{"id":"https://openalex.org/W7130726480","doi":"https://doi.org/10.1158/1557-3265.sabcs25-ps3-06-19","title":"Abstract PS3-06-19: Phylogenetic and Transcriptomic Analyses Reveal Specific Adaptations for Progression of Breast Cancer","display_name":"Abstract PS3-06-19: Phylogenetic and Transcriptomic Analyses Reveal Specific Adaptations for Progression of Breast Cancer","publication_year":2026,"publication_date":"2026-02-17","ids":{"openalex":"https://openalex.org/W7130726480","doi":"https://doi.org/10.1158/1557-3265.sabcs25-ps3-06-19"},"language":"en","primary_location":{"id":"doi:10.1158/1557-3265.sabcs25-ps3-06-19","doi":"https://doi.org/10.1158/1557-3265.sabcs25-ps3-06-19","is_oa":false,"landing_page_url":"https://doi.org/10.1158/1557-3265.sabcs25-ps3-06-19","pdf_url":null,"source":{"id":"https://openalex.org/S183149254","display_name":"Clinical Cancer Research","issn_l":"1078-0432","issn":["1078-0432","1557-3265"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","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":"Clinical Cancer Research","raw_type":"journal-article"},"volume":null,"type":"conference-abstract","is_traditional":false,"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/A5079711864","display_name":"Mariano Russo","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1321217177","display_name":"Windber Research Institute","ror":"https://ror.org/03w8j7142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1321217177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"M. Russo","raw_affiliation_strings":["1Bioinformatics, Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1Bioinformatics, Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA,","institution_ids":["https://openalex.org/I1321217177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5123389338","display_name":"Praveen-Kumar Raj-Kumar","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1321217177","display_name":"Windber Research Institute","ror":"https://ror.org/03w8j7142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1321217177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"P. Raj-Kumar","raw_affiliation_strings":["1Bioinformatics, Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1Bioinformatics, Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA,","institution_ids":["https://openalex.org/I1321217177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5126492304","display_name":"J. Liu","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1321217177","display_name":"Windber Research Institute","ror":"https://ror.org/03w8j7142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1321217177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J. Liu","raw_affiliation_strings":["1Bioinformatics, Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1Bioinformatics, Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA,","institution_ids":["https://openalex.org/I1321217177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036054543","display_name":"Anupama Praveen-Kumar","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1321217177","display_name":"Windber Research Institute","ror":"https://ror.org/03w8j7142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1321217177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"A. Praveen-Kumar","raw_affiliation_strings":["1Bioinformatics, Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1Bioinformatics, Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA,","institution_ids":["https://openalex.org/I1321217177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5126475320","display_name":"A. Kovatich","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1280259254","display_name":"Henry M. Jackson Foundation","ror":"https://ror.org/04q9tew83","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1280259254"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"A. Kovatich","raw_affiliation_strings":["2Murtha Cancer Center Research Program, The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"2Murtha Cancer Center Research Program, The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD,","institution_ids":["https://openalex.org/I1280259254"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019556057","display_name":"Aik