[Genome] question about SNPs in the UCSC browser

[Charla Lambert]

Hello there,

Do you know if there has been any discussion (by anyone) of including 
ancestral alleles as part of the SNP information in the UCSC browser? 
For example, an appropriate maximum likelihood method could be run for all 
SNPs (or all HapMap SNPs), using any orthologous information from primate 
sequence plus an accepted phylogenetic tree for all primates.

I know dbSNP includes ancestral information that was computed using the 
likelihood method described in the following paper:

Spencer CCA, et al. (2006). The influence of recombination on human 
genetic diversity.  PLoS Genetics 2(9): e148 
doi:10.1371/journal.pgen.0020148.
http://genetics.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pgen.0020148

However, the dbSNP documentation says the last batch of ancestral 
information they received was in May 2004.  A lot of orthologous data have 
been generated since then, and it seems like a good time to systematically 
compute the most likely ancestral allele for each SNP in the database. 
With all the genome-wide scans of publicly-available data that are being 
published right now, I imagine this would be very useful for a lot of 
researchers.

Thanks very much!
Charla

------
Charla Lambert
clambert at u.washington.edu
University of Washington
Genome Sciences Department
Foege Building, S-303
Tel: (206)321-8416
Lab: (206)897-1846