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July 29, 2011 New dataset of Amyotrophic lateral sclerosis(ALS) study has been released.
July 23, 2009 New dataset of Esophageal cancer study has been released.
June 12, 2008 The special datasets of 35 diseases study have been released.

This page

These datasets are the genotypic data of almost 200 or 92 Japanese samples from each of 36 diseases. Each dataset provides genotype frequency data of approximately 500,000 , 200,000 or 50,000 SNPs in autosomal chromosomes with genotyping information without individual genotype data. The genotyping was performed by in collaboration with the Center for Genomic Medicine of RIKEN (previously known as the SNP Research Center of RIKEN) and the University of Tokyo. These samples come from the Biobank Japan project on the implementation of personalized medicine.

Contents

Outline of project

  • The Biobank Japan project on the implementation of personalized medicine

    The project aims for construction of basic information for personalized medicine. The Center for Genomic Medicine of RIKEN (previously known as the SNP Research Center of RIKEN) functions as a core research organization for the personalized medicine project and plays a central role in genetic analysis. They will work in cooperation with patients by the words "Your understanding for our future" to provide better healthcare options for the benefit of patients.

  • Other useful dataset: "JSNP550typed (Control)"

    JSNP550typed provides data of 515,286 SNPs in autosomal chromosomes with genotyping information and annotation of 934 Japanese volunteers without individual genotype data. Genotyping was performed using the Illumina HumanHap550 BeadChip and quality control filters were applied

Data release

July 29, 2011 Amyotrophic lateral sclerosis (ALS) study
July 23, 2009 Esophageal cancer study
June 12, 2008 35 diseases study

Study list

Amyotrophic lateral sclerosis (ALS) study

Outline of study:
This study provides data of 48,939 SNPs in autosomal chromosomes with genotyping information and annotation of 92 Japanese ALS patients without individual genotype data. Genotyping was performed using the multiplex PCR-based invader assay (Third Wave Technologies) and quality control filters were applied.

Samples:
Samples were collected from 92 Japanese ALS patients after written informed consent. The study protocol was approved by the Ethical Committee at the Institute of Medical Science, the University of Tokyo and RIKEN.

Methods:
Genomic DNA was extracted from the peripheral blood leukocytes by standard method. SNPs were genotyped using the multiplex PCR-based invader assay (Third Wave Technologies) as described previously (Ohnishi et al. J Hum Genet, 2001).

Acknowledgements:
The genotyping, bioinformatics and data quality control have been performed in collaboration with the Center for Genomic Medicine of RIKEN (previously known as the SNP Research Center of RIKEN) and the University of Tokyo.This work was supported by Leading Project for personalized medicine in Ministry of Education, Culture, Sports, Science and Technology, Japan.

download links

File descriptions


Esophageal cancer study

Outline of study:
This study provides data of 503,734 SNPs in autosomal chromosomes with genotyping information and annotation of 182 Japanese Esophageal cancer patients without individual genotype data.
Genotyping was performed using the Illumina HumanHap550v3 Genotyping BeadChip plus and quality control filters were applied.

Samples:
Samples were collected from 182 Japanese volunteers after written informed consent.
The study protocol was approved by the Ethical Committee at the Institute of Medical Science, the University of Tokyo and RIKEN.

Methods:
Genomic DNA was extracted from whole blood by standard method.
We applied 750ng DNA (15ul DNA at concentration of 50ng/ul) of each sample to Illumina HumanHap550K BeadChip according to the manufacture's protocols.

Acknowledgements:
The genotyping, bioinformatics and data quality control have been performed in collaboration with the Center for Genomic Medicine of RIKEN (previously known as the SNP Research Center of RIKEN) and the University of Tokyo.This work was supported by Leading Project for personalized medicine in Ministry of Education, Culture, Sports, Science and Technology, Japan.

35 Diseases study

Outline of study:
These datasets are the genotypic data of 191- 195 Japanese samples from each of 35 diseases. Each dataset provides almost 200,000 SNPs in autosomal chromosomes with genotyping information without individual genotype data. The genotyping was performed by Perlegen Sciences, Inc. in collaboration with the Center for Genomic Medicine of RIKEN(previously known as the SNP Research Center of RIKEN) and the University of Tokyo. These samples come from the Biobank Japan project on the implementation of personalized medicine.



