NBDC Research ID: hum0182.v5
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])
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
| Dataset 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 |
| JGAS000180 | NGS (WGS): RK014-RK281 | Controlled-access (Type I) | 2021/01/06 |
| JGAS000180 |
NGS (WGS): RK014-RK281 (fast5 sequencing data) |
Controlled-access (Type I) | 2021/11/12 |
| JGAS000516 | NGS (RNA-seq) | Controlled-access (Type I) | 2022/05/27 |
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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
MOLECULAR DATA
| 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 |
| Japanese Genotype-phenotype Archive Dataset 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), 28 TB (fast5) |
| Comments (Policies) | NBDC policy |
| 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 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000261 |
| Total Data Volume | 3 GB (VCF [ref: hg19]) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
HCC (ICD10: C22.0): 42 cases tumor liver tissues: 42 samples matched non-tumor liver tissues: 42 samples Breast cancer cell line (MCF-7): 1 sample |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Nanopore [MinION] |
| Library Source | RNAs derived from tumor and matched non-tumor liver tissues and breast cancer cell line |
| Cell Lines | MCF-7; RNA was purchased from Cosmo Bio Co., Ltd. |
| Library Construction (kit name) | Ligation Sequencing Kit (SQK-LSK109) |
| Fragmentation Methods | - |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 1411.4 bp |
| Japanese Genotype-phenotype Archive Dataset ID / DDBJ Sequence Read Archive ID | JGAD000635 |
| Total Data Volume | 2.7 TB (fastq) |
| 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):
| 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 | 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 |
PUBLICATIONS
| Title | DOI | Dataset 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 | Whole-genome sequencing with long reads reveals complex structure and origin of structural variation in human genetic variations and somatic mutations in cancer | doi: 10.1186/s13073-021-00883-1 | JGAD000261 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Shuaicheng Li | City University of Hong Kong | A new method to construct the haplotypes of viral integration regions based on multiple sequencing data. | JGAS000180, DRA008482 | 2021/12/07-2022/11/01 | |
| Zeng Tianfu | Laboratory of Omics Technology and Bioinformatics, Sichuan University | China | Study on Heterogeneity of Hepatocellular Carcinoma Based on Nanopore Sequencing Technology | JGAD000635 | 2023/10/30-2024/09/28 |
