{"id":"https://openalex.org/W2954070001","doi":"https://doi.org/10.1158/1538-7445.am2019-5108","title":"Abstract 5108: Somatic small variant and copy number alteration calling with the Genome Analysis Toolkit","display_name":"Abstract 5108: Somatic small variant and copy number alteration calling with the Genome Analysis Toolkit","publication_year":2019,"publication_date":"2019-07-01","ids":{"openalex":"https://openalex.org/W2954070001","doi":"https://doi.org/10.1158/1538-7445.am2019-5108","mag":"2954070001"},"language":"en","primary_location":{"id":"doi:10.1158/1538-7445.am2019-5108","doi":"https://doi.org/10.1158/1538-7445.am2019-5108","is_oa":false,"landing_page_url":"https://doi.org/10.1158/1538-7445.am2019-5108","pdf_url":null,"source":{"id":"https://openalex.org/S168522863","display_name":"Cancer Research","issn_l":"0008-5472","issn":["0008-5472","1538-7445"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320273","host_organization_name":"American Association for Cancer Research","host_organization_lineage":["https://openalex.org/P4310320273"],"host_organization_lineage_names":["American Association for Cancer Research"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Cancer Research","raw_type":"journal-article"},"volume":null,"type":"conference-abstract","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5109952396","display_name":"Lee Lichtenstein","orcid":"https://orcid.org/0000-0003-0477-4401","observed_orcids":["https://orcid.org/0000-0003-0477-4401"]},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lee Lichtenstein","raw_affiliation_strings":["Broad Institute of MIT and Harvard, Cambridge, MA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Broad Institute of MIT and Harvard, Cambridge, MA","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5141658285","display_name":"Jonn Smith","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jonn Smith","raw_affiliation_strings":["Broad Institute of MIT and Harvard, Cambridge, MA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Broad Institute of MIT and Harvard, Cambridge, MA","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110511664","display_name":"David I. Benjamin","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David Benjamin","raw_affiliation_strings":["Broad Institute of MIT and Harvard, Cambridge, MA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Broad Institute of MIT and Harvard, Cambridge, MA","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075946443","display_name":"Aaron A. Chevalier","orcid":"https://orcid.org/0000-0002-3968-9250","observed_orcids":["https://orcid.org/0000-0002-3968-9250","https://orcid.org/0000-0002-3173-7350"]},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aaron Chevalier","raw_affiliation_strings":["Broad Institute of MIT and Harvard, Cambridge, MA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Broad Institute of MIT and Harvard, Cambridge, MA","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056650437","display_name":"Kristian Cibulskis","orcid":"https://orcid.org/0000-0003-1343-1582","observed_orcids":["https://orcid.org/0000-0003-1343-1582"]},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kristian Cibulskis","raw_affiliation_strings":["Broad Institute of MIT and Harvard, Cambridge, MA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Broad Institute of MIT and Harvard, Cambridge, MA","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081227382","display_name":"Samuel K. Lee","orcid":"https://orcid.org/0000-0001-6733-0547","observed_orcids":["https://orcid.org/0000-0001-6733-0547"]},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Samuel K. Lee","raw_affiliation_strings":["Broad Institute of MIT and Harvard, Cambridge, MA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Broad Institute of MIT and Harvard, Cambridge, MA","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5029475781","display_name":"Eric Banks","orcid":"https://orcid.org/0000-0001-9615-2372","observed_orcids":["https://orcid.org/0000-0001-9615-2372"]},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eric Banks","raw_affiliation_strings":["Broad Institute of MIT and Harvard, Cambridge, MA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Broad Institute of MIT and