How Does Dbsnp Record Allele Frequencies?

Question

[Andrea_Bio]

Hi

I've been reading about how dbSNP stores allele frequencies of a SNP. I've looked at the schema and the handbook but I can't find information about how they calculate frequency data

many thanks

Answer 1

[Pierre Lindenbaum]

See the page "Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters" : http://www.ncbi.nlm.nih.gov/projects/SNP/Hetfreq.html

Answer 2

[Larry_Parnell]

The data are indeed available for many different populations. SNP rs328 in LPL (lipoprotein lipase) has data from 23 different population-ss ID# combinations with regard to allele frequencies. The minor allele frequency ranges from 0.033 in YRI to 0.36 in a CEPH sample. Remember, ss IDs are folded into one rs ID.

Personally, I prefer to use data from HapMap when I am interested in genotypes of individual subjects. This allows us to calculate LD and such with tools in-house.

[Andrea_Bio]

thanks a lot. I've never seen an entry with that much information in.