• Wed. Sep 28th, 2022

GAWMerge expands GWAS sample size and diversity by combining matrix-based genotyping and whole genome sequencing

ByRandall B. Phelps

Aug 11, 2022

Primary support for the development of GAWMerge, performing analyses, and preparing the manuscript was provided by National Institute on Drug Abuse grants to EOJ: R01 DA044014 (PI: EOJ); R01 DA043980 (M-PI: Scacheri, EOJ, Akbarian); R01 DA051908 (M-PI: EOJ and Jacobson). Support for this work was provided by the National Institutes of Health, National Heart, Lung, and Blood Institute, through the BioData Catalyst program (award 1OT3HL142479-01, 1OT3HL142478-01, 1OT3HL142481-01, 1OT3HL142480-01, 1OT3HL147154 -01). All opinions expressed in this document are those of the authors and do not necessarily reflect the views of NHLBI, individual members of the BioData Catalyst team, or affiliated organizations and institutions. Molecular data from the Trans-Omics in Precision Medicine (TOPMed) program was supported by the National Heart, Lung and Blood Institute (NHLBI). Genome sequencing for NHLBI TOPMed: COPDGene (phs000179.v6.p2) was performed at NWGC (3R01HL089856-08S1, HHSN268201600032I and HHSN268201600032I) and Broad Genomics (HHSN268201500014C and HHSN2500204144C). Genome sequencing for NHLBI TOPMed: ECLIPSE (phs001252.v1.p1) was performed at MDI (HHSN268201600037I). Core support, including centralized genomic read mapping and genotype calling, as well as variant quality metrics and filtering, was provided by the TOPMed Informatics Research Center (3R01HL-117626-02S1; contract HHSN268201800002I ). Core support, including phenotype harmonization, data management, sample identity QC, and general program coordination, was provided by the TOPMed Data Coordination Center (R01HL-120393; U01HL -120393; contract HHSN268201800001I). We would like to thank the studies and participants who provided biological samples and data for TOPMed. The COPDGene project described was supported by award number U01 HL089897 and award number U01 HL089856 from the National Heart, Lung, and Blood Institute. The content is the sole responsibility of the authors and does not necessarily represent the official views of the National Heart, Lung, and Blood Institute or the National Institutes of Health. The COPDGene project is also supported by the COPD Foundation through contributions made to an industry advisory board that included AstraZeneca, Bayer Pharmaceuticals, Boehringer-Ingelheim, Genentech, GlaxoSmithKline, Novartis, Pfizer and Sunovion. A full list of COPDGene investigators can be found at: http://www.copdgene.org/directory. The ECLIPSE study (NCT00292552) was sponsored by GlaxoSmithKline. ECLIPSE investigators included: Bulgaria: Y. Ivanov, Pleven; K. Kostov, Sofia. Canada: J. Bourbeau, Montreal; M. Fitzgerald, Vancouver, BC; P. Hernandez, Halifax, NS; K. Killian, Hamilton, Ont.; R. Levy, Vancouver, BC; F. Maltais, Montreal; D. O’Donnell, Kingston, Ont. Czech Republic: J. Krepelka, Prague. Denmark: J. Vestbo, Hvidovre. Netherlands: E. Wouters, Horn-Maastricht. New Zealand: D. Quinn, Wellington. Norway: P. Bakke, Bergen. Slovenia: Mr. Kosnik, Golnik. Spain: A. Agusti, J. Sauleda, P. de Mallorca. Ukraine: Y. Feschenko, V. Gavrisyuk, L. Yashina, Kyiv; N. Monogarova, Donetsk. United Kingdom: P. Calverley, Liverpool; D. Lomas, Cambridge; W. MacNee, Edinburgh; D. Singh, Manchester; J. Wedzicha, London. United States: A. Anzueto, San Antonio, TX; S. Braman, Providence, RI; R. Casaburi, Torrance CA; B. Celli, Boston; G. Giessel, Richmond, Virginia; Mr. Gotfried, Phoenix, Arizona; G. Greenwald, Rancho Mirage, Calif.; N. Hanania, Houston; D. Mahler, Lebanon, NH; B. Make, Denver; S. Renard, Omaha, NE; C. Rochester, New Haven, CT; P. Scanlon, Rochester, MN; D. Schuller, Omaha, NE; F. Sciurba, Pittsburgh; A. Sharafkhaneh, Houston; T. Siler, St. Charles, MO; EKS, Boston; A. Wanner, Miami; R. Wise, Baltimore; R. ZuWallack, Hartford, CT. ECLIPSE Steering Committee: H. Coxson (Canada), C. Crim (GlaxoSmithKline, USA), L. Edwards (GlaxoSmithKline, USA), D. Lomas (UK), W. MacNee (UK) Uni), EKS (USA), R. Tal-Singer (Co-Chair, GlaxoSmithKline, USA), J. Vestbo (Co-Chair, Denmark), J. Yates (GlaxoSmithKline, USA). ECLIPSE Scientific Committee: A. Agusti (Spain), P. Calverley (UK), B. Celli (USA), C. Crim (GlaxoSmithKline, USA), B. Miller (GlaxoSmithKline, USA) , W. MacNee (Chairman, United Kingdom), S. Rennard (United States), R. Tal-Singer (GlaxoSmithKline, United States), E. Wouters (Netherlands), J. Yates (GlaxoSmithKline, United -United). COGEND was supported by grants from the National Cancer Institute (NCI; grant number P01 CA089392, PI: LJB) and NIDA (R01 DA036583 and R01 DA025888, PI: LJB), both National Institutes of Health (NIH). Genotype data is available via dbGaP as part of “The Genetic Architecture of Smoking and Smoking Cessation” (accession number phs000404.v1.p1) and “The Study of Addiction: Genetics and environment (SAGE)” (access number phs000092.v1.p1) . Financial support for the genotyping, which was performed at CIDR, was provided by 1×01 HG005274-01 and the NIH Genes, Environment and Health Initiative [GEI] (U01HG004422). CIDR is fully funded by a federal contract from the NIH to Johns Hopkins University, contract number HHSN268200782096C. Assistance in cleaning the genotypes as well as in the general coordination of the study was provided by the GENEVA Coordination Center (U01 HG004446).