Entering edit mode
2.9 years ago
nhaus
▴
300
I am currently reading up about Genotype Arrays and the different nomenclatures that are used to report genotypes. In that context, it is important if the SNP is ambiguous or not (https://emea.support.illumina.com/bulletins/2016/06/simple-guidelines-for-identifying-topbottom-topbot-strand-and-ab-allele.html).
However, I could not find anywhere why a A/T or C/G SNP is considered ambiguous. I did not quite get the explanation here
I would be very grateful if somebody could explain to me why a A/T or C/G SNP is considered ambiguous.
Cheers!
Thanks for you reply. In the answer that I linked in my original question, you say that A is the minor allele is ambiguous if we do not add any strand information (i.e. A on the + strand/ forward strand). That I understand.
What I do not understand is how a A/T SNP differs in that regard from a A/C SNP (which is considered to be non ambiguous). Isn't the situation the same?
Because A and T are complementary, A and C are not. So if you have A/T on the forward strand, that's the same as T/A on the reverse. If someone makes a statement about A without specifying the strand or which is the reference etc, it could be either allele. If you have A/C on the forward strand, that's T/G on the reverse, so if someone says something about G, you know they're referring to the non-reference allele on the reverse strand.