Over the past dozen years I have had several SNP studies conducted on my family. I am having a difficult time understanding how to compare my data to published studies about particular SNPs and their impact on risks for specific health issues. My peeves:
1. Different labs report results based on differing assumptions as to what the ancestral nucleotide is. Is there a central authority that declares for the purpose of standardization what the ancestral nucleotide is for each SNP? Genetics labs need to report only against a centralized standard.
2. The second problem is most disconcerting: I read a paper that says they observed G/A and they declare the ancestral allele as G and the frequency. When I look at my actual results I see the lab reports the choices are C/T and we have TT's in our actual results. I look at the dbSNP and I see reports of both G/A and C/T. WTF? What am I missing? Is this another case of labs picking one set of results versus what researchers choose to reference? What am I missing?