Survival GWAS: SNPs Associated with ESCC Patients’ Survival

Sample size

  • 1,006 ESCC patients with survival information
  • 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
  • Survival log-rank test was used to calculate the associations of SNPs and ESCC patients’ survival.
  • If the number of samples with homozygous genotype of minor allele is greater than 1% of all samples, the survival results using additive model are retained. Otherwise, the survival results using dominant model are retained.
  • SNPs in the final analysis after imputation and QC

  • 8,279,620 SNPs on autosomes

  • Additive model


    Dominant model

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

    The -log10 P values (y axis) of SNPs (P < 0.1) are shown according to their chromosomal positions (x axis), and the horizontal blue line represents the genome-wide significance threshold at P < 1.0 × 10-4.

    Significant SNPs associated with patients’ survival of ESCC included in CCGD-ESCC

  • 1,652 SNPs with P < 1.0× 10-4

  •   Related Sources

    1. Wu C, et al. (2013). Genome-wide association study identifies common variants in SLC39A6 associated with length of survival in esophageal squamous-cell carcinoma. Nat Genet. 45(6):632-8. PMID: 23644492.