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Grant Details

Grant Number: 5U01CA242954-03 Interpret this number
Primary Investigator: Cline, Melissa
Organization: University Of California Santa Cruz
Project Title: Eliminating Variants of Uncertain Significance in BRCA1, Brca2 and Beyond
Fiscal Year: 2021


Abstract

Abstract By current evidence, roughly one-third of all cancers are driven in part by germline variation. Genetic testing now enables individuals and their doctors to better understand and manage their genetic cancer risk. However, the effectiveness of these tests is limited by the many gaps in our knowledge about the clinical impact of individual variants. Even in the well-studiedBRCA1 and BRCA2 genes, 7280 of the 17156 variants currently in ClinVar are listed as “Variants of Uncertain Significance” (VUS). VUS test reports leave patients with anxiety, and often lead to clinical mismanagement: many doctors frequently recommend bilateral mastectomies for patients with uncertain variants, even though many of those variants will turn out to be benign. Genetic testing will not reach its potential while VUS test reports are still frequent, yet with global data sharing, novel functional screens, and integrative data analysis methods, we can envisage eliminating the VUS problem. We will produce methods for secure data sharing, and integrative analysis that leverages highly predictive modern functional assays. We will demonstrate these approaches on BRCA1 and BRCA2, while outlining their application to other high-penetrance cancer susceptibility genes. We will develop APIs to integrate this new knowledge into the ClinGen and CIViC repositories, to benefit the larger research community. Finally, we will extend the integrative data visualization of BRCA Exchange to additional genes implicated in breast, ovarian and colorectal cancers, which will ultimately benefit tens of thousands of cancer patients and previvors.



Publications

Federated analysis of BRCA1 and BRCA2 variation in a Japanese cohort.
Authors: Casaletto J. , Parsons M. , Markello C. , Iwasaki Y. , Momozawa Y. , Spurdle A.B. , Cline M. .
Source: Cell genomics, 2022-03-09; 2(3), .
PMID: 35373174
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U.S. Adult Perspectives on Facial Images, DNA, and Other Biometrics.
Authors: Katsanis S.H. , Claes P. , Doerr M. , Cook-Deegan R. , Tenenbaum J.D. , Evans B.J. , Lee M.K. , Anderton J. , Weinberg S.M. , Wagner J.K. .
Source: IEEE transactions on technology and society, 2022 Mar; 3(1), p. 9-15.
EPub date: 2021-10-18.
PMID: 35360665
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Closing the gap: Systematic integration of multiplexed functional data resolves variants of uncertain significance in BRCA1, TP53, and PTEN.
Authors: Fayer S. , Horton C. , Dines J.N. , Rubin A.F. , Richardson M.E. , McGoldrick K. , Hernandez F. , Pesaran T. , Karam R. , Shirts B.H. , et al. .
Source: American journal of human genetics, 2021-12-02; 108(12), p. 2248-2258.
EPub date: 2021-11-17.
PMID: 34793697
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The GA4GH Variation Representation Specification: A computational framework for variation representation and federated identification.
Authors: Wagner A.H. , Babb L. , Alterovitz G. , Baudis M. , Brush M. , Cameron D.L. , Cline M. , Griffith M. , Griffith O.L. , Hunt S.E. , et al. .
Source: Cell genomics, 2021-11-10; 1(2), .
PMID: 35311178
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International federation of genomic medicine databases using GA4GH standards.
Authors: Thorogood A. , Rehm H.L. , Goodhand P. , Page A.J.H. , Joly Y. , Baudis M. , Rambla J. , Navarro A. , Nyronen T.H. , Linden M. , et al. .
Source: Cell genomics, 2021-11-10; 1(2), .
PMID: 35128509
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GA4GH: International policies and standards for data sharing across genomic research and healthcare.
Authors: Rehm H.L. , Page A.J.H. , Smith L. , Adams J.B. , Alterovitz G. , Babb L.J. , Barkley M.P. , Baudis M. , Beauvais M.J.S. , Beck T. , et al. .
Source: Cell genomics, 2021-11-10; 1(2), .
PMID: 35072136
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A survey of U.S. public perspectives on facial recognition technology and facial imaging data practices in health and research contexts.
Authors: Katsanis S.H. , Claes P. , Doerr M. , Cook-Deegan R. , Tenenbaum J.D. , Evans B.J. , Lee M.K. , Anderton J. , Weinberg S.M. , Wagner J.K. .
Source: PloS one, 2021; 16(10), p. e0257923.
EPub date: 2021-10-14.
PMID: 34648520
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Recommendations for the collection and use of multiplexed functional data for clinical variant interpretation.
Authors: Gelman H. , Dines J.N. , Berg J. , Berger A.H. , Brnich S. , Hisama F.M. , James R.G. , Rubin A.F. , Shendure J. , Shirts B. , et al. .
Source: Genome medicine, 2019-12-20; 11(1), p. 85.
EPub date: 2019-12-20.
PMID: 31862013
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