Whole transcriptome sequencing of pediatric T-cell acute lymphoblastic leukemia

JGA Study Accession: JGAS000090.v1.p2

Study Version History

Study Release date
JGAS000090.v1.p1 2017-05-25
JGAS000090.v2.p1 2018-01-25

Study Description

Study Description

Aims: Identify disease-related genes in Japanese

Methods: Genomic DNA samples were genotyped by following methods: Human610-Quad BeadChip, HumanHap550v3 Genotyping BeadChip, HumanOmniExpress-12 BeadChip, HumanExome BeadChip, OmniExpressExome BeadChip (Illumina), high-density oligonucleotide arrays (Perlegen Sciences), or Invader (Hologic Japan). Genome-Wide Association Studies (GWAS) for myocardial infarction (MI) , type II diabetes mellitus (T2DM), Atopic dermatitis (AD), atrial fibrillation (AF), and Body Mass Index (BMI), primary open-angle glaucoma (POAG), 58 quantitative traits and age at menarche / menopause were performed using about 500-600K SNPs. A whole-genome sequencing analysis for 1,026 patients, who were registered Bio Bank Japan from 2003 - 2007 was performed with Illumina HiSeq2500.

Participants/Materials: Participants for the Tailor-made Medical Treatment Program (BioBank Japan: BBJ)

Study Type

Transcriptome Sequencing

Study History

Research milestones of the Framingham Heart Study can be found at http://www.framinghamheartstudy.org/about/milestones.html.

The Generation 1 (or Original) cohort Exam 1 took place between 1948 and 1953. Biennial exams have continued to the present. Exam 29 took place between 2006 and 2007. Exam 30 began in 2008.

Study Inclusion/Exclusion Criteria

A description of the Design of the Original Cohort can be found at Dawber TR, Meadors GF, and Moore FEJ. Epidemiological approaches to heart disease: the Framingham Study. Am J Public Health 1951; 41:279-86.

Project Name

Whole transcriptome sequencing of pediatric T-cell acute lymphoblastic leukemia Project

Related Studies

関連 ID は手作業で入力。JGA Study 番号を書くことでアンブレラのように使うことができる

Study Statistics

手作業で入力

  • Participants: 20
  • Subjects: 20
  • Samples: 40
  • Number of pediatric T-ALL patients: 12

Traits Related to Study

Sample Attributes

自動出力。Attribute に対して non NULL value を持っている Sample と Subject (subject id と sort | uniq 数) 数を表示

11 sample attributes

Sample attribute Samples Subjects
sample_name 20 10
title 20 10
description 20 10
donor_id 20 10
sex 20 10
affection_status 20 10
tissue 20 10
population 20 10
histological_type 20 10
is_tumor 20 10
age 20 10

Publicly Available Data

Public download site.

File accession Name Description Category Version Release date Last updated
JGAU000001.v1 all-patients-phenotypes phenotype data dictionary of all patients data_dictionary 1 2017-05-25 2017-05-25
JGAU000002.v1 association-analysis-results results of association analysis results (secondary accession: hum0014.v2.jsnp.934ctrl.v1) association_analysis_results 1 2017-05-25 2017-10-25

Data Use Restrictions

Data use policy Title Consent code Dataset
JGAP000001 NBDC Policy GRUC(CC) JGAD000079.v2.p1
JGAD000080.v2.p1
JGAP000004 Lung Cancer only GRUC(CC), GSO JGAD000080.v2.p1

Controlled-access Data

subject 数は subject id の sort | uniq 数

Datasets

Dataset Title Samples Subjects Files Total filesize File list
JGAD000079.v2.p1 WGS of cells 20 10 40 10 GB Download list
JGAD000080.v2.p1 WXS of cells 20 10 40 12 GB Download list

Publications

  1. Lucena MI, Molokhia M, Shen Y, Urban TJ, et al.
    Susceptibility to amoxicillin-clavulanate-induced liver injury is influenced by multiple HLA class I and II alleles.
    Gastroenterology. 2011 Jul; 141(1):338-47.
    PubMed link
  2. Urban TJ, Shen Y, Stolz A, Chalasani N, Fontana RJ et al.
    Limited contribution of common genetic variants to risk for liver injury due to a variety of drugs.
    Pharmacogenet Genomics. 2012 Nov; 22(11):784-95.
    PubMed link

Grants

Agency Name Title Grant ID
Ministry of Education, Culture, Sports, Science and Technology in Japan Tailor-made Medical Treatment Program (the 3rd phase) Tailor-made Medical Treatment Program (the 3rd phase) 11111
Japan Science and Technology Agency JST innovation program Innovation on medical research program A JP1234

Study Attributions

登録者ではなく貢献者として自由に記載してもらう

  • Principal Investigator:
    • Taro Mishima, PhD. DDBJ Center, National Institute of Genetics, Yata 1111, Shizuoka, Japan

Authorized Data Access Requests

申請管理 DB から公開情報 DB に格納し、動的に表示する

  1. Principal Investigator: Taro Mishima
    Affiliation: Naiotnal Institute of Genetics
    Data in Use (Dataset accession): JGAD000079,JGAD000080
    Period of Data Use: 2018-01-01 to 2020-01-01
  2. Principal Investigator: Taro Fuji
    Affiliation: Toyko University
    Data in Use (Dataset accession): JGAD000079
    Period of Data Use: 2018-04-01 to 2020-01-01