivity to inhibitors with variant 1 showing greater sensitivity than 3a in cell lines. EML4-ALK is crizotinib sensitive; however, several mutations that confer resistance mutations have been described in case studies. In the only clinical trial for crizotinib that included determination of EML4-ALK variant type in a subset of its participants, a very high response rate was observed, although the numbers were insufficient to validate correlation of variant type to outcome. Preclinical studies with this variant have indicated sensitivity to Hsp90 inhibitors."
#> 
#> $content$records[[1]]$variants[[6]]$gene_id
#> [1] 1
#> 
#> $content$records[[1]]$variants[[6]]$type
#> [1] "variant"
#> 
#> $content$records[[1]]$variants[[6]]$variant_types
#> $content$records[[1]]$variants[[6]]$variant_types[[1]]
#> $content$records[[1]]$variants[[6]]$variant_types[[1]]$id
#> [1] 120
#> 
#> $content$records[[1]]$variants[[6]]$variant_types[[1]]$name
#> [1] "transcript_fusion"
#> 
#> $content$records[[1]]$variants[[6]]$variant_types[[1]]$display_name
#> [1] "Transcript Fusion"
#> 
#> $content$records[[1]]$variants[[6]]$variant_types[[1]]$so_id
#> [1] "SO:0001886"
#> 
#> $content$records[[1]]$variants[[6]]$variant_types[[1]]$description
#> [1] "A feature fusion where the deletion brings together transcript regions."
#> 
#> $content$records[[1]]$variants[[6]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001886"
#> 
#> 
#> 
#> $content$records[[1]]$variants[[6]]$civic_actionability_score
#> [1] 48
#> 
#> $content$records[[1]]$variants[[6]]$coordinates
#> $content$records[[1]]$variants[[6]]$coordinates$chromosome
#> [1] "2"
#> 
#> $content$records[[1]]$variants[[6]]$coordinates$start
#> [1] 42396490
#> 
#> $content$records[[1]]$variants[[6]]$coordinates$stop
#> [1] 42522656
#> 
#> $content$records[[1]]$variants[[6]]$coordinates$reference_bases
#> NULL
#> 
#> $content$records[[1]]$variants[[6]]$coordinates$variant_bases
#> NULL
#> 
#> $content$records[[1]]$variants[[6]]$coordinates$representative_transcript
#> [1] "ENST00000318522.5"
#> 
#> $content$records[[1]]$variants[[6]]$coordinates$chromosome2
#> [1] "2"
#> 
#> $content$records[[1]]$variants[[6]]$coordinates$start2
#> [1] 29415640
#> 
#> $content$records[[1]]$variants[[6]]$coordinates$stop2
#> [1] 29446394
#> 
#> $content$records[[1]]$variants[[6]]$coordinates$representative_transcript2
#> [1] "ENST00000389048.3"
#> 
#> $content$records[[1]]$variants[[6]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[1]]$variants[[6]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[1]]$variants[[7]]
#> $content$records[[1]]$variants[[7]]$id
#> [1] 503
#> 
#> $content$records[[1]]$variants[[7]]$entrez_name
#> [1] "ALK"
#> 
#> $content$records[[1]]$variants[[7]]$entrez_id
#> [1] 238
#> 
#> $content$records[[1]]$variants[[7]]$name
#> [1] "EML4-ALK E6;A20"
#> 
#> $content$records[[1]]$variants[[7]]$description
#> [1] "The EML4-ALK variant 3a consists of the ALK kinase domain fused to EML4 exons 1-6, while the 3b variant has an additional 33bp of intronic EML4 sequence between EML4 and ALK regions. The two variants were found to originate from a single genomic rearrangement, and 3a/3b is found in ~ 30% of EML4-ALK positive NSCLC. Variant 3a has cytoplasmic and nuclear distribution. In vitro, these variants have shown sensitivity to ALK inhibitors TAE684 and crizotinib but less sensitive than other EML4-ALK variants. The H2228 cell line contains 3a and 3b variants and is described as having cyctostatic response to ALK inhibition as opposed to apoptotic. In a study of 31 NSCLC patients with EML4-ALK rearrangements, 4/5 patients with the 3a variant showed a partial response while 1 showed progressive disease (the only PD observed). In cells the 3a variant was reported to be more stable than other variants, less sensitive to crizotinib and not to respond to Hsp90 inhibition."
#> 
#> $content$records[[1]]$variants[[7]]$gene_id
#> [1] 1
#> 
#> $content$records[[1]]$variants[[7]]$type
#> [1] "variant"
#> 
#> $content$records[[1]]$variants[[7]]$variant_types
#> $content$records[[1]]$variants[[7]]$variant_types[[1]]
#> $content$records[[1]]$variants[[7]]$variant_types[[1]]$id
#> [1] 120
#> 
#> $content$records[[1]]$variants[[7]]$variant_types[[1]]$name
#> [1] "transcript_fusion"
#> 
#> $content$records[[1]]$variants[[7]]$variant_types[[1]]$display_name
#> [1] "Transcript Fusion"
#> 
#> $content$records[[1]]$variants[[7]]$variant_types[[1]]$so_id
#> [1] "SO:0001886"
#> 
#> $content$records[[1]]$variants[[7]]$variant_types[[1]]$description
#> [1] "A feature fusion where the deletion brings together transcript regions."
#> 
#> $content$records[[1]]$variants[[7]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001886"
#> 
#> 
#> 
#> $content$records[[1]]$variants[[7]]$civic_actionability_score
#> [1] 25
#> 
#> $content$records[[1]]$variants[[7]]$coordinates
#> $content$records[[1]]$variants[[7]]$coordinates$chromosome
#> [1] "2"
#> 
#> $content$records[[1]]$variants[[7]]$coordinates$start
#> [1] 42396490
#> 
#> $content$records[[1]]$variants[[7]]$coordinates$stop
#> [1] 42491871
#> 
#> $content$records[[1]]$variants[[7]]$coordinates$reference_bases
#> NULL
#> 
#> $content$records[[1]]$variants[[7]]$coordinates$variant_bases
#> NULL
#> 
#> $content$records[[1]]$variants[[7]]$coordinates$representative_transcript
#> [1] "ENST00000318522.5"
#> 
#> $content$records[[1]]$variants[[7]]$coordinates$chromosome2
#> [1] "2"
#> 
#> $content$records[[1]]$variants[[7]]$coordinates$start2
#> [1] 29415640
#> 
#> $content$records[[1]]$variants[[7]]$coordinates$stop2
#> [1] 29446394
#> 
#> $content$records[[1]]$variants[[7]]$coordinates$representative_transcript2
#> [1] "ENST00000389048.3"
#> 
#> $content$records[[1]]$variants[[7]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[1]]$variants[[7]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[1]]$variants[[8]]
#> $content$records[[1]]$variants[[8]]$id
#> [1] 499
#> 
#> $content$records[[1]]$variants[[8]]$entrez_name
#> [1] "ALK"
#> 
#> $content$records[[1]]$variants[[8]]$entrez_id
#> [1] 238
#> 
#> $content$records[[1]]$variants[[8]]$name
#> [1] "ALK FUSIONS"
#> 
#> $content$records[[1]]$variants[[8]]$description
#> [1] "Following the initial discovery and characterization of NPM-ALK fusion mutation in anaplastic large cell lymphoma (ALCL), EML4-ALK fusions were found to be driver mutations in a subset of lung adenocarcinomas. ALK fusions bring the C-terminal ALK kinase domain together with the N terminal region of the fusion partner, and have since been found in a range of cancers including inflammatory myofibroblastic tumor, renal cell carcinoma, diffuse large B cell lymphoma and colorectal cancer. \n\nIn a Phase I trial for crizotinib, a 92% response rate was seen in the subset of patients with a specific EML4-ALK variant, which was higher than the 57% rate in the overall ALK-rearranged population, but the subpopulation numbers were insufficient to correlate variant type with patient response. \n\nDue to restricted wild-type ALK expression, and also mild phenotypes seen in ALK knockout mice, ALK fusions are desirable targets.  ALK inhibitor TAE684 was used in initial characterizations of ALK fusion cancer drivers, and crizotinib – a small molecule ATP-competitor RTK inhibitor which is highly selective for ALK and MET - has been approved as first line therapy in ALK-rearranged NSCLC.   \n\nALK-rearrangement defines an NSCLC subtype that makes up 3-5% of NSCLC cases, and is characterized by higher proportions of younger patients and never smokers. EML4-ALK variant 1 is the most common ALK fusion in NSCLC and was the first to be discovered and demonstrate cancer driver properties in vitro and in mouse models. A Phase I study of crizotinib in ALK-rearranged NSCLC demonstrated an increase in overall survival when compared to standard chemotherapy. These and other initial results prompted accelerated approval for crizotinib in NSCLC.  Continued clinical work demonstrated benefit with crizotinib over chemotherapy in multi-armed studies, and as first line therapy. Crizotinib was also found to remain beneficial to NSCLC patients who had progressed on crizotinib. Additionally, crizotinib was shown to increase intracranial disease control in brain metastasis occurring from ALK-rearranged NSCLC."
#> 
#> $content$records[[1]]$variants[[8]]$gene_id
#> [1] 1
#> 
#> $content$records[[1]]$variants[[8]]$type
#> [1] "variant"
#> 
#> $content$records[[1]]$variants[[8]]$variant_types
#> $content$records[[1]]$variants[[8]]$variant_types[[1]]
#> $content$records[[1]]$variants[[8]]$variant_types[[1]]$id
#> [1] 120
#> 
#> $content$records[[1]]$variants[[8]]$variant_types[[1]]$name
#> [1] "transcript_fusion"
#> 
#> $content$records[[1]]$variants[[8]]$variant_types[[1]]$display_name
#> [1] "Transcript Fusion"
#> 
#> $content$records[[1]]$variants[[8]]$variant_types[[1]]$so_id
#> [1] "SO:0001886"
#> 
#> $content$records[[1]]$variants[[8]]$variant_types[[1]]$description
#> [1] "A feature fusion where the deletion brings together transcript regions."
#> 
#> $content$records[[1]]$variants[[8]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001886"
#> 
#> 
#> 
#> $content$records[[1]]$variants[[8]]$civic_actionability_score
#> [1] 470.5
#> 
#> $content$records[[1]]$variants[[8]]$coordinates
#> $content$records[[1]]$variants[[8]]$coordinates$chromosome
#> [1] "2"
#> 
#> $content$records[[1]]$variants[[8]]$coordinates$start
#> [1] 29415640
#> 
#> $content$records[[1]]$variants[[8]]$coordinates$stop
#> [1] 29446394
#> 
#> $content$records[[1]]$variants[[8]]$coordinates$reference_bases
#> NULL
#> 
#> $content$records[[1]]$variants[[8]]$coordinates$variant_bases
#> NULL
#> 
#> $content$records[[1]]$variants[[8]]$coordinates$representative_transcript
#> [1] "ENST00000389048.3"
#> 
#> $content$records[[1]]$variants[[8]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[1]]$variants[[8]]$coordinates$start2
#> NULL
#> 
#> $content$records[[1]]$variants[[8]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[1]]$variants[[8]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[1]]$variants[[8]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[1]]$variants[[8]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[1]]$variants[[9]]
#> $content$records[[1]]$variants[[9]]$id
#> [1] 6
#> 
#> $content$records[[1]]$variants[[9]]$entrez_name
#> [1] "ALK"
#> 
#> $content$records[[1]]$variants[[9]]$entrez_id
#> [1] 238
#> 
#> $content$records[[1]]$variants[[9]]$name
#> [1] "EML4-ALK C1156Y"
#> 
#> $content$records[[1]]$variants[[9]]$description
#> [1] "In patients with non-small cell lung cancer exhibiting EML4-ALK fusion, C1156Y has been shown to confer resistance to crizotinib. Case reports indicate that secondary mutations can modulate drug sensitivity. EML4-ALK C1156Y/L1196M maintained crizotinib resistance while the lorlatinib resistant combination EML4-ALK C1156Y/L1198F re-sensitized the tumor to crizotinib treatment."
#> 
#> $content$records[[1]]$variants[[9]]$gene_id
#> [1] 1
#> 
#> $content$records[[1]]$variants[[9]]$type
#> [1] "variant"
#> 
#> $content$records[[1]]$variants[[9]]$variant_types
#> $content$records[[1]]$variants[[9]]$variant_types[[1]]
#> $content$records[[1]]$variants[[9]]$variant_types[[1]]$id
#> [1] 120
#> 
#> $content$records[[1]]$variants[[9]]$variant_types[[1]]$name
#> [1] "transcript_fusion"
#> 
#> $content$records[[1]]$variants[[9]]$variant_types[[1]]$display_name
#> [1] "Transcript Fusion"
#> 
#> $content$records[[1]]$variants[[9]]$variant_types[[1]]$so_id
#> [1] "SO:0001886"
#> 
#> $content$records[[1]]$variants[[9]]$variant_types[[1]]$description
#> [1] "A feature fusion where the deletion brings together transcript regions."
#> 
#> $content$records[[1]]$variants[[9]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001886"
#> 
#> 
#> $content$records[[1]]$variants[[9]]$variant_types[[2]]
#> $content$records[[1]]$variants[[9]]$variant_types[[2]]$id
#> [1] 47
#> 
#> $content$records[[1]]$variants[[9]]$variant_types[[2]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[1]]$variants[[9]]$variant_types[[2]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[1]]$variants[[9]]$variant_types[[2]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[1]]$variants[[9]]$variant_types[[2]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[1]]$variants[[9]]$variant_types[[2]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[1]]$variants[[9]]$civic_actionability_score
#> [1] 19
#> 
#> $content$records[[1]]$variants[[9]]$coordinates
#> $content$records[[1]]$variants[[9]]$coordinates$chromosome
#> [1] "2"
#> 
#> $content$records[[1]]$variants[[9]]$coordinates$start
#> [1] 29445258
#> 
#> $content$records[[1]]$variants[[9]]$coordinates$stop
#> [1] 29445258
#> 
#> $content$records[[1]]$variants[[9]]$coordinates$reference_bases
#> [1] "C"
#> 
#> $content$records[[1]]$variants[[9]]$coordinates$variant_bases
#> [1] "T"
#> 
#> $content$records[[1]]$variants[[9]]$coordinates$representative_transcript
#> [1] "ENST00000389048.3"
#> 
#> $content$records[[1]]$variants[[9]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[1]]$variants[[9]]$coordinates$start2
#> NULL
#> 
#> $content$records[[1]]$variants[[9]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[1]]$variants[[9]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[1]]$variants[[9]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[1]]$variants[[9]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[1]]$variants[[10]]
#> $content$records[[1]]$variants[[10]]$id
#> [1] 7
#> 
#> $content$records[[1]]$variants[[10]]$entrez_name
#> [1] "ALK"
#> 
#> $content$records[[1]]$variants[[10]]$entrez_id
#> [1] 238
#> 
#> $content$records[[1]]$variants[[10]]$name
#> [1] "EML4-ALK L1196M"
#> 
#> $content$records[[1]]$variants[[10]]$description
#> [1] "In patients with non-small cell lung cancer exhibiting EML4-ALK fusion, L1196M has been shown to confer resistance to crizotinib. This was also true in a patient with both EML4-ALK C1156Y & L1196M."
