Grant Number:	1R03CA191447-01A1 Interpret this number
Primary Investigator:	Waldron, Levi
Organization:	Hunter College
Project Title:	Validation and Clinical Relevance of Ovarian Cancer Molecular Subtypes
Fiscal Year:	2015

¿ DESCRIPTION (provided by applicant): At least five major studies have reported molecular subtypes of high-grade, serous ovarian cancer, and these have the potential to guide development of targeted treatments. However, each study has proposed overlapping but different subtype algorithms, and have used small and differing subsets of publicly available data for validation. At least two other major ovarian cancer studies could not identify discrete subtypes in their gene expression data at all. Uncertainty in the clinical relevance of proposed subtypes is compounded by recent reports that most ovarian cancer tumors are multi-clonal, raising the possibility that multiple subtypes exist within a single tumor. Thus the nature of ovarian cancer subtypes remains controversial, even as they have spurred further investment in retrospective analysis of clinical trial specimens. This study aims to resolve controversy and uncertainty in the nature of ovarian cancer subtypes by two main approaches. First, subtype robustness and association to patient outcome are assessed by comparative meta-analysis using all relevant publicly available data. This will provide clarity on which definition of subtyps future research should focus on. Second, the likely ordering of subtype differentiation in tumor evolution is determined by analysis of the allele frequencies of subtype- associated DNA short variants in data from The Cancer Genome Atlas. This application moves the field of ovarian cancer research forward by resolving controversy around proposed subtypes using publicly available data, and by providing standardized definitions of subtype algorithms with documentation for their application to new patients.




Multiomic Analysis of Subtype Evolution and Heterogeneity in High-Grade Serous Ovarian Carcinoma.
Authors: Geistlinger L. , Oh S. , Ramos M. , Schiffer L. , LaRue R.S. , Henzler C.M. , Munro S.A. , Daughters C. , Nelson A.C. , Winterhoff B.J. , et al. .
Source: Cancer Research, 2020-08-03 00:00:00.0; , .
EPub date: 2020-08-03 00:00:00.0.
PMID: 32747365
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The Impact of Stroma Admixture on Molecular Subtypes and Prognostic Gene Signatures in Serous Ovarian Cancer.
Authors: Schwede M. , Waldron L. , Mok S.C. , Wei W. , Basunia A. , Merritt M.A. , Mitsiades C.S. , Parmigiani G. , Harrington D.P. , Quackenbush J. , et al. .
Source: Cancer Epidemiology, Biomarkers & Prevention : A Publication Of The American Association For Cancer Research, Cosponsored By The American Society Of Preventive Oncology, 2020 02; 29(2), p. 509-519.
EPub date: 2019-12-23 00:00:00.0.
PMID: 31871106
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MetaGxData: Clinically Annotated Breast, Ovarian and Pancreatic Cancer Datasets and their Use in Generating a Multi-Cancer Gene Signature.
Authors: Gendoo D.M.A. , Zon M. , Sandhu V. , Manem V.S.K. , Ratanasirigulchai N. , Chen G.M. , Waldron L. , Haibe-Kains B. .
Source: Scientific Reports, 2019-06-19 00:00:00.0; 9(1), p. 8770.
EPub date: 2019-06-19 00:00:00.0.
PMID: 31217513
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Consensus on Molecular Subtypes of High-Grade Serous Ovarian Carcinoma.
Authors: Chen G.M. , Kannan L. , Geistlinger L. , Kofia V. , Safikhani Z. , Gendoo D.M.A. , Parmigiani G. , Birrer M. , Haibe-Kains B. , Waldron L. .
Source: Clinical Cancer Research : An Official Journal Of The American Association For Cancer Research, 2018-10-15 00:00:00.0; 24(20), p. 5037-5047.
EPub date: 2018-07-03 00:00:00.0.
PMID: 30084834
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Continuity of transcriptomes among colorectal cancer subtypes based on meta-analysis.
Authors: Ma S. , Ogino S. , Parsana P. , Nishihara R. , Qian Z. , Shen J. , Mima K. , Masugi Y. , Cao Y. , Nowak J.A. , et al. .
Source: Genome Biology, 2018-09-25 00:00:00.0; 19(1), p. 142.
EPub date: 2018-09-25 00:00:00.0.
PMID: 30253799
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The impact of different sources of heterogeneity on loss of accuracy from genomic prediction models.
Authors: Zhang Y. , Bernau C. , Parmigiani G. , Waldron L. .
Source: Biostatistics (oxford, England), 2018-09-06 00:00:00.0; , .
EPub date: 2018-09-06 00:00:00.0.
PMID: 30202918
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The Doppelgänger Effect: Hidden Duplicates in Databases of Transcriptome Profiles.
Authors: Waldron L. , Riester M. , Ramos M. , Parmigiani G. , Birrer M. .
Source: Journal Of The National Cancer Institute, 2016 Nov; 108(11), .
PMID: 27381624
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Racial/Ethnic Disparities in Genomic Sequencing.
Authors: Spratt D.E. , Chan T. , Waldron L. , Speers C. , Feng F.Y. , Ogunwobi O.O. , Osborne J.R. .
Source: Jama Oncology, 2016-08-01 00:00:00.0; 2(8), p. 1070-4.
PMID: 27366979
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