{"id":"https://openalex.org/W2886842871","doi":"https://doi.org/10.1158/1538-7445.am2018-2346","title":"Abstract 2346: ARDE: Detecting selectively expressed cancer driver mutations through integration of exome and transcriptome sequencing data","display_name":"Abstract 2346: ARDE: Detecting selectively expressed cancer driver mutations through integration of exome and transcriptome sequencing data","publication_year":2018,"publication_date":"2018-07-01","ids":{"openalex":"https://openalex.org/W2886842871","doi":"https://doi.org/10.1158/1538-7445.am2018-2346","mag":"2886842871"},"language":"en","primary_location":{"id":"doi:10.1158/1538-7445.am2018-2346","doi":"https://doi.org/10.1158/1538-7445.am2018-2346","is_oa":false,"landing_page_url":"https://doi.org/10.1158/1538-7445.am2018-2346","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/A5100321405","display_name":"Fang Wang","orcid":"https://orcid.org/0000-0002-3510-4550","observed_orcids":["https://orcid.org/0000-0002-3510-4550"]},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fang Wang","raw_affiliation_strings":["UT MD Anderson Cancer Ctr., Houston, TX"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UT MD Anderson Cancer Ctr., Houston, TX","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100607393","display_name":"Shaojun Zhang","orcid":"https://orcid.org/0000-0002-2176-6174","observed_orcids":["https://orcid.org/0000-0002-2176-6174","https://orcid.org/0000-0001-6138-0308","https://orcid.org/0000-0003-3284-9546"]},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shaojun Zhang","raw_affiliation_strings":["UT MD Anderson Cancer Ctr., Houston, TX"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UT MD Anderson Cancer Ctr., Houston, TX","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100439331","display_name":"Yiwen Chen","orcid":"https://orcid.org/0000-0002-7706-7540","observed_orcids":["https://orcid.org/0000-0002-7706-7540"]},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yiwen Chen","raw_affiliation_strings":["UT MD Anderson Cancer Ctr., Houston, TX"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UT MD Anderson Cancer Ctr., Houston, TX","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033882667","display_name":"Traver Hart","orcid":"https://orcid.org/0000-0002-1880-3341","observed_orcids":["https://orcid.org/0000-0002-1880-3341"]},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Traver Hart","raw_affiliation_strings":["UT MD Anderson Cancer Ctr., Houston, TX"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UT MD Anderson Cancer Ctr., Houston, TX","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113847984","display_name":"Kenna Shaw","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kenna Shaw","raw_affiliation_strings":["UT MD Anderson Cancer Ctr., Houston, TX"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UT MD Anderson Cancer Ctr., Houston, TX","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076426660","display_name":"Funda Meric\u2010Bernstam","orcid":"https://orcid.org/0000-0001-6816-6072","observed_orcids":["https://orcid.org/0000-0001-6816-6072"]},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Funda Meric-Bernstam","raw_affiliation_strings":["UT MD Anderson Cancer Ctr., Houston, TX"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UT MD Anderson Cancer Ctr., Houston, TX","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005221518","display_name":"Gordon Brent Mills","orcid":"https://orcid.org/0000-0002-0144-9614","observed_orcids":["https://orcid.org/0000-0002-0144-9614"]},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gordon Mills","raw_affiliation_strings":["UT MD Anderson Cancer Ctr., Houston, TX"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UT MD Anderson Cancer Ctr., Houston, TX","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100420347","display_name":"Ken Chen","orcid":"https://orcid.org/0000-0003-4013-5279","observed_orcids":["https://orcid.org/0000-0003-4013-5279"]},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ken Chen","raw_affiliation_strings":["UT MD Anderson Cancer Ctr., Houston, TX"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UT MD Anderson Cancer