#> 
#> $content$records[[1]]$variants[[10]]$gene_id
#> [1] 1
#> 
#> $content$records[[1]]$variants[[10]]$type
#> [1] "variant"
#> 
#> $content$records[[1]]$variants[[10]]$variant_types
#> $content$records[[1]]$variants[[10]]$variant_types[[1]]
#> $content$records[[1]]$variants[[10]]$variant_types[[1]]$id
#> [1] 120
#> 
#> $content$records[[1]]$variants[[10]]$variant_types[[1]]$name
#> [1] "transcript_fusion"
#> 
#> $content$records[[1]]$variants[[10]]$variant_types[[1]]$display_name
#> [1] "Transcript Fusion"
#> 
#> $content$records[[1]]$variants[[10]]$variant_types[[1]]$so_id
#> [1] "SO:0001886"
#> 
#> $content$records[[1]]$variants[[10]]$variant_types[[1]]$description
#> [1] "A feature fusion where the deletion brings together transcript regions."
#> 
#> $content$records[[1]]$variants[[10]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001886"
#> 
#> 
#> $content$records[[1]]$variants[[10]]$variant_types[[2]]
#> $content$records[[1]]$variants[[10]]$variant_types[[2]]$id
#> [1] 47
#> 
#> $content$records[[1]]$variants[[10]]$variant_types[[2]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[1]]$variants[[10]]$variant_types[[2]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[1]]$variants[[10]]$variant_types[[2]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[1]]$variants[[10]]$variant_types[[2]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[1]]$variants[[10]]$variant_types[[2]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[1]]$variants[[10]]$civic_actionability_score
#> [1] 31
#> 
#> $content$records[[1]]$variants[[10]]$coordinates
#> $content$records[[1]]$variants[[10]]$coordinates$chromosome
#> [1] "2"
#> 
#> $content$records[[1]]$variants[[10]]$coordinates$start
#> [1] 29443631
#> 
#> $content$records[[1]]$variants[[10]]$coordinates$stop
#> [1] 29443631
#> 
#> $content$records[[1]]$variants[[10]]$coordinates$reference_bases
#> [1] "G"
#> 
#> $content$records[[1]]$variants[[10]]$coordinates$variant_bases
#> [1] "T"
#> 
#> $content$records[[1]]$variants[[10]]$coordinates$representative_transcript
#> [1] "ENST00000389048.3"
#> 
#> $content$records[[1]]$variants[[10]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[1]]$variants[[10]]$coordinates$start2
#> NULL
#> 
#> $content$records[[1]]$variants[[10]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[1]]$variants[[10]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[1]]$variants[[10]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[1]]$variants[[10]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> 
#> $content$records[[1]]$type
#> [1] "variant_group"
#> 
#> 
#> $content$records[[2]]
#> $content$records[[2]]$id
#> [1] 12
#> 
#> $content$records[[2]]$name
#> [1] "EGFR TKI Resistance"
#> 
#> $content$records[[2]]$description
#> [1] "EGFR pathway activation is a nearly ubiquitous hallmark of cancer. Many tyrosine kinase inhibitors have been developed to target EGFR pathway activity. One such inhibitor, erlotinib, has demonstrated efficacy in an EGFR over-active setting. However, the T790M missense mutation has shown to confer resistance to this inhibitor in cell lines and case studies.  "
#> 
#> $content$records[[2]]$variants
#> $content$records[[2]]$variants[[1]]
#> $content$records[[2]]$variants[[1]]$id
#> [1] 148
#> 
#> $content$records[[2]]$variants[[1]]$entrez_name
#> [1] "KRAS"
#> 
#> $content$records[[2]]$variants[[1]]$entrez_id
#> [1] 3845
#> 
#> $content$records[[2]]$variants[[1]]$name
#> [1] "G12A"
#> 
#> $content$records[[2]]$variants[[1]]$description
#> [1] "KRAS G12A, like EGFR T790M, has been shown to be capable of driving acquired resistance to tyrosine kinase inhibitors in lung adenocarcinoma."
#> 
#> $content$records[[2]]$variants[[1]]$gene_id
#> [1] 30
#> 
#> $content$records[[2]]$variants[[1]]$type
#> [1] "variant"
#> 
#> $content$records[[2]]$variants[[1]]$variant_types
#> $content$records[[2]]$variants[[1]]$variant_types[[1]]
#> $content$records[[2]]$variants[[1]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[2]]$variants[[1]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[2]]$variants[[1]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[2]]$variants[[1]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[2]]$variants[[1]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[2]]$variants[[1]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[2]]$variants[[1]]$civic_actionability_score
#> [1] 48
#> 
#> $content$records[[2]]$variants[[1]]$coordinates
#> $content$records[[2]]$variants[[1]]$coordinates$chromosome
#> [1] "12"
#> 
#> $content$records[[2]]$variants[[1]]$coordinates$start
#> [1] 25398284
#> 
#> $content$records[[2]]$variants[[1]]$coordinates$stop
#> [1] 25398284
#> 
#> $content$records[[2]]$variants[[1]]$coordinates$reference_bases
#> [1] "C"
#> 
#> $content$records[[2]]$variants[[1]]$coordinates$variant_bases
#> [1] "G"
#> 
#> $content$records[[2]]$variants[[1]]$coordinates$representative_transcript
#> [1] "ENST00000256078.4"
#> 
#> $content$records[[2]]$variants[[1]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[2]]$variants[[1]]$coordinates$start2
#> NULL
#> 
#> $content$records[[2]]$variants[[1]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[2]]$variants[[1]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[2]]$variants[[1]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[2]]$variants[[1]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[2]]$variants[[2]]
#> $content$records[[2]]$variants[[2]]$id
#> [1] 78
#> 
#> $content$records[[2]]$variants[[2]]$entrez_name
#> [1] "KRAS"
#> 
#> $content$records[[2]]$variants[[2]]$entrez_id
#> [1] 3845
#> 
#> $content$records[[2]]$variants[[2]]$name
#> [1] "G12C"
#> 
#> $content$records[[2]]$variants[[2]]$description
#> [1] "While the KRAS G12 region is a widely studied recurrent region in cancer, its impact on clinical action is still debated. Often associated with tumors that are wild-type for other drivers (EGFR and ALK specifically), the prognosis for patients with this mutation seems to be worse than the KRAS wild-type cohort in patients with colorectal and pancreatic cancer, however this hypothesis is in need of further validation. This mutation, along with the mutations affecting the neighboring G13 position, may result in a less responsive tumor when treated with first-generation TKI's like gefitinib. However, cetuximab treatment was shown to extend survival in a cohort of colorectal patients."
#> 
#> $content$records[[2]]$variants[[2]]$gene_id
#> [1] 30
#> 
#> $content$records[[2]]$variants[[2]]$type
#> [1] "variant"
#> 
#> $content$records[[2]]$variants[[2]]$variant_types
#> $content$records[[2]]$variants[[2]]$variant_types[[1]]
#> $content$records[[2]]$variants[[2]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[2]]$variants[[2]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[2]]$variants[[2]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[2]]$variants[[2]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[2]]$variants[[2]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[2]]$variants[[2]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[2]]$variants[[2]]$civic_actionability_score
#> [1] 74
#> 
#> $content$records[[2]]$variants[[2]]$coordinates
#> $content$records[[2]]$variants[[2]]$coordinates$chromosome
#> [1] "12"
#> 
#> $content$records[[2]]$variants[[2]]$coordinates$start
#> [1] 25398285
#> 
#> $content$records[[2]]$variants[[2]]$coordinates$stop
#> [1] 25398285
#> 
#> $content$records[[2]]$variants[[2]]$coordinates$reference_bases
#> [1] "C"
#> 
#> $content$records[[2]]$variants[[2]]$coordinates$variant_bases
#> [1] "A"
#> 
#> $content$records[[2]]$variants[[2]]$coordinates$representative_transcript
#> [1] "ENST00000256078.4"
#> 
#> $content$records[[2]]$variants[[2]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[2]]$variants[[2]]$coordinates$start2
#> NULL
#> 
#> $content$records[[2]]$variants[[2]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[2]]$variants[[2]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[2]]$variants[[2]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[2]]$variants[[2]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[2]]$variants[[3]]
#> $content$records[[2]]$variants[[3]]$id
#> [1] 34
#> 
#> $content$records[[2]]$variants[[3]]$entrez_name
#> [1] "EGFR"
#> 
#> $content$records[[2]]$variants[[3]]$entrez_id
#> [1] 1956
#> 
#> $content$records[[2]]$variants[[3]]$name
#> [1] "T790M"
#> 
#> $content$records[[2]]$variants[[3]]$description
#> [1] "EGFR T790M was one of the very first mutations recognized to confer resistance to targeted therapies in non-small cell lung cancer. While successful in amplified EGFR, the efficacy of the first and second generation TKI's (erlotinib, gefitinib, neratinib) in treating patients harboring this mutation before treatment is notably lower. This lack of efficacy can likely be to blame for the poorer prognosis for patients with this mutation as compared to patients with wildtype EGFR or other types of EGFR mutations. Approximately half of EGFR mutant tumors with acquired resistance to TKI inhibition have been shown to harbor this mutation, implicating it as a mechanism of acquired therapy resistence. A third generation TKI (osimertinib) has been approved for the treatment of EGFR T790M mutant NSCLC. Patients positive for T790M in a plasma-based test have similar outcomes like those with tumor biopsy testing."
#> 
#> $content$records[[2]]$variants[[3]]$gene_id
#> [1] 19
#> 
#> $content$records[[2]]$variants[[3]]$type
#> [1] "variant"
#> 
#> $content$records[[2]]$variants[[3]]$variant_types
#> $content$records[[2]]$variants[[3]]$variant_types[[1]]
#> $content$records[[2]]$variants[[3]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[2]]$variants[[3]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[2]]$variants[[3]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[2]]$variants[[3]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[2]]$variants[[3]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[2]]$variants[[3]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[2]]$variants[[3]]$civic_actionability_score
#> [1] 376.25
#> 
#> $content$records[[2]]$variants[[3]]$coordinates
#> $content$records[[2]]$variants[[3]]$coordinates$chromosome
#> [1] "7"
#> 
#> $content$records[[2]]$variants[[3]]$coordinates$start
#> [1] 55249071
#> 
#> $content$records[[2]]$variants[[3]]$coordinates$stop
#> [1] 55249071
#> 
#> $content$records[[2]]$variants[[3]]$coordinates$reference_bases
#> [1] "C"
#> 
#> $content$records[[2]]$variants[[3]]$coordinates$variant_bases
#> [1] "T"
#> 
#> $content$records[[2]]$variants[[3]]$coordinates$representative_transcript
#> [1] "ENST00000275493.2"
#> 
#> $content$records[[2]]$variants[[3]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[2]]$variants[[3]]$coordinates$start2
#> NULL
#> 
#> $content$records[[2]]$variants[[3]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[2]]$variants[[3]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[2]]$variants[[3]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[2]]$variants[[3]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[2]]$variants[[4]]
#> $content$records[[2]]$variants[[4]]$id
#> [1] 79
#> 
#> $content$records[[2]]$variants[[4]]$entrez_name
#> [1] "KRAS"
#> 
#> $content$records[[2]]$variants[[4]]$entrez_id
#> [1] 3845
#> 
#> $content$records[[2]]$variants[[4]]$name
#> [1] "G12D"
#> 
#> $content$records[[2]]$variants[[4]]$description
#> [1] "While the KRAS G12 region is a widely studied recurrent region in cancer, its impact on clinical action is still actively debated. Often associated with tumors that are wild-type for other drivers (EGFR and ALK specifically), the prognosis for patients with this mutation seems to be worse than the KRAS wild-type cohort in patients with colorectal and pancreatic cancer, however this hypothesis is in need of further validation. This mutation, along with the mutations affecting the neighboring G13 position, may result in a less responsive tumor when treated with first-generation TKI's like gefitinib. The NCCN guidelines for colorectal cancer contain recommendations that the targeted therapies cetuximab and panitumumab should only be used in the context of wild type KRAS. However, cetuximab treatment was shown to extend survival in a single cohort of colorectal patients with G12D mutations. Overall, the interpretation for KRAS mutations in most clinical scenarios is still undecided."
#> 
#> $content$records[[2]]$variants[[4]]$gene_id
#> [1] 30
#> 
#> $content$records[[2]]$variants[[4]]$type
#> [1] "variant"
#> 
#> $content$records[[2]]$variants[[4]]$variant_types
#> $content$records[[2]]$variants[[4]]$variant_types[[1]]
#> $content$records[[2]]$variants[[4]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[2]]$variants[[4]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[2]]$variants[[4]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[2]]$variants[[4]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[2]]$variants[[4]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[2]]$variants[[4]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[2]]$variants[[4]]$civic_actionability_score
#> [1] 135.5
#> 
#> $content$records[[2]]$variants[[4]]$coordinates
#> $content$records[[2]]$variants[[4]]$coordinates$chromosome
#> [1] "12"
#> 
#> $content$records[[2]]$variants[[4]]$coordinates$start
#> [1] 25398284
#> 
#> $content$records[[2]]$variants[[4]]$coordinates$stop
#> [1] 25398284
#> 
#> $content$records[[2]]$variants[[4]]$coordinates$reference_bases
#> [1] "C"
#> 
#> $content$records[[2]]$variants[[4]]$coordinates$variant_bases
#> [1] "T"
#> 
#> $content$records[[2]]$variants[[4]]$coordinates$representative_transcript
#> [1] "ENST00000256078.4"
#> 
#> $content$records[[2]]$variants[[4]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[2]]$variants[[4]]$coordinates$start2
#> NULL
#> 
#> $content$records[[2]]$variants[[4]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[2]]$variants[[4]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[2]]$variants[[4]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[2]]$variants[[4]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> 
#> $content$records[[2]]$type
#> [1] "variant_group"
#> 
#> 
#> $content$records[[3]]
#> $content$records[[3]]$id
#> [1] 13
#> 
#> $content$records[[3]]$name
#> [1] "ESR1 Ligand-Binding Domain"
#> 
#> $content$records[[3]]$description
#> [1] "ER-positive breast cancer is the most common of the breast cancer subtypes. Hormone therapy has been widely effective in treating the disease, however sequencing of resistant patients has uncovered a number of missense mutations in mediating this resistance. Many of these mutations lie within the ligand-binding domain, and contribute to constitutive activity of the receptor. This has lead to the development of estrogen receptor degrading agents such as fulvestrant, which have shown early efficacy in clinical trials.  "
#> 
#> $content$records[[3]]$variants
#> $content$records[[3]]$variants[[1]]
#> $content$records[[3]]$variants[[1]]$id
#> [1] 46
#> 
#> $content$records[[3]]$variants[[1]]$entrez_name
#> [1] "ESR1"
#> 
#> $content$records[[3]]$variants[[1]]$entrez_id
#> [1] 2099
#> 
#> $content$records[[3]]$variants[[1]]$name
#> [1] "L536Q"
#> 
#> $content$records[[3]]$variants[[1]]$description
#> [1] "ESR1 biology has become a central focus in breast cancer therapy. In ER+ tumors, mutations in the ESR1 ligand binding domain have been shown to confer resistance to hormone therapy. This evidence has led to an increased use of targeted sequencing of the estrogen receptor in breast and ovarian cancer. Y536Q is one of these ligand binding domain mutations, and is commonly implicated in this hormone resistance. Preliminary data suggests ER-degrading agents, such as fulvestrant, may be beneficial in treating ESR1 mutant, hormone resistant breast cancers."
