Autologous reference types affect detection of hepatocellular carcinoma-associated somatic mutation

Abstract

Objective To investigate the effect of autologous reference types on somatic mutation analysis of hepatocellular carcinoma whole exon sequencing. Methods The clinical data of 364 patients with hepatocellular carcinoma were downloaded from The Cancer Genome Atlas (TCGA) database. R software (version 3.4.1) was used for classification and preliminary statistical analysis. The total number of SNVs in each patient, the number of SNVs with different somatic mutation patterns and types, and the number of SNVs with different biological types and effect types caused by somatic mutations were preliminarily summarized. The effects of autologous reference types on the outcomes of somatic mutation were determined by generalized linear model (GLM) . Results Autologous peripheral blood and adjacent normal tissues were used as reference. The median number of somatic mutations in hepatocellular carcinoma tissues was 122.50 and 99.00, respectively, and there was statistically significant difference in the distribution (Z=-3.149, P=0.002) . After adjusting for the influences of age, gender, race, pathological grade, and BMI by GLM, the frequency of 3′UTR mutation (β=0.373, P=0.002) , 5′Flank mutation (β=0.477, P=0.017) , 5′UTR mutation (β=0.482, P<0.001) , frame shift deletion (β=0.344, P=0.008) , in-frame insertion (β=0.288, P=0.016) , intron mutation (β=0.390, P=0.001) , missense mutation (β=0.332, P=0.002) , silent mutation (β=0.282, P=0.009) , and splicing region mutation (β=0.861, P=0.001) significantly increased compared with that in the adjacent normal tissues and peripheral blood as a reference, respectively. Furthermore, the distribution frequency of somatic mutation significantly increased on effects of high protein coding influence (β=0.269, P=0.014) , moderately protein coding influence (β=0.328, P=0.002) , low protein coding influence (β=0.305, P=0.005) , and noncoding RNA regulation (β=0.404, P<0.001) . Conclusion As autologous reference types, tumor-associated somatic mutations in different types of normal tissues affect the outcomes of somatic mutation of hepatocellular carcinoma, with significant differences in the distribution. Key words: Hepatocellular carcinoma; Peripheral blood; Tissue; Whole exon sequencing; Mutation