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Study Description

This project aims to conduct genome-wide association studies (GWAS) in two anatomically different upper gastrointestinal (UGI) cancer sites in two populations with distinctly different disease rates and genetic profiles. One population has very high rates for both esophageal squamous cell carcinomas (ESCCs) and gastric cancers (GCs) and is comprised of Asians (the "Asian UGI GWAS"), while the other population has low rates of ESCC and GC and includes non-Asians from the Americas, Europe, and Australia (the "Non-Asian UGI GWAS").

Study participants for the Asian UGI GWAS reported here (Illumina 660W Quad chip) were drawn from 2 studies, the Shanxi Upper Gastrointestinal Cancer Genetics Project (Shanxi) and the Linxian Nutrition Intervention Trial (NIT), a prospective cohort, and included a total of 1898 ESCCs, 1625 GCs, and 2100 controls. For the 2nd phase (8 TaqMan SNPs), additional subjects from Shanxi and NIT as well as subjects from the Shanghai Men's Health Study (SMHS), the Shanghai Women's Health Study (SWHS), and the Singapore Chinese Health Study (SCHS) were also included (217 ESCCs, 615 GCs, 1202 controls). Altogether 2115 ESCCs, 2240 GCs, and 3302 controls were genotyped in this study.

  • Study Types: Case-Control, Case Set, Cohort
  • Number of study subjects that have individual level data available through Authorized Access: 5623

Authorized Access
Publicly Available Data (Public ftp)

Connect to the public download site. The site contains release notes and manifests. If available, the site also contains data dictionaries, variable summaries, documents, and truncated analyses.

Study Inclusion/Exclusion Criteria

Esophageal squamous cell carcinomas (ESCCs) include incident, primary esophageal cancers with squamous histology.

Gastric cancers (GCs) include incident, primary gastric adenocarcinomas.

Controls were all cancer-free at the time of enrollment (and blood draw).

Molecular Data
TypeSourcePlatformNumber of Oligos/SNPsSNP Batch IdComment
Whole Genome Genotyping Illumina Human660W-Quad_v1_A 592839 1048965
Study History

See "Study Description"

Selected publications
Diseases/Traits Related to Study (MESH terms)
Links to Other NCBI Resources
Authorized Data Access Requests
Study Attribution
  • Principal Investigator
    • Philip R. Taylor. National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
  • Study Coordinators
    • Christian C. Abnet. National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
    • Neal D. Freedman. National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
    • Nan Hu. National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
    • Alisa M. Goldstein. National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
    • Linda M. Dong. National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
  • Genomics
    • Zhaoming Wang. National Cancer Institute and SAIC-Frederick, National Institutes of Health, Bethesda, MD, USA
    • Laurie Burdett. National Cancer Institute and SAIC-Frederick, National Institutes of Health, Bethesda, MD, USA
    • Stephen J. Chanock. National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
  • Statistician
    • Kai Yu. National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
  • Study Representatives
    • Jian-Min Yuan. University of Minnesota, Minneapolis, MN, USA
    • Xiao-Ou Shu. Vanderbilt University, Nashville, TN, USA
    • Wei Zheng. Vanderbilt University, Nashville, TN, USA
  • Funding Source
    • Funding sources are listed in the acknowledgements of Abnet et al., Nature Genetics 2010;42:764. PMID: 20729852