#> 
#> $content$records[[3]]$variants[[1]]$gene_id
#> [1] 21
#> 
#> $content$records[[3]]$variants[[1]]$type
#> [1] "variant"
#> 
#> $content$records[[3]]$variants[[1]]$variant_types
#> $content$records[[3]]$variants[[1]]$variant_types[[1]]
#> $content$records[[3]]$variants[[1]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[3]]$variants[[1]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[3]]$variants[[1]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[3]]$variants[[1]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[3]]$variants[[1]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[3]]$variants[[1]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[3]]$variants[[1]]$civic_actionability_score
#> [1] 8
#> 
#> $content$records[[3]]$variants[[1]]$coordinates
#> $content$records[[3]]$variants[[1]]$coordinates$chromosome
#> [1] "6"
#> 
#> $content$records[[3]]$variants[[1]]$coordinates$start
#> [1] 152419920
#> 
#> $content$records[[3]]$variants[[1]]$coordinates$stop
#> [1] 152419921
#> 
#> $content$records[[3]]$variants[[1]]$coordinates$reference_bases
#> [1] "TC"
#> 
#> $content$records[[3]]$variants[[1]]$coordinates$variant_bases
#> [1] "AG"
#> 
#> $content$records[[3]]$variants[[1]]$coordinates$representative_transcript
#> [1] "ENST00000440973.1"
#> 
#> $content$records[[3]]$variants[[1]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[3]]$variants[[1]]$coordinates$start2
#> NULL
#> 
#> $content$records[[3]]$variants[[1]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[3]]$variants[[1]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[3]]$variants[[1]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[3]]$variants[[1]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[3]]$variants[[2]]
#> $content$records[[3]]$variants[[2]]$id
#> [1] 49
#> 
#> $content$records[[3]]$variants[[2]]$entrez_name
#> [1] "ESR1"
#> 
#> $content$records[[3]]$variants[[2]]$entrez_id
#> [1] 2099
#> 
#> $content$records[[3]]$variants[[2]]$name
#> [1] "Y537N"
#> 
#> $content$records[[3]]$variants[[2]]$description
#> [1] "ESR1 biology has become a central focus in breast cancer therapy. In ER+ tumors, mutations in the ESR1 ligand binding domain have been shown to confer resistance to hormone therapy. This evidence has led to an increased use of targeted sequencing of the estrogen receptor in breast and ovarian cancer. Y537N is one of these ligand binding domain mutations, and is commonly implicated in this hormone resistance. Preliminary data suggests ER-degrading agents, such as fulvestrant, may be beneficial in treating ESR1 mutant, hormone resistant breast cancers."
#> 
#> $content$records[[3]]$variants[[2]]$gene_id
#> [1] 21
#> 
#> $content$records[[3]]$variants[[2]]$type
#> [1] "variant"
#> 
#> $content$records[[3]]$variants[[2]]$variant_types
#> $content$records[[3]]$variants[[2]]$variant_types[[1]]
#> $content$records[[3]]$variants[[2]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[3]]$variants[[2]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[3]]$variants[[2]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[3]]$variants[[2]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[3]]$variants[[2]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[3]]$variants[[2]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[3]]$variants[[2]]$civic_actionability_score
#> [1] 8
#> 
#> $content$records[[3]]$variants[[2]]$coordinates
#> $content$records[[3]]$variants[[2]]$coordinates$chromosome
#> [1] "6"
#> 
#> $content$records[[3]]$variants[[2]]$coordinates$start
#> [1] 152419922
#> 
#> $content$records[[3]]$variants[[2]]$coordinates$stop
#> [1] 152419922
#> 
#> $content$records[[3]]$variants[[2]]$coordinates$reference_bases
#> [1] "T"
#> 
#> $content$records[[3]]$variants[[2]]$coordinates$variant_bases
#> [1] "A"
#> 
#> $content$records[[3]]$variants[[2]]$coordinates$representative_transcript
#> [1] "ENST00000206249.3"
#> 
#> $content$records[[3]]$variants[[2]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[3]]$variants[[2]]$coordinates$start2
#> NULL
#> 
#> $content$records[[3]]$variants[[2]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[3]]$variants[[2]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[3]]$variants[[2]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[3]]$variants[[2]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[3]]$variants[[3]]
#> $content$records[[3]]$variants[[3]]$id
#> [1] 47
#> 
#> $content$records[[3]]$variants[[3]]$entrez_name
#> [1] "ESR1"
#> 
#> $content$records[[3]]$variants[[3]]$entrez_id
#> [1] 2099
#> 
#> $content$records[[3]]$variants[[3]]$name
#> [1] "D538G"
#> 
#> $content$records[[3]]$variants[[3]]$description
#> [1] "ESR1 biology has become a central focus in breast cancer therapy. In ER+ tumors, mutations in the ESR1 ligand binding domain have been shown to confer resistance to hormone therapy. This evidence has led to an increased use of targeted sequencing of the estrogen receptor in breast and ovarian cancer. D538G is one of these ligand binding domain mutations, and is commonly implicated in this hormone resistance. Preliminary data suggests ER-degrading agents, such as fulvestrant, may be beneficial in treating ESR1 mutant, hormone resistant breast cancers."
#> 
#> $content$records[[3]]$variants[[3]]$gene_id
#> [1] 21
#> 
#> $content$records[[3]]$variants[[3]]$type
#> [1] "variant"
#> 
#> $content$records[[3]]$variants[[3]]$variant_types
#> $content$records[[3]]$variants[[3]]$variant_types[[1]]
#> $content$records[[3]]$variants[[3]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[3]]$variants[[3]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[3]]$variants[[3]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[3]]$variants[[3]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[3]]$variants[[3]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[3]]$variants[[3]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[3]]$variants[[3]]$civic_actionability_score
#> [1] 18
#> 
#> $content$records[[3]]$variants[[3]]$coordinates
#> $content$records[[3]]$variants[[3]]$coordinates$chromosome
#> [1] "6"
#> 
#> $content$records[[3]]$variants[[3]]$coordinates$start
#> [1] 152419926
#> 
#> $content$records[[3]]$variants[[3]]$coordinates$stop
#> [1] 152419926
#> 
#> $content$records[[3]]$variants[[3]]$coordinates$reference_bases
#> [1] "A"
#> 
#> $content$records[[3]]$variants[[3]]$coordinates$variant_bases
#> [1] "G"
#> 
#> $content$records[[3]]$variants[[3]]$coordinates$representative_transcript
#> [1] "ENST00000206249.3"
#> 
#> $content$records[[3]]$variants[[3]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[3]]$variants[[3]]$coordinates$start2
#> NULL
#> 
#> $content$records[[3]]$variants[[3]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[3]]$variants[[3]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[3]]$variants[[3]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[3]]$variants[[3]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[3]]$variants[[4]]
#> $content$records[[3]]$variants[[4]]$id
#> [1] 50
#> 
#> $content$records[[3]]$variants[[4]]$entrez_name
#> [1] "ESR1"
#> 
#> $content$records[[3]]$variants[[4]]$entrez_id
#> [1] 2099
#> 
#> $content$records[[3]]$variants[[4]]$name
#> [1] "Y537S"
#> 
#> $content$records[[3]]$variants[[4]]$description
#> [1] "ESR1 biology has become a central focus in breast cancer therapy. In ER+ tumors, mutations in the ESR1 ligand binding domain have been shown to confer resistance to hormone therapy. This evidence has led to an increased use of targeted sequencing of the estrogen receptor in breast and ovarian cancer. Y537S is one of these ligand binding domain mutations, and is commonly implicated in this hormone resistance. Preliminary data suggests ER-degrading agents, such as fulvestrant, may be beneficial in treating ESR1 mutant, hormone resistant breast cancers."
#> 
#> $content$records[[3]]$variants[[4]]$gene_id
#> [1] 21
#> 
#> $content$records[[3]]$variants[[4]]$type
#> [1] "variant"
#> 
#> $content$records[[3]]$variants[[4]]$variant_types
#> $content$records[[3]]$variants[[4]]$variant_types[[1]]
#> $content$records[[3]]$variants[[4]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[3]]$variants[[4]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[3]]$variants[[4]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[3]]$variants[[4]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[3]]$variants[[4]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[3]]$variants[[4]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[3]]$variants[[4]]$civic_actionability_score
#> [1] 8
#> 
#> $content$records[[3]]$variants[[4]]$coordinates
#> $content$records[[3]]$variants[[4]]$coordinates$chromosome
#> [1] "6"
#> 
#> $content$records[[3]]$variants[[4]]$coordinates$start
#> [1] 152419923
#> 
#> $content$records[[3]]$variants[[4]]$coordinates$stop
#> [1] 152419923
#> 
#> $content$records[[3]]$variants[[4]]$coordinates$reference_bases
#> [1] "A"
#> 
#> $content$records[[3]]$variants[[4]]$coordinates$variant_bases
#> [1] "C"
#> 
#> $content$records[[3]]$variants[[4]]$coordinates$representative_transcript
#> [1] "ENST00000206249.3"
#> 
#> $content$records[[3]]$variants[[4]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[3]]$variants[[4]]$coordinates$start2
#> NULL
#> 
#> $content$records[[3]]$variants[[4]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[3]]$variants[[4]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[3]]$variants[[4]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[3]]$variants[[4]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[3]]$variants[[5]]
#> $content$records[[3]]$variants[[5]]$id
#> [1] 48
#> 
#> $content$records[[3]]$variants[[5]]$entrez_name
#> [1] "ESR1"
#> 
#> $content$records[[3]]$variants[[5]]$entrez_id
#> [1] 2099
#> 
#> $content$records[[3]]$variants[[5]]$name
#> [1] "Y537C"
#> 
#> $content$records[[3]]$variants[[5]]$description
#> [1] "ESR1 biology has become a central focus in breast cancer therapy. In ER+ tumors, mutations in the ESR1 ligand binding domain have been shown to confer resistance to hormone therapy. This evidence has led to an increased use of targeted sequencing of the estrogen receptor in breast and ovarian cancer. Y537C is one of these ligand binding domain mutations, and is commonly implicated in this hormone resistance. Preliminary data suggests ER-degrading agents, such as fulvestrant, may be beneficial in treating ESR1 mutant, hormone resistant breast cancers."
#> 
#> $content$records[[3]]$variants[[5]]$gene_id
#> [1] 21
#> 
#> $content$records[[3]]$variants[[5]]$type
#> [1] "variant"
#> 
#> $content$records[[3]]$variants[[5]]$variant_types
#> $content$records[[3]]$variants[[5]]$variant_types[[1]]
#> $content$records[[3]]$variants[[5]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[3]]$variants[[5]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[3]]$variants[[5]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[3]]$variants[[5]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[3]]$variants[[5]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[3]]$variants[[5]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[3]]$variants[[5]]$civic_actionability_score
#> [1] 8
#> 
#> $content$records[[3]]$variants[[5]]$coordinates
#> $content$records[[3]]$variants[[5]]$coordinates$chromosome
#> [1] "6"
#> 
#> $content$records[[3]]$variants[[5]]$coordinates$start
#> [1] 152419923
#> 
#> $content$records[[3]]$variants[[5]]$coordinates$stop
#> [1] 152419923
#> 
#> $content$records[[3]]$variants[[5]]$coordinates$reference_bases
#> [1] "A"
#> 
#> $content$records[[3]]$variants[[5]]$coordinates$variant_bases
#> [1] "G"
#> 
#> $content$records[[3]]$variants[[5]]$coordinates$representative_transcript
#> [1] "ENST00000206249.3"
#> 
#> $content$records[[3]]$variants[[5]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[3]]$variants[[5]]$coordinates$start2
#> NULL
#> 
#> $content$records[[3]]$variants[[5]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[3]]$variants[[5]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[3]]$variants[[5]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[3]]$variants[[5]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> 
#> $content$records[[3]]$type
#> [1] "variant_group"
#> 
#> 
#> $content$records[[4]]
#> $content$records[[4]]$id
#> [1] 14
#> 
#> $content$records[[4]]$name
#> [1] "HER2 Activating"
#> 
#> $content$records[[4]]$description
#> [1] "HER2-positive breast cancer is widely recognized as a molecular subtype of breast cancer. While amplification of ERBB2 is a common mechanism for activation of the pathway, missense mutations have also demonstrated activation potential. These activating missense mutations also confer sensitivity to the targeted therapeutic neratinib."
#> 
#> $content$records[[4]]$variants
#> $content$records[[4]]$variants[[1]]
#> $content$records[[4]]$variants[[1]]$id
#> [1] 38
#> 
#> $content$records[[4]]$variants[[1]]$entrez_name
#> [1] "ERBB2"
#> 
#> $content$records[[4]]$variants[[1]]$entrez_id
#> [1] 2064
#> 
#> $content$records[[4]]$variants[[1]]$name
#> [1] "G309A"
#> 
#> $content$records[[4]]$variants[[1]]$description
#> [1] "ERBB2 G309A was one of the first ERBB2 variants to be functionally classified (Bose et al. 2013). This mutation was shown to be an activating mutation in an in vitro assay. In the same paper, this mutation (along with other ERBB2 activating mutations) in MCF10A breast cancer cell lines have been shown to be sensitive to the kinase inhibitor neratinib. More recent evidence may show that HER2 acitivating mutations confer sensitivity to a host of tyrosine kinase inhibitors, which is the topic of current clinical trials and research."
#> 
#> $content$records[[4]]$variants[[1]]$gene_id
#> [1] 20
#> 
#> $content$records[[4]]$variants[[1]]$type
#> [1] "variant"
#> 
#> $content$records[[4]]$variants[[1]]$variant_types
#> $content$records[[4]]$variants[[1]]$variant_types[[1]]
#> $content$records[[4]]$variants[[1]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[4]]$variants[[1]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[4]]$variants[[1]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[4]]$variants[[1]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[4]]$variants[[1]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[4]]$variants[[1]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[4]]$variants[[1]]$civic_actionability_score
#> [1] 5
#> 
#> $content$records[[4]]$variants[[1]]$coordinates
#> $content$records[[4]]$variants[[1]]$coordinates$chromosome
#> [1] "17"
#> 
#> $content$records[[4]]$variants[[1]]$coordinates$start
#> [1] 37868205
#> 
#> $content$records[[4]]$variants[[1]]$coordinates$stop
#> [1] 37868205
#> 
#> $content$records[[4]]$variants[[1]]$coordinates$reference_bases
#> [1] "G"
#> 
#> $content$records[[4]]$variants[[1]]$coordinates$variant_bases
#> [1] "C"
#> 
#> $content$records[[4]]$variants[[1]]$coordinates$representative_transcript
#> [1] "ENST00000269571.5"
#> 
#> $content$records[[4]]$variants[[1]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[4]]$variants[[1]]$coordinates$start2
#> NULL
#> 
#> $content$records[[4]]$variants[[1]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[4]]$variants[[1]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[4]]$variants[[1]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[4]]$variants[[1]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[4]]$variants[[2]]
#> $content$records[[4]]$variants[[2]]$id
#> [1] 43
#> 
#> $content$records[[4]]$variants[[2]]$entrez_name
#> [1] "ERBB2"
#> 
#> $content$records[[4]]$variants[[2]]$entrez_id
#> [1] 2064
#> 
#> $content$records[[4]]$variants[[2]]$name
#> [1] "R896C"
#> 
#> $content$records[[4]]$variants[[2]]$description
#> [1] "ERBB2 R896C was one of the first ERBB2 variants to be functionally classified (Bose et al. 2013). This mutation was shown to be an activating mutation in an in vitro assay. In the same paper, this mutation (along with other ERBB2 activating mutations) in MCF10A breast cancer cell lines have been shown to be sensitive to the kinase inhibitor neratinib. More recent evidence may show that HER2 acitivating mutations confer sensitivity to a host of tyrosine kinase inhibitors, which is the topic of current clinical trials and research."
