Winner's Curse Correction and Variable Thresholding Improve Performance of Polygenic Risk Modeling Based on Genome-Wide Association Study Summary-Level Data

• Jianxin Shi ,

  * E-mail: Jianxin.Shi@nih.gov (JS); nilanjan@jhu.edu (NC)

  Affiliation Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America

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• Ju-Hyun Park,

  Affiliation Department of Statistics, Dongguk University, Seoul, Korea

  http://orcid.org/0000-0001-9675-6475

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• Jubao Duan,

  Affiliation Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, North Shore University Health System Research Institute, University of Chicago Pritzker School of Medicine, Evanston, Illinois, United States of America

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• Sonja T. Berndt,

  Affiliation Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America

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• Winton Moy,

  Affiliation Dept. of Statistics, Northern Illinois University, DeKalb, Illinois, United States of America

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• Kai Yu,

  Affiliation Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America

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• Lei Song,

  Affiliation Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America

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• William Wheeler,

  Affiliation Information Management Services, Inc., Rockville, Maryland, United States of America

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• Xing Hua,

  Affiliation Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America

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• Debra Silverman,

  Affiliation Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America

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• Montserrat Garcia-Closas,

  Affiliation Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America

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• Chao Agnes Hsiung,

  Affiliation Institute of Population Health Sciences, National Health Research Institutes, Miaoli, Taiwan

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• Jonine D. Figueroa,

  Affiliations Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America, Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Medical School, Edinburgh, United Kingdom

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• Victoria K. Cortessis,

  Affiliations Department of Preventive Medicine and Department of Obstetrics and Gynecology, USC Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America, Norris Comprehensive Cancer Center, USC Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America

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• Núria Malats,

  Affiliation Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain

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• Margaret R. Karagas,

  Affiliation Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, United States of America

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• Paolo Vineis,

  Affiliations Human Genetics Foundation, Turin, Italy, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, United Kingdom

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• I-Shou Chang,

  Affiliation National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan

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• Dongxin Lin,

  Affiliations Department of Etiology & Carcinogenesis, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China, State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China

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• Baosen Zhou,

  Affiliation Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China

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• Adeline Seow,

  Affiliation Saw Swee Hock School of Public Health, National University of Singapore, Singapore

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• Keitaro Matsuo,

  Affiliation Division of Molecular Medicine, Aichi Cancer Center Research Institute, Chikusa-ku, Nagoya, Japan

  http://orcid.org/0000-0003-1761-6314

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• Yun-Chul Hong,

  Affiliation Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea

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• Neil E. Caporaso,

  Affiliation Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America

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• Brian Wolpin,

  Affiliations Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America

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• Eric Jacobs,

  Affiliation Epidemiology Research Program, American Cancer Society, Atlanta, Georgia, United States of America

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• Gloria M. Petersen,

  Affiliation Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America

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• Alison P. Klein,

  Affiliations Department of Oncology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America, Department of Epidemiology, the Bloomberg School of Public Health, Baltimore, Maryland, United States of America

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• Donghui Li,

  Affiliation Department of Gastrointestinal Medical Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas, United States of America

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• Harvey Risch,

  Affiliation Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, Connecticut, United States of America

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• Alan R. Sanders,

  Affiliation Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, North Shore University Health System Research Institute, University of Chicago Pritzker School of Medicine, Evanston, Illinois, United States of America

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• Li Hsu,

  Affiliation Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America

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• Robert E. Schoen,

  Affiliation Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America

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• Hermann Brenner,

  Affiliations Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany, Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany

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• MGS (Molecular Genetics of Schizophrenia) GWAS Consortium ,

  ¶Members of MGS Consortium, GECCO Consortium, GAME-ON/TRICL Consortium, PRACTICAL Consortium, PanScan Consortium and GAME-ON/ ELLIPSE are provided in S1 Text.

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• GECCO (The Genetics and Epidemiology of Colorectal Cancer Consortium) ,

  ¶Members of MGS Consortium, GECCO Consortium, GAME-ON/TRICL Consortium, PRACTICAL Consortium, PanScan Consortium and GAME-ON/ ELLIPSE are provided in S1 Text.

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• The GAME-ON/TRICL (Transdisciplinary Research in Cancer of the Lung) GWAS Consortium ,

  ¶Members of MGS Consortium, GECCO Consortium, GAME-ON/TRICL Consortium, PRACTICAL Consortium, PanScan Consortium and GAME-ON/ ELLIPSE are provided in S1 Text.

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• PRACTICAL (PRostate cancer AssoCiation group To Investigate Cancer Associated aLterations) Consortium ,

  ¶Members of MGS Consortium, GECCO Consortium, GAME-ON/TRICL Consortium, PRACTICAL Consortium, PanScan Consortium and GAME-ON/ ELLIPSE are provided in S1 Text.

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• PanScan Consortium ,

  ¶Members of MGS Consortium, GECCO Consortium, GAME-ON/TRICL Consortium, PRACTICAL Consortium, PanScan Consortium and GAME-ON/ ELLIPSE are provided in S1 Text.

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• The GAME-ON/ELLIPSE Consortium ,

  ¶Members of MGS Consortium, GECCO Consortium, GAME-ON/TRICL Consortium, PRACTICAL Consortium, PanScan Consortium and GAME-ON/ ELLIPSE are provided in S1 Text.

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• Rachael Stolzenberg-Solomon,

  Affiliation Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America

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• Pablo Gejman,

  Affiliation Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, North Shore University Health System Research Institute, University of Chicago Pritzker School of Medicine, Evanston, Illinois, United States of America

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• Qing Lan,

  Affiliation Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America

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• Nathaniel Rothman,

  Affiliation Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America

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• Laufey T. Amundadottir,

  Affiliation Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America

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• Maria Teresa Landi,

  Affiliation Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America

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• Douglas F. Levinson,

  Affiliation Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, California, United States of America

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• Stephen J. Chanock,

  Affiliation Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America

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•  [ ... ],
• Nilanjan Chatterjee

  * E-mail: Jianxin.Shi@nih.gov (JS); nilanjan@jhu.edu (NC)

  Affiliations Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America, Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America, Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America

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