NBDC Research ID: hum0222.v1
SUMMARY
Aims: To clarify risk of germline variants of known causal genes for Hereditary Breast Ovarian Cancer Syndrome in Japan by combinatorial analysis of somatic and germline variants in the breast cancer tissue.
Methods: Target caputure analysis by using Illumina HiSeq 2000
Participants/Materials: 108 whole blood and 124 primary tumor samples from familial breast cancer patients
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000224 | NGS (Target Capture) | Controlled-access (Type I) | 2020/03/13 |
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MOLECULAR DATA
| Participants/Materials |
breast cancer (ICD10: C50): 115 cases (124 samples) primary tumor tissues and paired blood: 108 cases (116 samples) primary tumor tissues only: 7 cases (8 samples) |
| Targets | Target Capture |
| Target Loci for Capture Methods | 119 genes including known causal genes of HBOC syndrome (BRCA1, BRCA2, STK11, NBN, ATM, CHEK2, PALB2, TP53, PTEN, CDH1, RAD51D, RAD51C, BRIP1, RAD50, XRCC2, RAD51B, NF1, EPCAM, MLH1, MSH2, MSH6, PMS2, BARD1, MRE11A, FANCC, BLM, FAM175A, RINT1, FANCM, RECQL, etc.) |
| Platform | Illumina [HiSeq 2000] |
| Library Source | DNAs extracted from primary tumor tissues and peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect XT Custom |
| Fragmentation Methods |
blood 108 samples : Ultrasonic fragmentation (Covaris) tumor 49 samples : Ultrasonic fragmentation (Covaris) tumor 75 samples : Enzymatic fragmentation (DNase included in KAPA HyperPlus Kit) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 101 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000315 |
| Total Data Volume | 222 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Shinji Ohno
Affiliation: The Cancer Institute Hospital of JFCR
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED) | Identification of responsible genes and development of standardized medicine for familial breast cancer by genetic analysis with NGS technology | JP16cm0106503 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Prevalence of disease-causing genes in Japanese patients with BRCA1/2-wildtype hereditary breast and ovarian cancer syndrome | doi: 10.1038/s41523-020-0163-1 | JGAD000315 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