#> 
#> $content$records[[4]]$variants[[2]]$gene_id
#> [1] 20
#> 
#> $content$records[[4]]$variants[[2]]$type
#> [1] "variant"
#> 
#> $content$records[[4]]$variants[[2]]$variant_types
#> $content$records[[4]]$variants[[2]]$variant_types[[1]]
#> $content$records[[4]]$variants[[2]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[4]]$variants[[2]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[4]]$variants[[2]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[4]]$variants[[2]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[4]]$variants[[2]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[4]]$variants[[2]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[4]]$variants[[2]]$civic_actionability_score
#> [1] 5
#> 
#> $content$records[[4]]$variants[[2]]$coordinates
#> $content$records[[4]]$variants[[2]]$coordinates$chromosome
#> [1] "17"
#> 
#> $content$records[[4]]$variants[[2]]$coordinates$start
#> [1] 37881616
#> 
#> $content$records[[4]]$variants[[2]]$coordinates$stop
#> [1] 37881616
#> 
#> $content$records[[4]]$variants[[2]]$coordinates$reference_bases
#> [1] "C"
#> 
#> $content$records[[4]]$variants[[2]]$coordinates$variant_bases
#> [1] "T"
#> 
#> $content$records[[4]]$variants[[2]]$coordinates$representative_transcript
#> [1] "ENST00000269571.5"
#> 
#> $content$records[[4]]$variants[[2]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[4]]$variants[[2]]$coordinates$start2
#> NULL
#> 
#> $content$records[[4]]$variants[[2]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[4]]$variants[[2]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[4]]$variants[[2]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[4]]$variants[[2]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[4]]$variants[[3]]
#> $content$records[[4]]$variants[[3]]$id
#> [1] 44
#> 
#> $content$records[[4]]$variants[[3]]$entrez_name
#> [1] "ERBB2"
#> 
#> $content$records[[4]]$variants[[3]]$entrez_id
#> [1] 2064
#> 
#> $content$records[[4]]$variants[[3]]$name
#> [1] "V777L"
#> 
#> $content$records[[4]]$variants[[3]]$description
#> [1] "ERBB2 V777L was one of the first ERBB2 variants to be functionally classified (Bose et al. 2013). This mutation was shown to be an activating mutation in an in vitro assay. In the same paper, this mutation (along with other ERBB2 activating mutations) in MCF10A breast cancer cell lines have been shown to be sensitive to the kinase inhibitor neratinib. More recent evidence may show that HER2 acitivating mutations confer sensitivity to a host of tyrosine kinase inhibitors, which is the topic of current clinical trials and research."
#> 
#> $content$records[[4]]$variants[[3]]$gene_id
#> [1] 20
#> 
#> $content$records[[4]]$variants[[3]]$type
#> [1] "variant"
#> 
#> $content$records[[4]]$variants[[3]]$variant_types
#> $content$records[[4]]$variants[[3]]$variant_types[[1]]
#> $content$records[[4]]$variants[[3]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[4]]$variants[[3]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[4]]$variants[[3]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[4]]$variants[[3]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[4]]$variants[[3]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[4]]$variants[[3]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[4]]$variants[[3]]$civic_actionability_score
#> [1] 9
#> 
#> $content$records[[4]]$variants[[3]]$coordinates
#> $content$records[[4]]$variants[[3]]$coordinates$chromosome
#> [1] "17"
#> 
#> $content$records[[4]]$variants[[3]]$coordinates$start
#> [1] 37881000
#> 
#> $content$records[[4]]$variants[[3]]$coordinates$stop
#> [1] 37881000
#> 
#> $content$records[[4]]$variants[[3]]$coordinates$reference_bases
#> [1] "G"
#> 
#> $content$records[[4]]$variants[[3]]$coordinates$variant_bases
#> [1] "T"
#> 
#> $content$records[[4]]$variants[[3]]$coordinates$representative_transcript
#> [1] "ENST00000269571.5"
#> 
#> $content$records[[4]]$variants[[3]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[4]]$variants[[3]]$coordinates$start2
#> NULL
#> 
#> $content$records[[4]]$variants[[3]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[4]]$variants[[3]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[4]]$variants[[3]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[4]]$variants[[3]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[4]]$variants[[4]]
#> $content$records[[4]]$variants[[4]]$id
#> [1] 45
#> 
#> $content$records[[4]]$variants[[4]]$entrez_name
#> [1] "ERBB2"
#> 
#> $content$records[[4]]$variants[[4]]$entrez_id
#> [1] 2064
#> 
#> $content$records[[4]]$variants[[4]]$name
#> [1] "V842I"
#> 
#> $content$records[[4]]$variants[[4]]$description
#> [1] "ERBB2 V842I was one of the first ERBB2 variants to be functionally classified (Bose et al. 2013). This mutation was shown to be an activating mutation in an in vitro assay. In the same paper, this mutation (along with other ERBB2 activating mutations) in MCF10A breast cancer cell lines have been shown to be sensitive to the kinase inhibitor neratinib. More recent evidence may show that HER2 acitivating mutations confer sensitivity to a host of tyrosine kinase inhibitors, which is the topic of current clinical trials and research."
#> 
#> $content$records[[4]]$variants[[4]]$gene_id
#> [1] 20
#> 
#> $content$records[[4]]$variants[[4]]$type
#> [1] "variant"
#> 
#> $content$records[[4]]$variants[[4]]$variant_types
#> $content$records[[4]]$variants[[4]]$variant_types[[1]]
#> $content$records[[4]]$variants[[4]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[4]]$variants[[4]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[4]]$variants[[4]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[4]]$variants[[4]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[4]]$variants[[4]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[4]]$variants[[4]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[4]]$variants[[4]]$civic_actionability_score
#> [1] 9
#> 
#> $content$records[[4]]$variants[[4]]$coordinates
#> $content$records[[4]]$variants[[4]]$coordinates$chromosome
#> [1] "17"
#> 
#> $content$records[[4]]$variants[[4]]$coordinates$start
#> [1] 37881332
#> 
#> $content$records[[4]]$variants[[4]]$coordinates$stop
#> [1] 37881332
#> 
#> $content$records[[4]]$variants[[4]]$coordinates$reference_bases
#> [1] "G"
#> 
#> $content$records[[4]]$variants[[4]]$coordinates$variant_bases
#> [1] "A"
#> 
#> $content$records[[4]]$variants[[4]]$coordinates$representative_transcript
#> [1] "ENST00000269571.5"
#> 
#> $content$records[[4]]$variants[[4]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[4]]$variants[[4]]$coordinates$start2
#> NULL
#> 
#> $content$records[[4]]$variants[[4]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[4]]$variants[[4]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[4]]$variants[[4]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[4]]$variants[[4]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[4]]$variants[[5]]
#> $content$records[[4]]$variants[[5]]$id
#> [1] 35
#> 
#> $content$records[[4]]$variants[[5]]$entrez_name
#> [1] "ERBB2"
#> 
#> $content$records[[4]]$variants[[5]]$entrez_id
#> [1] 2064
#> 
#> $content$records[[4]]$variants[[5]]$name
#> [1] "D769H"
#> 
#> $content$records[[4]]$variants[[5]]$description
#> [1] "ERBB2 D769H was one of the first ERBB2 variants to be functionally classified (Bose et al. 2013). This mutation was shown to be an activating mutation in an in vitro assay. In the same paper, this mutation (along with other ERBB2 activating mutations) in MCF10A breast cancer cell lines were shown to be sensitive to the kinase inhibitor neratinib. More recent evidence may show that HER2 activating mutations confer sensitivity to a host of tyrosine kinase inhibitors, which is the topic of current clinical trials and research."
#> 
#> $content$records[[4]]$variants[[5]]$gene_id
#> [1] 20
#> 
#> $content$records[[4]]$variants[[5]]$type
#> [1] "variant"
#> 
#> $content$records[[4]]$variants[[5]]$variant_types
#> $content$records[[4]]$variants[[5]]$variant_types[[1]]
#> $content$records[[4]]$variants[[5]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[4]]$variants[[5]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[4]]$variants[[5]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[4]]$variants[[5]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[4]]$variants[[5]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[4]]$variants[[5]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[4]]$variants[[5]]$civic_actionability_score
#> [1] 4
#> 
#> $content$records[[4]]$variants[[5]]$coordinates
#> $content$records[[4]]$variants[[5]]$coordinates$chromosome
#> [1] "17"
#> 
#> $content$records[[4]]$variants[[5]]$coordinates$start
#> [1] 37880261
#> 
#> $content$records[[4]]$variants[[5]]$coordinates$stop
#> [1] 37880261
#> 
#> $content$records[[4]]$variants[[5]]$coordinates$reference_bases
#> [1] "G"
#> 
#> $content$records[[4]]$variants[[5]]$coordinates$variant_bases
#> [1] "C"
#> 
#> $content$records[[4]]$variants[[5]]$coordinates$representative_transcript
#> [1] "ENST00000269571.5"
#> 
#> $content$records[[4]]$variants[[5]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[4]]$variants[[5]]$coordinates$start2
#> NULL
#> 
#> $content$records[[4]]$variants[[5]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[4]]$variants[[5]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[4]]$variants[[5]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[4]]$variants[[5]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[4]]$variants[[6]]
#> $content$records[[4]]$variants[[6]]$id
#> [1] 41
#> 
#> $content$records[[4]]$variants[[6]]$entrez_name
#> [1] "ERBB2"
#> 
#> $content$records[[4]]$variants[[6]]$entrez_id
#> [1] 2064
#> 
#> $content$records[[4]]$variants[[6]]$name
#> [1] "P780INS"
#> 
#> $content$records[[4]]$variants[[6]]$description
#> [1] "ERBB2 P780 insertion was one of the first ERBB2 variants to be functionally classified (Bose et al. 2013). This mutation was shown to be an activating mutation in an in vitro assay. In the same paper, this mutation (along with other ERBB2 activating mutations) in MCF10A breast cancer cell lines have been shown to be sensitive to the kinase inhibitor neratinib. More recent evidence may show that HER2 activating mutations confer sensitivity to a host of tyrosine kinase inhibitors, which is the topic of current clinical trials and research."
#> 
#> $content$records[[4]]$variants[[6]]$gene_id
#> [1] 20
#> 
#> $content$records[[4]]$variants[[6]]$type
#> [1] "variant"
#> 
#> $content$records[[4]]$variants[[6]]$variant_types
#> $content$records[[4]]$variants[[6]]$variant_types[[1]]
#> $content$records[[4]]$variants[[6]]$variant_types[[1]]$id
#> [1] 106
#> 
#> $content$records[[4]]$variants[[6]]$variant_types[[1]]$name
#> [1] "inframe_insertion"
#> 
#> $content$records[[4]]$variants[[6]]$variant_types[[1]]$display_name
#> [1] "Inframe Insertion"
#> 
#> $content$records[[4]]$variants[[6]]$variant_types[[1]]$so_id
#> [1] "SO:0001821"
#> 
#> $content$records[[4]]$variants[[6]]$variant_types[[1]]$description
#> [1] "An inframe non synonymous variant that inserts bases into in the coding sequence."
#> 
#> $content$records[[4]]$variants[[6]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001821"
#> 
#> 
#> 
#> $content$records[[4]]$variants[[6]]$civic_actionability_score
#> [1] 12.5
#> 
#> $content$records[[4]]$variants[[6]]$coordinates
#> $content$records[[4]]$variants[[6]]$coordinates$chromosome
#> [1] "17"
#> 
#> $content$records[[4]]$variants[[6]]$coordinates$start
#> [1] 37881011
#> 
#> $content$records[[4]]$variants[[6]]$coordinates$stop
#> [1] 37881012
#> 
#> $content$records[[4]]$variants[[6]]$coordinates$reference_bases
#> NULL
#> 
#> $content$records[[4]]$variants[[6]]$coordinates$variant_bases
#> [1] "GGCTCCCCA"
#> 
#> $content$records[[4]]$variants[[6]]$coordinates$representative_transcript
#> [1] "ENST00000269571.5"
#> 
#> $content$records[[4]]$variants[[6]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[4]]$variants[[6]]$coordinates$start2
#> NULL
#> 
#> $content$records[[4]]$variants[[6]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[4]]$variants[[6]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[4]]$variants[[6]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[4]]$variants[[6]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[4]]$variants[[7]]
#> $content$records[[4]]$variants[[7]]$id
#> [1] 36
#> 
#> $content$records[[4]]$variants[[7]]$entrez_name
#> [1] "ERBB2"
#> 
#> $content$records[[4]]$variants[[7]]$entrez_id
#> [1] 2064
#> 
#> $content$records[[4]]$variants[[7]]$name
#> [1] "D769Y"
#> 
#> $content$records[[4]]$variants[[7]]$description
#> [1] "ERBB2 D769Y was one of the first ERBB2 variants to be functionally classified (Bose et al., 2013). This mutation was shown to be an activating mutation in an in vitro assay. In the same paper, this mutation (along with other ERBB2 activating mutations) in MCF10A breast cancer cell lines have been shown to be sensitive to the kinase inhibitor neratinib. More recent evidence may show that HER2 acitivating mutations confer sensitivity to a host of tyrosine kinase inhibitors, which is the topic of current clinical trials and research."
#> 
#> $content$records[[4]]$variants[[7]]$gene_id
#> [1] 20
#> 
#> $content$records[[4]]$variants[[7]]$type
#> [1] "variant"
#> 
#> $content$records[[4]]$variants[[7]]$variant_types
#> $content$records[[4]]$variants[[7]]$variant_types[[1]]
#> $content$records[[4]]$variants[[7]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[4]]$variants[[7]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[4]]$variants[[7]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[4]]$variants[[7]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[4]]$variants[[7]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[4]]$variants[[7]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[4]]$variants[[7]]$civic_actionability_score
#> [1] 4
#> 
#> $content$records[[4]]$variants[[7]]$coordinates
#> $content$records[[4]]$variants[[7]]$coordinates$chromosome
#> [1] "17"
#> 
#> $content$records[[4]]$variants[[7]]$coordinates$start
#> [1] 37880261
#> 
#> $content$records[[4]]$variants[[7]]$coordinates$stop
#> [1] 37880261
#> 
#> $content$records[[4]]$variants[[7]]$coordinates$reference_bases
#> [1] "G"
#> 
#> $content$records[[4]]$variants[[7]]$coordinates$variant_bases
#> [1] "T"
#> 
#> $content$records[[4]]$variants[[7]]$coordinates$representative_transcript
#> [1] "ENST00000269571.5"
#> 
#> $content$records[[4]]$variants[[7]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[4]]$variants[[7]]$coordinates$start2
#> NULL
#> 
#> $content$records[[4]]$variants[[7]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[4]]$variants[[7]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[4]]$variants[[7]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[4]]$variants[[7]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> 
#> $content$records[[4]]$type
#> [1] "variant_group"
#> 
#> 
#> $content$records[[5]]
#> $content$records[[5]]$id
#> [1] 15
#> 
#> $content$records[[5]]$name
#> [1] "PTEN Loss-of-Function"
#> 
#> $content$records[[5]]$description
#> [1] "PTEN loss is a common event in breast cancer, as well as others. The most common single nucleotide variant resulting in PTEN loss is a R233 nonsense mutation. Cell lines harboring this mutation behave similarly to cell lines harboring larger insertion or deletion events, in that they both respond to PI3K-mTOR inhibitors with impeded growth. "
#> 
#> $content$records[[5]]$variants
#> $content$records[[5]]$variants[[1]]
#> $content$records[[5]]$variants[[1]]$id
#> [1] 110
#> 
#> $content$records[[5]]$variants[[1]]$entrez_name
#> [1] "PTEN"
#> 
#> $content$records[[5]]$variants[[1]]$entrez_id
#> [1] 5728
#> 
#> $content$records[[5]]$variants[[1]]$name
#> [1] "R233*"
#> 
#> $content$records[[5]]$variants[[1]]$description
#> [1] "PTEN R233* has been shown to be a loss of function mutation, and PTEN loss has been the subject of considerable research in breast cancer. PTEN loss may sensitize cells to PI3K-mTOR inhibition. While still being debated, there is data to support that PTEN loss is both associated with poorer prognosis, and no change in prognosis."
