Determine ethnicity from exome sequence

[rbagnall]

I have data from 40 exomes and they are from de-identified post-mortem samples.

There are many SNPs that have a higher frequency in Asian populations compared to Europeans, for example. When I compare my data to available SNP frequencies I would like to match the ethnicity. Have the collective observed alleles at such sites been used to determine the ethnicity from exome data?

Also, I have been able to reconstruct the Mitochondrial DNA sequence from off-target reads, using MitoSeek. I can determine the mitochondrial haplotype using Mitotool website, and since particular mitochondrial haplogroups can be enriched in ethnic groups, can this extra information support ethnicity?

Any thoughts or comments welcome.

[GenoMax]

http://genomemedicine.com/content/5/7/69