NBDC Research ID: hum0163.v3
SUMMARY
Aims: Identification of biomarkers associated with efficacy and adverse drug reactions in therapeutics for psychiatric/neurological disorders or cancers, leading to establishment of stratified medicine based on pharmacogenomic information.
Methods: DNA/plasma samples and clinical information are collected from patients with psychiatric/neurological disorders or cancers. Targeted NGS analysis focusing on 100 pharmacogenes, HLA typing, metabolome analysis, and pharmacokinetic analysis were conducted to identify biomarkers associated with drug responses.
Participants/Materials:
Patients receiving psychotropic drugs (lamotrigine and clozapine), and patients receiving anti-cancer molecular targeted drugs (regorafenib, trastuzumab and nivolumab)
90 bullous pemphigoid cases; 737 general populations derived from Epstein-Barr virus-transformed B-lymphoblast cell lines of unrelated Japanese individuals established by the Pharma SNP Consortium (PSC)
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| hum0163.v1.freq.v1 | NGS (Target Capture) | Unrestricted-access | 2018/12/14 |
| hum0163.v2.nat2.v1 | NGS (NAT2 haplotype) | Unrestricted-access | 2021/02/09 |
| hum0163.v3.BPgwas.v1 | GWAS for bullous pemphigoid | Unrestricted-access | 2023/04/21 |
*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
hum0163.v1.freq.v1 / hum0163.v2.nat2.v1
| Participants/Materials |
990 patients with psychiatric/neurological disorders or cancers - epilepsy (ICD10: G402) / bipolar disorder (ICD10: F319): 343 cases (receiving lamotrigine) - schizophrenia (ICD10: F209): 454 cases - breast cancer (ICD10: C509): 65 cases (receiving trastuzumab) - colorectal cancer (ICD10: C189): 83 cases (receiving regorafenib) - malignant melanoma (ICD10: C439): 45 cases (receiving nivolumab) |
| Targets | Target Capture |
| Target Loci for Capture Methods | diplotype of coding regions of 100 pharmacogenes (1846 variants), CYP2D6 gene and NAT2 gene |
| Platform | Illumina [MiSeq] |
| Library Source | DNAs extracted from peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) | in-house MultiplexPCR |
| Fragmentation Methods | - |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 250 bp x 2 |
| NBDC Dataset ID |
(Click the Dataset ID to download the file) |
| Total Data Volume |
hum0163.v1.freq.v1: 55 KB (csv.zip) hum0163.v2.nat2.v1: 1 KB (csv.zip) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
bullous pemphigoid (ICD10: L12.0): 90 cases 737 healthy controls |
| Targets | genome wide SNPs |
| Target Loci for Capture Methods | - |
| Platform | Illumina [Infinium OmniExpressExome BeadChip] |
| Source | DNA extracted from peripheral blood cells of bullous pemphigoid patients and B-lymphoblast cell lines |
| Cell Lines | 737 general populations derived from Epstein-Barr virus-transformed B-lymphoblast cell lines of unrelated Japanese individuals established by the Pharma SNP Consortium (PSC) |
| Reagents (Kit, Version) | Illumina Infinium OmniExpressExome BeadChip |
| Genotype Call Methods (software) | GenCall software (GenomeStudio) |
| Filtering Methods | sample call rate < 0.99, SNP call rate < 0.99, HWE-P < 1x10^-6 |
| Marker Number (after QC) | 526,267 SNPs (on autosomal chromosomes, hg19) |
| NBDC Dataset ID |
(Click the Dataset ID to download the file) |
| Total Data Volume | 6 MB (txt.zip) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Taisei Mushiroda
Affiliation: RIKEN Center for Integrative Medical Sciences, Laboratory for Pharmacogenomics
Project / Group Name: -
URL: http://www.riken.jp/en/research/labs/ims/pharmacogen/
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Advanced Genome Research and Bioinformatics Study to Facilitate Medical Innovation (GRIFIN), Platform Program for Promotion of Genome Medicine, Japan Agency for Medical Research and Development (AMED) | Pharmacogenomics research for therapeutics in psychiatry, neurology and oncology | JP16km0405201 |
| Practical Research Project for Rare / Intractable Diseases | Elucidation of the pathogenesis and risk factors of bullous pemphigoid | JP22ek0109430 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | GSTP1 rs1695 is associated with both hematological toxicity and prognosis of ovarian cancer treated with paclitaxel plus carboplatin combination chemotherapy: a comprehensive analysis using targeted resequencing of 100 pharmacogenes. | doi: 10.18632/oncotarget.25712 | hum0163.v1.freq.v1 |
| 2 | Association of Genetic Variants of HLA-DQA1 with Bullous Pemphigoid Induced by Dipeptidyl Peptidase-4 Inhibitors | doi: 10.1016/j.jid.2023.04.017 | hum0163.v3.BPgwas.v1 |