#> 
#> $content$records[[5]]$variants[[1]]$gene_id
#> [1] 41
#> 
#> $content$records[[5]]$variants[[1]]$type
#> [1] "variant"
#> 
#> $content$records[[5]]$variants[[1]]$variant_types
#> $content$records[[5]]$variants[[1]]$variant_types[[1]]
#> $content$records[[5]]$variants[[1]]$variant_types[[1]]$id
#> [1] 161
#> 
#> $content$records[[5]]$variants[[1]]$variant_types[[1]]$name
#> [1] "loss_of_function_variant"
#> 
#> $content$records[[5]]$variants[[1]]$variant_types[[1]]$display_name
#> [1] "Loss Of Function Variant"
#> 
#> $content$records[[5]]$variants[[1]]$variant_types[[1]]$so_id
#> [1] "SO:0002054"
#> 
#> $content$records[[5]]$variants[[1]]$variant_types[[1]]$description
#> [1] "A sequence variant whereby the gene product has diminished or abolished function."
#> 
#> $content$records[[5]]$variants[[1]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0002054"
#> 
#> 
#> $content$records[[5]]$variants[[1]]$variant_types[[2]]
#> $content$records[[5]]$variants[[1]]$variant_types[[2]]$id
#> [1] 50
#> 
#> $content$records[[5]]$variants[[1]]$variant_types[[2]]$name
#> [1] "stop_gained"
#> 
#> $content$records[[5]]$variants[[1]]$variant_types[[2]]$display_name
#> [1] "Stop Gained"
#> 
#> $content$records[[5]]$variants[[1]]$variant_types[[2]]$so_id
#> [1] "SO:0001587"
#> 
#> $content$records[[5]]$variants[[1]]$variant_types[[2]]$description
#> [1] "A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened polypeptide."
#> 
#> $content$records[[5]]$variants[[1]]$variant_types[[2]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001587"
#> 
#> 
#> 
#> $content$records[[5]]$variants[[1]]$civic_actionability_score
#> [1] 19
#> 
#> $content$records[[5]]$variants[[1]]$coordinates
#> $content$records[[5]]$variants[[1]]$coordinates$chromosome
#> [1] "10"
#> 
#> $content$records[[5]]$variants[[1]]$coordinates$start
#> [1] 89717672
#> 
#> $content$records[[5]]$variants[[1]]$coordinates$stop
#> [1] 89717672
#> 
#> $content$records[[5]]$variants[[1]]$coordinates$reference_bases
#> [1] "C"
#> 
#> $content$records[[5]]$variants[[1]]$coordinates$variant_bases
#> [1] "T"
#> 
#> $content$records[[5]]$variants[[1]]$coordinates$representative_transcript
#> [1] "ENST00000371953.3"
#> 
#> $content$records[[5]]$variants[[1]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[5]]$variants[[1]]$coordinates$start2
#> NULL
#> 
#> $content$records[[5]]$variants[[1]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[5]]$variants[[1]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[5]]$variants[[1]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[5]]$variants[[1]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> 
#> $content$records[[5]]$type
#> [1] "variant_group"
#> 
#> 
#> $content$records[[6]]
#> $content$records[[6]]$id
#> [1] 16
#> 
#> $content$records[[6]]$name
#> [1] "SYT-SSX fusions"
#> 
#> $content$records[[6]]$description
#> [1] "Several fusions between SYT (SS18) and various SSX genes are created by a t(X,18; p11,q11) event (especially SSX1 and SSX2)."
#> 
#> $content$records[[6]]$variants
#> $content$records[[6]]$variants[[1]]
#> $content$records[[6]]$variants[[1]]$id
#> [1] 450
#> 
#> $content$records[[6]]$variants[[1]]$entrez_name
#> [1] "SSX4"
#> 
#> $content$records[[6]]$variants[[1]]$entrez_id
#> [1] 6759
#> 
#> $content$records[[6]]$variants[[1]]$name
#> [1] "SS18-SSX4"
#> 
#> $content$records[[6]]$variants[[1]]$description
#> [1] ""
#> 
#> $content$records[[6]]$variants[[1]]$gene_id
#> [1] 5503
#> 
#> $content$records[[6]]$variants[[1]]$type
#> [1] "variant"
#> 
#> $content$records[[6]]$variants[[1]]$variant_types
#> $content$records[[6]]$variants[[1]]$variant_types[[1]]
#> $content$records[[6]]$variants[[1]]$variant_types[[1]]$id
#> [1] 120
#> 
#> $content$records[[6]]$variants[[1]]$variant_types[[1]]$name
#> [1] "transcript_fusion"
#> 
#> $content$records[[6]]$variants[[1]]$variant_types[[1]]$display_name
#> [1] "Transcript Fusion"
#> 
#> $content$records[[6]]$variants[[1]]$variant_types[[1]]$so_id
#> [1] "SO:0001886"
#> 
#> $content$records[[6]]$variants[[1]]$variant_types[[1]]$description
#> [1] "A feature fusion where the deletion brings together transcript regions."
#> 
#> $content$records[[6]]$variants[[1]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001886"
#> 
#> 
#> 
#> $content$records[[6]]$variants[[1]]$civic_actionability_score
#> [1] 5
#> 
#> $content$records[[6]]$variants[[1]]$coordinates
#> $content$records[[6]]$variants[[1]]$coordinates$chromosome
#> [1] "18"
#> 
#> $content$records[[6]]$variants[[1]]$coordinates$start
#> [1] 23612363
#> 
#> $content$records[[6]]$variants[[1]]$coordinates$stop
#> [1] 23670589
#> 
#> $content$records[[6]]$variants[[1]]$coordinates$reference_bases
#> NULL
#> 
#> $content$records[[6]]$variants[[1]]$coordinates$variant_bases
#> NULL
#> 
#> $content$records[[6]]$variants[[1]]$coordinates$representative_transcript
#> [1] "ENST00000415083.2"
#> 
#> $content$records[[6]]$variants[[1]]$coordinates$chromosome2
#> [1] "X"
#> 
#> $content$records[[6]]$variants[[1]]$coordinates$start2
#> [1] 48261524
#> 
#> $content$records[[6]]$variants[[1]]$coordinates$stop2
#> [1] 48265521
#> 
#> $content$records[[6]]$variants[[1]]$coordinates$representative_transcript2
#> [1] "ENST00000376884.2"
#> 
#> $content$records[[6]]$variants[[1]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[6]]$variants[[1]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[6]]$variants[[2]]
#> $content$records[[6]]$variants[[2]]$id
#> [1] 448
#> 
#> $content$records[[6]]$variants[[2]]$entrez_name
#> [1] "SSX1"
#> 
#> $content$records[[6]]$variants[[2]]$entrez_id
#> [1] 6756
#> 
#> $content$records[[6]]$variants[[2]]$name
#> [1] "SS18-SSX1"
#> 
#> $content$records[[6]]$variants[[2]]$description
#> [1] ""
#> 
#> $content$records[[6]]$variants[[2]]$gene_id
#> [1] 5500
#> 
#> $content$records[[6]]$variants[[2]]$type
#> [1] "variant"
#> 
#> $content$records[[6]]$variants[[2]]$variant_types
#> $content$records[[6]]$variants[[2]]$variant_types[[1]]
#> $content$records[[6]]$variants[[2]]$variant_types[[1]]$id
#> [1] 120
#> 
#> $content$records[[6]]$variants[[2]]$variant_types[[1]]$name
#> [1] "transcript_fusion"
#> 
#> $content$records[[6]]$variants[[2]]$variant_types[[1]]$display_name
#> [1] "Transcript Fusion"
#> 
#> $content$records[[6]]$variants[[2]]$variant_types[[1]]$so_id
#> [1] "SO:0001886"
#> 
#> $content$records[[6]]$variants[[2]]$variant_types[[1]]$description
#> [1] "A feature fusion where the deletion brings together transcript regions."
#> 
#> $content$records[[6]]$variants[[2]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001886"
#> 
#> 
#> 
#> $content$records[[6]]$variants[[2]]$civic_actionability_score
#> [1] 145
#> 
#> $content$records[[6]]$variants[[2]]$coordinates
#> $content$records[[6]]$variants[[2]]$coordinates$chromosome
#> NULL
#> 
#> $content$records[[6]]$variants[[2]]$coordinates$start
#> NULL
#> 
#> $content$records[[6]]$variants[[2]]$coordinates$stop
#> NULL
#> 
#> $content$records[[6]]$variants[[2]]$coordinates$reference_bases
#> NULL
#> 
#> $content$records[[6]]$variants[[2]]$coordinates$variant_bases
#> NULL
#> 
#> $content$records[[6]]$variants[[2]]$coordinates$representative_transcript
#> NULL
#> 
#> $content$records[[6]]$variants[[2]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[6]]$variants[[2]]$coordinates$start2
#> NULL
#> 
#> $content$records[[6]]$variants[[2]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[6]]$variants[[2]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[6]]$variants[[2]]$coordinates$ensembl_version
#> NULL
#> 
#> $content$records[[6]]$variants[[2]]$coordinates$reference_build
#> NULL
#> 
#> 
#> 
#> $content$records[[6]]$variants[[3]]
#> $content$records[[6]]$variants[[3]]$id
#> [1] 449
#> 
#> $content$records[[6]]$variants[[3]]$entrez_name
#> [1] "SSX2"
#> 
#> $content$records[[6]]$variants[[3]]$entrez_id
#> [1] 6757
#> 
#> $content$records[[6]]$variants[[3]]$name
#> [1] "SS18-SSX2"
#> 
#> $content$records[[6]]$variants[[3]]$description
#> [1] ""
#> 
#> $content$records[[6]]$variants[[3]]$gene_id
#> [1] 5501
#> 
#> $content$records[[6]]$variants[[3]]$type
#> [1] "variant"
#> 
#> $content$records[[6]]$variants[[3]]$variant_types
#> $content$records[[6]]$variants[[3]]$variant_types[[1]]
#> $content$records[[6]]$variants[[3]]$variant_types[[1]]$id
#> [1] 120
#> 
#> $content$records[[6]]$variants[[3]]$variant_types[[1]]$name
#> [1] "transcript_fusion"
#> 
#> $content$records[[6]]$variants[[3]]$variant_types[[1]]$display_name
#> [1] "Transcript Fusion"
#> 
#> $content$records[[6]]$variants[[3]]$variant_types[[1]]$so_id
#> [1] "SO:0001886"
#> 
#> $content$records[[6]]$variants[[3]]$variant_types[[1]]$description
#> [1] "A feature fusion where the deletion brings together transcript regions."
#> 
#> $content$records[[6]]$variants[[3]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001886"
#> 
#> 
#> 
#> $content$records[[6]]$variants[[3]]$civic_actionability_score
#> [1] 85
#> 
#> $content$records[[6]]$variants[[3]]$coordinates
#> $content$records[[6]]$variants[[3]]$coordinates$chromosome
#> NULL
#> 
#> $content$records[[6]]$variants[[3]]$coordinates$start
#> NULL
#> 
#> $content$records[[6]]$variants[[3]]$coordinates$stop
#> NULL
#> 
#> $content$records[[6]]$variants[[3]]$coordinates$reference_bases
#> NULL
#> 
#> $content$records[[6]]$variants[[3]]$coordinates$variant_bases
#> NULL
#> 
#> $content$records[[6]]$variants[[3]]$coordinates$representative_transcript
#> NULL
#> 
#> $content$records[[6]]$variants[[3]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[6]]$variants[[3]]$coordinates$start2
#> NULL
#> 
#> $content$records[[6]]$variants[[3]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[6]]$variants[[3]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[6]]$variants[[3]]$coordinates$ensembl_version
#> NULL
#> 
#> $content$records[[6]]$variants[[3]]$coordinates$reference_build
#> NULL
#> 
#> 
#> 
#> 
#> $content$records[[6]]$type
#> [1] "variant_group"
#> 
#> 
#> $content$records[[7]]
#> $content$records[[7]]$id
#> [1] 17
#> 
#> $content$records[[7]]$name
#> [1] "PML-RARa B2 Domain"
#> 
#> $content$records[[7]]$description
#> [1] "The B2 domain of PML is the binding site for ATRA in the PML-RARa fusion protein. Early clinical data may suggest that mutations in this domain may confer resistance to ATRA in patients with APL."
#> 
#> $content$records[[7]]$variants
#> $content$records[[7]]$variants[[1]]
#> $content$records[[7]]$variants[[1]]$id
#> [1] 461
#> 
#> $content$records[[7]]$variants[[1]]$entrez_name
#> [1] "PML"
#> 
#> $content$records[[7]]$variants[[1]]$entrez_id
#> [1] 5371
#> 
#> $content$records[[7]]$variants[[1]]$name
#> [1] "B2 DOMAIN MUTATION"
#> 
#> $content$records[[7]]$variants[[1]]$description
#> [1] "The B2 domain in PML is the binding site for ATRA. Point mutations in this region have been associated with ATRA resistance in patients with APL."
#> 
#> $content$records[[7]]$variants[[1]]$gene_id
#> [1] 39
#> 
#> $content$records[[7]]$variants[[1]]$type
#> [1] "variant"
#> 
#> $content$records[[7]]$variants[[1]]$variant_types
#> $content$records[[7]]$variants[[1]]$variant_types[[1]]
#> $content$records[[7]]$variants[[1]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[7]]$variants[[1]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[7]]$variants[[1]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[7]]$variants[[1]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[7]]$variants[[1]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[7]]$variants[[1]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[7]]$variants[[1]]$civic_actionability_score
#> [1] 20
#> 
#> $content$records[[7]]$variants[[1]]$coordinates
#> $content$records[[7]]$variants[[1]]$coordinates$chromosome
#> [1] "15"
#> 
#> $content$records[[7]]$variants[[1]]$coordinates$start
#> [1] 74315213
#> 
#> $content$records[[7]]$variants[[1]]$coordinates$stop
#> [1] 74315219
#> 
#> $content$records[[7]]$variants[[1]]$coordinates$reference_bases
#> NULL
#> 
#> $content$records[[7]]$variants[[1]]$coordinates$variant_bases
#> NULL
#> 
#> $content$records[[7]]$variants[[1]]$coordinates$representative_transcript
#> [1] "ENST00000268058.3"
#> 
#> $content$records[[7]]$variants[[1]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[7]]$variants[[1]]$coordinates$start2
#> NULL
#> 
#> $content$records[[7]]$variants[[1]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[7]]$variants[[1]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[7]]$variants[[1]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[7]]$variants[[1]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[7]]$variants[[2]]
#> $content$records[[7]]$variants[[2]]$id
#> [1] 463
#> 
#> $content$records[[7]]$variants[[2]]$entrez_name
#> [1] "PML"
#> 
#> $content$records[[7]]$variants[[2]]$entrez_id
#> [1] 5371
#> 
#> $content$records[[7]]$variants[[2]]$name
#> [1] "PML-RARA L218P"
#> 
#> $content$records[[7]]$variants[[2]]$description
#> [1] "L218P in the B2 domain of PML is one of the variants found in a patient with ATRA-resistant APL."