Choon Tan","orcid":"https://orcid.org/0000-0003-2955-8369","observed_orcids":["https://orcid.org/0000-0003-2955-8369"]},"institutions":[{"id":"https://openalex.org/I2801159745","display_name":"Huntsman Cancer Institute","ror":"https://ror.org/03v7tx966","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2801159745","https://openalex.org/I4210148268"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"A. Tan","raw_affiliation_strings":["3Oncological Sciences & Biomedical Informatics, Huntsman Cancer Institute, Salt Lake City, UT,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"3Oncological Sciences & Biomedical Informatics, Huntsman Cancer Institute, Salt Lake City, UT,","institution_ids":["https://openalex.org/I2801159745"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5126495906","display_name":"Hai Hu","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1321217177","display_name":"Windber Research Institute","ror":"https://ror.org/03w8j7142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1321217177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"H. Hu","raw_affiliation_strings":["1Bioinformatics, Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1Bioinformatics, Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA,","institution_ids":["https://openalex.org/I1321217177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014595154","display_name":"Craig D. Shriver","orcid":"https://orcid.org/0000-0001-8993-5811","observed_orcids":["https://orcid.org/0000-0001-8993-5811"]},"institutions":[{"id":"https://openalex.org/I2800363604","display_name":"Walter Reed National Military Medical Center","ror":"https://ror.org/025cem651","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1330347796","https://openalex.org/I2800250139","https://openalex.org/I2800363604","https://openalex.org/I2800386880"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"C. Shriver","raw_affiliation_strings":["4Murtha Cancer Center Research Program, Walter Reed National Military Medical Center, Bethesda, MD"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"4Murtha Cancer Center Research Program, Walter Reed National Military Medical Center, Bethesda, MD","institution_ids":["https://openalex.org/I2800363604"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5113674726","display_name":"Xiaoying Lin","orcid":"https://orcid.org/0009-0009-8780-1807","observed_orcids":["https://orcid.org/0009-0009-8780-1807"]},"institutions":[{"id":"https://openalex.org/I1321217177","display_name":"Windber Research Institute","ror":"https://ror.org/03w8j7142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1321217177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"X. Lin","raw_affiliation_strings":["1Bioinformatics, Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1Bioinformatics, Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA,","institution_ids":["https://openalex.org/I1321217177"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"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":"32","issue":"4_Supplement","first_page":"PS3","last_page":"06"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9965999722480774,"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":0.9965999722480774,"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/T10183","display_name":"Breast Cancer Treatment Studies","score":0.0010000000474974513,"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/T10336","display_name":"Cancer Cells and Metastasis","score":0.0007999999797903001,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/breast-cancer-metastasis","display_name":"breast cancer metastasis","score":0.8759999871253967},{"id":"https://openalex.org/keywords/metastatic-progression","display_name":"metastatic progression","score":0.7789999842643738},{"id":"https://openalex.org/keywords/clonal-evolution","display_name":"clonal evolution","score":0.7440000176429749},{"id":"https://openalex.org/keywords/tumor-phylogeny","display_name":"tumor phylogeny","score":0.9549999833106995},{"id":"https://openalex.org/keywords/copy-number-alterations","display_name":"copy number alterations","score":0.9089999794960022},{"id":"https://openalex.org/keywords/positive-selection","display_name":"positive