NBDC Research ID: hum0182.v2
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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])
Data Set ID | Type of Data | Criteria | Release 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 |
* Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data.
MOLECULAR DATA
Participants/Materials |
1) RK067 (a liver cancer patient): 1 case 2) NA18943 (HapMap): 1 sample |
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 |
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) 7463 bp 2) 3479 bp |
Japan Genotype-Phenotype Archive Data Set ID / DDBJ Sequence Read Archive ID |
1) JGAD000261 2) DRA008482 |
Total Data Volume |
1) 128 GB (fastq) 2) 79.7 GB (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
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 Drug Discovery Medicine, Graduate School of Medicine, Kyoto University
Project / Group Name: Japan Agency for Medical Research and Development (AMED)
Funds / Grants (Research Project Number):
Name | Title | Project 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 |
PUBLICATIONS
Title | DOI | Data 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 |
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