NBDC Research ID: hum0319.v1
SUMMARY
Aims: To prospectively evaluate a prostate cancer risk prediction model combining multiple genetic polymorphisms using blood samples from patients who have high serum prostate-specific antigen (PSA) or abnormalities on rectal examination and undergo prostate biopsy for the definitive diagnosis of prostate cancer, and to evaluate its performance as a diagnostic marker for prostate cancer. In addition, to identify rare variants involved in the development of prostate cancer in Japanese by searching for rare variants.
Methods: DNA was extracted from peripheral blood samples taken prior to prostate biopsy. Targeted sequencing using multiplex PCR was performed to genotype 55 SNPs (16 SNPs used in the existing risk model and 39 additional SNPs) that have been reported to be associated with prostate cancer in Japan. We also performed targeted sequencing of all exonic regions of 8 genes (ATM, BRCA1, BRCA2, BRIP1, CHEK2, HOXB13, NBN, and PALB2) that have been reported to be associated with prostate cancer development.
Participants/Materials: 1,336 men with suspected prostate cancer scheduled for prostate biopsy
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000487 | NGS (Target Capture) | Controlled-access (Type I) | 2021/01/21 |
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| Participants/Materials | 1,336 men with suspected prostate cancer (ICD10: C61) scheduled for prostate biopsy |
| Targets | Target Capture |
| Target Loci for Capture Methods | 55 SNPs and all exonic regions of 8 genes (ATM, BRCA1, BRCA2, BRIP1, CHEK2, HOXB13, NBN, and PALB2) |
| Platform | Illumina [HiSeq2500] |
| Library Source | DNAs extracted from peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) | Target gene region was amplified by multiplex PCR using 2X Platinum Multiplex PCR Master Mix (Thermo Fisher Scientific), and 2nd PCR was conducted to attach barcode and adaptor sequences necessary for sequencing by HiSeq using KAPA HiFi DNA Polymerase. |
| Fragmentation Methods | - |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp x 2 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000604 |
| Total Data Volume | 83.9 GB (fastq, vcf [ref: hg19]) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Shusuke Akamatsu
Affiliation: Department of Urology, Graduate School of Medicine, Kyoto University
Project / Group Name: Prostate Cancer Susceptibility Single Nucleotide Polymorphism (PCSSNP) study
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Tailor-Made Medical Treatment with the BioBank Japan Project (BBJ), Japan Agency for Medical Research and Development (AMED) | Research project for exploring genetic susceptibility to cancer and biomarkers for personalized cancer medicine | JP17km0506001 |
| Externally Sponsored Research by AstraZeneca | Prevalence of germline and somatic DNA repair gene mutations in Japanese prostate cancer patients. | NCR-17-13159 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Clinical Utility of Germline Genetic Testing in Japanese Men Undergoing Prostate Biopsy | doi: 10.1093/jncics/pkac001 | JGAD000604 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