selection","score":0.8019999861717224},{"id":"https://openalex.org/keywords/oncogenes","display_name":"oncogenes","score":0.6919999718666077},{"id":"https://openalex.org/keywords/tumor-suppressor-genes","display_name":"tumor suppressor","score":0.7829999923706055},{"id":"https://openalex.org/keywords/epithelial-mesenchymal-transition","display_name":"epithelial-mesenchymal transition","score":0.8989999890327454},{"id":"https://openalex.org/keywords/immune-regulation","display_name":"immune regulation","score":0.7089999914169312},{"id":"https://openalex.org/keywords/primary-versus-metastatic-tumors","display_name":"primary tumor versus metastasis","score":0.628000020980835},{"id":"https://openalex.org/keywords/driver-genes","display_name":"driver genes","score":0.5419999957084656},{"id":"https://openalex.org/keywords/gata3","display_name":"GATA3","score":0.7580000162124634},{"id":"https://openalex.org/keywords/tp53","display_name":"TP53","score":0.9990000128746033},{"id":"https://openalex.org/keywords/mutational-signatures","display_name":"mutational signatures","score":0.6930000185966492},{"id":"https://openalex.org/keywords/tumor-microenvironment","display_name":"tumor microenvironment","score":0.9079999923706055}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7483999729156494},{"id":"https://openalex.org/C2779013556","wikidata":"https://www.wikidata.org/wiki/Q181876","display_name":"Metastasis","level":3,"score":0.6808000206947327},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.6718000173568726},{"id":"https://openalex.org/C530470458","wikidata":"https://www.wikidata.org/wiki/Q128581","display_name":"Breast cancer","level":3,"score":0.5964999794960022},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.5616999864578247},{"id":"https://openalex.org/C113968399","wikidata":"https://www.wikidata.org/wiki/Q7559241","display_name":"Somatic evolution in cancer","level":3,"score":0.5404999852180481},{"id":"https://openalex.org/C2780283643","wikidata":"https://www.wikidata.org/wiki/Q2110267","display_name":"Primary tumor","level":4,"score":0.5339000225067139},{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.47780001163482666},{"id":"https://openalex.org/C120821319","wikidata":"https://www.wikidata.org/wiki/Q1501491","display_name":"Copy-number variation","level":4,"score":0.4742000102996826},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4652000069618225},{"id":"https://openalex.org/C81089528","wikidata":"https://www.wikidata.org/wiki/Q5134986","display_name":"clone (Java method)","level":3,"score":0.46459999680519104},{"id":"https://openalex.org/C2779256057","wikidata":"https://www.wikidata.org/wiki/Q16909647","display_name":"Tumor progression","level":3,"score":0.4602999985218048},{"id":"https://openalex.org/C7386963","wikidata":"https://www.wikidata.org/wiki/Q3954859","display_name":"Negative selection","level":4,"score":0.3917999863624573},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.3917999863624573},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.38690000772476196},{"id":"https://openalex.org/C502942594","wikidata":"https://www.wikidata.org/wiki/Q3421914","display_name":"Cancer research","level":1,"score":0.37299999594688416},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.34040001034736633},{"id":"https://openalex.org/C2776187077","wikidata":"https://www.wikidata.org/wiki/Q1888235","display_name":"Mammary tumor","level":4,"score":0.32589998841285706},{"id":"https://openalex.org/C2775930923","wikidata":"https://www.wikidata.org/wiki/Q12859063","display_name":"Metastatic breast cancer","level":4,"score":0.325300008058548},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.3165999948978424},{"id":"https://openalex.org/C8415881","wikidata":"https://www.wikidata.org/wiki/Q6839217","display_name":"Microarray analysis techniques","level":4,"score":0.3154999911785126},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.3116999864578247},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.30469998717308044},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2976999878883362},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.29339998960494995},{"id":"https://openalex.org/C186836561","wikidata":"https://www.wikidata.org/wiki/Q1931516","display_name":"Microarray","level":4,"score":0.2915000021457672},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.28780001401901245},{"id":"https://openalex.org/C69991583","wikidata":"https://www.wikidata.org/wiki/Q1423575","display_name":"Candidate