NBDC Research ID: hum0261.v2
SUMMARY
Aims: Genome-wide search for susceptibility genes for primary biliary cholangitis (PBC)
Methods: Regional Heritability Mapping (RHM) and Genome-wide Association Study (GWAS)
Participants/Materials: 1,953 PBCs and 3,690 healthy controls
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| hum0261.v1.rhm.v1 | RHM for 1,953 PBCs and 3,690 healthy controls | Unrestricted-access | 2021/01/08 |
| hum0261.v1.gwas.v1 | GWAS for 1,953 PBCs and 3,690 healthy controls | Unrestricted-access | 2021/01/08 |
| hum0261.v2.gwas.v1 | GWAS for 1,920 PBCs and 1,770 healthy controls | Unrestricted-access | 2021/01/19 |
*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
hum0261.v1.rhm.v1 / hum0261.v1.gwas.v1
| Participants/Materials | 1,953 PBCs (ICD10: K743) and 3,690 healthy controls |
| Targets | genome wide SNPs |
| Target Loci for Capture Methods | - |
| Platform | Affymetrix [Axiom Genome-Wide ASI 1 Array, Japonica Array v1] |
| Library Source | DNAs extracted from peripheral blood cells |
| Cell Lines | - |
| Reagents (Kit, Version) | Axiom 2.0 Reagent Kit |
| Genotype Call Methods (software) |
ASI: Genotyping Console ver. 4.2.0.26 Japonica: Affymetrix Power Tools ver. 1.18.2 IMPUTE4 (with 2KJPN reference panel) |
| Filtering Methods |
HWE: P≥10^-6、Imputation info score: ≥ 0.5 Individuals call rate ≥ 98%, SNPs call rate ≥ 98%, MAF ≥ 1% |
| Marker Number (after QC) | 1,022,237 SNPs |
| Analysis Method (software) |
RHM: GCTA GWAS: PLINK |
| NBDC Dataset ID |
RHM: hum0261.v1.rhm.v1 GWAS: hum0261.v1.gwas.v1 (Click the Dataset ID to download the file) RHM: Dictionary file GWAS: Dictionary file |
| Total Data Volume | 17 MB (csv.zip) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | 1,920 PBCs (ICD10: K743) and 1,770 healthy controls |
| Targets | genome wide SNPs |
| Target Loci for Capture Methods | - |
| Platform | Affymetrix [Axiom Genome-Wide ASI 1 Array, Japonica Array v1] |
| Library Source | DNAs extracted from peripheral blood cells |
| Cell Lines | - |
| Reagents (Kit, Version) | Axiom 2.0 Reagent Kit |
| Genotype Call Methods (software) |
ASI: Genotyping Console ver. 4.2.0.26 Japonica: Affymetrix Power Tools ver. 1.18.2 Eagle v2.3.2 for haplotype phasing IMPUTE4 v1.0 for genotype imputation with 2KJPN reference panel |
| Filtering Methods |
Sample QCs: sample call rate < 0.97, closely related samples by PRIMUS (PI_HAT > 0.09375), outlier from Japanese cluster by PCA (Smirnov‐Grubbs test with a Bonferroni corrected P < 0.05) SNP QCs: SNP call rate < 0.99, HWE P < 0.0001, MAF < 0.05 |
| Marker Number (after QC) | 4,902,084 SNPs (hg19) |
| Analysis Method (software) | PLINK (v1.9) |
| NBDC Dataset ID |
(Click the Dataset ID to download the file) |
| Total Data Volume | 81.6 MB (tsv.zip) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Minoru Nakamura
Affiliation: NHO Nagasaki Medical Center & Nagasaki University Graduate School of Biomedical Sciences Division of Advanced Research, Department of Hepatology
Project / Group Name: PBC Consortium in Japan (PBCCJP)
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (C) | New clinical classification and the criteria for predicting long-term outcome in primary biliary cirrhosis | 20590800 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Genome-wide association study to detect disease-associated genes in Japanese patients with primary biliary cirrhosis | 23591006 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | Analysis of disease-pathways and molecular targets by disease-susceptibility genes in primary biliary cholangitis | 26293181 |
| KAKENHI Grant-in-Aid for Early-Career Scientists | Genomic analysis of traits related to metabolic syndrome and chronic kidney disease | 18K14757 |
| KAKENHI Grant-in-Aid for Young Scientists (B) | Analysis of molecular mechanisms involved in progression to jaundice and liver failure in primary biliary cholangitis | 15K19357 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | The role of cathepsin Z for liver failure-type progression in primary biliary cholangitis | 17K09449 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | GWAS-based integrated analysis of PBC to dissect the mechanism of development and progression of primary biliary cholangitis | 17H04169 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Integrated GWAS and mRNA Microarray Analysis Identified IFNG and CD40L as the Central Upstream Regulators in Primary Biliary Cholangitis. | doi: 10.1002/hep4.1497 | hum0261.v2.gwas.v1 |
| 2 |
