eQTL: SNPs Associated with Gene Expression
Sample size
Tumor and their adjacent normal tissues from 94 patients with ESCC
Sequencing platform
RNA sequencing was accomplished with Illumina HiSeq2000
Whole-genome sequencing was accomplished on Illumina HiSeq X Ten System
Quality control criteria
SNP
Called by Freebayes
Minor allele frequency (MAF) > 0.05
Hardy-Weinberg equilibrium with P > 1.0 × 10−6
Gene expression
Quantified for the transcript models corresponding to the TCGA GAF2.1 and normalized to a fixed upper quartile of total reads within the sample using RSEM
Only retained genes expressed in more than 9 (10%) samples
Statistical methods
Linear regression with additive model to evaluate the associations of all SNPs within a 100 kb window of upstream and downstream of the transcription start site (TSS) of a given gene in ESCC tumor tissues and adjacent normal tissues, respectively.
SNPs and genes in the final analysis after QC
6,092,313 SNPs & 18,085 genes on autosomes
Counts of eQTL, SNP, and gene in ESCC
tumor tissues and adjacent normal tissues
Significant eQTLs with FDR < 0.05 included in CCGD-ESCC
16,984 eQTLs: the associations of 15,742 SNPs with 645 genes in ESCC tumor tissue
54,445 eQTLs: the associations of 46,361 SNPs with 2,286 genes in adjacent normal tissue