NBDC Research ID: hum0434.v1
SUMMARY
Aims: The aim of this study is to identify somatic gene mutations associated with various diseases involving T cells or NK cells, and to perform integrated analyses with clinical data in order to elucidate gene sets that contribute to disease onset or treatment resistance. These findings are expected to provide fundamental data for the development of novel diagnostic criteria and therapeutic agents.
Methods: whole exome sequencing and target capture sequencing
Participants/Materials:
- whole exome sequencing: CD4-positive cells and CD8-positive cells were isolated from 10 patients with pure red cell aplasia were used.
- targeted capture sequencing: Peripheral blood mononuclear cells (PBMCs) from 53 patients with pure red cell aplasia, 10 patients with aplastic anemia, 2 healthy controls, and 55 patients with large granular lymphocytic leukemia were used. For 4 patients with pure red cell aplasia, PBMCs were collected at 2 different time points (Case 1: onset and 9y later, Case 2: onset and 5y later, Case 3: onset and 6y later, Case 4: onset and 3y later).
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000658 | Controlled-access (Type I) | 2025/04/17 | |
| JGAS000709 | NGS (Target Capture) | Controlled-access (Type I) | 2025/04/17 |
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MOLECULAR DATA
| Participants/Materials |
pure red cell aplasia (ICD10: D600): 10 cases CD4-positive cells: 10 samples CD8-positive cells: 10 samples |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Thermo Fisher Scientific [Ion Torrent S5] |
| Library Source | DNAs extracted from CD4-positive cells and CD8-positive cells of patients |
| Cell Lines | - |
| Library Construction (kit name) | Ion AmpliSeq Exome RDY Kit |
| Fragmentation Methods | - |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 200 bp |
| Mapping Methods | Torrent Suite software program |
| Mapping Quality | MAPQ = 6.5 |
| Reference Genome Sequence | hg19 |
| Coverage (Depth) |
CD4-positive cells: 84x CD8-positive cells: 136x |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000788 |
| Total Data Volume | 701.6 GB (bam) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
[JGAS000658] pure red cell aplasia (ICD10: D600): 53 cases PBMCs were collected at 2 different time points from the 4 patients with pure red cell aplasia (C1: onset and 9y later, C2: onset and 5y later, C3: onset and 6y later, C4: onset and 3y later) aplastic anemia (ICD10: D61.3): 10 cases 2 healthy controls PBMCs: 69 samples Buccal swab, CD4-positive cells and neutrophils from 1 pure red cell aplasia case included above cases: total 3 samples [JGAS000709] large granular lymphocytic leukemia (ICD10: C917): 55 cases PBMCs: 55 samples |
| Targets | Target Capture |
| Target Loci for Capture Methods | 52 genes (Gene list) |
| Platform | Thermo Fisher Scientific [Ion GeneStudio S5] |
| Library Source | DNAs extracted from PBMCs, buccal swab, CD4-positive cells and neutrophils |
| Cell Lines | - |
| Library Construction (kit name) | Ion AmpliSeq Library Kit Plus |
| Fragmentation Methods | - |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 200 bp |
| Japanese Genotype-phenotype Archive Dataset ID | |
| Total Data Volume |
JGAD000788: 701.6 GB (fastq) JGAD000842: 169 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Fumihiro Ishida
Affiliation: Department of Biomedical Laboratory Sciences, Shinshu University School of Medicine
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (C) | Mutational profiles of T cells in bone marrro failure syndrome as clinical markers | 20K08709 |
| KAKENHI Grant-in-Aid for Young Scientists | Elucidation of immune abnormalities in thymoma and related autoimmune diseases through comprehensive genetic analysis of T cells | 21K16302 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Mutational heterogeneities in STAT3 and clonal hematopoiesis-related genes in acquired pure red cell aplasia | doi: 10.1007/s00277-025-06356-4 | JGAD000788 JGAD000842 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
