{"id":"https://openalex.org/W2017531104","doi":"https://doi.org/10.1158/1538-7445.am2013-5133","title":"Abstract 5133: Inference of tumor phylogenetic markers from large copy number datasets.","display_name":"Abstract 5133: Inference of tumor phylogenetic markers from large copy number datasets.","publication_year":2013,"publication_date":"2013-04-01","ids":{"openalex":"https://openalex.org/W2017531104","doi":"https://doi.org/10.1158/1538-7445.am2013-5133","mag":"2017531104"},"language":"en","primary_location":{"id":"doi:10.1158/1538-7445.am2013-5133","doi":"https://doi.org/10.1158/1538-7445.am2013-5133","is_oa":false,"landing_page_url":"https://doi.org/10.1158/1538-7445.am2013-5133","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/A5031387460","display_name":"Ayshwarya Subramanian","orcid":"https://orcid.org/0000-0002-4134-7612","observed_orcids":["https://orcid.org/0000-0002-4134-7612"]},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ayshwarya Subramanian","raw_affiliation_strings":["1Carnegie Mellon Univ., Pittsburgh, PA;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1Carnegie Mellon Univ., Pittsburgh, PA;","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027859218","display_name":"Stanley E. Shackney","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Stanley Shackney","raw_affiliation_strings":["2Intelligent Oncotherapeutics, Pittsburgh, PA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"2Intelligent Oncotherapeutics, Pittsburgh, PA","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051953313","display_name":"Russell S. Schwartz","orcid":"https://orcid.org/0000-0002-4970-2252","observed_orcids":["https://orcid.org/0000-0002-4970-2252"]},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Russell Schwartz","raw_affiliation_strings":["1Carnegie Mellon Univ., Pittsburgh, PA;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1Carnegie Mellon Univ., Pittsburgh, PA;","institution_ids":["https://openalex.org/I74973139"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":[],"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":"73","issue":"8_Supplement","first_page":"5133","last_page":"5133"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9624000191688538,"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":0.9624000191688538,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.027499999850988388,"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"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.002199999988079071,"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/tumor-phylogeny","display_name":"tumor phylogeny","score":0.7599999904632568},{"id":"https://openalex.org/keywords/tumor-evolution","display_name":"tumor evolution","score":0.7319999933242798},{"id":"https://openalex.org/keywords/copy-number-profiles","display_name":"copy number profiles","score":0.6830000281333923},{"id":"https://openalex.org/keywords/hidden-markov-models","display_name":"hidden Markov models","score":0.9810000061988831},{"id":"https://openalex.org/keywords/tumor-progression-markers","display_name":"tumor progression markers","score":0.6629999876022339},{"id":"https://openalex.org/keywords/breast-cancer","display_name":"breast cancer","score":0.6859999895095825},{"id":"https://openalex.org/keywords/tumor-heterogeneity","display_name":"tumor heterogeneity","score":0.8109999895095825},{"id":"https://openalex.org/keywords/state-space-reduction","display_name":"state space reduction","score":0.6150000095367432},{"id":"https://openalex.org/keywords/tumor-subtypes","display_name":"tumor subtypes","score":0.5019999742507935}],"concepts":[{"id":"https://openalex.org/C8185291","wikidata":"https://www.wikidata.org/wiki/Q2844457","display_name":"Amplicon","level":4,"score":0.6507803201675415},{"id":"https://openalex.org/C124942203","wikidata":"https://www.wikidata.org/wiki/Q656638","display_name":"Comparative genomic hybridization","level":4,"score":0.6435565948486328},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6398472785949707},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.5975649952888489},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5915287733078003},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5332806706428528},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5277931094169617},{"id":"https://openalex.org/C120821319","wikidata":"https://www.wikidata.org/wiki/Q1501491","display_name":"Copy-number variation","level":4,"score":0.5138561725616455},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.47188130021095276},{"id":"https://openalex.org/C166608930","wikidata":"https://www.wikidata.org/wiki/Q5169175","display_name":"Copy number analysis","level":5,"score":0.45272377133369446},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.4437374174594879},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.43641984462738037},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.4218951165676117},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3354441821575165},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.33214983344078064},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.3103887438774109},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.29305094480514526},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.17873528599739075},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.16285094618797302},{"id":"https://openalex.org/C49105822","wikidata":"https://www.wikidata.org/wiki/Q176996","display_name":"Polymerase chain