#> 
#> $content$records[[7]]$variants[[2]]$gene_id
#> [1] 39
#> 
#> $content$records[[7]]$variants[[2]]$type
#> [1] "variant"
#> 
#> $content$records[[7]]$variants[[2]]$variant_types
#> $content$records[[7]]$variants[[2]]$variant_types[[1]]
#> $content$records[[7]]$variants[[2]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[7]]$variants[[2]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[7]]$variants[[2]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[7]]$variants[[2]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[7]]$variants[[2]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[7]]$variants[[2]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[7]]$variants[[2]]$civic_actionability_score
#> [1] 7.5
#> 
#> $content$records[[7]]$variants[[2]]$coordinates
#> $content$records[[7]]$variants[[2]]$coordinates$chromosome
#> [1] "15"
#> 
#> $content$records[[7]]$variants[[2]]$coordinates$start
#> [1] 74315219
#> 
#> $content$records[[7]]$variants[[2]]$coordinates$stop
#> [1] 74315219
#> 
#> $content$records[[7]]$variants[[2]]$coordinates$reference_bases
#> [1] "T"
#> 
#> $content$records[[7]]$variants[[2]]$coordinates$variant_bases
#> [1] "C"
#> 
#> $content$records[[7]]$variants[[2]]$coordinates$representative_transcript
#> [1] "ENST00000268058.3"
#> 
#> $content$records[[7]]$variants[[2]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[7]]$variants[[2]]$coordinates$start2
#> NULL
#> 
#> $content$records[[7]]$variants[[2]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[7]]$variants[[2]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[7]]$variants[[2]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[7]]$variants[[2]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[7]]$variants[[3]]
#> $content$records[[7]]$variants[[3]]$id
#> [1] 462
#> 
#> $content$records[[7]]$variants[[3]]$entrez_name
#> [1] "PML"
#> 
#> $content$records[[7]]$variants[[3]]$entrez_id
#> [1] 5371
#> 
#> $content$records[[7]]$variants[[3]]$name
#> [1] "PML-RARA A216V"
#> 
#> $content$records[[7]]$variants[[3]]$description
#> [1] "A216V in the B2 domain of PML is one of the variants found in a patient with ATRA-resistant APL."
#> 
#> $content$records[[7]]$variants[[3]]$gene_id
#> [1] 39
#> 
#> $content$records[[7]]$variants[[3]]$type
#> [1] "variant"
#> 
#> $content$records[[7]]$variants[[3]]$variant_types
#> $content$records[[7]]$variants[[3]]$variant_types[[1]]
#> $content$records[[7]]$variants[[3]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[7]]$variants[[3]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[7]]$variants[[3]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[7]]$variants[[3]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[7]]$variants[[3]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[7]]$variants[[3]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[7]]$variants[[3]]$civic_actionability_score
#> [1] 10
#> 
#> $content$records[[7]]$variants[[3]]$coordinates
#> $content$records[[7]]$variants[[3]]$coordinates$chromosome
#> [1] "15"
#> 
#> $content$records[[7]]$variants[[3]]$coordinates$start
#> [1] 74315213
#> 
#> $content$records[[7]]$variants[[3]]$coordinates$stop
#> [1] 74315213
#> 
#> $content$records[[7]]$variants[[3]]$coordinates$reference_bases
#> [1] "C"
#> 
#> $content$records[[7]]$variants[[3]]$coordinates$variant_bases
#> [1] "T"
#> 
#> $content$records[[7]]$variants[[3]]$coordinates$representative_transcript
#> [1] "ENST00000268058.3"
#> 
#> $content$records[[7]]$variants[[3]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[7]]$variants[[3]]$coordinates$start2
#> NULL
#> 
#> $content$records[[7]]$variants[[3]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[7]]$variants[[3]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[7]]$variants[[3]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[7]]$variants[[3]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> 
#> $content$records[[7]]$type
#> [1] "variant_group"
#> 
#> 
#> $content$records[[8]]
#> $content$records[[8]]$id
#> [1] 18
#> 
#> $content$records[[8]]$name
#> [1] "BRAF Fusions"
#> 
#> $content$records[[8]]$description
#> [1] "BRAF fusions are a rare event in several cancer types but enriched in spitzoid melanoma, pilocytic astrocytomas, pancreatic acinar and papillary thyroid cancers. In a large study, they were observed in 55 (0.3%) of 20,573 tumors, across 12 distinct tumor types. Responses to sorafenib and MEK inhibitors have been described.\nRoss et al., Int. J. Cancer: 138, 881–890 (2016)"
#> 
#> $content$records[[8]]$variants
#> $content$records[[8]]$variants[[1]]
#> $content$records[[8]]$variants[[1]]$id
#> [1] 184
#> 
#> $content$records[[8]]$variants[[1]]$entrez_name
#> [1] "BRAF"
#> 
#> $content$records[[8]]$variants[[1]]$entrez_id
#> [1] 673
#> 
#> $content$records[[8]]$variants[[1]]$name
#> [1] "AKAP9-BRAF"
#> 
#> $content$records[[8]]$variants[[1]]$description
#> [1] ""
#> 
#> $content$records[[8]]$variants[[1]]$gene_id
#> [1] 5
#> 
#> $content$records[[8]]$variants[[1]]$type
#> [1] "variant"
#> 
#> $content$records[[8]]$variants[[1]]$variant_types
#> $content$records[[8]]$variants[[1]]$variant_types[[1]]
#> $content$records[[8]]$variants[[1]]$variant_types[[1]]$id
#> [1] 120
#> 
#> $content$records[[8]]$variants[[1]]$variant_types[[1]]$name
#> [1] "transcript_fusion"
#> 
#> $content$records[[8]]$variants[[1]]$variant_types[[1]]$display_name
#> [1] "Transcript Fusion"
#> 
#> $content$records[[8]]$variants[[1]]$variant_types[[1]]$so_id
#> [1] "SO:0001886"
#> 
#> $content$records[[8]]$variants[[1]]$variant_types[[1]]$description
#> [1] "A feature fusion where the deletion brings together transcript regions."
#> 
#> $content$records[[8]]$variants[[1]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001886"
#> 
#> 
#> 
#> $content$records[[8]]$variants[[1]]$civic_actionability_score
#> [1] 20
#> 
#> $content$records[[8]]$variants[[1]]$coordinates
#> $content$records[[8]]$variants[[1]]$coordinates$chromosome
#> [1] "7"
#> 
#> $content$records[[8]]$variants[[1]]$coordinates$start
#> [1] 91570181
#> 
#> $content$records[[8]]$variants[[1]]$coordinates$stop
#> [1] 91625114
#> 
#> $content$records[[8]]$variants[[1]]$coordinates$reference_bases
#> NULL
#> 
#> $content$records[[8]]$variants[[1]]$coordinates$variant_bases
#> NULL
#> 
#> $content$records[[8]]$variants[[1]]$coordinates$representative_transcript
#> [1] "ENST00000356239.3"
#> 
#> $content$records[[8]]$variants[[1]]$coordinates$chromosome2
#> [1] "7"
#> 
#> $content$records[[8]]$variants[[1]]$coordinates$start2
#> [1] 140434279
#> 
#> $content$records[[8]]$variants[[1]]$coordinates$stop2
#> [1] 140487384
#> 
#> $content$records[[8]]$variants[[1]]$coordinates$representative_transcript2
#> [1] "ENST00000288602.6"
#> 
#> $content$records[[8]]$variants[[1]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[8]]$variants[[1]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[8]]$variants[[2]]
#> $content$records[[8]]$variants[[2]]$id
#> [1] 2229
#> 
#> $content$records[[8]]$variants[[2]]$entrez_name
#> [1] "BRAF"
#> 
#> $content$records[[8]]$variants[[2]]$entrez_id
#> [1] 673
#> 
#> $content$records[[8]]$variants[[2]]$name
#> [1] "CUX1-BRAF"
#> 
#> $content$records[[8]]$variants[[2]]$description
#> [1] ""
#> 
#> $content$records[[8]]$variants[[2]]$gene_id
#> [1] 5
#> 
#> $content$records[[8]]$variants[[2]]$type
#> [1] "variant"
#> 
#> $content$records[[8]]$variants[[2]]$variant_types
#> $content$records[[8]]$variants[[2]]$variant_types[[1]]
#> $content$records[[8]]$variants[[2]]$variant_types[[1]]$id
#> [1] 120
#> 
#> $content$records[[8]]$variants[[2]]$variant_types[[1]]$name
#> [1] "transcript_fusion"
#> 
#> $content$records[[8]]$variants[[2]]$variant_types[[1]]$display_name
#> [1] "Transcript Fusion"
#> 
#> $content$records[[8]]$variants[[2]]$variant_types[[1]]$so_id
#> [1] "SO:0001886"
#> 
#> $content$records[[8]]$variants[[2]]$variant_types[[1]]$description
#> [1] "A feature fusion where the deletion brings together transcript regions."
#> 
#> $content$records[[8]]$variants[[2]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001886"
#> 
#> 
#> 
#> $content$records[[8]]$variants[[2]]$civic_actionability_score
#> [1] 5
#> 
#> $content$records[[8]]$variants[[2]]$coordinates
#> $content$records[[8]]$variants[[2]]$coordinates$chromosome
#> NULL
#> 
#> $content$records[[8]]$variants[[2]]$coordinates$start
#> NULL
#> 
#> $content$records[[8]]$variants[[2]]$coordinates$stop
#> NULL
#> 
#> $content$records[[8]]$variants[[2]]$coordinates$reference_bases
#> NULL
#> 
#> $content$records[[8]]$variants[[2]]$coordinates$variant_bases
#> NULL
#> 
#> $content$records[[8]]$variants[[2]]$coordinates$representative_transcript
#> NULL
#> 
#> $content$records[[8]]$variants[[2]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[8]]$variants[[2]]$coordinates$start2
#> NULL
#> 
#> $content$records[[8]]$variants[[2]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[8]]$variants[[2]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[8]]$variants[[2]]$coordinates$ensembl_version
#> NULL
#> 
#> $content$records[[8]]$variants[[2]]$coordinates$reference_build
#> NULL
#> 
#> 
#> 
#> $content$records[[8]]$variants[[3]]
#> $content$records[[8]]$variants[[3]]$id
#> [1] 286
#> 
#> $content$records[[8]]$variants[[3]]$entrez_name
#> [1] "BRAF"
#> 
#> $content$records[[8]]$variants[[3]]$entrez_id
#> [1] 673
#> 
#> $content$records[[8]]$variants[[3]]$name
#> [1] "PAPSS1-BRAF"
#> 
#> $content$records[[8]]$variants[[3]]$description
#> [1] ""
#> 
#> $content$records[[8]]$variants[[3]]$gene_id
#> [1] 5
#> 
#> $content$records[[8]]$variants[[3]]$type
#> [1] "variant"
#> 
#> $content$records[[8]]$variants[[3]]$variant_types
#> $content$records[[8]]$variants[[3]]$variant_types[[1]]
#> $content$records[[8]]$variants[[3]]$variant_types[[1]]$id
#> [1] 120
#> 
#> $content$records[[8]]$variants[[3]]$variant_types[[1]]$name
#> [1] "transcript_fusion"
#> 
#> $content$records[[8]]$variants[[3]]$variant_types[[1]]$display_name
#> [1] "Transcript Fusion"
#> 
#> $content$records[[8]]$variants[[3]]$variant_types[[1]]$so_id
#> [1] "SO:0001886"
#> 
#> $content$records[[8]]$variants[[3]]$variant_types[[1]]$description
#> [1] "A feature fusion where the deletion brings together transcript regions."
#> 
#> $content$records[[8]]$variants[[3]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001886"
#> 
#> 
#> $content$records[[8]]$variants[[3]]$variant_types[[2]]
#> $content$records[[8]]$variants[[3]]$variant_types[[2]]$id
#> [1] 31
#> 
#> $content$records[[8]]$variants[[3]]$variant_types[[2]]$name
#> [1] "gene_fusion"
#> 
#> $content$records[[8]]$variants[[3]]$variant_types[[2]]$display_name
#> [1] "Gene Fusion"
#> 
#> $content$records[[8]]$variants[[3]]$variant_types[[2]]$so_id
#> [1] "SO:0001565"
#> 
#> $content$records[[8]]$variants[[3]]$variant_types[[2]]$description
#> [1] "A sequence variant whereby a two genes have become joined."
#> 
#> $content$records[[8]]$variants[[3]]$variant_types[[2]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001565"
#> 
#> 
#> 
#> $content$records[[8]]$variants[[3]]$civic_actionability_score
#> [1] 6
#> 
#> $content$records[[8]]$variants[[3]]$coordinates
#> $content$records[[8]]$variants[[3]]$coordinates$chromosome
#> [1] "4"
#> 
#> $content$records[[8]]$variants[[3]]$coordinates$start
#> [1] 108603171
#> 
#> $content$records[[8]]$variants[[3]]$coordinates$stop
#> [1] 108641608
#> 
#> $content$records[[8]]$variants[[3]]$coordinates$reference_bases
#> NULL
#> 
#> $content$records[[8]]$variants[[3]]$coordinates$variant_bases
#> NULL
#> 
#> $content$records[[8]]$variants[[3]]$coordinates$representative_transcript
#> [1] "ENST00000265174.4"
#> 
#> $content$records[[8]]$variants[[3]]$coordinates$chromosome2
#> [1] "7"
#> 
#> $content$records[[8]]$variants[[3]]$coordinates$start2
#> [1] 140434279
#> 
#> $content$records[[8]]$variants[[3]]$coordinates$stop2
#> [1] 140487384
#> 
#> $content$records[[8]]$variants[[3]]$coordinates$representative_transcript2
#> [1] "ENST00000288602.6"
#> 
#> $content$records[[8]]$variants[[3]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[8]]$variants[[3]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[8]]$variants[[4]]
#> $content$records[[8]]$variants[[4]]$id
#> [1] 287
#> 
#> $content$records[[8]]$variants[[4]]$entrez_name
#> [1] "BRAF"
#> 
#> $content$records[[8]]$variants[[4]]$entrez_id
#> [1] 673
#> 
#> $content$records[[8]]$variants[[4]]$name
#> [1] "TRIM24-BRAF"
#> 
#> $content$records[[8]]$variants[[4]]$description
#> [1] ""
#> 
#> $content$records[[8]]$variants[[4]]$gene_id
#> [1] 5
#> 
#> $content$records[[8]]$variants[[4]]$type
#> [1] "variant"
#> 
#> $content$records[[8]]$variants[[4]]$variant_types
#> $content$records[[8]]$variants[[4]]$variant_types[[1]]
#> $content$records[[8]]$variants[[4]]$variant_types[[1]]$id
#> [1] 120
#> 
#> $content$records[[8]]$variants[[4]]$variant_types[[1]]$name
#> [1] "transcript_fusion"
#> 
#> $content$records[[8]]$variants[[4]]$variant_types[[1]]$display_name
#> [1] "Transcript Fusion"
#> 
#> $content$records[[8]]$variants[[4]]$variant_types[[1]]$so_id
#> [1] "SO:0001886"
#> 
#> $content$records[[8]]$variants[[4]]$variant_types[[1]]$description
#> [1] "A feature fusion where the deletion brings together transcript regions."
