8.2 years ago by
Boston, MA USA
Question: Which human variation database has the best coverage of SNPs.
Tough to answer because what do you mean? If you're looking across the human genome, then mine dbSNP. If you're interested in something more specific, say variants in CYP (P450) genes or mitochondrial genome differences, then you're best served by specialised databases.
The SNPs in clinical setting question is really hard, in my mind, because this is evolving quite rapidly. Do you want the 200,000 or so SNPs that 23andMe, for example, adds to their chip because there is evidence for an association of some type? For those SNPs, is premature gray hair or detecting asparagus byproducts in urine really relevant? Do you want those SNPs that are in OMIM because they have been found in medical cases? Do you want those that are routinely tested for in terms of metabolic health of newborns or pre-pregnancy counseling? Or do you want to think about the loads of new variants found from sequencing cancer genomes, especially the SNPs that can "tag" a copy number variant? This is not a pool of SNPs, but an amorphous cloud - boundaries are not well defined.
I know this is not an answer, per se. I don't have one because I don't need such SNPs for my research. These are just some thoughts I'd pose to my colleagues before we tried to capture such information. Good luck!