Ctr., Houston, TX","institution_ids":["https://openalex.org/I1343551460"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I1343551460"],"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":"78","issue":"13_Supplement","first_page":"2346","last_page":"2346"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9980000257492065,"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":0.9980000257492065,"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":0.00039999998989515007,"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/T12820","display_name":"Chromatin Remodeling and Cancer","score":0.00019999999494757503,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/cancer-driver-mutations","display_name":"cancer driver mutations","score":0.9459999799728394},{"id":"https://openalex.org/keywords/allele-specific-expression","display_name":"allele-specific expression","score":0.8370000123977661},{"id":"https://openalex.org/keywords/tumor-purity-estimation","display_name":"tumor purity estimation","score":0.800000011920929},{"id":"https://openalex.org/keywords/intratumor-heterogeneity","display_name":"intratumoral heterogeneity","score":0.9589999914169312},{"id":"https://openalex.org/keywords/allele-specific-copy-number","display_name":"allele-specific copy number","score":0.8230000138282776},{"id":"https://openalex.org/keywords/multi-omics-integration","display_name":"multi-omics integration","score":0.6740000247955322},{"id":"https://openalex.org/keywords/melanoma","display_name":"melanoma","score":0.6669999957084656},{"id":"https://openalex.org/keywords/breast-cancer","display_name":"breast cancer","score":0.9990000128746033},{"id":"https://openalex.org/keywords/braf-v600e-mutation","display_name":"BRAF V600E mutation","score":0.9570000171661377},{"id":"https://openalex.org/keywords/gain-of-function-mutations","display_name":"gain-of-function mutations","score":0.8539999723434448},{"id":"https://openalex.org/keywords/survival-stratification","display_name":"survival stratification","score":0.5889999866485596},{"id":"https://openalex.org/keywords/single-cell-rna-sequencing","display_name":"single-cell RNA sequencing","score":0.35600000619888306},{"id":"https://openalex.org/keywords/the-cancer-genome-atlas","display_name":"TCGA","score":0.4230000078678131}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6124054193496704},{"id":"https://openalex.org/C10590036","wikidata":"https://www.wikidata.org/wiki/Q417664","display_name":"Exome","level":5,"score":0.601276695728302},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.5297535061836243},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.520839512348175},{"id":"https://openalex.org/C16671776","wikidata":"https://www.wikidata.org/wiki/Q5420592","display_name":"Exome sequencing","level":4,"score":0.5125699043273926},{"id":"https://openalex.org/C530470458","wikidata":"https://www.wikidata.org/wiki/Q128581","display_name":"Breast cancer","level":3,"score":0.501591682434082},{"id":"https://openalex.org/C13514818","wikidata":"https://www.wikidata.org/wiki/Q5552256","display_name":"Germline mutation","level":4,"score":0.4942028820514679},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.42066118121147156},{"id":"https://openalex.org/C180754005","wikidata":"https://www.wikidata.org/wiki/Q80726","display_name":"Allele","level":3,"score":0.4198967218399048},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.41741248965263367},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4113609492778778},{"id":"https://openalex.org/C502942594","wikidata":"https://www.wikidata.org/wiki/Q3421914","display_name":"Cancer research","level":1,"score":0.37082862854003906},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.3054787814617157},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2918016314506531}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1158/1538-7445.am2018-2346","doi":"https://doi.org/10.1158/1538-7445.am2018-2346","is_oa":false,"landing_page_url":"https://doi.org/10.1158/1538-7445.am2018-2346","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":0.8371999859809875,"id":"https://metadata.un.org/sdg/3"}],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2092245530","https://openalex.org/W4410925636","https://openalex.org/W1794109707","https://openalex.org/W2397992771","https://openalex.org/W3205518740","https://openalex.org/W7099299999","https://openalex.org/W2971410098","https://openalex.org/W3166714444","https://openalex.org/W4399674117","https://openalex.org/W2031496088"],"abstract_inverted_index":{"Abstract":[0],"Integrating":[1],"multi-omics":[2],"data":[3,314],"from":[4,39,81,124