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

  •   Related Sources

    1. Chang J, et al. (2017). Genomic analysis of esophageal squamous-cell carcinoma identifies alcohol drinking-related mutation signature and genomic alterations. Nat Commun. 8, 15290. PMID: 28548104.