Harvard, Cambridge, MA","institution_ids":["https://openalex.org/I107606265"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I107606265"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"79","issue":"13_Supplement","first_page":"5108","last_page":"5108"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.8324999809265137,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.8324999809265137,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.13729999959468842,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.019099999219179153,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/somatic-variant-calling","display_name":"somatic variant calling","score":0.9890000224113464},{"id":"https://openalex.org/keywords/copy-number-alterations","display_name":"copy number alterations","score":0.8899999856948853},{"id":"https://openalex.org/keywords/gatk","display_name":"GATK","score":0.7369999885559082},{"id":"https://openalex.org/keywords/single-nucleotide-variants","display_name":"single nucleotide variants","score":0.9100000262260437},{"id":"https://openalex.org/keywords/indels","display_name":"indels","score":0.8840000033378601},{"id":"https://openalex.org/keywords/cancer-genomics","display_name":"cancer genomics","score":0.7689999938011169},{"id":"https://openalex.org/keywords/sequencing-artifacts","display_name":"sequencing artifacts","score":0.36000001430511475},{"id":"https://openalex.org/keywords/dream-challenge","display_name":"DREAM challenge","score":0.5460000038146973}],"concepts":[{"id":"https://openalex.org/C119054055","wikidata":"https://www.wikidata.org/wiki/Q1576681","display_name":"Indel","level":5,"score":0.8657413721084595},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.586677074432373},{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.5808266997337341},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5446169376373291},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5167409777641296},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.47820234298706055},{"id":"https://openalex.org/C120821319","wikidata":"https://www.wikidata.org/wiki/Q1501491","display_name":"Copy-number variation","level":4,"score":0.47500407695770264},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4304802715778351},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.43006718158721924},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2963252663612366},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.2537849545478821},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.10951080918312073},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.09000661969184875},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.08563381433486938}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1158/1538-7445.am2019-5108","doi":"https://doi.org/10.1158/1538-7445.am2019-5108","is_oa":false,"landing_page_url":"https://doi.org/10.1158/1538-7445.am2019-5108","pdf_url":null,"source":{"id":"https://openalex.org/S168522863","display_name":"Cancer Research","issn_l":"0008-5472","issn":["0008-5472","1538-7445"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320273","host_organization_name":"American Association for Cancer Research","host_organization_lineage":["https://openalex.org/P4310320273"],"host_organization_lineage_names":["American Association for Cancer Research"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Cancer Research","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.46810001134872437,"id":"https://metadata.un.org/sdg/3"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4360943990","https://openalex.org/W7154749304","https://openalex.org/W2740463006","https://openalex.org/W3083170382","https://openalex.org/W7098607783","https://openalex.org/W2162116127","https://openalex.org/W2739529365","https://openalex.org/W1590169480","https://openalex.org/W7152669504","https://openalex.org/W2763341612"],"abstract_inverted_index":{"Abstract":[0],"Somatic":[1,435],"small":[2,34,73,193,201,436],"mutations,":[3],"SNVs":[4,240],"or":[5,58,95,167],"Indels,":[6],"and":[7,37,62,75,107,129,175,198,207,210,236,241,253,258,261,294,320,335,355,387,438],"copy":[8,38,439],"number":[9,39,440],"alterations":[10,40],"are":[11,98,155,158,170],"the":[12,18,44,103,144,275,343,363,406,414,444,452],"two":[13],"categories":[14],"of":[15,51,102,112,150,186,215,226,248,274,284,299,312,325,346,392,416,451],"mutations":[16,35],"with":[17,306,395,443],"largest":[19],"impact":[20],"on":[21,43,164,204,211,233,266,302,378],"cancer":[22],"tumors.":[23],"The":[24,49,153,223,243,272,309,339,399],"Broad":[25],"Institute":[26],"has":[27],"released":[28],"somatic