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Due to system maintenance, the application system, application review by the Data Access Committee will be unavailable during the following period.
Schedule: October 5th (Mon), 2026, 9:00 - October 7th (Wed), 2026, 15:00 (JST)
We apologize for any inconvenience this may cause and appreciate your understanding.

We are currently receiving a large number of applications for data submission, and the review process is taking longer than usual.We sincerely apologize for the delay and kindly ask for your understanding. When submitting an application, we would greatly appreciate it if you could allow sufficient time for the processing.

Following a change to our organizational structure effective April 1, 2026, this division has been renamed from the "Database Center for Life Science, Joint Support-Center for Data Science Research" to the "Database Division for Life Science (DBCLS), BioData Science Initiative (BSI), National Institute of Genetics (NIG)". Where the former name still appears in the guidelines, please read it as the new name.

Research ID

hum0182-v4Release info

This page is a past version (v4). The latest version is v5.
Latest version (v5)

Research title

Comprehansive analysis of somatic mutations and genetic variations with whole genome sequencing

Research overview

Aims
Indetification of stractural variations by using of long read whole genome sequencing data
Methods
Whole genome sequencing with Nanopore sequencer, HiSeq 2000 and Genome Analyzer IIx (Illumina)
Participants/materials
DNA samples from 2 Japanese individuals.
1) DNA extracted from normal blood cell of a liver cancer patient (ICGC: RK067 [hum0158])
2) HapMap sample (NA18943)
3) DNA extracted from normal blood cell of 174 liver cancer patients (ICGC: RK001-RK338 [hum0158])
4) DNA extracted from tumor tissues and normal blood cell of 11 liver cancer patients (ICGC: RK014, RK019, RK020, RK067, RK085, RK0143, RK147, RK156, RK157, RK167, RK281 [hum0158])
5) RNAs derived from 42 Japanese HCCs and 42 matched non-tumor liver tissues collected by ICGC
RNA from breast cancer cell line MCF-7
URL
N/A

Datasets

The list is the one this version published; each dataset's content is shown as it is now.

CartDataset IDType of dataAnalysis methodAccess criteriaDate published
JGAD000261NGS (WGS): RK067
  • WGS
Controlled-access (Type I)2020-10-21
DRA008482NGS (WGS): NA18943
  • WGS
Unrestricted-access2019-06-21

Data provider

Principal investigator
Akihiro Fujimoto
Affiliation
Department of Human Genetics, Graduate School of Medicine,The University of Tokyo

Research projects

NameURL
Japan Agency for Medical Research and Development (AMED)
N/A

Grants

NameTitleProject number
Platform Program for Promotion of Genome Medicine, Japan Agency for Medical Research and Development (AMED)
Development of advanced data analysis methods for genome sequencing
  • JP18km0405207
KAKENHI Grant-in-Aid for Scientific Research (B)
Comprehensive analysis of full-length transcriptome of liver cancer with a long-reads sequencing technology
  • 18H02680
KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
Yaponesian genome
  • 18H05511
Program for Integrated Database of Clinical and Genomic Information, Japan Agency for Medical Research and Development (AMED)
Construction of integrated clinical genome database regarding hepatitis B related diseases
  • JP18kk0205007

Related publications

TitleDOIDataset ID
Identification of intermediate-sized deletions and inference of their impact on gene expression in a human population.
https://doi.org/10.1186/s13073-019-0656-4 (opens in a new tab)
Whole-genome sequencing with long reads reveals complex structure and origin of structural variation in human genetic variations and somatic mutations in cancer
https://doi.org/10.1186/s13073-021-00883-1 (opens in a new tab)

Controlled access users

Principal investigatorAffiliationCountry/RegionResearch titlePeriod of data useDataset ID
Shuaicheng LiHong Kong A new method to construct the haplotypes of viral integration regions based on multiple sequencing data.2021-12-13 – 2023-01-05
zeng tianfuLaboratory of Omics Technology and Bioinformatics, Sichuan UniversityChinaStudy on Heterogeneity of Hepatocellular Carcinoma Based on Nanopore Sequencing Technology2023-10-30 – 2024-09-18