NBDC Research ID: hum0041.v1



Aims: Advanced cancers with metastasis and/or recurrence are usually resistant and refractory to treatment. In our studies, whole exome sequencing analysis, comprehensive epigenetic analysis and genome-wide expression analysis were performed using cancerous and non-cancerous tissues derived from multicentric cohort study of hepatocellular carcinoma (HCC). The aim of the studies is identification of the refractoriness-related deriver genes for application to novel molecular targeted therapy and preventive medicine.

Methods: The materials were obtained from thirty three patients underwent curative hepatectomy for HCC at Department of Hepato-Biliary-Pancreatic Surgery, Tokyo Medical and Dental University Hospital. Written informed consent from these patients, as well as the institutional review board approved was obtained. The determination of the refractory HCC group (16 cases) was based on the point of the recurrence patterns in accordance with Milan criteria for the recurrent tumor (solitary <5cm, or up to 3 nodules <3 cm, without major vascular invasion or distant metastasis) that has been proposed as the useful criteria of the liver transplantation for HCC. The cellular DNA was extracted from the cancerous and non-cancerous tissues of primary HCC by the phenol-chloroform method. After SNP certification using Genome-Wide Human SNP Array 6.0 (Affymetrix), whole exome sequencing was performed at the Cancer Institute of JFCR, as the support infrastructure. Exome sequencing was performed using HiSeq 2000 (Illumina), and the obtained reads were mapped to the human reference genome (hg19) using BWA software. GATK software was used for local realignment base call recalibration. Single nucleotide variants (SNVs) and indels were analyzed by VarScan, MuTect, SomaticIndelDetector and FATHMM software, as well as visual confirmation by IGV software.

Participants/Materials: The studies are intended for refractory HCC. High frequency of the tumor recurrence even after curative resection is one of the major difficulties in the treatment of HCC. According to our previous studies, not the recurrence itself, but the recurrence pattern has critical effects on prognosis of the patient with HCC. Then, we analyzed the cancerous and non-cancerous tissues of primary HCC on the point of the recurrence patterns in accordance with or without Milan criteria.


Dataset IDType of DataCriteriaRelease Date
JGAS000052 NGS (Exome, Target Capture) Controlled-access (Type I) 2017/01/12

*Release Note

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33 cancerous and non-cancerous tissues of primary HCC 

・Recurrence patterns in accordance without Milan criteria : 16 cases

・Recurrence patterns in accordance with Milan criteria : 17 cases

Targets Exome, Target Capture
Target Loci for Capture Methods SureSelect Human All Exon V4, HBVgemone, lincRNA
Platform Illumina [HiSeq 2000]
Library Source

gDNA extracted from cancerous and non-cancerous tissues

(Phenol–chloroform extraction)

Cell Lines -
Library Construction (kit name) SureSelect Human All Exon V4
Fragmentation Methods Covaris S220
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 100 bp x 2
Japanese Genotype-phenotype Archive Dataset ID JGAD000052
Total Data Volume 1759 GB (fastq.gz)
Comments (Policies) NBDC policy



Principal Investigator: Shinji Tanaka

Affiliation: Department of Molecular Oncology, Graduate School of Medicine, Tokyo Medical and Dental University

Project / Group Name: Project for Development of Innovative Research on Cancer Therapeutics

URL: http://www.tmd.ac.jp/grad/monc/en/index.html

Funds / Grants (Research Project Number):

NameTitleProject Number
Project for Development of Innovative Research on Cancer Therapeutics (P-DIRECT), Japan Agency for Medical Research and Development (AMED) Development of the Intractable Cancer Therapies through the New Target Identification by the Molecular Profiling JP15cm0106064



TitleDOIDataset ID
1 under publishing


USERS (Controlled-sccess Data)

Principal InvestigatorAffiliationCountry/RegionResearch TitleData in Use (Dataset ID)Period of Data Use