gene","level":3,"score":0.27079999446868896},{"id":"https://openalex.org/C99983632","wikidata":"https://www.wikidata.org/wiki/Q1087765","display_name":"Chromothripsis","level":5,"score":0.26989999413490295},{"id":"https://openalex.org/C96232424","wikidata":"https://www.wikidata.org/wiki/Q4118072","display_name":"Cancer cell","level":3,"score":0.2687999904155731},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.26570001244544983},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.2632000148296356},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.2621000111103058},{"id":"https://openalex.org/C166608930","wikidata":"https://www.wikidata.org/wiki/Q5169175","display_name":"Copy number analysis","level":5,"score":0.25380000472068787}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1158/1557-3265.sabcs25-ps3-06-19","doi":"https://doi.org/10.1158/1557-3265.sabcs25-ps3-06-19","is_oa":false,"landing_page_url":"https://doi.org/10.1158/1557-3265.sabcs25-ps3-06-19","pdf_url":null,"source":{"id":"https://openalex.org/S183149254","display_name":"Clinical Cancer Research","issn_l":"1078-0432","issn":["1078-0432","1557-3265"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","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":"Clinical Cancer Research","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.8048999905586243,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"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/W2984655944","https://openalex.org/W3083274762","https://openalex.org/W3083411944","https://openalex.org/W7064548644","https://openalex.org/W3204988959","https://openalex.org/W2793109979","https://openalex.org/W7074191857","https://openalex.org/W3042260992","https://openalex.org/W2788302995","https://openalex.org/W2560102897"],"abstract_inverted_index":{"Abstract":[0],"Introduction:":[1],"Metastatic":[2],"spread":[3],"and":[4,37,103,109,162,178,185,207,220,258,265,283,300,316,332,337,353,364,397,409,425,508],"cancer":[5,21,71,140,288,384,407],"evolution":[6,408],"in":[7,53,75,87,136,302,326,383],"response":[8],"to":[9,14,56,63,66,173,201,229,239,343,360,386],"treatment":[10],"represent":[11],"major":[12],"obstacles":[13],"positive":[15,231,269],"patient":[16],"outcomes.":[17],"Preliminary":[18],"evidence":[19],"on":[20,156,183],"metastatic":[22,125,305],"progression":[23,72,135,327,346,390],"supports":[24],"evolutionary":[25,373],"selection":[26,76,83,270,303],"from":[27,148],"primary":[28,57,161,206],"tumors":[29,118,253],"as":[30,91,330],"a":[31,78,142,191,295,394],"proposed":[32],"mechanism":[33],"for":[34,77,271,298,304,368,449,514],"metastasis.":[35,377],"PanCancer":[36],"focused":[38,155],"studies":[39],"have":[40],"demonstrated":[41],"an":[42],"overall":[43],"pattern":[44],"of":[45,114,134,138,144,160,190,193,247,250,276,311,348,415,422,435,439,452,458,464,472,516,522],"increased":[46,51],"genomic":[47,88,112,396],"alterations":[48,213],"concurrent":[49],"with":[50,141,195,216,393],"clonality":[52],"metastasis":[54,137,163,208,392],"compared":[55],"tumors.":[58],"This":[59,82,400],"circumstance":[60],"is":[61],"likely":[62],"arise":[64],"due":[65],"ongoing":[67],"mutational":[68],"processes":[69],"during":[70],"that":[73,375],"result":[74],"specific":[79,256,323],"subclone":[80],"seeding.":[81],"process":[84],"will":[85,357],"manifest":[86],"adaptations":[89],"such":[90,329],"small":[92],"mutations,":[93],"copy":[94],"number":[95,212,292],"alterations,":[96],"or":[97,167,218,433,461,468,477],"epigenetic":[98],"modifications":[99],"regulating":[100],"gene":[101],"expression":[102,204],"directed":[104],"towards":[105],"enhancing":[106],"tumor":[107,180,259],"survival":[108],"proliferation.":[110],"The":[111,152,413],"composition":[113],"seeding":[115,175,365],"clones":[116],"across":[117],"may":[119],"give":[120],"us":[121],"unique":[122,296],"insight":[123],"into":[124,371,391,406],"progression.":[