":[29,194],"variant":[30,437],"calling":[31,442],"workflows":[32,52,104,145,154],"for":[33,138,172,192,200,238,256,264,281,318,342,352,455],"(M2)":[36],"(ModelSegments)":[41],"based":[42],"Genome":[45,445],"Analysis":[46,446],"Toolkit":[47,447],"(GATK).":[48],"suite":[50],"can":[53,146,161,176],"call":[54],"variants":[55,196],"in":[56,83,405,413],"capture":[57],"whole-genome":[59],"sequencing":[60,84],"data":[61],"will":[63],"include":[64],"functional":[65],"annotations":[66],"(Funcotator),":[67],"such":[68,86],"as":[69,87,122,124,368],"protein":[70],"change":[71],"(for":[72,78],"variants)":[74],"impacted":[76],"gene":[77],"all":[79],"variants).":[80],"Common":[81],"artifacts":[82],"data,":[85],"those":[88],"arising":[89],"from":[90,229],"oxidative":[91],"DNA":[92],"damage,":[93],"FFPE/deamination,":[94],"mapping":[96],"errors,":[97],"corrected":[99],"automatically.":[100],"Evaluation":[101],"is":[105,135,278],"standardized":[106],"repeatable,":[108],"which":[109],"allows":[110],"tracking":[111],"performance":[113,118,126],"across":[114,322],"versions,":[115],"both":[116,239,353],"detection":[117],"(e.g.":[119,127],"sensitivity,":[120],"precision),":[121],"well":[123],"runtime":[125],"CPU":[128,300,393],"RAM":[130,400],"usage).":[131],"A":[132],"matched":[133,287],"normal":[134],"not":[136],"required":[137,295,388],"a":[139,212,282,303,369,379,396],"given":[140],"tumor":[141],"sample,":[142],"since":[143],"leverage":[147,181],"pre-processed":[148],"panels":[149],"normals":[151],"(PoNs).":[152],"freely":[156],"available,":[157],"portable":[159],"(i.e.":[160],"be":[162,177],"run":[163],"local,":[165],"on-prem,":[166],"cloud":[168],"compute),":[169],"optimized":[171],"cost":[173,273,374],"reduction,":[174],"tuned":[178],"to":[179,231,408],"optimally":[180],"available":[182],"compute.The":[183],"measured":[184,224,310,340],"sensitivity":[185,311],"M2":[187,227,249,276],"was":[188,250,314,348,375,402,412],"at":[189,315,349],"least":[190,316,350],"0.93":[191],"nucleotide":[195],"(SNVs)":[197],"0.83":[199],"insertions/deletions":[202],"(Indels)":[203],"DREAM1,":[205,234],"DREAM2,":[206,235],"DREAM3":[208,237],"challenges,":[209],"titrated":[213],"mixture":[214],"germline":[216],"samples":[217,328],"(>=100x":[218],"depth,":[219],"AF":[220],"=":[221],"0.2).":[222],"precision":[225],"ranged":[228],"0.91":[230,317],"0.98":[232],"Indels.":[242],"false":[244],"positive":[245],"rate":[246],"(FPR)":[247],"between":[251,259],"0.03":[252],"0.21":[254],"FP/Mb":[255,263],"SNVs,":[257],"0.0":[260],"0.1":[262],"indels,":[265],"twelve":[267],"paired,":[268],"replicate":[269],"normal-normal":[270],"samples.":[271],"workflow":[277,407],"about":[279,296,389],"USD$1.15":[280],"pair":[283,382],"35x":[285],"WGS":[286,381],"tumor-normal":[288],"samples,":[289],"using":[290,362,383],"Google":[291,384],"Cloud":[292,385],"Compute,":[293],"32":[297],"hours":[298,391],"time":[301,394],"single":[304,397],"core":[305],"3GB":[307],"RAM.":[308],"ModelSegments":[313],"deletions":[319,354],"amplifications":[321],"three":[323],"cohorts":[324,347],"TCGA":[326],"whole-exome":[327],"(Stomach":[329],"adenocarcinoma":[330,337],"N=39,":[331],"Thyroid":[332],"carcinoma":[333],"N=50,":[334],"Lung":[336],"N=60).":[338],"specificity":[341],"same":[344],"set":[345],"0.96":[351],"amplifications.":[356],"All":[357],"results":[358,367],"reported":[359],"here":[360],"were":[361],"corresponding":[364],"SNP":[365],"Array":[366],"truth":[370],"set.":[371],"GATK":[372],"MS":[373],"approximately":[376],"USD$0.65":[377],"30x":[380],"Compute":[386],"6":[390],"core.":[398],"usage":[401],"varied":[403],"automatically":[404],"minimize":[409],"cost,":[410],"but":[411],"range":[415],"2-13GB.":[417],"Citation":[418],"Format:":[419],"Lee":[420],"Lichtenstein,":[421],"Jonn":[422],"Smith,":[423],"David":[424],"Benjamin,":[425],"Aaron":[426],"Chevalier,":[427],"Kristian":[428],"Cibulskis,":[429],"Samuel":[430],"K.":[431],"Lee,":[432],"Eric":[433],"Banks.":[434],"alteration":[441],"[abstract].":[448],"In:":[449],"Proceedings":[450],"American":[453],"Association":[454],"Cancer":[456,470],"Research":[457],"Annual":[458],"Meeting":[459],"2019;":[460],"2019":[461],"Mar":[462],"29-Apr":[463],"3;":[464],"Atlanta,":[465],"GA.":[466],"Philadelphia":[467],"(PA):":[468],"AACR;":[469],"Res":[471],"2019;79(13":[472],"Suppl):Abstract":[473],"nr":[474],"5108.":[475]},"counts_by_year":[],"updated_date":"2026-11-03T10:50:19.383937","created_date":"2019-07-12T00:00:00"}
