Question: How Does Dbsnp Record Allele Frequencies?
2
gravatar for Andrea_Bio
9.0 years ago by
Andrea_Bio2.6k
Andrea_Bio2.6k wrote:

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

frequency allele • 2.9k views
ADD COMMENTlink modified 8.5 years ago by Larry_Parnell16k • written 9.0 years ago by Andrea_Bio2.6k
4
gravatar for Pierre Lindenbaum
9.0 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum123k wrote:

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

ADD COMMENTlink written 9.0 years ago by Pierre Lindenbaum123k
4
gravatar for Larry_Parnell
9.0 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

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.

ADD COMMENTlink written 9.0 years ago by Larry_Parnell16k

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

ADD REPLYlink written 9.0 years ago by Andrea_Bio2.6k
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