Development and Validation of the Gene Expression Predictor of High-grade Serous Ovarian Carcinoma Molecular SubTYPE (PrOTYPE).
| Title: | Development and Validation of the Gene Expression Predictor of High-grade Serous Ovarian Carcinoma Molecular SubTYPE (PrOTYPE). |
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| Authors: | Talhouk A; British Columbia's Gynecological Cancer Research Program (OVCARE), BC Cancer, Vancouver General Hospital, and University of British Columbia, Vancouver, British Columbia, Canada.; University of British Columbia, Department of Obstetrics and Gynecology, Vancouver, British Columbia, Canada.; George J; The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut.; Wang C; Mayo Clinic, Division of Biomedical Statistics and Informatics, Department of Health Science Research, Rochester, Minnesota.; Budden T; University of NSW Sydney, School of Women's and Children's Health, Faculty of Medicine, Sydney, New South Wales, Australia.; The University of Manchester, CRUK Manchester Institute, Manchester, United Kingdom.; Tan TZ; National University of Singapore, Cancer Science Institute of Singapore, Center for Translational Medicine, Singapore, Singapore.; Chiu DS; British Columbia's Gynecological Cancer Research Program (OVCARE), BC Cancer, Vancouver General Hospital, and University of British Columbia, Vancouver, British Columbia, Canada.; Kommoss S; Tuebingen University Hospital, Department of Women's Health, Tuebingen, Germany.; Leong HS; Peter MacCallum Cancer Center, Melbourne, Victoria, Australia.; Chen S; Cedars-Sinai Medical Center, Center for Cancer Prevention and Translational Genomics, Samuel Oschin Comprehensive Cancer Institute, Los Angeles, California.; Intermaggio MP; University of NSW Sydney, School of Women's and Children's Health, Faculty of Medicine, Sydney, New South Wales, Australia.; Gilks B; British Columbia's Gynecological Cancer Research Program (OVCARE), BC Cancer, Vancouver General Hospital, and University of British Columbia, Vancouver, British Columbia, Canada.; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.; Nazeran TM; British Columbia's Gynecological Cancer Research Program (OVCARE), BC Cancer, Vancouver General Hospital, and University of British Columbia, Vancouver, British Columbia, Canada.; Volchek M; Royal Women's Hospital, Anatomical Pathology, Parkville, Victoria, Australia.; Elatre W; Department of Pathology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California.; Bentley RC; Department of Pathology, Duke University Hospital, Durham, North Carolina.; Senz J; British Columbia's Gynecological Cancer Research Program (OVCARE), BC Cancer, Vancouver General Hospital, and University of British Columbia, Vancouver, British Columbia, Canada.; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.; Lum A; British Columbia's Gynecological Cancer Research Program (OVCARE), BC Cancer, Vancouver General Hospital, and University of British Columbia, Vancouver, British Columbia, Canada.; Chow V; British Columbia's Gynecological Cancer Research Program (OVCARE), BC Cancer, Vancouver General Hospital, and University of British Columbia, Vancouver, British Columbia, Canada.; Sudderuddin H; British Columbia's Gynecological Cancer Research Program (OVCARE), BC Cancer, Vancouver General Hospital, and University of British Columbia, Vancouver, British Columbia, Canada.; Mackenzie R; British Columbia's Gynecological Cancer Research Program (OVCARE), BC Cancer, Vancouver General Hospital, and University of British Columbia, Vancouver, British Columbia, Canada.; Leong SCY; British Columbia's Gynecological Cancer Research Program (OVCARE), BC Cancer, Vancouver General Hospital, and University of British Columbia, Vancouver, British Columbia, Canada.; Liu G; British Columbia's Gynecological Cancer Research Program (OVCARE), BC Cancer, Vancouver General Hospital, and University of British Columbia, Vancouver, British Columbia, Canada.; Johnson D; British Columbia's Gynecological Cancer Research Program (OVCARE), BC Cancer, Vancouver General Hospital, and University of British Columbia, Vancouver, British Columbia, Canada.; Chen B; British Columbia's Gynecological Cancer Research Program (OVCARE), BC Cancer, Vancouver General Hospital, and University of British Columbia, Vancouver, British Columbia, Canada.; Group A; Peter MacCallum Cancer Center, Melbourne, Victoria, Australia.; QIMR Berghofer Medical Research Institute, Department of Genetics and Computational Biology, Brisbane, Queensland, Australia.; Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, New South Wales, Australia.; Alsop J; Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom.; Banerjee SN; The Royal Marsden NHS Foundation Trust and Institute of Cancer Research, Gynaecology Unit, London, United Kingdom.; Behrens S; German Cancer Research Center (DKFZ), Division of Cancer Epidemiology, Heidelberg, Germany.; Bodelon