Entering edit mode
8.6 years ago
Dear all,
Fortunately, I've learned how to use available databases to choose the Tagging SNPs in order to include them in the study. Kindly, I need the answer of the following question:
Which population should be chosen if the population in question is not found in HapMap database, since there are limited number of populations? That is to say, how to know the most genetically related population to a given one, so that its information can be used as a predictive one for the required population?
Thanks a lot.
Do you already have (a limited) number of genotypes available for you population of interest? If so, you could perform PCA using genotype data of the population present in HapMap and see to which population your samples cluster, if at all.
Actually, I'm now in the step of candidate gene(s) and SNPs selection, but in order to do so, you have to determine which population its genotype you want to use in Haploview to pick the Tagging SNPs among others. I'm now designing the study and I want to choose SNPs correctly and based on proper criteria. BUT!! The population of interest in not listed in the drag drop list!! So, which population should I select??
So not a single genetic study has been performed before? You haven't revealed anything about your population, so it's hard to guess whether you work on an out bred population comparable to 'ehm' New-York, or you are working on a genetically isolated tribe. Which will make a difference.
Firstly, I highly appreciate your kind responses and patience. I think that you are exactly around my question!! I'm asking about genotypic information -to be used in proper SNPs selection- of relatively homogeneous populations like middle east populations (e.g. Arab, Turkish, Kurdish or Iranian population). As you know, these populations are not yet listed in HapMap population drop down list!! So, for example if you want to work on association of SNPs with a disease in (ARAB) population, then which of the listed populations will you choose?? (Most related to Arab population).
Great thanks.