NBDC Research ID: hum0164.v1
SUMMARY
Aims: Identify the genetic factors related to tanning ability in Japanese
Methods: Genome-wide association study
Participants/Materials: Genotypedata and quetionnaire based skin tanning ability information of 9,187 participants of Tohoku Medical Megabank Organization cohort study
URL: https://www.megabank.tohoku.ac.jp/english/
URL: http://iwate-megabank.org/en/
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000160 | GWAS for skin tanning ability of 9,187 participants | Controlled-access (Type I) | 2018/12/14 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials | 9,187 participants of Tohoku Medical Megabank Organization cohort study |
| Targets | genome wide SNPs |
| Target Loci for Capture Methods | - |
| Platform | Illumina [Infinium OmniExpressExome-8] |
| Library Source | DNAs extracted from peripheral blood cells |
| Cell Lines | - |
| Reagents (Kit, Version) | Illumina Infinium OmniExpressExome-8 Beadchip Kit |
| Genotype Call Methods (software) | GenCall software (GenomeStudio) |
| Association Analysis (software) |
linear mixed model (software: BOLT-LMM v2.3.2) adjusted by age, sex and 1-10 principal component scores |
| Filtering Methods |
Sample: Call rate > 0.98 SNP: HWE P < 0.0001, MAF < 0.01, Missing rate > 0.05 |
| Marker Number (after QC) | 6,193,994 SNPs (reference: hg19) |
| Japanese Genotype-phenotype Archive Dataset ID |
* GWAS_summary_statistics_JST_Combined_set.txt.gz GWAS summary statistics of Japanese Skin Type for 9,187 Japanese individuals in Miyagi and Iwate prefectures * GWAS_summary_statistics_JST_Miyagi.txt.gz GWAS summary statistics of Japanese Skin Type for 4,475 Japanese individuals in Miyagi prefecture * GWAS_summary_statistics_JST_Iwate.txt.gz GWAS summary statistics of Japanese Skin Type for 4,712 Japanese individuals in Iwate prefecture |
| Total Data Volume | 463 MB (txt) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Masao Nagasaki
Affiliation: Department of Integrative Genomics, Tohoku Medical Megabank Organization
Project / Group Name: -
URL: https://www.megabank.tohoku.ac.jp/english/
URL: http://iwate-megabank.org/en/
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Japan Agency for Medical Research and Development (AMED) | Tohoku Medical Megabank Project (Tohoku University) Special account of the Great East Japan Earthquake disaster recovery | JP18km0105001 |
| Japan Agency for Medical Research and Development (AMED) | Tohoku Medical Megabank Project (Tohoku University) General accounting | JP18km0105002 |
| Platform Program for Promotion of Genome Medicine, Japan Agency for Medical Research and Development (AMED) | Facilitation of R&D Platform for AMED Genome Mecidine Support | JP18km0405001 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | |||
| 2 |
USERS (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Seishi Ogawa | Department of Medical Science, Kyoto University | - | Comprehensive analysis of genetic alterations in hematological malignancies | JGAD000238 | 2019/11/14-2024/03/31 |
