Large-Scale GWAS of Esophageal Diseases

The BEACON GWAS included men and women diagnosed with EA or BE, and control participants pooled from 14 individual studies conducted in Western Europe, Australia, and North America over the past 20 years. Detailed study population characteristics and genotyping protocols have been published [24 (link)]. The current analysis employed a pooled dataset [30 (link)] that included participants of European ancestry from the BEACON GWAS, additional BE and EA patients from the UK Barrett’s Esophagus Gene Study and the UK Stomach and Oesophageal Cancer Study (SOCS), respectively [24 (link)], and additional control participants from a hospital-based case-control study of melanoma conducted at the MD Anderson Cancer Center (Houston, TX) [31 (link)]. Genotyping of buffy coat or whole blood DNA from all participants was conducted using the Illumina Omni1M Quad platform, in accordance with standard quality control procedures [32 (link)]. All participants gave written informed consent, and this project was approved by the ethics review board of the Fred Hutchinson Cancer Research Center. We selected all unrelated participants with <2% missing genotyping calls; thus the final study sample included 2,515 EA cases, 3,295 BE cases, and 3,207 controls. Three control participants were excluded from analyses involving BE cases, because of familial relation to cases.

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Buas M.F., He Q., Johnson L.G., Onstad L., Levine D.M., Thrift A.P., Gharahkhani P., Palles C., Lagergren J., Fitzgerald R.C., Ye W., Caldas C., Bird N.C., Shaheen N.J., Bernstein L., Gammon M.D., Wu A.H., Hardie L.J., Pharoah P.D., Liu G., Iyer P., Corley D.A., Risch H.A., Chow W.H., Prenen H., Chegwidden L., Love S., Attwood S., Moayyedi P., MacDonald D., Harrison R., Watson P., Barr H., deCaestecker J., Tomlinson I., Jankowski J., Whiteman D.C., MacGregor S., Vaughan T.L, & Madeleine M.M. (2016). Germline variation in inflammation-related pathways and risk of Barrett’s esophagus and esophageal adenocarcinoma. Gut, 66(10), 1739-1747.

Publication 2016

Omni1M Quad platform

Barrett esophagus Blood Cancer European Gene Gwas Melanoma Oesophageal cancer Patients Socs Stomach Women

Corresponding Organization : Fred Hutch Cancer Center

Other organizations : University of Washington, Baylor College of Medicine, QIMR Berghofer Medical Research Institute, Wellcome Centre for Human Genetics, King's College London, Karolinska Institutet, MRC Cancer Unit, Hutchison/MRC Research Centre, Medical Research Council, Cancer Research UK Cambridge Center, University of Sheffield, University of North Carolina at Chapel Hill, City of Hope, University of Southern California, University of Leeds, University of Cambridge, Ontario Institute for Cancer Research, Mayo Clinic, WinnMed, Kaiser Permanente, Kaiser Permanente San Francisco Medical Center, Yale University, The University of Texas MD Anderson Cancer Center, Wellcome/MRC Institute of Metabolic Science, Addenbrooke's Hospital, Wellcome Trust, MRC Clinical Trials Unit at UCL, North Tyneside General Hospital, McMaster University, University of British Columbia, Leicester Royal Infirmary, University of Ulster, Royal Victoria Hospital, Gloucestershire Royal Hospital, Leicester General Hospital

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Variable analysis

independent variables

Independent variables not explicitly mentioned.

dependent variables

Dependent variables not explicitly mentioned.

control variables

European ancestry
Unrelated participants with <2% missing genotyping calls
Three control participants excluded from analyses involving BE cases due to familial relation to cases

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