Survival GWAS: SNPs Associated with ESCC Patients’ Survival
1,006 ESCC patients with survival information
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
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
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