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 GAIIx, 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

 

Data Set IDType of DataCriteriaRelease Date
JGAS00000000023 NGS (Exome) Controlled-Access (Type I) 2015/04/16

*Release Note

* Data users need to apply the Form 2 (Application Form for Using NBDC Human Data) to reach the Controlled Access Data. Learn more

 

MOLECULAR DATA

JGAS00000000023

Participants/Materials: 13 MDSs and 1 CMML
Targets Exome
Target Loci for Capture Methods -
Platform Illumina [GAIIx, 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 Data set ID JGAD00000000023
Total Data Volume 300 GB
Comments (Policies) NBDC policy & P-DIRECT 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):

NameTitleProject 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

TitleDOIData Set ID
1 Frequent pathway mutations of splicing machinery in myelodysplasia. doi: 10.1038/nature10496 JGAD00000000023
2 Recurrent mutations in multiple components of the cohesin complex in myeloid neoplasms. doi: 10.1038/ng.2731 JGAD00000000023
3 The landscape of somatic mutations in Down syndrome-related myeloid disorders. doi: 10.1038/ng.2759 JGAD00000000023
4 Landscape of genetic lesions in 944 patients with myelodysplastic syndromes. doi: 10.1038/leu.2013.336 JGAD00000000023

 

USERS (Controlled-Access Data)

Principal Investigator: Affiliation: Data in Use (Data Set ID)Period of Data Use