NBDC Research ID: hum0426.v1
SUMMARY
Aims: This study aims to 1) identify unknown causative genes, modifier genes, and their mutations in cancers suspected to be hereditary, and 2) accumulate knowledge on genotype-phenotype relationships, based on a multicenter cooperative system and network for genetic diagnosis of hereditary tumors.
Methods: DNA sequencing using adaptive sampling with GridION nanopore sequencer
Participants/Materials: 33 cases of hereditary cancer syndromes (blood)
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000654 | NGS (WGS) | Controlled-access (Type I) | 2024/08/01 |
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MOLECULAR DATA
| Participants/Materials |
hereditary cancer syndromes (ICD10: C00-C97): 33 cases peripheral blood cells (normal leukocytes): 33 samples |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | Nanopore [GridION] |
| Library Source | DNAs extracted from peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) | SQK-LSK110 or SQK-LSK114 |
| Fragmentation Methods | g-TUBE (Covaris) |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | N50 is approximately 600 bp (N50 of reads sequenced as long-read is approximately 9,000 bp). |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000784 |
| Total Data Volume | 270.7 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Yuichi Shiraishi
Affiliation: Division of Genome Analysis Platform Development, National Cancer Center Research Institute
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| National Cancer Center Research and Development Funds | Establishing a Research Foundation and Verifying Clinical Utility Using Long-Read Sequencing | 2021-A-3 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Assessing the efficacy of target adaptive sampling long-read sequencing through hereditary cancer patient genomes. | doi: 10.1038/s41525-024-00394-z | JGAD000784 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
