GWAS: SNPs Associated with ESCC Risk

Sample size

2,022 ESCC cases and 2,039 controls

Genotyping platform

SNPs were typed with Affymetrix GeneChip Human Mapping 6.0 set

Quality control criteria

Minor allele frequency (MAF) > 0.01

Hardy-Weinberg equilibrium with P > 1.0 × 10⁻⁶

Statistical methods

Imputed by MACH software based on the 1000 Genomes Project Phase 3 ASN (Asian) panel

An additive model in a logistic regression framework with age, sex, smoking and drinking as covariates

SNPs in the final analysis after imputation and QC

8,252,518 SNPs on autosomes

Manhattan plot of the genome-wide
P values of risk associations

The -log₁₀ P values (y axis) of SNPs (P < 0.01) are shown according to their chromosomal positions (x axis), and the horizontal blue line represents the genome-wide significance threshold at P < 1.0 × 10^-5.

Significant SNPs associated with risk of ESCC included in CCGD-ESCC

16,544 SNPs with P < 1.0 × 10^-5

  Related Sources

1. Wu C, et al. (2011). Genome-wide association study identifies three new susceptibility loci for esophageal squamous-cell carcinoma in Chinese populations. Nat Genet. 43(7):679-84. PMID: 21642993.
2. Wu C, et al. (2012). Genome-wide association analyses of esophageal squamous cell carcinoma in Chinese identify multiple susceptibility loci and gene-environment interactions. Nat Genet. 44(10):1090-7. PMID: 22960999.
3. Wu C, et al. (2014). Joint analysis of three genome-wide association studies of esophageal squamous cell carcinoma in Chinese populations. Nat Genet. 46(9):1001-6. PMID: 25129146.