NBDC Research ID: hum0074.v2
SUMMARY
Aims: Genome-wide association studies on Hepatitis C virus-related diseases and construction of genome database
Methods: SNP-based genome-wide association studies
Participants/Materials:
1. virologic response to PEG-INF/RBV treatment
78 null virologic response (NVR)
64 virologic response (VR)
51 sustained virologic response (SVR)
2. decrease of PLT in response to PEG-IFN/RBV treatment
107 HCV patients with decrease of PLT in response to PEG-IFN/RBV treatment
196 HCV patients without decrease of PLT in response to PEG-IFN/RBV treatment
3. Hb reduction
94 HCV patients with Hb reduction
209 HCV patients without Hb reduction
4. hepatocellular carcinoma (HCC) development after eradication of HCV by IFN-based treatment
123 patients who developed HCC at ≥1 year since the end of treatment
333 patients who did not develop HCC at ≥5 years since the end of treatment
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| hum0074.v1.vr.v1 |
GWAS for 78 NVR and 64 VR GWAS for 78 NVR and 51 SVR |
Unrestricted-access | 2018/02/27 |
| hum0074.v1.plt.v1 | GWAS for 107 HCV patients with decrease of PLT in response to PEG-IFN/RBV treatment and 196 HCV patients without decrease of PLT in response to PEG-IFN/RBV treatment | Unrestricted-access | 2018/02/27 |
| hum0074.v1.Hb.v1 | GWAS for 94 HCV patients with Hb reduction and 209 HCV patients without Hb reduction | Unrestricted-access | 2018/02/27 |
| hum0074.v2.hcc.v1 |
GWAS for HCC development after eradication of HCV by IFN-based treatment 123 patients who developed HCC 333 patients who did not develop HCC |
Unrestricted-access | 2018/09/25 |
*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 |
virologic response 78 null virologic response 64 virologic response 51 sustained virologic response |
| Targets | genome wide SNPs |
| Target Loci for Capture Methods | - |
| Platform | Affymetrix [Genome-Wide Human SNP Array 6.0] |
| Library Source | gDNA extracted from peripheral blood cells |
| Cell Lines | - |
| Reagents (Kit, Version) | Affymetrix Genome-Wide Human SNP Nsp/Sty Assay Kit 6.0 |
| Genotype Call Methods (software) | Birdseed version 3 |
| Filtering Methods |
Sample call rate < 0.95, SNP call rate < 0.95, HWE P < 0.001, Chi-square test (allelic model) P < 1 x 10^-4 |
| Marker Number (after QC) |
NVR vs VR: 43 SNPs (hg18) NVR vs SVR: 2 SNPs (hg18) |
| NBDC Dataset ID |
(Click the Dataset ID to download the file) |
| Total Data Volume | 3 KB |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
decrease of PLT in response to PEG-IFN/RBV treatment 107 HCV patients with decrease of PLT 196 HCV patients without decrease of PLT |
| Targets | genome wide SNPs |
| Target Loci for Capture Methods | - |
| Platform | Affymetrix [Genome-Wide Human SNP Array 6.0] |
| Library Source | gDNA extracted from peripheral blood cells |
| Cell Lines | - |
| Reagents (Kit, Version) | Affymetrix Genome-Wide Human SNP Nsp/Sty Assay Kit 6.0 |
| Genotype Call Methods (software) | Birdseed version 3 |
| Filtering Methods |
Sample call rate < 0.95, SNP call rate < 0.95, HWE P < 0.001, Chi-square test (allelic model) P < 1 x 10^-4 |
| Marker Number (after QC) | 66 SNPs (hg18) |
| NBDC Dataset ID |
(Click the Dataset ID to download the file) |
| Total Data Volume |
9 KB |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Hb reduction 94 HCV patients with Hb reduction 209 HCV patients without Hb reduction |
| Targets | genome wide SNPs |
| Target Loci for Capture Methods | - |
| Platform | Affymetrix [Genome-Wide Human SNP Array 6.0] |
| Library Source | gDNA extracted from peripheral blood cells |
| Cell Lines | - |
| Reagents (Kit, Version) | Affymetrix Genome-Wide Human SNP Nsp/Sty Assay Kit 6.0 |
| Genotype Call Methods (software) | Birdseed version 3 |
| Filtering Methods |
Sample call rate < 0.95, SNP call rate < 0.95, HWE P < 0.001, Chi-square test (allelic model) P < 1 x 10^-4 |
| Marker Number (after QC) | 32 SNPs (hg18) |
| NBDC Dataset ID |
(Click the Dataset ID to download the file) |
| Total Data Volume | 5 KB |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
HCC development after eradication of HCV by IFN-based treatment (ICD10: C220) 123 patients who developed HCC 333 patients who did not develop HCC |
| Targets | genome wide SNPs |
| Target Loci for Capture Methods | - |
| Platform | Affymetrix [Axiom Genome-Wide ASI 1 Array Plate], DigiTag2 Assay, TaqMan SNP Genotyping Assays |
| Library Source | gDNA extracted from peripheral blood cells |
| Cell Lines | - |
| Reagents (Kit, Version) | Affymetrix Axiom 2.0 Reagent Kit |
| Genotype Call Methods (software) | Genotyping Console v4.1 |
| Filtering Methods |
Sample call rate < 0.95, SNP call rate < 0.95, MAF < 0.05, HWE P < 0.001, Chi-square test (allelic model) P < 1 x 10^-4 |
| Marker Number (after QC) | 70 SNPs (hg18) |
| NBDC Dataset ID |
(Click the Dataset ID to download the file) |
| Total Data Volume | 22 KB (xslx) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Yasuhito Tanaka
Affiliation: Department of Gastroenterology and Hepatology, Graduate School of Medical Sciences, Kumamoto University
Project / Group Name: -
URL: https://researchmap.jp/Yasuhito_Tanaka?lang=en
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Grant-in-aid from the Ministry of Health, Labour, and Welfare of Japan | Construction of hepatitis virus related database aiming at personalized medicine | H19-kanen-013 |
| Grant-in-aid from the Ministry of Health, Labour, and Welfare of Japan | Database construction and therapeuitic applications including host genetic factors for hepatitis virus related diseases | H22-kanen-005 |
| Grant-in-aid from the Ministry of Health, Labour, and Welfare of Japan | Genome-wide research on identification of host genetic factors to develop novel diagnostic and therapeutic methods for hepatitis. | JP15fk0210018 |
| Research Program on Hepatitis, Japan Agency for Medical Research and Development (AMED) | Genome-wide research for identification of host factors associated with liver disease progression or improvement after hepatitis C virus eradication. | 18fk0210001h0003 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Genome-wide association of IL28B with response to pegylated interferon-α and ribavirin therapy for chronic hepatitis C | doi: 10.1038/ng.449 | hum0074.v1.vr.v1 |
| 2 | Genome-wide association study identified ITPA/DDRGK1 variants reflecting thrombocytopenia in pegylated interferon and ribavirin therapy for chronic hepatitis C | doi: 10.1093/hmg/ddr249 |
hum0074.v1.plt.v1 hum0074.v1.Hb.v1 |
| 3 | Genome-wide Association Study Identifies TLL1 Variant Associated With Development of Hepatocellular Carcinoma After Eradication of Hepatitis C Virus Infection | doi: 10.1053/j.gastro.2017.01.041 | hum0074.v2.hcc.v1 |