reaction","level":3,"score":0.11360993981361389},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1158/1538-7445.am2013-5133","doi":"https://doi.org/10.1158/1538-7445.am2013-5133","is_oa":false,"landing_page_url":"https://doi.org/10.1158/1538-7445.am2013-5133","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":[],"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/W2324719779","https://openalex.org/W2179893475","https://openalex.org/W2038927641","https://openalex.org/W104023327","https://openalex.org/W2065288894","https://openalex.org/W7096396252","https://openalex.org/W2153603480","https://openalex.org/W2005623215","https://openalex.org/W2066721762","https://openalex.org/W7095749919"],"abstract_inverted_index":{"Abstract":[0],"Understanding":[1],"tumors":[2],"as":[3],"evolutionary":[4,33],"systems":[5],"is":[6,22,206],"an":[7,171,254],"important":[8],"area":[9],"of":[10,32,49,65,91,102,147,185,214,230,239,249,256,294,310,318,320,343,354,393,411,420,438,450,455],"study":[11],"with":[12,246],"far-reaching":[13],"implications":[14],"in":[15,30,38,55,86,109,120,227,346],"diagnostic":[16],"and":[17,52,63,112,132,140,166,180,204,222,349,396],"treatment":[18],"paradigms.":[19],"Computational":[20],"phylogenetics":[21],"a":[23,39,70,125,153,158,181,210,265,351,361],"valuable":[24],"method":[25,359,383],"for":[26,75,129,174,340,400,459],"inferring":[27],"tumor":[28,44,61,71,81,103,148,363,412,439],"evolution":[29,104],"terms":[31],"trees,":[34],"phylogenies,":[35],"where":[36],"paths":[37,108],"tree":[40,57],"correspond":[41],"to":[42,116,144,161,259,268,272,386,423],"possible":[43,186,192,240,311],"progression":[45,93],"pathways.":[46],"The":[47,292,404],"location":[48],"specific":[50],"cell-types":[51],"patient":[53],"samples":[54,231,374],"the":[56,87,96,106,110,117,175,228,232,237,247,257,269,274,298,308,316,321,341,347,358,389,418,421,451,456],"provide":[58],"information":[59],"on":[60,170,301,315,360],"sub-types":[62],"development":[64],"heterogeneity.":[66],"We":[67,123,189,263,305,356],"previously":[68],"developed":[69],"phylogeny":[72,402],"inference":[73],"pipeline":[74,88],"array":[76,334],"comparative":[77],"genome":[78,290,335],"hybridization":[79],"(aCGH)-based":[80],"copy":[82,177,367,444],"number":[83,178,229,238,248,368,445],"profiles.":[84,150],"Steps":[85],"included":[89],"extraction":[90],"robust":[92,394],"markers":[94,119,138,410,441],"from":[95,139,371,442],"data,":[97],"which":[98,135],"could":[99],"differentiate":[100],"stages":[101],"or":[105,199,333],"different":[107,427],"tree,":[111],"assigning":[113],"amplification":[114,142,187,193,215,242,282,312],"states":[115,143,168,179,194,216,243,283,313,322,327],"inferred":[118,406],"those":[121,326],"stages.":[122],"introduced":[124],"novel":[126],"multi-sample":[127],"model":[128],"amplicon":[130],"identification":[131],"calling,":[133],"HMMCNA,":[134],"jointly":[136],"extracted":[137],"assigned":[141],"small":[145],"sets":[146,392],"aCGH":[149,331,364],"HMMCNA":[151],"employs":[152],"Hidden":[154],"Markov":[155],"Model":[156],"(HMM),":[157],"probabilistic":[159],"model,":[160],"classify":[162],"data":[163,348,390],"into":[164,391],"normal":[165,197,395],"amplified":[167,200,397],"based":[169,314],"underlying":[172],"distribution":[173],"two":[176,191],"hidden":[182,241,275],"state":[183,276,299],"space":[184,277,300],"states.":[188],"assumed":[190],"per":[195],"sample:":[196],"(0)":[198],"(1).":[201],"Joint":[202],"segmentation":[203],"calling":[205],"performed":[207],"by":[208,278,303,323],"identifying":[209],"most":[211],"likely":[212],"sequence":[213],"across":[217,426],"all":[218],"genomic":[219],"sites":[220],"probes":[221,332],"samples.":[223,250],"This":[224,337],"approach":[225,258],"limits":[226],"HMM":[233,270,422],"can":[234],"handle":[235,260,424],"since":[236],"increases":[244],"exponentially":[245],"Here,":[251],"we":[252],"present":[253],"extension":[255],"large":[261,443],"datasets.":[262,428,446],"incorporate":[264],"heuristic":[266,296],"prior":[267],"classification":[271],"reduce":[273,307],"first":[279],"screening":[280],"out":[281],"not":[284],"strongly":[285],"supported":[286],"at":[287,329],"any":[288],"individual":[289],"coordinates.":[291],"introduction":[293],"this":[295],"reduces":[297],"average":[302],"99%.":[304],"further":[306,352],"set":[309],"frequency":[317],"occurrence":[319],"only":[324],"allowing":[325],"occuring":[328],"multiple":[330],"coordinate.":[336],"step":[338],"accounts":[339],"presence":[342],"random":[344],"noise":[345],"gives":[350],"reduction":[353],"80%.":[355],"demonstrate":[357],"breast":[362],"dataset":[365],"comprising":[366],"profiles":[369],"derived":[370],"sectioned":[372],"biopsy":[373],"(NCBI":[375],"GEO":[376],"GSE16672,":[377],"Navin":[378],"et":[379],"al.,":[380],"2010).":[381],"Our":[382],"was":[384],"able":[385],"quickly":[387],"segment":[388],"segments":[398],"suitable":[399],"downstream":[401],"building.":[403],"amplicons":[405],"carried":[407],"several":[408],"known":[409],"progression.":[413],"Further":[414],"steps":[415],"include":[416],"tuning":[417],"parameters":[419],"noise-levels":[425],"Citation":[429],"Format:":[430],"Ayshwarya":[431],"Subramanian,":[432],"Stanley":[433],"Shackney,":[434],"Russell":[435],"Schwartz.":[436],"Inference":[437],"phylogenetic":[440],"[abstract].":[447],"In:":[448],"Proceedings":[449],"104th":[452],"Annual":[453],"Meeting":[454],"American":[457],"Association":[458],"Cancer":[460,470],"Research;":[461],"2013":[462],"Apr":[463],"6-10;":[464],"Washington,":[465],"DC.":[466],"Philadelphia":[467],"(PA):":[468],"AACR;":[469],"Res":[471],"2013;73(8":[472],"Suppl):Abstract":[473],"nr":[474],"5133.":[475],"doi:10.1158/1538-7445.AM2013-5133":[476]},"counts_by_year":[],"updated_date":"2026-09-22T06:50:58.402377","created_date":"2016-06-24T00:00:00"}