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The HapMap ENCODE resequencing and genotyping project aims to produce a dense set of genotypes across large genomic regions. Ten 500-kilobase regions of the genome were resequenced in 48 unrelated DNA samples (16 Yoruba, 8 Japanese, 8 Han Chinese, and 16 CEPH). All SNPs identified, along with SNPs in dbSNP, were genotyped in the 269 HapMap DNA samples (90 Yoruba, 44 Japanese, 45 Han Chinese, and 90 CEPH). The new SNPs discovered were deposited in dbSNP and all genotype data were sent to the HapMap Data Coordination Center. In addition, Perlegen will genotype all SNPs in the remaining 34 ENCODE regions in all of the HapMap DNA samples as part of its genotyping for the HapMap Project. This study will provide dense genotype data to allow the development and assessment of methods of analysis. A second plate of samples was collected from each population in order to allow studies of how general the results are from the first plate of samples. Of the 16 Yoruba samples resequenced, 8 are on the first plate and 8 are on the second plate; of the 8 Han Chinese samples resequenced, 7 are on the first plate and 1 is on the second plate; the 8 Japanese samples and 16 CEPH samples that were resequenced are on the first plates. A complete list of the sample ID's can be found here.
CEU |
JPT+CHB |
YRI |
ENr112 |
2p16.3 |
Chr2:51512208..52012208 |
2,601 |
2,573 |
2,608 |
McGill-GQIC, Perlegen |
ENr131 |
2q37.1 |
Chr2:234156563..234656627 |
2,214 |
2,107 |
2,129 |
McGill-GQIC, Perlegen |
ENr113 |
4q26 |
Chr4:118466103..118966103 |
2,538 |
2,401 |
2,405 |
Broad, Perlegen |
ENm010 |
7p15.2 |
Chr7:26924045..27424045 |
1,830 |
1,787 |
1,742 |
UCSF-WU, Perlegen |
ENm013(500Kb) |
7q21.13 |
Chr7:89621624..90121624 |
1,770 |
1,678 |
1,680 |
Broad, Perlegen |
ENm014(500Kb) |
7q31.33 |
chr7:126368183..126865324 |
3,343 |
3,239 |
3,232 |
Broad, Perlegen |
ENr321 |
8q24.11 |
Chr8:118882220..119382220 |
2,128 |
2,100 |
2,092 |
Illumina, Perlegen |
ENr232 |
9q34.11 |
Chr9:130725122..131225122 |
1,909 |
1,828 |
1,808 |
Illumina, Perlegen |
ENr123 |
12q12 |
Chr12:38626477..39126476 |
2,189 |
2,181 |
2,035 |
BCM, Perlegen |
ENr213 |
18q12.1 |
Chr18:23719231..24219231 |
1,990 |
1,969 |
1,966 |
Illumina, Perlegen |
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Total |
22,512 |
21,863 |
21,697 |
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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 Apr 13 13:44:05 EDT 2007
- 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.
- 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.
- PCR-based sequencing across the regions for each sample.
- The regions are the same ten regions being resequenced.
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Each group genotyped all known SNPs (with rs# in dbSNP) and newly discovered SNPs in the 500kb ENCODE regions in their assigned chromosomes.
- 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.
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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.
- Initially the SNPs currently in dbSNP build 121 were genotyped.
- All SNPs found from the resequencing project and other sources were also genotyped.
- The genotype data were sent to the DCC and distributed in the same way as the other HapMap genotype data.
- Initially, the ten 500kb regions.
- Perlegen will genotype all SNPs in the remaining 34 ENCODE regions.
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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.
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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.
-
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
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