126,277],"Methods:":[127],"Our":[128,245,379],"study":[129,380],"aims":[130],"at":[131,273],"defining":[132],"networks":[133,347,374],"breast":[139,252,287,349],"total":[143],"2077":[145],"patients":[146],"participating":[147],"the":[149,308,345,372,388,419,423,430,440,444,450,456,462,465,484,523],"ORIEN":[150],"consortium.":[151],"current":[153],"analysis":[154,189,246,293,320],"112":[157,248],"paired":[158,251],"cases":[159,194,249],"(regional":[164],"lymph":[165],"node":[166],"distal).":[168],"Subclonal":[169],"deconvolution":[170],"was":[171,199,237],"used":[172,228,238,359],"define":[174],"clone":[176,366],"clusters":[177],"reconstruct":[179],"phylogenies":[181],"based":[182],"PyClone":[184],"CONIPHER":[186],"modeling.":[187],"Transcriptomics":[188,319],"subset":[192],"successful":[196],"RNASeq":[197],"(N=62)":[198],"performed":[200],"identify":[202,240],"differential":[203],"between":[205],"using":[209,222],"limma.":[210],"Copy":[211,291],"were":[214,227],"identified":[215,255,294],"ASCAT":[217],"Sequenza":[219],"analyzed":[221,342],"GISTIC2.":[223],"dNdS":[224],"mutation":[225,272,338],"rates":[226],"model":[230,361],"selection.":[232],"Gene":[233],"Set":[234],"Enrichment":[235],"Analysis":[236],"differentially":[241],"expressed":[242],"pathways.":[243],"Results:":[244],"has":[254],"oncogenes":[257],"suppressors,":[260],"including":[261,307],"transcription":[262],"factors,":[263],"kinases,":[264],"chromatin":[266],"remodelers,":[267],"under":[268],"different":[274],"stages":[275],"These":[278],"genes":[279],"include":[280],"GATA3,":[281],"TP53,":[282],"4":[284],"potentially":[285],"novel":[286],"driver":[289],"genes.":[290],"profile":[297],"amplifications":[299],"deletions":[301],"progression,":[306],"early":[309],"acquisition":[310],"broad":[312],"chromosome":[313],"arm":[314],"events":[315],"focal":[317],"enrichment.":[318],"revealed":[321],"5":[322],"pathways":[324],"enriched":[325],"programs":[328],"EMT":[331],"immune":[333],"regulation.":[334],"Tumor":[335],"microenvironment":[336],"signatures":[339],"are":[340,418],"being":[341],"elucidate":[344],"cancer.":[350],"Hierarchical":[351],"clustering":[352],"machine":[354],"learning":[355],"approaches":[356],"be":[358],"clinical,":[362],"molecular,":[363],"features":[367],"additional":[369],"insights":[370,405],"drive":[376],"Conclusion:":[378],"uses":[381],"innovations":[382],"genomics":[385],"determine":[387],"subclonal":[389],"comprehensive":[395],"transcriptomic":[398],"profile.":[399],"approach":[401],"can":[402],"yield":[403],"valuable":[404],"therapeutic":[410],"markers.":[411],"Disclaimer:":[412],"contents":[414],"this":[416],"publication":[417],"sole":[420],"responsibility":[421],"author(s)":[424],"do":[426],"not":[427,480],"necessarily":[428],"reflect":[429],"views,":[431],"opinions,":[432],"policies":[434],"Uniformed":[436],"Services":[437],"University":[438],"Health":[441],"Sciences":[442],"(USUHS),":[443],"Henry":[445],"M.":[446,489],"Jackson":[447],"Foundation":[448],"Advancement":[451],"Military":[453],"Medicine,":[454],"Inc.,":[455],"Department":[457],"Defense":[459],"(DoD)":[460],"Departments":[463],"Army,":[466],"Navy,":[467],"Air":[469],"Force.":[470],"Mention":[471],"trade":[473],"names,":[474],"commercial":[475],"products,":[476],"organizations":[478],"does":[479],"imply":[481],"endorsement":[482],"by":[483],"U.S.":[485],"government.":[486],"Citation":[487],"Format:":[488],"Russo,":[490],"P.":[491],"Raj-Kumar,":[492],"J.":[493],"Liu,":[494],"A.":[495,497,499],"Praveen-Kumar,":[496],"Kovatich,":[498],"Tan,":[500],"H.":[501],"Hu,":[502],"C.":[503],"Shriver,":[504],"X.":[505],"Lin.":[506],"Phylogenetic":[507],"Transcriptomic":[509],"Analyses":[510],"Reveal":[511],"Specific":[512],"Adaptations":[513],"Progression":[515],"Breast":[517,526],"Cancer":[518,527,540],"[abstract].":[519],"In:":[520],"Proceedings":[521],"San":[524,533],"Antonio":[525],"Symposium":[528],"2025;":[529],"2025":[530],"Dec":[531],"9-12;":[532],"Antonio,":[534],"TX.":[535],"Philadelphia":[536],"(PA):":[537],"AACR;":[538],"Clin":[539],"Res":[541],"2026;32(4":[542],"Suppl):Abstract":[543],"nr":[544],"PS3-06-19.":[545]},"counts_by_year":[],"updated_date":"2026-10-14T16:39:01.820549","created_date":"2026-02-21T00:00:00"}