Improving reporting standards for polygenic scores in risk prediction studies

被引:231
|
作者
Wand, Hannah [1 ,2 ]
Lambert, Samuel A. [3 ,4 ,5 ,6 ,7 ,8 ]
Tamburro, Cecelia [9 ]
Iacocca, Michael A. [1 ]
O'Sullivan, Jack W. [1 ,2 ]
Sillari, Catherine [9 ]
Kullo, Iftikhar J. [10 ]
Rowley, Robb [9 ]
Dron, Jacqueline S. [11 ,12 ]
Brockman, Deanna [11 ]
Venner, Eric [13 ]
McCarthy, Mark I. [14 ,15 ]
Antoniou, Antonis C. [16 ]
Easton, Douglas F. [16 ]
Hegele, Robert A. [12 ]
Khera, Amit V. [11 ]
Chatterjee, Nilanjan [17 ,18 ]
Kooperberg, Charles [19 ]
Edwards, Karen [20 ]
Vlessis, Katherine [21 ]
Kinnear, Kim [21 ]
Danesh, John N. [5 ,6 ,7 ,22 ,23 ]
Parkinson, Helen [6 ,7 ,8 ]
Ramos, Erin M. [9 ]
Roberts, Megan C. [24 ]
Ormond, Kelly E. [21 ,25 ]
Khoury, Muin J. [26 ]
Janssens, A. Cecile J. W. [27 ]
Goddard, Katrina A. B. [28 ,29 ]
Kraft, Peter [30 ]
MacArthur, Jaqueline A. L. [8 ]
Inouye, Michael [3 ,4 ,5 ,6 ,7 ,31 ]
Wojcik, Genevieve L. [22 ,23 ,32 ]
机构
[1] Stanford Univ, Sch Med, Stanford, CA 94305 USA
[2] Stanford Ctr Inherited Cardiovasc Dis, Stanford, CA USA
[3] Univ Cambridge, Dept Publ Hlth & Primary Care, Cambridge Baker Syst Genom Initiat, Cambridge, England
[4] Baker Heart & Diabet Inst, Cambridge Baker Syst Genom Initiat, Melbourne, Vic, Australia
[5] Univ Cambridge, Dept Publ Hlth & Primary Care, BHF Cardiovasc Epidemiol Unit, Cambridge, England
[6] Wellcome Genome Campus, Hlth Data Res UK Cambridge, Cambridge, England
[7] Univ Cambridge, Cambridge, England
[8] European Bioinformat Inst, European Mol Biol Lab, Wellcome Genome Campus, Hinxton, England
[9] NHGRI, Bethesda, MD 20892 USA
[10] Mayo Clin, Dept Cardiovasc Med, Rochester, MN USA
[11] Massachusetts Gen Hosp, Ctr Genom Med, Boston, MA 02114 USA
[12] Western Univ, London, ON, Canada
[13] Baylor Coll Med, Houston, TX 77030 USA
[14] Genentech Inc, Dept Human Genet, San Francisco, CA USA
[15] Wellcome Ctr Human Genet, Oxford, England
[16] Univ Cambridge, Dept Publ Hlth & Primary Care, Cambridge, England
[17] Johns Hopkins Bloomberg Sch Publ Hlth, Dept Biostat, Baltimore, MD USA
[18] Johns Hopkins Sch Med, Dept Oncol, Baltimore, MD USA
[19] Fred Hutchinson Canc Res Ctr, Div Publ Hlth Sci, 1124 Columbia St, Seattle, WA 98104 USA
[20] Univ Calif Irvine, Dept Epidemiol, Irvine, CA USA
[21] Stanford Univ, Sch Med, Dept Genet, Stanford, CA 94305 USA
[22] Univ Cambridge, Natl Inst Hlth Res, Cambridge Biomed Res Ctr, Cambridge, England
[23] Cambridge Univ Hosp, Cambridge, England
[24] UNC Eshelman Sch Pharm, Div Pharmaceut Outcomes & Policy, Chapel Hill, NC USA
[25] Stanford Univ, Sch Med, Stanford Ctr Biomed Eth, Stanford, CA 94305 USA
[26] Ctr Dis Control & Prevent, Atlanta, GA USA
[27] Emory Univ, Dept Epidemiol, Rollins Sch Publ Hlth, Atlanta, GA 30322 USA
[28] Kaiser Permanente Northwest, Dept Translat & Appl Genom, Portland, OR USA
[29] Kaiser Permanente Northwest, Ctr Hlth Res, Portland, OR USA
[30] Harvard TH Chan Sch Publ Hlth, Dept Epidemiol, Boston, MA USA
[31] Alan Turing Inst, London, England
[32] Johns Hopkins Bloomberg Sch Publ Hlth, Dept Epidemiol, Baltimore, MD 21205 USA
基金
英国医学研究理事会; 英国经济与社会研究理事会; 加拿大健康研究院; 英国工程与自然科学研究理事会;
关键词
GENOME-WIDE ASSOCIATION; BREAST-CANCER; DISEASE; SUSCEPTIBILITY; ACCURACY; GENES; MODEL;
D O I
10.1038/s41586-021-03243-6
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Polygenic risk scores (PRSs), which often aggregate results from genome-wide association studies, can bridge the gap between initial discovery efforts and clinical applications for the estimation of disease risk using-genetics. However, there is notable heterogeneity in the application and reporting of these risk scores, which hinders the translation of PRSs into clinical care. Here, in a collaboration between the Clinical Genome Resource (ClinGen) Complex Disease Working Group and the Polygenic Score (PGS) Catalog, we present the Polygenic Risk Score Reporting Standards (PRS-RS), in which we update the Genetic Risk Prediction Studies (GRIPS) Statement to reflect the present state of the field. Drawing on the input of experts in epidemiology, statistics, disease-specific applications, implementation and policy, this comprehensive reporting framework defines the minimal information that is needed to interpret and evaluate PRSs, especially with respect to downstream clinical applications. Items span detailed descriptions of study populations, statistical methods for the development and validation of PRSs and considerations for the potential limitations of these scores. In addition, we emphasize the need for data availability and transparency, and we encourage researchers to deposit and share PRSs through the PGS Catalog to facilitate reproducibility and comparative bench marking. By providing these criteria in a structured format that builds on existing standards and ontologies, the use of this framework in publishing PRSs will facilitate translation into clinical care and progress towards defining best practice.
引用
收藏
页码:211 / 219
页数:9
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