Disease list and download links

Download the subsets with the data relevant to each disease in Excel and flat file in aZIP archive.


  Cancer
  Cerebrovascular disorders
  Cardiovascular diseases
  Respiratory tract diseases
  Chronic liver diseases
  Eye diseases
  Other diseases

File discriptions

Excel sheets are split by chromosome, multimapped SNPs and unmapped SNPs according to dbSNP mapping information. In each sheet data are sorted by dbSNP rsID. Flat text file is divided by chromosome, multimapped SNPs and unmapped SNPs. In each division data are sorted by dbSNP rsID.
Column number Field name Description
1 dbSNP_rsID rsID corresponding dbSNP version
2 allele_A nucleotide code corresponding to perlegen_allel_1 based on dbSNP orientation or Illumina HumanHap550 allele A
3 allele_B nucleotide code corresponding to perlegen_allel_2 based on dbSNP orientation or Illumina HumanHap550 allele B
4 genotype_AA_count AA genotype count
5 genotype_AB_count AB genotype count
6 genotype_BB_count BB genotype count
7 genotype_XX_count count of undetermined data
8 genotype_AA_freq AA genotype frequency
9 genotype_AB_freq AB genotype frequency
10 genotype_BB_freq BB genotype frequency
11 allele_A_freq allele A frequency
12 allele_B_freq allele B frequency
13 allele_of_MAF nucleotide code for minor allele frequency
14 HWE_p_value p-value for Hardy-Weinberg Equilibrium by exact test
15 genotype_suspicious * for possible genotyping error
16 number_of_mapped number of positions in dbSNP
17 chromosome chromosome
18 position_in_chromosome nucleotide position in chromosome according to dbSNP mapping information
19 duplicate_SNP duplicated rsID due to SNP merged in dbSNP
20 perlegen_rsID or HumanHap550v3_rsID rsID used by perlegen or Illumina HumanHap550v3
21 perlegen_allele_1 or HumanHap550v3_alleleA nucleotide code for allele 1 used by perlegen or alleleA used by HumanHap550v3
22 perlegen_allele_2 or HumanHap550v3_alleleB nucleotide code for allele 2 used by perlegen or alleleB used by HumanHap550v3
23 perlegen_chromosome or HumanHap550v3_chromosome chromosome used by perlegen or not available used by HumanHap550v3
24 perlegen_accession_id or HumanHap550v3_accession_id accession number from NCBI Build 35 of the contig to which the SNP aligns;may be null or not available used by HumanHap550v3
25 perlegen_contig_position or HumanHap550v3_contig_position nucleotide position in NCBI build 35 contig of the reference base in the alignment;may be null or not available used by HumanHap550v3
26 perlegen_strand or HumanHap550v3_strand + or -, based on the strand for the reported alleles on NCBI Build 35 or 36
27 perlegen_Assayed_sequence or HumanHap550v3_AlleleA_ProbeSeq the 29mer assayed for this SNP, with an ambiguity character representing the SNP at the middle base or HumanHap550v3_AlleleA_ProbeSeq


File discriptions(ALS datasets using the multiplex PCR-based invader assay (Third Wave Technologies))

Column number Field name Description
0 Probe_ID ID used by RIKEN
1 dbSNP_rsID rsID of dbSNP or "ambiguous" without rsID
2 allele_A nucleotide code corresponding to TWT_Invader allele A
3 allele_B nucleotide code corresponding to TWT_Invader allele B
4 genotype_AA_count AA genotype count
5 genotype_AB_count AB genotype count
6 genotype_BB_count BB genotype count
7 genotype_XX_count count of undetermined data
8 genotype_AA_freq AA genotype frequency
9 genotype_AB_freq AB genotype frequency
10 genotype_BB_freq BB genotype frequency
11 allele_A_freq allele A frequency
12 allele_B_freq allele B frequency
13 allele_of_MAF nucleotide code for minor allele frequency
14 HWE_p_value p-value for Hardy-Weinberg Equilibrium by exact test
15 flanking_sequnce SNP flanking sequence


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