Study: JGAS00000000151

Identifier

AccessionJGAS00000000151

Description

TitleWGS analysis of Japanese liver cancer
AbstractLiver cancer is prevalent worldwide, mainly associated with virus infection, and its underlying etiology and genomic structure are heterogeneous. Here we provide a whole-genome landscape of somatic alterations in 300 Japanese liver cancers. Our comprehensive analysis elucidated point mutations in non-coding regions, structural variants (SVs), and virus integrations, in addition to coding mutations, and demonstrated new mutational signatures related with liver carcinogenesis, novel recurrently mutated coding and non-coding regions such as lincRNA NEAT1/MALAT1, promoters, CTCF binding sites, and regulatory regions. SV analysis found a significant association with replication timing, and revealed that known cancer genes (CDKN2A, CCND1, APC, and TERT) and new cancer genes (ASH1L, NCOR1, MACROD2) were recurrently affected by SVs, leading to altered expression of nearby genes. These results emphasize the value of whole genome sequencing analysis to discover cancer driver mutations and to understand comprehensive molecular profiles of liver cancer, especially for SVs and non-coding mutations.
Study Type
Study TypeTumor vs. Matched-Normal

Publication

PubMed ID27064257
Publication Statuspublished
DB TypePUBMED

Study Attribute

NBDC Numberhum0158
Registration date2018-03-26
Submitting organizationRIKEN Center for Integrative Medical Sciences
Principal InvestigatorHidewaki Nakagawa
Molecular Data TypeWhole Genome Sequencing
PlatformGenome Analyzer IIx
VendorIllumina
Comment
Molecular Data TypeWhole Genome Sequencing
PlatformHiSeq2000
VendorIllumina
Comment
Primary PhenotypeLiver cancer
Disease TypeNeoplasms
Dataset
Accession Title Dataset type Data objects Policy
JGAD00000000228 Whole Genome Sequencing analysis of japanense liver cancer (WGS) Whole genome sequencing 580 JGAP00000000001
JGAD00000000229 Whole Genome Sequencing analysis of japanense liver cancer (RNA-Seq) Transcriptome profiling by high-throughput sequencing 439 JGAP00000000001