NBDC Research ID: hum0119.v1

 

SUMMARY

Aims: Discovery of genetic factors for NAFLD, NASH and NASH derived hepatocellular carcinoma

Methods: Genome scan by SNP array

Participants/Materials: NAFLD patients (include 580 NASH and 58 NASH-HCC) : 902, controls : 7672

 

Data Set IDType of DataCriteriaRelease Date
JGAS00000000126 GWAS for NAFLD, NASH, and NASH-HCC Controlled Access (Type I) 2019/01/31

*Release Note

* Data users need to apply the Form 2 (Application Form for Using NBDC Human Data) to reach the Controlled Access Data. Learn more

 

MOLECULAR DATA

JGAS00000000126

Participants/Materials

NAFLD (ICD10: K76.0): 264 patients

NASH (ICD10: K75.81): 580 patients

NASH-HCC (ICD10: C220): 58 patients

7672 healthy controls

Targets genome wide SNPs
Target Loci for Capture Methods -
Platform

Illumina [Human610-Quad BeadChip]

Illumina [HumanCoreExome BeadChip]

Illumina [HumanOmni2.5-Quad BeadChip]

Library Source DNAs extracted from peripheral blood cells
Cell Lines -
Reagents (Kit, Version)

Illumina Human610-Quad BeadChip Kit

Illumina HumanCoreExome BeadChip Kit

Illumina HumanOmni2.5-Quad BeadChip Kit

Genotype Call Methods (software) GenomeStudio (Illumina)
Filtering Methods

Exclusion criteria : sample call-rate < 0.95, PCA outlier of Japanese population, encrypted relatedness (pihat > 0.38)

SNP call-rate < 0.99, HWE-p < 1e-6, MAF< 0.01

Marker Number (after QC) 93,606 SNPs (hg19)
Japanese Genotype-phenotype Archive Data set ID JGAD00000000137
Total Data Volume 26 MB (xlsx)
Comments (Policies) NBDC policy

 

DATA PROVIDER

Principal Investigator: Fumihiko Matsuda

Affiliation: Center for Genomic Medicine, Kyoto University Graduate School of Medicine

Project / Group Name: -

Funds / Grants (Research Project Number):

NameTitleProject Number
Health and Labour Sciences Research Grant for Research on Hepatitis Research and development of pathophysiology, diagnostic tool and treatment in nonalcoholic fatty liver disease H20-Hepatitis-general-008

 

PUBLICATIONS

TitleDOIData Set ID
1 Risk estimation model for nonalcoholic fatty liver disease in the Japanese using multiple genetic markers doi: https://doi.org/10.1371/journal.pone.0185490 JGAD00000000137
2

 

USERS (Controlled-Access Data)

Principal Investigator: Affiliation: Data in Use (Data Set ID)Period of Data Use