#> 
#> $content$records[[8]]$variants[[4]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001886"
#> 
#> 
#> 
#> $content$records[[8]]$variants[[4]]$civic_actionability_score
#> [1] 6
#> 
#> $content$records[[8]]$variants[[4]]$coordinates
#> $content$records[[8]]$variants[[4]]$coordinates$chromosome
#> [1] "7"
#> 
#> $content$records[[8]]$variants[[4]]$coordinates$start
#> [1] 138145079
#> 
#> $content$records[[8]]$variants[[4]]$coordinates$stop
#> [1] 138239711
#> 
#> $content$records[[8]]$variants[[4]]$coordinates$reference_bases
#> NULL
#> 
#> $content$records[[8]]$variants[[4]]$coordinates$variant_bases
#> NULL
#> 
#> $content$records[[8]]$variants[[4]]$coordinates$representative_transcript
#> [1] "ENST00000343526.4"
#> 
#> $content$records[[8]]$variants[[4]]$coordinates$chromosome2
#> [1] "7"
#> 
#> $content$records[[8]]$variants[[4]]$coordinates$start2
#> [1] 140434279
#> 
#> $content$records[[8]]$variants[[4]]$coordinates$stop2
#> [1] 140487384
#> 
#> $content$records[[8]]$variants[[4]]$coordinates$representative_transcript2
#> [1] "ENST00000288602.6"
#> 
#> $content$records[[8]]$variants[[4]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[8]]$variants[[4]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[8]]$variants[[5]]
#> $content$records[[8]]$variants[[5]]$id
#> [1] 617
#> 
#> $content$records[[8]]$variants[[5]]$entrez_name
#> [1] "BRAF"
#> 
#> $content$records[[8]]$variants[[5]]$entrez_id
#> [1] 673
#> 
#> $content$records[[8]]$variants[[5]]$name
#> [1] "PPFIBP2-BRAF"
#> 
#> $content$records[[8]]$variants[[5]]$description
#> [1] ""
#> 
#> $content$records[[8]]$variants[[5]]$gene_id
#> [1] 5
#> 
#> $content$records[[8]]$variants[[5]]$type
#> [1] "variant"
#> 
#> $content$records[[8]]$variants[[5]]$variant_types
#> $content$records[[8]]$variants[[5]]$variant_types[[1]]
#> $content$records[[8]]$variants[[5]]$variant_types[[1]]$id
#> [1] 120
#> 
#> $content$records[[8]]$variants[[5]]$variant_types[[1]]$name
#> [1] "transcript_fusion"
#> 
#> $content$records[[8]]$variants[[5]]$variant_types[[1]]$display_name
#> [1] "Transcript Fusion"
#> 
#> $content$records[[8]]$variants[[5]]$variant_types[[1]]$so_id
#> [1] "SO:0001886"
#> 
#> $content$records[[8]]$variants[[5]]$variant_types[[1]]$description
#> [1] "A feature fusion where the deletion brings together transcript regions."
#> 
#> $content$records[[8]]$variants[[5]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001886"
#> 
#> 
#> 
#> $content$records[[8]]$variants[[5]]$civic_actionability_score
#> [1] 5
#> 
#> $content$records[[8]]$variants[[5]]$coordinates
#> $content$records[[8]]$variants[[5]]$coordinates$chromosome
#> [1] "11"
#> 
#> $content$records[[8]]$variants[[5]]$coordinates$start
#> [1] 7535001
#> 
#> $content$records[[8]]$variants[[5]]$coordinates$stop
#> [1] 7586998
#> 
#> $content$records[[8]]$variants[[5]]$coordinates$reference_bases
#> NULL
#> 
#> $content$records[[8]]$variants[[5]]$coordinates$variant_bases
#> NULL
#> 
#> $content$records[[8]]$variants[[5]]$coordinates$representative_transcript
#> [1] "ENST00000299492.4"
#> 
#> $content$records[[8]]$variants[[5]]$coordinates$chromosome2
#> [1] "7"
#> 
#> $content$records[[8]]$variants[[5]]$coordinates$start2
#> [1] 140434279
#> 
#> $content$records[[8]]$variants[[5]]$coordinates$stop2
#> [1] 140481493
#> 
#> $content$records[[8]]$variants[[5]]$coordinates$representative_transcript2
#> [1] "ENST00000288602.6"
#> 
#> $content$records[[8]]$variants[[5]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[8]]$variants[[5]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[8]]$variants[[6]]
#> $content$records[[8]]$variants[[6]]$id
#> [1] 656
#> 
#> $content$records[[8]]$variants[[6]]$entrez_name
#> [1] "BRAF"
#> 
#> $content$records[[8]]$variants[[6]]$entrez_id
#> [1] 673
#> 
#> $content$records[[8]]$variants[[6]]$name
#> [1] "BRAF-CUL1"
#> 
#> $content$records[[8]]$variants[[6]]$description
#> [1] ""
#> 
#> $content$records[[8]]$variants[[6]]$gene_id
#> [1] 5
#> 
#> $content$records[[8]]$variants[[6]]$type
#> [1] "variant"
#> 
#> $content$records[[8]]$variants[[6]]$variant_types
#> $content$records[[8]]$variants[[6]]$variant_types[[1]]
#> $content$records[[8]]$variants[[6]]$variant_types[[1]]$id
#> [1] 120
#> 
#> $content$records[[8]]$variants[[6]]$variant_types[[1]]$name
#> [1] "transcript_fusion"
#> 
#> $content$records[[8]]$variants[[6]]$variant_types[[1]]$display_name
#> [1] "Transcript Fusion"
#> 
#> $content$records[[8]]$variants[[6]]$variant_types[[1]]$so_id
#> [1] "SO:0001886"
#> 
#> $content$records[[8]]$variants[[6]]$variant_types[[1]]$description
#> [1] "A feature fusion where the deletion brings together transcript regions."
#> 
#> $content$records[[8]]$variants[[6]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001886"
#> 
#> 
#> 
#> $content$records[[8]]$variants[[6]]$civic_actionability_score
#> [1] 5
#> 
#> $content$records[[8]]$variants[[6]]$coordinates
#> $content$records[[8]]$variants[[6]]$coordinates$chromosome
#> [1] "7"
#> 
#> $content$records[[8]]$variants[[6]]$coordinates$start
#> [1] 140434279
#> 
#> $content$records[[8]]$variants[[6]]$coordinates$stop
#> [1] 140487384
#> 
#> $content$records[[8]]$variants[[6]]$coordinates$reference_bases
#> NULL
#> 
#> $content$records[[8]]$variants[[6]]$coordinates$variant_bases
#> NULL
#> 
#> $content$records[[8]]$variants[[6]]$coordinates$representative_transcript
#> [1] "ENST00000288602.6"
#> 
#> $content$records[[8]]$variants[[6]]$coordinates$chromosome2
#> [1] "7"
#> 
#> $content$records[[8]]$variants[[6]]$coordinates$start2
#> [1] 148395737
#> 
#> $content$records[[8]]$variants[[6]]$coordinates$stop2
#> [1] 148457588
#> 
#> $content$records[[8]]$variants[[6]]$coordinates$representative_transcript2
#> [1] "ENST00000602748.1"
#> 
#> $content$records[[8]]$variants[[6]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[8]]$variants[[6]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[8]]$variants[[7]]
#> $content$records[[8]]$variants[[7]]$id
#> [1] 657
#> 
#> $content$records[[8]]$variants[[7]]$entrez_name
#> [1] "BRAF"
#> 
#> $content$records[[8]]$variants[[7]]$entrez_id
#> [1] 673
#> 
#> $content$records[[8]]$variants[[7]]$name
#> [1] "ZKSCAN1-BRAF"
#> 
#> $content$records[[8]]$variants[[7]]$description
#> [1] ""
#> 
#> $content$records[[8]]$variants[[7]]$gene_id
#> [1] 5
#> 
#> $content$records[[8]]$variants[[7]]$type
#> [1] "variant"
#> 
#> $content$records[[8]]$variants[[7]]$variant_types
#> $content$records[[8]]$variants[[7]]$variant_types[[1]]
#> $content$records[[8]]$variants[[7]]$variant_types[[1]]$id
#> [1] 120
#> 
#> $content$records[[8]]$variants[[7]]$variant_types[[1]]$name
#> [1] "transcript_fusion"
#> 
#> $content$records[[8]]$variants[[7]]$variant_types[[1]]$display_name
#> [1] "Transcript Fusion"
#> 
#> $content$records[[8]]$variants[[7]]$variant_types[[1]]$so_id
#> [1] "SO:0001886"
#> 
#> $content$records[[8]]$variants[[7]]$variant_types[[1]]$description
#> [1] "A feature fusion where the deletion brings together transcript regions."
#> 
#> $content$records[[8]]$variants[[7]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001886"
#> 
#> 
#> 
#> $content$records[[8]]$variants[[7]]$civic_actionability_score
#> [1] 7.5
#> 
#> $content$records[[8]]$variants[[7]]$coordinates
#> $content$records[[8]]$variants[[7]]$coordinates$chromosome
#> [1] "7"
#> 
#> $content$records[[8]]$variants[[7]]$coordinates$start
#> [1] 99613222
#> 
#> $content$records[[8]]$variants[[7]]$coordinates$stop
#> [1] 99627575
#> 
#> $content$records[[8]]$variants[[7]]$coordinates$reference_bases
#> NULL
#> 
#> $content$records[[8]]$variants[[7]]$coordinates$variant_bases
#> NULL
#> 
#> $content$records[[8]]$variants[[7]]$coordinates$representative_transcript
#> [1] "ENST00000426572.1"
#> 
#> $content$records[[8]]$variants[[7]]$coordinates$chromosome2
#> [1] "7"
#> 
#> $content$records[[8]]$variants[[7]]$coordinates$start2
#> [1] 140434279
#> 
#> $content$records[[8]]$variants[[7]]$coordinates$stop2
#> [1] 140482957
#> 
#> $content$records[[8]]$variants[[7]]$coordinates$representative_transcript2
#> [1] "ENST00000288602.6"
#> 
#> $content$records[[8]]$variants[[7]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[8]]$variants[[7]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[8]]$variants[[8]]
#> $content$records[[8]]$variants[[8]]$id
#> [1] 285
#> 
#> $content$records[[8]]$variants[[8]]$entrez_name
#> [1] "BRAF"
#> 
#> $content$records[[8]]$variants[[8]]$entrez_id
#> [1] 673
#> 
#> $content$records[[8]]$variants[[8]]$name
#> [1] "AGK-BRAF"
#> 
#> $content$records[[8]]$variants[[8]]$description
#> [1] ""
#> 
#> $content$records[[8]]$variants[[8]]$gene_id
#> [1] 5
#> 
#> $content$records[[8]]$variants[[8]]$type
#> [1] "variant"
#> 
#> $content$records[[8]]$variants[[8]]$variant_types
#> $content$records[[8]]$variants[[8]]$variant_types[[1]]
#> $content$records[[8]]$variants[[8]]$variant_types[[1]]$id
#> [1] 120
#> 
#> $content$records[[8]]$variants[[8]]$variant_types[[1]]$name
#> [1] "transcript_fusion"
#> 
#> $content$records[[8]]$variants[[8]]$variant_types[[1]]$display_name
#> [1] "Transcript Fusion"
#> 
#> $content$records[[8]]$variants[[8]]$variant_types[[1]]$so_id
#> [1] "SO:0001886"
#> 
#> $content$records[[8]]$variants[[8]]$variant_types[[1]]$description
#> [1] "A feature fusion where the deletion brings together transcript regions."
#> 
#> $content$records[[8]]$variants[[8]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001886"
#> 
#> 
#> 
#> $content$records[[8]]$variants[[8]]$civic_actionability_score
#> [1] 7
#> 
#> $content$records[[8]]$variants[[8]]$coordinates
#> $content$records[[8]]$variants[[8]]$coordinates$chromosome
#> [1] "7"
#> 
#> $content$records[[8]]$variants[[8]]$coordinates$start
#> [1] 141250989
#> 
#> $content$records[[8]]$variants[[8]]$coordinates$stop
#> [1] 141255367
#> 
#> $content$records[[8]]$variants[[8]]$coordinates$reference_bases
#> NULL
#> 
#> $content$records[[8]]$variants[[8]]$coordinates$variant_bases
#> NULL
#> 
#> $content$records[[8]]$variants[[8]]$coordinates$representative_transcript
#> [1] "ENST00000355413.4"
#> 
#> $content$records[[8]]$variants[[8]]$coordinates$chromosome2
#> [1] "7"
#> 
#> $content$records[[8]]$variants[[8]]$coordinates$start2
#> [1] 140434279
#> 
#> $content$records[[8]]$variants[[8]]$coordinates$stop2
#> [1] 140494267
#> 
#> $content$records[[8]]$variants[[8]]$coordinates$representative_transcript2
#> [1] "ENST00000288602.6"
#> 
#> $content$records[[8]]$variants[[8]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[8]]$variants[[8]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[8]]$variants[[9]]
#> $content$records[[8]]$variants[[9]]$id
#> [1] 618
#> 
#> $content$records[[8]]$variants[[9]]$entrez_name
#> [1] "BRAF"
#> 
#> $content$records[[8]]$variants[[9]]$entrez_id
#> [1] 673
#> 
#> $content$records[[8]]$variants[[9]]$name
#> [1] "KIAA1549-BRAF"
#> 
#> $content$records[[8]]$variants[[9]]$description
#> [1] ""
#> 
#> $content$records[[8]]$variants[[9]]$gene_id
#> [1] 5
#> 
#> $content$records[[8]]$variants[[9]]$type
#> [1] "variant"
#> 
#> $content$records[[8]]$variants[[9]]$variant_types
#> $content$records[[8]]$variants[[9]]$variant_types[[1]]
#> $content$records[[8]]$variants[[9]]$variant_types[[1]]$id
#> [1] 120
#> 
#> $content$records[[8]]$variants[[9]]$variant_types[[1]]$name
#> [1] "transcript_fusion"
#> 
#> $content$records[[8]]$variants[[9]]$variant_types[[1]]$display_name
#> [1] "Transcript Fusion"
#> 
#> $content$records[[8]]$variants[[9]]$variant_types[[1]]$so_id
#> [1] "SO:0001886"
#> 
#> $content$records[[8]]$variants[[9]]$variant_types[[1]]$description
#> [1] "A feature fusion where the deletion brings together transcript regions."
