NBDC Research ID: hum0024.v1
SUMMARY
Aims: To perform a comprehensive analysis of genetic alterations of myelodysplastic syndromes (MDS) and related myeloid neoplasms (myelodysplasia).
Methods: Whole-exome sequencing of gDNAs extracted from leukemic cells and paired non-leukemic cells (Illumina Genome Analyzer IIx, HiSeq 2000, and HiSeq 2500).
Participants/Materials: 13 MDSs and 1 chronic myelomonocytic leukemia (CMML) (leukemic cells and paired non-leukemic cells)
URL: http://www.h.u-tokyo.ac.jp/vcms_lf/release_20110912.pdf
http://www.kyoto-u.ac.jp/static/ja/news_data/h/h1/news6/2013/130819_1.htm
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000023 | NGS (Exome) | Controlled-access (Type I) | 2015/04/16 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials: | 13 MDSs and 1 CMML |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [Genome Analyzer IIx, HiSeq 2000/2500] |
| Library Source |
Leukemic cells: peripheral blood, bone marrow aspirate Non-leukemic cells: oral mucosa |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect Human ALL Exon kit (38Mb, 50Mb kit, v4) |
| Fragmentation Methods | Covaris (S220) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 75-108 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000023 |
| Total Data Volume | 300 GB |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Seishi Ogawa
Affiliation: Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University
Project / Group Name:
URL： http://plaza.umin.ac.jp/kyoto_tumorpatho/
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Project for Development of Innovative Research on Cancer Therapeutics (P-DIRECT) | 骨髄異形成症候群におけるエピゲノム関連マーカーの探索と実用化 | - |
| Health and Labour Science Research Grants from the Japanese Ministry of Health, Labour and Welfare, and Research on Measures for Intractable Disease | 不応性貧血の治癒率向上を目指した分子・免疫 病態研究 | - |
| KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas | システム的統合理解に基づくがんの先端的診断、治療、予防法の開発 | 22134006 |
| KAKENHI Grant-in-Aid for Scientific Research (A) | Analysis on genetic basis of leukemia relapse and therapy resistance | 23249052 |
| KAKENHI Grant-in-Aid for Young Scientists (B) | Exploring new gene target of 4q-UPD in Myelodysplastic syndromes | 21790907 |
| New Energy and Industrial Technology Development Organization (NEDO) | 機能性アレルのデジタルカウントによる次世代"ExpressGenotype法"とその産業応用 | 08C46598a |
|
Cabinet Office, Government of Japan Funding Program for World-Leading Innovative R&D on Science and Technology (FIRST) |
Development of medical technologies for treating intractable cancers and cardiovascular diseases | - |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Frequent pathway mutations of splicing machinery in myelodysplasia. | doi: 10.1038/nature10496 | JGAD000023 |
| 2 | Recurrent mutations in multiple components of the cohesin complex in myeloid neoplasms. | doi: 10.1038/ng.2731 | JGAD000023 |
| 3 | The landscape of somatic mutations in Down syndrome-related myeloid disorders. | doi: 10.1038/ng.2759 | JGAD000023 |
| 4 | Landscape of genetic lesions in 944 patients with myelodysplastic syndromes. | doi: 10.1038/leu.2013.336 | JGAD000023 |
USERS (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
