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HapMap ENCODE Data

 
rs    = SNP exists in dbSNP b124 (as of June 2005) as refSNP cluster
nonrs = SNP does not exist yet in dbSNP, but expected to appear in dbSNP b125

Population descriptors:    
   YRI     : Yoruba in Ibadan, Nigeria  
   JPT+CHB : Japanese in Tokyo, Japan + Han Chinese in Beijing, China (combined on one plate)
   CEU     : CEPH (Utah residents with ancestry from northern and western Europe)

Generated Fri Jun 17 13:44:05 EDT 2005

Groups

• David Altshuler and Stacey Gabriel, Broad Institute of Harvard and MIT
• Richard Gibbs and George Weinstock, Baylor College of Medicine

ENCODE Regions

• Each group resequenced five 500kb regions.
• These regions were chosen by the Analysis Group from among the ENCODE regions; they include a range of chromosomes, recombination rates, gene density, and values of non-transcribed conservation with mouse. For more information on the ENCODE Project see http://www.genome.gov/10005107.

Samples

• Resequencing was done for 16 CEPH, 16 Yoruba, 8 Japanese, and 8 Han Chinese samples. Please click here to view the Coriell Catalog ID for each DNA sample.
• The samples are currently available and may be ordered from the Coriell Institute.

Strategy

• PCR-based sequencing across the regions for each sample.

Data Release

• All SNPs found were deposited in dbSNP (http://www.ncbi.nlm.nih.gov/projects/SNP/).

Groups

• David Altshuler and Stacey Gabriel, Broad Institute of Harvard and MIT
• Mark Chee, Illumina
• Richard Gibbs and John Belmont, Baylor College of Medicine
• Thomas Hudson, McGill University & Génome Québec Innovation Centre
• Pui Kwok, UCSF

ENCODE Regions

• The regions are the same ten regions being resequenced.
• Each group genotyped all known SNPs (with rs# in dbSNP) and newly discovered SNPs in the 500kb ENCODE regions in their assigned chromosomes.

Samples

• The samples genotyped are the same 270 (plus the 5 duplicates for each plate) used for the HapMap Project:
• 90 CEPH samples: including the 16 that were resequenced.
• 90 Yoruba samples: including the 8 that were resequenced.
• 44 Japanese samples: including the 8 that were resequenced.
• 45 Han Chinese samples: including the 7 that were resequenced.
• All of the samples listed above may be ordered from the Coriell Institute.
• The 8 Yoruba samples and 1 Chinese sample that were not genotyped on the first plates, are included on the second plates.

Strategy

• Initially the SNPs currently in dbSNP build 121 were genotyped.
• All SNPs found from the resequencing project and other sources were also genotyped.

Data Release

• The genotype data were sent to the DCC and distributed in the same way as the other HapMap genotype data.

Groups

• Perlegen

ENCODE regions

• Initially, the ten 500kb regions.
• Perlegen will genotype all SNPs in the remaining 34 ENCODE regions.

Samples

• 90 HapMap CEPH samples (plus 5 duplicates) in the ten 500kb regions.
• All samples (90 Yoruba, 45 Japanese, 45 Han Chinese, and 90 CEPH samples) in the remaining 34 ENCODE regions as part of its genotyping for the HapMap Project.

Strategy

• In the CEPH samples, Perlegen genotyped the ten 500kb regions for all the SNPs in dbSNP and for the SNPs it had.
• Perlegen will genotype all SNPs in the remaining 34 ENCODE regions in all 270 samples.

Data Release

• Perlegen sent its SNPs in the ten 500kb regions to dbSNP (as new SNPs or as validation of ones in dbSNP).
• The genotype data were sent to the DCC and distributed in the same way as the other HapMap genotype data.
• The data for the remaining 34 ENCODE regions will be sent to the DCC when they become available.

Last updated : encode1.html.en,v 1.6 2005/06/29 16:31:35 krishnan Exp