NBDC Research ID: hum0467.v1
SUMMARY
Aims: To clarify the genetic background behind the onset of pelvic organ prolapse (POP), enable identification of high-risk groups, and provide early therapeutic intervention.
Methods: Samples were devided into four groups (1~4) based on study groups (BioBank Japan: BBJ, Okinawa Bio-information Bank: OBi, and POP registry: POP) and Japanese sub-populations (Hondo, Ryukyu). Associations studies for POP were analyzed in each group and meta-analysis was performed.
Participants/Materials: [Case] female participants with a medical history of POP. Total 771 patients (BBJ n = 447, POP n = 324)
[Control] female participants with no history of POP or general population. Total 76,625 individuals (BBJ: n =73,892, OBi: n = 2,733)
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| hum0467.v1.gwas.v1 | GWAS for POP | Unrestricted-access | 2024/10/02 |
*When the research results including the data which were downloaded from NHA/DRA, 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 |
[GWAS-1] POP (ICD-10: N81): BBJ_Hondo n = 418, Controls: BBJ_Hondo n = 68,040 [GWAS-2] POP: POP_Hondo n = 128, Controls: OBi_Hondo n = 387 [GWAS-3] POP: BBJ_Ryukyu n = 29, Controls: BBJ_Ryukyu n = 5,852 [GWAS-4] POP: POP_Ryukyu n = 196, Controls: OBi_Ryukyu n = 2,346 |
| Targets | Genome wide SNPs |
| Target Loci for Capture Methods | - |
| Platform |
OBi, POP: Illumina [Asian Screening Array] BBJ: Illumina [Infinium OmniExpress, HumanExome, Infinium OmniExpressExome v1.0, Infinium OmniExpressExome v1.2] |
| Source | DNAs extracted from peripheral blood cells |
| Cell Lines | - |
| Reagents (Kit, Version) | - |
| Genotype Call Methods (software) |
minimac4 Imputation: reference 1KGP3+JEWEL_3K |
| Association Analysis & Meta Analysis (software) |
Association Analysis: SAIGE version 1.0.5 Meta Analysis: METAL |
| Filtering Methods |
Sample QC: sample call rates ≧ 0.98 Genotyping QC: SNP call rate ≧ 0.98 (OBi, POP) or 0.99 (BBJ), MAF ≧ 0.01, p-values for Hardy–Weinberg equilibrium (HWE) test ≧ 1×10-6 Imputation QC: MAF ≥ 0.005 and imputation score (Rsq) ≥ 0.7 |
| Marker Number (after QC) | 9,862,117 variants |
| NBDC Dataset ID |
(Click the gwas number to download files) |
| Total Data Volume | 0.66 MB (txt) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Shiro Maeda
Affiliation: Faculty of Medicine, University of the Ryukyus
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Project for Whole Implementation to Support and Ensure the Female Life (Wise), Japan Agency for Medical Research and Development (AMED) | Stratification of patients with pelvic organ prolapse or lower urinary tract diseases based on comprehensive information and goals of individualized treatment strategies | JP22gk0210025 |
| Promotion project of innovation-eco system collaborating organization from the Okinawa prefecture | Disease Genome Research and Genomic Medicine for the Health and Longevity of Okinawans | - |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Genome-wide association studies for pelvic organ prolapse in the Japanese population | doi: 10.1038/s42003-024-06875-2 | hum0467.v1.gwas.v1 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
