Somatic Mutation: SNVs/indels Associated with ESCC Patients’ Survival

Sample size

  • 675 ESCC patients with survival information
  • Quality control criteria

  • Genes mutated in more than 1% of all samples
  • Statistical methods

  • Survival log-rank test in each study, respectively, and in the combined samples
  • Samples and genes in the final analysis after QC

  • 675 samples and 2,203 genes on autosomes

  • Mutational landscape of somatic
    alterations in 704 ESCC samples

    Significant genes with SNVs/indels associated with ESCC patients’ survival included in CCGD-ESCC

  • 662 genes with P < 0.05

  • StudySequencing platformSomatic mutation calling toolsSamples analyzed
    Chang J, et al. (PMID: 28548104), 2017WGS: Illumina HiSeq X Ten SystemStrelka 94
    Cancer Genome Atlas Research. (PMID: 28052061), 2017WES: Illumina HiSeq 2000 MuTect, indel locator; RADIA; Strelka; Samtools1, Strelka3, VarScan4, GATK5, Pindel690
    Qin HD, et al. (PMID: 27058444), 2016WGS & WES: Illumina HiSeq 2000 VarScan 2 66
    Sawada G, et al. (PMID: 26873401), 2016WES: Illumina HiSeq 2000 Genomon-exome144
    Zhang L, et al. (PMID: 25839328), 2015WGS & WES: Illumina HiSeq 2000SAMtools and VarScan 2.2.5 80
    Gao YB, et al. (PMID: 25151357), 2014WES: Illumina HiSeq 2000 CASAVA 1.7113
    Song Y, et al. (PMID: 24670651), 2014WGS & WES: Illumina HiSeq 2000 VarScan 2.2.5 and GATK SomaticIndelDetector88
    Combined 675

    WGS: whole-genome sequencing; WES: whole-exome sequencing.

      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.
    2. Cancer Genome Atlas Research. (2017). Integrated genomic characterization of oesophageal carcinoma. Nature. 541(7636):169-175. PMID: 28052061.
    3. Qin HD, et al. (2016). Genomic characterization of esophageal squamous cell carcinoma reveals critical genes underlying tumorigenesis and poor prognosis. Am J Hum Genet. 98(4):709-27. PMID: 27058444.
    4. Sawada G, et al. (2016). Genomic landscape of esophageal squamous cell carcinoma in a Japanese population. Gastroenterology. 150(5):1171-82. PMID: 26873401.
    5. Zhang L, et al. (2015). Genomic analyses reveal mutational signatures and frequently altered genes in esophageal squamous cell carcinoma. Am J Hum Genet. 96(4):597-611. PMID: 25839328.
    6. Gao YB, et al. (2014). Genetic landscape of esophageal squamous cell carcinoma. Nat Genet. 46(10):1097-102. PMID: 25151357.
    7. Song Y, et al. (2014). Identification of genomic alterations in oesophageal squamous cell cancer. Nature. 509(7498):91-5.  PMID: 24670651.