C; NCI, Division of Cancer Epidemiology and Genetics, Bethesda, Maryland.; Brand AH; Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia.; Brinton L; NCI, Division of Cancer Epidemiology and Genetics, Bethesda, Maryland.; Carney ME; Department of Obstetrics and Gynecology, University of Hawaii, John A. Burns School of Medicine, Honolulu, Hawaii.; Chiew YE; Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, New South Wales, Australia.; Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia.; Cushing-Haugen KL; Fred Hutchinson Cancer Research Center, Program in Epidemiology, Division of Public Health Sciences, Seattle, Washington.; Cybulski C; Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland.; Ennis D; Imperial College London, Division of Cancer and Ovarian Cancer Action Research Centre, Department Surgery & Cancer, London, United Kingdom.; Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom.; Fereday S; Peter MacCallum Cancer Center, Melbourne, Victoria, Australia.; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia.; Fortner RT; German Cancer Research Center (DKFZ), Division of Cancer Epidemiology, Heidelberg, Germany.; García-Donas J; HM Hospitales Centro Integral Oncológico Clara Campal (HM CIOCC), Madrid, Spain.; Gentry-Maharaj A; University College London, MRC Clinical Trials Unit at UCL, Institute of Clinical Trials & Methodology, London, United Kingdom.; Glasspool R; Department of Medical Oncology, Beatson West of Scotland Cancer Centre and University of Glasgow, Glasgow, United Kingdom.; Goranova T; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom.; Greene CS; Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.; Haluska P; Mayo Clinic, Department of Oncology, Rochester, Minnesota.; Harris HR; Fred Hutchinson Cancer Research Center, Program in Epidemiology, Division of Public Health Sciences, Seattle, Washington.; Department of Epidemiology, University of Washington, Seattle, Washington.; Hendley J; Peter MacCallum Cancer Center, Melbourne, Victoria, Australia.; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia.; Hernandez BY; University of Hawaii Cancer Center, Cancer Epidemiology Program, Honolulu, Hawaii.; Herpel E; Institute of Pathology and NCT Tissue Bank, University Hospital Heidelberg, Heidelberg, Germany.; Jimenez-Linan M; Addenbrooke's Hospital NHS Trust, Department of Pathology, Cambridge, United Kingdom.; Karpinskyj C; University College London, MRC Clinical Trials Unit at UCL, Institute of Clinical Trials & Methodology, London, United Kingdom.; Kaufmann SH; Mayo Clinic, Department of Oncology, Rochester, Minnesota.; Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota.; Keeney GL; Division of Anatomic Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.; Kennedy CJ; Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, New South Wales, Australia.; Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia.; Köbel M; Department of Pathology and Laboratory Medicine, Foothills Medical Center, University of Calgary, Calgary, Alberta, Canada.; Koziak JM; Alberta Health Services-Cancer Care, Calgary, Alberta, Canada.; Larson MC; Mayo Clinic, Division of Biomedical Statistics and Informatics, Department of Health Science Research, Rochester, Minnesota.; Lester J; David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California at Los Angeles, Los Angeles, California.; Cedars-Sinai Medical Center, Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Los Angeles, California.; Lewsley LA; Cancer Research UK Clinical Trials Unit, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom.; Lissowska J; M Sklodowska Curie National Research Institute of Oncology, Department of Cancer Epidemiology and Prevention, Warsaw, Poland.; Lubiński J; Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland.; Luk H; University of Hawaii Cancer Center, Cancer Epidemiology Program, Honolulu, Hawaii.; Macintyre G; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom.; Mahner S; Department of Obstetrics and Gynecology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany.; McNeish IA; Imperial College London, Division of Cancer and Ovarian Cancer Action Research Centre, Department Surgery & Cancer, London, United Kingdom.; Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom.; Menkiszak J; Department of Gynecological Surgery and Gynecological Oncology of Adults and Adolescents, Pomeranian Medical University, Szczecin, Poland.; Nevins N; Department of Gynaecological Oncology, Westmead Hospital and Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, New South Wales, Australia.; Osorio A; Centro de Investigación en Red de Enfermedades Raras (CIBERER), Madrid, Spain.; Spanish National Cancer Research Centre (CNIO), Human Cancer Genetics Programme, Madrid, Spain.; Oszurek O; Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland.; Palacios J; Hospital Universitario Ramón y Cajal, Pathology Department. 