[HapMap announcements] HapMap Release #21a available

[Marcela K. Tello-Ruiz]

  --  HapMap data release #21a, January 2007, on NCBI B35 assembly, 
dbSNP b125

*New Data. *This release contains all processed data from phases I+II of 
the HapMap project. In addition, it also contains genotypes, frequencies 
and assays from the Illumina Infinium* 100k and 300k genotyping arrays, 
Affymetrix non-synonymous SNPs (nsSNPs), and SNPs typed for a 
high-resolution map (De Bakker et al. 2006) of the extended MHC locus. 
Data is available for bulk download and browsing, as well as HapMart.

Populations

	

CEU

	

CHB+JPT

	

YRI

Total Non-Redundant

	

3,904,218 

	

3,936,482 

	

3,846,092 

Total QC+ SNPs

	

4,871,127 

	

4,881,441 

	

4,774,448 

Total Genotyped SNPs

	

6,838,923 

	

6,799,238 

	

6,798,546 



Summary of nsSNPs in hapmap.org:

_Category						Count

_Total genotyped nsSNPs					21003
Total QC+ nsSNPs 					18191
Total nsSNPs polymorphic in at least one population	12217
Total untyped nsSNPs (dbSNP 125)			13025


NOTE: The new genotyping data included in this release has not been 
processed further. Thus, LD data and phased haplotypes currently 
available at hapmap.org correspond to the previous release #21 data 
(phases I+II).


* Illumina Infinium arrays: The 100K array covers the entire genome with 
109K SNPs with a focus on exonic regions, and the 300K array (also known 
as HumanHap300) contains 319K tag SNPs derived from the Phase I of the 
HapMap project.

*New Features*. New genomic variation data sets available for 
visualization in the HapMap genome browser are: Segmental Duplications 
and Structural Variation (Copy Number Variation; CNV). Segmental 
Duplications correspond to High-Depth Celera Reads (She et al. 2004; 
Bailey et al. 2001 &2002). Structural Variation datasets include:

    * CNV regions determined in HapMap samples (Redon et al. 2006)
    * CNV datasets (Iafrate et al. 2004, Sebat et al. 2004, Sharp et al.
      2005, Tuzun et al. 2005)
    * Deletions (Hinds et al. 2006, Conrad et al. 2006; McCarroll et al.
      2006)


The HapMap database is updated with data submitted to the DCC by centers 
funded by agencies in the UK, Japan, US, China and Canada.  New data are 
submitted to NCBI's dbSNP database within days and should become 
available also at http://www.ncbi.nih.gov/SNP/ soon thereafter, once 
NCBI has incorporated this submission into the next build of dbSNP.

-- 
Marcela Karey Tello-Ruiz
HapMap Data Coordination Center

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://osceola.cshl.edu/pipermail/announcements/attachments/20070116/95b7885a/attachment.html