{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Biswas D"],"funding":["Austrian Science Fund FWF","Cancer Research UK","International Association for the Study of Lung Cancer (IASLC)","Hungarian Academy of Sciences | Magyar Tudományos Akadémia Számítástechnikai és Automatizálási Kutatóintézet (Számítástechnikai és Automatizálási Kutatóintézet)","Japan Society for the Promotion of Science London (JSPS London)","The Francis Crick Institute","University College London (UCL)","Wellcome Trust","Novo Nordisk Foundation Center for Basic Metabolic Research (NovoNordisk Foundation Center for Basic Metabolic Research)"],"pagination":["86-101"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC11779643"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["6(1)"],"pubmed_abstract":["Human tumors are diverse in their natural history and response to treatment, which in part results from genetic and transcriptomic heterogeneity. In clinical practice, single-site needle biopsies are used to sample this diversity, but cancer biomarkers may be confounded by spatiogenomic heterogeneity within individual tumors. Here we investigate clonally expressed genes as a solution to the sampling bias problem by analyzing multiregion whole-exome and RNA sequencing data for 450 tumor regions from 184 patients with lung adenocarcinoma in the TRACERx study. We prospectively validate the survival association of a clonal expression biomarker, Outcome Risk Associated Clonal Lung Expression (ORACLE), in combination with clinicopathological risk factors, and in stage I disease. We expand our me"],"journal":["Nature cancer"],"pubmed_title":["Prospective validation of ORACLE, a clonal expression biomarker associated with survival of patients with lung adenocarcinoma."],"pmcid":["PMC11779643"],"funding_grant_id":["UCL/12/0279","CC2088","202060447","C11496/A17786, C416/A21999","220589/Z/20/Z","CC1064","CC2040","CC2041","Young Investigator Grant","ID16584","CTUQQR-DEC22/100009","EDDCPJT\\100008","I4677","Bolyai Research Scholarship"],"pubmed_authors":["Litovchenko M","Osman A","Bailey C","Stavrou G","Atkin A","Stephens RCM","Fraioli F","Stone RK","Thakrar RM","Pilotti C","Biswas D","Sivakumar M","Prymas P","McGranahan N","Zaidi R","Thol K","Liu YH","Alzetani A","Brown KD","Yuan Y","Lindberg A","Hackshaw A","De Sousa P","Chavan H","Wilson GA","Rowan A","Asif M","Chaturvedi A","Gronroos E","Langman G","Russell P","Fennell DA","Naito Y","East P","Martinez-Ruiz C","Forster MD","Malima M","Kerr KM","Novasio J","Khiroya R","Shackleford H","Summers Y","Benafif S","Nicod J","Watkins TBK","Veeriah S","Lee SM","Grapa A","Mussa B","Leonce D","Bishop P","Kaplar Z","Dwornik A","Usaite I","Bola SK","Le Quesne J","Djearaman M","Black JRM","Downward J","Paiva-Correia A","Hill W","Bajaj A","Patrini D","Spanswick V","Colliver E","Pich O","Kostoulas N","Tugwood J","Carter M","AbdulJabbar K","Blyth KG","Bakir MA","Demeulemeester J","Proli C","Fernandes N","Collins-Fekete CA","Rathinam S","Taylor MN","Escudero M","Gilbert K","Pawlik P","Janes SM","Begum S","Dome B","Szallasi Z","Swanton C","Sangha M","Chuter D","Bhayani H","Boeing S","Rammohan K","Lindsay CR","Lu WT","Moore DA","Liu WK","Khalil M","Monk F","Patel AJ","Naceur-Lombardelli C","Toncheva A","Jordan S","Scott R","Shackcloth MJ","Rane JK","Koh K","Angelova M","Chee S","Herrero J","Hobson P","Kassiotis G","Kidd A","Grigoriadis K","Malhi A","Boleti E","Moldvay J","Oliveira P","Lim E","Scotland M","Kaufmann TL","Dulloo S","Shah M","Papadatos-Pastos D","Bandula S","Shah P","Hiley CT","Zhang H","Wilson J","Whiteley J","Crosbie P","Bilancia R","Quezada SA","Leek A","Leslie R","Goldman J","Sahai E","Totton N","Weeden CE","Royle G","Lucas O","Bhakhri K","Pisciella MC","Ahmed A","Selvaraju K","Gorman P","Tufail M","Waplington S","Richardson S","Beck S","Fontaine E","Wong YNS","Hacker AM","Castignani C","Megyesfalvi Z","Kanu N","Murphy C","Kaniu D","Cheyne H","Saghafinia S","Choudhary J","Rice A","Danson S","Bunkum A","Dive C","Schwarz RF","MacKenzie M","Harries S","Jones TP","Holding JW","Reading JL","Keene E","Hewish M","Hessey S","Dick C","Lee C","Zagorulya M","Hartley JA","Georg P","Thomas M","Pearce DR","Navani N","Matharu G","Veiga C","Booth S","Lester JF","Nicholson AG","Kirk A","Price G","Noorani I","Kittel J","Buderi SI","Karamani A","Richard C","Ashford P","Falzon M","Wilson C","Snell DM","Birkbak NJ","Ung SKA","Cave J","Nakas A","Karagianni D","Leung MM","Zaccaria S","Barbe V","Sodha-Ramdeen A","Karasaki T","Mastrokalos GT","Patruno L","Ahmad T","Aerts HJWL","O'Neill O","Middleton G","Marafioti T","Enfield KSS","Ensell L","Hodgkinson JD","Wu Y","Micke P","Shaw JA","Puttick C","Blackhall FH","Lowe HL","Gimeno-Valiente F","Magala M","Procter AJ","Jamal-Hanjani M","Haase K","Vendramin R","de Carne Trecesson S","Krebs MG","Gamble S","Peggs KS","Bentham R","Ramsden Z","Raubenheimer H","Chain B","Huebner A","Rosenthal R","Van Loo P","Magno N","French J","Naidu B","Ward S","Hill MS","Walker A","Joshi V","Thakkar K","Denner T","Lawrence D","Frankell AM","Boyles R","Vanloo S","Pan X","TRACERx Consortium","Robinson L","Hoogenboom EM","Ambrose L","Devaraj A","Diossy M","Joseph L","Fillinger J","Granato F","Smith S","Borg E","Salgado R","Mattsson J","Nye E","Lim EL","Cruickshank T","Nair A"],"additional_accession":[]},"is_claimable":false,"name":"Prospective validation of ORACLE, a clonal expression biomarker associated with survival of patients with lung adenocarcinoma.","description":"Human tumors are diverse in their natural history and response to treatment, which in part results from genetic and transcriptomic heterogeneity. In clinical practice, single-site needle biopsies are used to sample this diversity, but cancer biomarkers may be confounded by spatiogenomic heterogeneity within individual tumors. Here we investigate clonally expressed genes as a solution to the sampling bias problem by analyzing multiregion whole-exome and RNA sequencing data for 450 tumor regions from 184 patients with lung adenocarcinoma in the TRACERx study. We prospectively validate the survival association of a clonal expression biomarker, Outcome Risk Associated Clonal Lung Expression (ORACLE), in combination with clinicopathological risk factors, and in stage I disease. We expand our me","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Jan","modification":"2026-06-01T20:07:23.595Z","creation":"2025-04-04T14:05:48.412Z"},"accession":"S-EPMC11779643","cross_references":{"pubmed":["39789179"],"doi":["10.1038/s43018-024-00883-1"]}}