Construction of a Comprehensive Multiomics Map of Hepatocellular Carcinoma and Screening of Possible Driver Genes

Frontiers in Genetics
Ziyu LiuRong Liang

Abstract

Objectives: The occurrence of hepatocellular carcinoma (HCC) is a complex process involving genetic mutations, epigenetic variation, and abnormal gene expression. However, a comprehensive multiomics investigation of HCC is lacking, and the available multiomics evidence has not led to improvements in clinical practice. Therefore, we explored the molecular mechanism underlying the development of HCC through an integrative analysis of multiomics data obtained at multiple levels to provide innovative perspectives and a new theoretical basis for the early diagnosis, personalized treatment and medical guidance of HCC. Methods: In this study, we collected whole-exome sequencing data, RNA (mRNA and miRNA) sequencing data, DNA methylation array data, and single nucleotide polymorphism (SNP) array data from The Cancer Genome Atlas (TCGA). We analyzed the copy number variation (CNV) in HCC using GISTIC2. MutSigCV was applied to identify significantly mutated genes (SMGs). Functional enrichment analyses were performed using the clusterProfiler package in R software. The prognostic values of discrete variables were estimated using Kaplan-Meier survival curves. Results: By analyzing the HCC data in TCGA, we constructed a comprehensive multio...Continue Reading

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Methods Mentioned

BETA
exome sequencing
RNA-seq
Chip
chromosomal aberrations

Software Mentioned

DEseq2
maftools
ggplot2
ChAMP R
ChAMP
ConsensusClusterPlus
pheatmap
GISTIC
R
R language package

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