Germline and somatic variations influence the somatic mutational signatures of esophageal squamous cell carcinomas in a Chinese population

BMC Genomics
Jintao GuoQiyuan Li

Abstract

Esophageal squamous cell carcinomas (ESCC) is the fourth most lethal cancer in China. Previous studies reveal several highly conserved mutational processes in ESCC. However, it remains unclear what are the true regulators of the mutational processes. We analyzed the somatic mutational signatures in 302 paired whole-exome sequencing data of ESCC in a Chinese population for potential regulators of the mutational processes. We identified three conserved subtypes based on the mutational signatures with significantly different clinical outcomes. Our results show that patients of different subpopulations of Chinese differ significantly in the activity of the "NpCpG" signature (FDR = 0.00188). In addition, we report ZNF750 and CDC27, of which the somatic statuses and the genetic burdens consistently influence the activities of specific mutational signatures in ESCC: the somatic ZNF750 status is associated with the AID/APOBEC-related mutational process (FDR = 0.0637); the somatic CDC27 copy-number is associated with the "NpCpG" (FDR = 0.00615) and the AID/APOBEC-related mutational processes (FDR = 8.69 × 10- 4). The burdens of germline variants in the two genes also significantly influence the activities of the same somatic mutational ...Continue Reading

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Citations

Mar 23, 2021·Cancer Cell International·Golnaz Ensieh Kazemi-SefatKazem Mousavizadeh
Jul 22, 2021·Scientific Reports·Hayriye Verda ErkizanRobert G Wadleigh

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JISTIC
HaplotypeCaller
Picard Tools
MutSigCV
Oncotator
SKAT
VarScan2
pmsignature
HotNet2
BWA

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