NBDC Research ID: hum0182.v3

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SUMMARY

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])

 

Data Set IDType of DataCriteriaRelease Date
JGAS000180 NGS (WGS): RK067 Controlled-Access (Type I) 2019/06/20
DRA008482 NGS (WGS): NA18943 Unrestricted Access 2019/06/20
JGAS000180 NGS (WGS): RK001-RK338 Controlled-Access (Type I) 2020/05/12
JGAS000180 NGS (WGS): RK014-RK281 Controlled-Access (Type I) 2021/01/06

*Release Note

*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more

 

MOLECULAR DATA

JGAS000180 / DRA008482

Participants/Materials

1) RK067 (a liver cancer patient): 1 case

2) NA18943 (HapMap): 1 sample

4) RK014, RK019, RK020, RK067, RK085, RK0143, RK147, RK156, RK157, RK167, RK281 (liver cancer patients): 11 cases

Targets WGS
Target Loci for Capture Methods -
Platform Nanopore [MinION]
Library Source

1) DNA extracted from blood sample (normal cell) of a liver cancer patient

2) HapMap DNA sample

4) RK014, RK019, RK020, RK085, RK0143, RK147, RK156, RK157, RK167, RK281: DNA extracted from blood samples (normal cell) of liver cancer patients

   RK014, RK019, RK020, RK067, RK085, RK0143, RK147, RK156, RK157, RK167, RK281: DNA extracted from tumor tissues of liver cancer patients

Cell Lines https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=NA18943&Product=DNA
Library Construction (kit name) 1D Ligation Sequencing Kit (Cat#SQK-LSK108)
Fragmentation Methods g-TUBE (Covaris)
Spot Type Single-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers)

1, 4) 7463 bp

2) 3479 bp

Japan Genotype-Phenotype Archive Data Set ID / DDBJ Sequence Read Archive ID

1, 4) JGAD000261

2) DRA008482

Total Data Volume

1) 128 GB (fastq)

2) 79.7 GB (fastq)

4) 2.3 TGB (fastq)

Comments (Policies) NBDC policy

When the research results including the data which were downloaded from NHA/DRA/JGA, are published or presented somewhere, the data user must refer the papers which are related to the data, or include in the acknowledgment. Learn more

 

JGAS000180

Participants/Materials 3) RK001-RK338 (liver cancer patients): 174 cases
Targets WGS
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2000, Genome Analyzer IIx]
Library Source DNA extracted from blood sample (normal cell) of liver cancer patients
Cell Lines -
Library Construction (kit name) TruSeq DNA LT Sample Prep Kit, TruSeq Nano DNA Low Throughput Library Prep Kit, Paired-End DNA Sample Prep Kit, TruSeq Nano DNA Library Preparation Kit
Fragmentation Methods Ultrasonic fragmentation (Covaris)
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 100 bp
QC/Filtering Methods -
Deduplication Picard
Mapping Methods bwa
Reference Genome Sequence hg19
Coverage (Depth) 30X
Detecting Methods for Variation VCMM (Shigemizu et al. Sci Rep (2013))
Detecting Methods for Structural Variation IMSindel and joint-call recovery method (Shigemizu et al. Sci Rep (2018), Wong et al. Genome Med (2019)*ref1)
SNV Numbers (after QC) 5,239,921
SV Numbers (after QC) 4,378
Japan Genotype-Phenotype Archive Data Set ID JGAD000261
Total Data Volume 3 GB (VCF [ref: hg19])
Comments (Policies) NBDC policy

 

DATA PROVIDER

Principal Investigators: Akihiro Fujimoto

Affiliation: Department of Human Genetics, Graduate School of Medicine,The University of Tokyo

Project / Group Name: Japan Agency for Medical Research and Development (AMED)

Funds / Grants (Research Project Number):

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 18km0405207h0003
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 18kk0205007h0003

 

PUBLICATIONS

TitleDOIData Set ID
1 Identification of intermediate-sized deletions and inference of their impact on gene expression in a human population. doi: 10.1186/s13073-019-0656-4 JGAD000261
DRA008482
2

 

USERS (Controlled-Access Data)

Principal Investigator: Affiliation: Data in Use (Data Set ID)Period of Data Use