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Wilkens LR; University of Hawaii Cancer Center, Cancer Epidemiology Program, Honolulu, Hawaii.; Winham SJ; Mayo Clinic, Division of Biomedical Statistics and Informatics, Department of Health Science Research, Rochester, Minnesota.; Winterhoff B; Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, Minnesota.; Beeghly-Fadiel A; Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee.; Benitez J; Centro de Investigación en Red de Enfermedades Raras (CIBERER), Madrid, Spain.; Spanish National Cancer Research Centre (CNIO), Human Cancer Genetics Programme, Madrid, Spain.; Berchuck A; Department of Gynecologic Oncology, Duke University Hospital, Durham, North Carolina.; Brenton JD; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom.; Brown R; Division of Cancer and Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London, United Kingdom.; Chang-Claude J; German Cancer Research Center (DKFZ), Division of Cancer Epidemiology, Heidelberg, Germany.; University Medical Center Hamburg-Eppendorf, Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), Hamburg, Germany.; Chenevix-Trench G; QIMR Berghofer Medical Research Institute, Department of Genetics and Computational Biology, Brisbane, Queensland, Australia.; deFazio A; Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, New South Wales, Australia.; Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia.; Fasching PA; Division of Hematology and Oncology, Department of Medicine, University of California at Los Angeles, David Geffen School of Medicine, Los Angeles, California.; Department of Gynecology and Obstetrics, Comprehensive Cancer Center ER-EMN, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany.; García MJ; Spanish National Cancer Research Centre (CNIO), Human Cancer Genetics Programme, Madrid, Spain.; Biomedical Network on Rare Diseases (CIBERER), Madrid, Spain.; Gayther SA; Cedars-Sinai Medical Center, Center for Bioinformatics and Functional Genomics and the Cedars Sinai Genomics Core, Los Angeles, California.; Goodman MT; Cedars-Sinai Medical Center, Samuel Oschin Comprehensive Cancer Institute, Cancer Prevention and Genetics Program, Los Angeles, California.; Gronwald J; Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland.; Henderson MJ; Children's Cancer Institute, Lowy Cancer Research Centre, University of NSW Sydney, Sydney, New South Wales, Australia.; Karlan BY; David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California at Los Angeles, Los Angeles, California.; Cedars-Sinai Medical Center, Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Los Angeles, California.; Kelemen LE; Hollings Cancer Center and Department of Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina.; 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Rossing MA; Fred Hutchinson Cancer Research Center, Program in Epidemiology, Division of Public Health Sciences, Seattle, Washington.; Department of Epidemiology, University of Washington, Seattle, Washington.; Konecny GE; Division of Hematology and Oncology, Department of Medicine, University of California at Los Angeles, David Geffen School of Medicine, Los Angeles, California.; Huntsman DG; British Columbia's Gynecological Cancer Research Program (OVCARE), BC Cancer, Vancouver General Hospital, and University of British Columbia, Vancouver, British Columbia, Canada.; University of British Columbia, Department of Obstetrics and Gynecology, Vancouver, British Columbia, Canada.; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.; Department of Molecular Oncology, BC Cancer Research Centre, Vancouver, British Columbia, Canada.; Huang RY; National University of Singapore, Cancer Science Institute of Singapore, Center for Translational Medicine, Singapore, Singapore.; National Taiwan University, School of Medicine, College of Medicine, Taipei City, Taiwan.; Goode EL; Division of Epidemiology, Department of Health Science Research, Mayo Clinic, Rochester, Minnesota. m.anglesio@ubc.ca David.bowtell@petermac.org jen.doherty@hci.utah.edu s.ramus@unsw.edu.au egoode@mayo.edu.; Ramus SJ; University of NSW Sydney, School of Women's and Children's Health, Faculty of Medicine, Sydney, New South Wales, Australia. m.anglesio@ubc.ca David.bowtell@petermac.org jen.doherty@hci.utah.edu s.ramus@unsw.edu.au egoode@mayo.edu.; Adult Cancer Program, Lowy Cancer Research Centre, University of NSW Sydney, Sydney, New South Wales, Australia.; Doherty JA; Department of Population Health Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah. m.anglesio@ubc.ca David.bowtell@petermac.org jen.doherty@hci.utah.edu s.ramus@unsw.edu.au egoode@mayo.edu.; Bowtell DD; Peter MacCallum Cancer Center, Melbourne, Victoria, Australia. m.anglesio@ubc.ca David.bowtell@petermac.org jen.doherty@hci.utah.edu s.ramus@unsw.edu.au egoode@mayo.edu.; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia.; Anglesio MS; British Columbia's Gynecological Cancer Research Program (OVCARE), BC Cancer, Vancouver General Hospital, and University of British Columbia, Vancouver, British Columbia, Canada. m.anglesio@ubc.ca David.bowtell@petermac.org jen.doherty@hci.utah.edu s.ramus@unsw.edu.au egoode@mayo.edu.; University of British Columbia, Department of Obstetrics and Gynecology, Vancouver, British Columbia, Canada.; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada. |