,140,250],"cancer":[5,14,23,159,304],"patient":[6],"samples":[7,123],"can":[8,155],"potentially":[9],"advance":[10],"the":[11,108,176,215,319],"discovery":[12,52,247],"of":[13,53,111,164,192,218,227,248,273,309,318],"driver":[15,305],"mutations":[16,194,266,306],"(CDM)":[17],"towards":[18],"establishing":[19],"a":[20,61,96,224],"knowledgebase":[21],"for":[22,245,322],"precision":[24],"medicine.":[25],"However,":[26],"it":[27],"remains":[28],"unclear":[29],"whether":[30,44],"CDMs":[31,249],"are":[32,195,202],"selectively":[33,103,196,302],"expressed":[34,104,197,264,303],"at":[35],"RNA":[36,67],"levels":[37,92,180],"unexpected":[38],"DNA":[40,68,143],"copy":[41,75],"numbers":[42],"and":[43,77,84,94,121,149,161,207,311],"identifying":[45],"such":[46],"selectivity":[47,217],"will":[48,237],"enable":[49],"more":[50],"accurate":[51,246],"CDMs.":[54],"To":[55],"answer":[56],"this":[57],"question,":[58],"we":[59],"developed":[60],"novel":[62],"statistical":[63],"algorithm,":[64],"ARDE":[65,117,134,236],"(Allelic":[66],"expression),":[69],"which":[70],"estimates":[71],"tumor":[72,89,109,113,169,184,251],"purity,":[73],"allele-specific":[74,90],"number":[76],"intratumor":[78],"heterogeneity":[79],"(ITH)":[80],"matched":[82],"whole-exome":[83],"whole-transcriptome":[85],"sequencing":[86,253,313],"data,":[87],"deconvolutes":[88],"expression":[91,147,179,216],"(ASEL)":[93],"uses":[95],"two-component":[97],"mixture":[98],"probability":[99],"model":[100],"to":[101,118],"identify":[102],"alleles":[105],"(SEAs)":[106],"in":[107,181,187,205,223,229],"compartment":[110],"heterogeneous":[112],"tissues.":[114],"We":[115],"applied":[116],"analyze":[119],"melanoma":[120,165,212],"breast":[122,158],"The":[125,167],"Cancer":[126,323,336],"Genome":[127],"Atlas":[128],"(TCGA).":[129],"Tumor":[130],"purities":[131],"estimated":[132],"by":[133,214],"were":[135],"highly":[136,203],"correlated":[137],"with":[138,175],"estimation":[139],"pathology":[141],"review,":[142],"methylation":[144],"array,":[145],"gene":[146,178],"microarray":[148],"SNP":[150],"array":[151],"data.":[152,254],"ITH":[153],"scores":[154],"significantly":[156],"stratify":[157],"subtypes":[160],"survival":[162,230],"time":[163],"patients.":[166],"deconvoluted":[168],"ASEL":[170],"showed":[171],"consistently":[172],"higher":[173],"correlation":[174],"averaged":[177],"tissue-matched":[182],"single":[183],"cells":[185],"than":[186,198],"normal":[188],"cells.":[189],"Higher":[190],"proportions":[191],"somatic":[193,265],"germline.":[199],"Top":[200,260],"SEAs":[201],"enriched":[204],"deleterious":[206],"gain-of-function":[208],"(GOF)":[209],"mutations.":[210],"Stratifying":[211],"patients":[213],"BRAF":[219],"V600E":[220],"mutation":[221],"resulted":[222],"10-fold":[225],"improvement":[226],"significance":[228],"analysis.":[231],"These":[232],"results":[233],"indicate":[234],"that":[235],"likely":[238],"be":[239],"an":[240],"effective,":[241],"widely":[242],"applicable":[243],"approach":[244],"tissue":[252],"(See":[255],"Table":[256,258],"1.)":[257],"1.":[259],"10":[261],"significant":[262],"positive-selectively":[263],"MelanomaBreast":[267],"cancerGenepSNVFunctionSIFTGenepSNVFunctionSIFTBRAFp.":[268],"V600EGOFDAKT1p.E17KGOFDNRASp.":[269],"Q61RGOFDPIK3CAp.H1047RGOFTCDKN2Ap.":[270],"R114LGOFDERBB2p.L755SGOFDIDH1p.":[271],"R132CSwitch":[272],"functionDTP53p.R273HGOFDEEF1A1p.":[274],"H349YDGATA3p.M293KDRAC1p.":[275],"P29SGOFDTP53p.P278TDNRASp.":[276],"Q61KGOFDFOXA1p.S250FDSF3B1p.":[277],"R625HGOFDTP53p.":[278],"R175HGOFDNRASp.":[279],"Q61LGOFDPIK3CAp.H1047LGOFTMAP2K1p.":[280],"P124SGOFDERBB2p.V777LGOFT":[281],"Citation":[282],"Format:":[283],"Fang":[284],"Wang,":[285],"Shaojun":[286],"Zhang,":[287],"Yiwen":[288],"Chen,":[289],"Traver":[290],"Hart,":[291],"Kenna":[292],"Shaw,":[293],"Funda":[294],"Meric-Bernstam,":[295],"Gordon":[296],"Mills,":[297],"Ken":[298],"Chen.":[299],"ARDE:":[300],"Detecting":[301],"through":[307],"integration":[308],"exome":[310],"transcriptome":[312],"[abstract].":[315],"In:":[316],"Proceedings":[317],"American":[320],"Association":[321],"Research":[324],"Annual":[325],"Meeting":[326],"2018;":[327],"2018":[328],"Apr":[329],"14-18;":[330],"Chicago,":[331],"IL.":[332],"Philadelphia":[333],"(PA):":[334],"AACR;":[335],"Res":[337],"2018;78(13":[338],"Suppl):Abstract":[339],"nr":[340],"2346.":[341]},"counts_by_year":[],"updated_date":"2026-09-24T07:57:37.273135","created_date":"2018-08-22T00:00:00"}