#> 
#> $content$records[[8]]$variants[[9]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001886"
#> 
#> 
#> 
#> $content$records[[8]]$variants[[9]]$civic_actionability_score
#> [1] 35.5
#> 
#> $content$records[[8]]$variants[[9]]$coordinates
#> $content$records[[8]]$variants[[9]]$coordinates$chromosome
#> [1] "7"
#> 
#> $content$records[[8]]$variants[[9]]$coordinates$start
#> [1] 138545885
#> 
#> $content$records[[8]]$variants[[9]]$coordinates$stop
#> [1] 138666064
#> 
#> $content$records[[8]]$variants[[9]]$coordinates$reference_bases
#> NULL
#> 
#> $content$records[[8]]$variants[[9]]$coordinates$variant_bases
#> NULL
#> 
#> $content$records[[8]]$variants[[9]]$coordinates$representative_transcript
#> [1] "ENST00000440172.1"
#> 
#> $content$records[[8]]$variants[[9]]$coordinates$chromosome2
#> [1] "7"
#> 
#> $content$records[[8]]$variants[[9]]$coordinates$start2
#> [1] 140434279
#> 
#> $content$records[[8]]$variants[[9]]$coordinates$stop2
#> [1] 140487384
#> 
#> $content$records[[8]]$variants[[9]]$coordinates$representative_transcript2
#> [1] "ENST00000288602.6"
#> 
#> $content$records[[8]]$variants[[9]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[8]]$variants[[9]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> 
#> $content$records[[8]]$type
#> [1] "variant_group"
#> 
#> 
#> $content$records[[9]]
#> $content$records[[9]]$id
#> [1] 19
#> 
#> $content$records[[9]]$name
#> [1] "Kinase Dead BRAF Mutation"
#> 
#> $content$records[[9]]$description
#> [1] "Several BRAF mutations lead to an inactive form of the BRAF kinase domain and paradoxically lead to MEK-ERK signalling via CRAF binding. \nHeidorn et al., Cell. 2010 Jan 22;140(2):209-21. doi: 10.1016/j.cell.2009.12.040."
#> 
#> $content$records[[9]]$variants
#> $content$records[[9]]$variants[[1]]
#> $content$records[[9]]$variants[[1]]$id
#> [1] 581
#> 
#> $content$records[[9]]$variants[[1]]$entrez_name
#> [1] "BRAF"
#> 
#> $content$records[[9]]$variants[[1]]$entrez_id
#> [1] 673
#> 
#> $content$records[[9]]$variants[[1]]$name
#> [1] "K483M"
#> 
#> $content$records[[9]]$variants[[1]]$description
#> [1] "The K483M variant is a kinase dead loss-of-function variant in the catalytic site of BRAF. This engineered variant is often used as a control when evaluating other BRAF variants."
#> 
#> $content$records[[9]]$variants[[1]]$gene_id
#> [1] 5
#> 
#> $content$records[[9]]$variants[[1]]$type
#> [1] "variant"
#> 
#> $content$records[[9]]$variants[[1]]$variant_types
#> $content$records[[9]]$variants[[1]]$variant_types[[1]]
#> $content$records[[9]]$variants[[1]]$variant_types[[1]]$id
#> [1] 161
#> 
#> $content$records[[9]]$variants[[1]]$variant_types[[1]]$name
#> [1] "loss_of_function_variant"
#> 
#> $content$records[[9]]$variants[[1]]$variant_types[[1]]$display_name
#> [1] "Loss Of Function Variant"
#> 
#> $content$records[[9]]$variants[[1]]$variant_types[[1]]$so_id
#> [1] "SO:0002054"
#> 
#> $content$records[[9]]$variants[[1]]$variant_types[[1]]$description
#> [1] "A sequence variant whereby the gene product has diminished or abolished function."
#> 
#> $content$records[[9]]$variants[[1]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0002054"
#> 
#> 
#> $content$records[[9]]$variants[[1]]$variant_types[[2]]
#> $content$records[[9]]$variants[[1]]$variant_types[[2]]$id
#> [1] 47
#> 
#> $content$records[[9]]$variants[[1]]$variant_types[[2]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[9]]$variants[[1]]$variant_types[[2]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[9]]$variants[[1]]$variant_types[[2]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[9]]$variants[[1]]$variant_types[[2]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[9]]$variants[[1]]$variant_types[[2]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[9]]$variants[[1]]$civic_actionability_score
#> [1] 0.75
#> 
#> $content$records[[9]]$variants[[1]]$coordinates
#> $content$records[[9]]$variants[[1]]$coordinates$chromosome
#> [1] "7"
#> 
#> $content$records[[9]]$variants[[1]]$coordinates$start
#> [1] 140477859
#> 
#> $content$records[[9]]$variants[[1]]$coordinates$stop
#> [1] 140477860
#> 
#> $content$records[[9]]$variants[[1]]$coordinates$reference_bases
#> [1] "TT"
#> 
#> $content$records[[9]]$variants[[1]]$coordinates$variant_bases
#> [1] "CA"
#> 
#> $content$records[[9]]$variants[[1]]$coordinates$representative_transcript
#> [1] "ENST00000288602.6"
#> 
#> $content$records[[9]]$variants[[1]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[9]]$variants[[1]]$coordinates$start2
#> NULL
#> 
#> $content$records[[9]]$variants[[1]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[9]]$variants[[1]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[9]]$variants[[1]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[9]]$variants[[1]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[9]]$variants[[2]]
#> $content$records[[9]]$variants[[2]]$id
#> [1] 579
#> 
#> $content$records[[9]]$variants[[2]]$entrez_name
#> [1] "BRAF"
#> 
#> $content$records[[9]]$variants[[2]]$entrez_id
#> [1] 673
#> 
#> $content$records[[9]]$variants[[2]]$name
#> [1] "D594A"
#> 
#> $content$records[[9]]$variants[[2]]$description
#> [1] ""
#> 
#> $content$records[[9]]$variants[[2]]$gene_id
#> [1] 5
#> 
#> $content$records[[9]]$variants[[2]]$type
#> [1] "variant"
#> 
#> $content$records[[9]]$variants[[2]]$variant_types
#> $content$records[[9]]$variants[[2]]$variant_types[[1]]
#> $content$records[[9]]$variants[[2]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[9]]$variants[[2]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[9]]$variants[[2]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[9]]$variants[[2]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[9]]$variants[[2]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[9]]$variants[[2]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[9]]$variants[[2]]$civic_actionability_score
#> [1] 0.75
#> 
#> $content$records[[9]]$variants[[2]]$coordinates
#> $content$records[[9]]$variants[[2]]$coordinates$chromosome
#> [1] "7"
#> 
#> $content$records[[9]]$variants[[2]]$coordinates$start
#> [1] 140453154
#> 
#> $content$records[[9]]$variants[[2]]$coordinates$stop
#> [1] 140453154
#> 
#> $content$records[[9]]$variants[[2]]$coordinates$reference_bases
#> [1] "T"
#> 
#> $content$records[[9]]$variants[[2]]$coordinates$variant_bases
#> [1] "G"
#> 
#> $content$records[[9]]$variants[[2]]$coordinates$representative_transcript
#> [1] "ENST00000288602.6"
#> 
#> $content$records[[9]]$variants[[2]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[9]]$variants[[2]]$coordinates$start2
#> NULL
#> 
#> $content$records[[9]]$variants[[2]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[9]]$variants[[2]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[9]]$variants[[2]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[9]]$variants[[2]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[9]]$variants[[3]]
#> $content$records[[9]]$variants[[3]]$id
#> [1] 580
#> 
#> $content$records[[9]]$variants[[3]]$entrez_name
#> [1] "BRAF"
#> 
#> $content$records[[9]]$variants[[3]]$entrez_id
#> [1] 673
#> 
#> $content$records[[9]]$variants[[3]]$name
#> [1] "D594V"
#> 
#> $content$records[[9]]$variants[[3]]$description
#> [1] ""
#> 
#> $content$records[[9]]$variants[[3]]$gene_id
#> [1] 5
#> 
#> $content$records[[9]]$variants[[3]]$type
#> [1] "variant"
#> 
#> $content$records[[9]]$variants[[3]]$variant_types
#> $content$records[[9]]$variants[[3]]$variant_types[[1]]
#> $content$records[[9]]$variants[[3]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[9]]$variants[[3]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[9]]$variants[[3]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[9]]$variants[[3]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[9]]$variants[[3]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[9]]$variants[[3]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[9]]$variants[[3]]$civic_actionability_score
#> [1] 0.75
#> 
#> $content$records[[9]]$variants[[3]]$coordinates
#> $content$records[[9]]$variants[[3]]$coordinates$chromosome
#> [1] "7"
#> 
#> $content$records[[9]]$variants[[3]]$coordinates$start
#> [1] 140453154
#> 
#> $content$records[[9]]$variants[[3]]$coordinates$stop
#> [1] 140453154
#> 
#> $content$records[[9]]$variants[[3]]$coordinates$reference_bases
#> [1] "T"
#> 
#> $content$records[[9]]$variants[[3]]$coordinates$variant_bases
#> [1] "A"
#> 
#> $content$records[[9]]$variants[[3]]$coordinates$representative_transcript
#> [1] "ENST00000288602.6"
#> 
#> $content$records[[9]]$variants[[3]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[9]]$variants[[3]]$coordinates$start2
#> NULL
#> 
#> $content$records[[9]]$variants[[3]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[9]]$variants[[3]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[9]]$variants[[3]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[9]]$variants[[3]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> 
#> $content$records[[9]]$type
#> [1] "variant_group"
#> 
#> 
#> $content$records[[10]]
#> $content$records[[10]]$id
#> [1] 20
#> 
#> $content$records[[10]]$name
#> [1] "HEAT domain mutation"
#> 
#> $content$records[[10]]$description
#> [1] ""
#> 
#> $content$records[[10]]$variants
#> $content$records[[10]]$variants[[1]]
#> $content$records[[10]]$variants[[1]]$id
#> [1] 114
#> 
#> $content$records[[10]]$variants[[1]]$entrez_name
#> [1] "SF3B1"
#> 
#> $content$records[[10]]$variants[[1]]$entrez_id
#> [1] 23451
#> 
#> $content$records[[10]]$variants[[1]]$name
#> [1] "K666N"
#> 
#> $content$records[[10]]$variants[[1]]$description
#> [1] "SF3B1 K666N is a variant found in myelodysplastic syndromes, chronic leukemias, and more recently, breast cancer. This somatic mutation has been linked to better overall outcome and event-free survival in MDS patients."
#> 
#> $content$records[[10]]$variants[[1]]$gene_id
#> [1] 44
#> 
#> $content$records[[10]]$variants[[1]]$type
#> [1] "variant"
#> 
#> $content$records[[10]]$variants[[1]]$variant_types
#> $content$records[[10]]$variants[[1]]$variant_types[[1]]
#> $content$records[[10]]$variants[[1]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[10]]$variants[[1]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[10]]$variants[[1]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[10]]$variants[[1]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[10]]$variants[[1]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[10]]$variants[[1]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[10]]$variants[[1]]$civic_actionability_score
#> [1] 2
#> 
#> $content$records[[10]]$variants[[1]]$coordinates
#> $content$records[[10]]$variants[[1]]$coordinates$chromosome
#> [1] "2"
#> 
#> $content$records[[10]]$variants[[1]]$coordinates$start
#> [1] 198267359
#> 
#> $content$records[[10]]$variants[[1]]$coordinates$stop
#> [1] 198267359
#> 
#> $content$records[[10]]$variants[[1]]$coordinates$reference_bases
#> [1] "C"
#> 
#> $content$records[[10]]$variants[[1]]$coordinates$variant_bases
#> [1] "A"
#> 
#> $content$records[[10]]$variants[[1]]$coordinates$representative_transcript
#> [1] "ENST00000335508.6"
#> 
#> $content$records[[10]]$variants[[1]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[10]]$variants[[1]]$coordinates$start2
#> NULL
#> 
#> $content$records[[10]]$variants[[1]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[10]]$variants[[1]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[10]]$variants[[1]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[10]]$variants[[1]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> $content$records[[10]]$variants[[2]]
#> $content$records[[10]]$variants[[2]]$id
#> [1] 565
#> 
#> $content$records[[10]]$variants[[2]]$entrez_name
#> [1] "SF3B1"
#> 
#> $content$records[[10]]$variants[[2]]$entrez_id
#> [1] 23451
#> 
#> $content$records[[10]]$variants[[2]]$name
#> [1] "K700E"
#> 
#> $content$records[[10]]$variants[[2]]$description
#> [1] ""
#> 
#> $content$records[[10]]$variants[[2]]$gene_id
#> [1] 44
#> 
#> $content$records[[10]]$variants[[2]]$type
#> [1] "variant"
#> 
#> $content$records[[10]]$variants[[2]]$variant_types
#> $content$records[[10]]$variants[[2]]$variant_types[[1]]
#> $content$records[[10]]$variants[[2]]$variant_types[[1]]$id
#> [1] 47
#> 
#> $content$records[[10]]$variants[[2]]$variant_types[[1]]$name
#> [1] "missense_variant"
#> 
#> $content$records[[10]]$variants[[2]]$variant_types[[1]]$display_name
#> [1] "Missense Variant"
#> 
#> $content$records[[10]]$variants[[2]]$variant_types[[1]]$so_id
#> [1] "SO:0001583"
#> 
#> $content$records[[10]]$variants[[2]]$variant_types[[1]]$description
#> [1] "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved."
#> 
#> $content$records[[10]]$variants[[2]]$variant_types[[1]]$url
#> [1] "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583"
#> 
#> 
#> 
#> $content$records[[10]]$variants[[2]]$civic_actionability_score
#> [1] 2
#> 
#> $content$records[[10]]$variants[[2]]$coordinates
#> $content$records[[10]]$variants[[2]]$coordinates$chromosome
#> [1] "2"
#> 
#> $content$records[[10]]$variants[[2]]$coordinates$start
#> [1] 198266834
#> 
#> $content$records[[10]]$variants[[2]]$coordinates$stop
#> [1] 198266834
#> 
#> $content$records[[10]]$variants[[2]]$coordinates$reference_bases
#> [1] "T"
#> 
#> $content$records[[10]]$variants[[2]]$coordinates$variant_bases
#> [1] "C"
#> 
#> $content$records[[10]]$variants[[2]]$coordinates$representative_transcript
#> [1] "ENST00000335508.6"
#> 
#> $content$records[[10]]$variants[[2]]$coordinates$chromosome2
#> NULL
#> 
#> $content$records[[10]]$variants[[2]]$coordinates$start2
#> NULL
#> 
#> $content$records[[10]]$variants[[2]]$coordinates$stop2
#> NULL
#> 
#> $content$records[[10]]$variants[[2]]$coordinates$representative_transcript2
#> NULL
#> 
#> $content$records[[10]]$variants[[2]]$coordinates$ensembl_version
#> [1] 75
#> 
#> $content$records[[10]]$variants[[2]]$coordinates$reference_build
#> [1] "GRCh37"
#> 
#> 
#> 
#> 
#> $content$records[[10]]$type
#> [1] "variant_group"
#> 
#> 
#> 
#> 
#> $url
#> [1] "https://civicdb.org/api/variant_groups"
#> 
#> $response
#> Response [https://civicdb.org/api/variant_groups?page=2&count=10]
#>   Date: 2019-09-03 16:44
#>   Status: 200
#>   Content-Type: application/json; charset=utf-8
#>   Size: 56.5 kB
#> 
#> 
#> attr(,"class")
#> [1] "civic_api"