| Source: | Clinical cancer research : an official journal of the American Association for Cancer Research [Clin Cancer Res] 2020 Oct 15; Vol. 26 (20), pp. 5411-5423. Date of Electronic Publication: 2020 Jun 17. |
| Publication Type: | Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S. |
| Language: | English |
| Journal Info: | Publisher: American Association for Cancer Research Country of Publication: United States NLM ID: 9502500 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1557-3265 (Electronic) Linking ISSN: 10780432 NLM ISO Abbreviation: Clin Cancer Res Subsets: MEDLINE |
| Imprint Name(s): | Original Publication: Denville, NJ : American Association for Cancer Research, c1995- |
| MeSH Terms: | Cystadenoma, Serous/*genetics ; Neoplasm Proteins/*genetics ; Ovarian Neoplasms/*genetics ; Transcriptome/*genetics; Cystadenoma, Serous/classification ; Cystadenoma, Serous/pathology ; Gene Expression Regulation, Neoplastic/genetics ; Lymphocytes, Tumor-Infiltrating/pathology ; Neoplasm, Residual/classification ; Neoplasm, Residual/genetics ; Neoplasm, Residual/pathology ; Ovarian Neoplasms/classification ; Ovarian Neoplasms/pathology ; Aged ; Algorithms ; Female ; Humans ; Middle Aged ; Neoplasm Grading |
| Abstract: | Purpose: Gene expression-based molecular subtypes of high-grade serous tubo-ovarian cancer (HGSOC), demonstrated across multiple studies, may provide improved stratification for molecularly targeted trials. However, evaluation of clinical utility has been hindered by nonstandardized methods, which are not applicable in a clinical setting. We sought to generate a clinical grade minimal gene set assay for classification of individual tumor specimens into HGSOC subtypes and confirm previously reported subtype-associated features.; Experimental Design: Adopting two independent approaches, we derived and internally validated algorithms for subtype prediction using published gene expression data from 1,650 tumors. We applied resulting models to NanoString data on 3,829 HGSOCs from the Ovarian Tumor Tissue Analysis consortium. We further developed, confirmed, and validated a reduced, minimal gene set predictor, with methods suitable for a single-patient setting.; Results: Gene expression data were used to derive the predictor of high-grade serous ovarian carcinoma molecular subtype (PrOTYPE) assay. We established a de facto standard as a consensus of two parallel approaches. PrOTYPE subtypes are significantly associated with age, stage, residual disease, tumor-infiltrating lymphocytes, and outcome. The locked-down clinical grade PrOTYPE test includes a model with 55 genes that predicted gene expression subtype with >95% accuracy that was maintained in all analytic and biological validations.; Conclusions: We validated the PrOTYPE assay following the Institute of Medicine guidelines for the development of omics-based tests. This fully defined and locked-down clinical grade assay will enable trial design with molecular subtype stratification and allow for objective assessment of the predictive value of HGSOC molecular subtypes in precision medicine applications.See related commentary by McMullen et al., p. 5271.; (©2020 American Association for Cancer Research.) |
| Comments: | Comment in: Clin Cancer Res. 2020 Oct 15;26(20):5271-5273. doi: 10.1158/1078-0432.CCR-20-2429.. (PMID: 32816948) |
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| Grant Information: | R01 CA172404 United States CA NCI NIH HHS; MC_UU_12023/20 United Kingdom MRC_ Medical Research Council; P30 CA034196 United States CA NCI NIH HHS; UL1 TR000124 United States TR NCATS NIH HHS; 15601 United Kingdom CRUK_ Cancer Research UK; R01 CA200854 United States CA NCI NIH HHS; 22905 United Kingdom CRUK_ Cancer Research UK; 13086 United Kingdom CRUK_ Cancer Research UK; UL1 TR001881 United States TR NCATS NIH HHS; P30 CA042014 United States CA NCI NIH HHS; P30 CA008748 United States CA NCI NIH HHS; K22 CA193860 United States CA NCI NIH HHS; R01 CA168758 United States CA NCI NIH HHS; P30 CA071789 United States CA NCI NIH HHS; P50 CA136393 United States CA NCI NIH HHS |
| Substance Nomenclature: | 0 (Neoplasm Proteins) |
| Entry Date(s): | Date Created: 20200620 Date Completed: 20211123 Latest Revision: 20250530 |
| Update Code: | 20260130 |
| PubMed Central ID: | PMC7572656 |
| DOI: | 10.1158/1078-0432.CCR-20-0103 |
| PMID: | 32554541 |
| Database: | MEDLINE |
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.