NBDC Research ID: hum0196.v1

 

SUMMARY

Aims: Identification of biomarkers for risk of suicide and application to clinical use

Methods: GWAS

Participants/Materials: Individuals who died by suicide

 

Dataset IDType of DataCriteriaRelease Date
hum0196.v1.gwas.v1 meta-analyses of GWAS datasets for suicides vs. non-suicide individuals and for age at suicide Unrestricted-access 2019/12/20

*Release Note

*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

hum0196.v1.gwas.v1

Participants/Materials

[Suicide (ICD10:X83) vs. Non-suicide]

  1st set: Suicide: 386 cases, Non-suicide: 7,458 cases

  2nd set: Suicide: 360 cases, Non-suicide: 6,591 cases

  Total: Suicide: 746 cases, Non-suicide: 14,049 cases

[Age at Suicide]

  1st set: Suicide: 366 cases, 2nd set: Suicide: 353 cases

  Total: Suicide: 719 cases

Targets genome wide SNVs
Target Loci for Capture Methods -
Platform

1st set: Illumina [HumanOmniExpress-24 BeadChip]

2nd set: Illumina [HumanOmniExpressExome-8 BeadChip]

Library Source gDNAs extracted from postmortem tissues or peripheral blood cells
Cell Lines -
Reagents (Kit, Version) HumanOmniExpress / OmniExpressExome Beadchip kit
Genotype Call Methods (software)

minimac [imputation (1000 genomes Phase 3)]

GenCall software (GenomeStudio)

Association Analysis (software)

Rvtests software

METAL software

Filtering Methods

Variants which match the following criteria were excluded:

- sample call rate < 0.98, SNV call rate < 0.98, MAF < 0.01,

- HWE P < 1 x 10-6 in control

- imputation quality of Rsq < 0.7 in each of the 1st and 2nd dataset

Marker Number (after QC)

[Suicide vs. Non-suicide] 8,381,404 SNPs (hg19)

[Age at Suicide] 8,555,734 SNPs (hg19)

NBDC Dataset ID

hum0196.v1.gwas.v1

(Click the Dataset ID to download the file)

Dictionary file

Total Data Volume 420 MB
Comments (Policies) NBDC policy

 

DATA PROVIDER

Principal Investigator: Akitoyo Hishimoto

Affiliation: Department of Psychiatry, Kobe University Graduate School of Medicine

Project / Group Name: -

Funds / Grants (Research Project Number):

NameTitleProject Number
KAKENHI Grant-in-Aid for Scientific Research (B) Investigation on molecular mechanism causing the downward spiral of Stress, Depression, and Suicide 17H04249

 

PUBLICATIONS

TitleDOIDataset ID
1 Genome-wide association studies identify polygenic effects for completed suicide in the Japanese population doi: 10.1038/s41386-019-0506-5 hum0196.v1.gwas.v1
2