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 will resequence 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.
- 16 HapMap CEPH samples: The DNA is currently available from Coriell.
- 16 Yoruba, 8 Japanese, and 8 Han Chinese samples: From the HapMap samples being transformed at Coriell.
- Resequencing will start with the CEPH samples; when the other samples become available they will be resequenced as well.
- PCR-based sequencing across the regions for each sample.
All SNPs found will be sent to dbSNP.
- The regions are the same ten regions being resequenced.
- Each group will resequence the 500kb ENCODE regions in their assigned chromosomes.
- The samples genotyped will be the same 270 (plus the 5 duplicates for each plate) used for the HapMap Project:
- 90 CEPH samples: including the 16 that were resequenced: these are currently available and the genotyping can start immediately.
- 90 Yoruba samples: being transformed at Coriell.
- 45 Japanese samples: being transformed at Coriell.
- 45 Han Chinese samples: being transformed at Coriell.
- All SNPs in these regions will be genotyped.
- Initially the SNPs currently in dbSNP will be genotyped.
- As more SNPs are found from the resequencing project and other sources, they will then also be genotyped.
- When the non-CEPH samples become available, they will be genotyped for all the known SNPs, and the CEPH samples will be genotyped for any new SNPs.
The genotype data will be sent to the DCC and distributed in the same way as the other HapMap genotype data.
- Initially the 90 HapMap CEPH samples (plus 5 duplicates).
- If the Analysis Group is interested, then Perlegen might genotype these SNPs in the other samples when they become available.
- Perlegen will genotype all the regions, for all the SNPs in dbSNP and for the SNPs it has.
- Perlegen will send its SNPs in these regions to dbSNP (as new SNPs or as validation of ones in dbSNP).
- The genotype data will be sent to the DCC and distributed in the same way as the other HapMap genotype data.
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