Ambiguous SNPs
1
0
Entering edit mode
7 weeks ago
nhaus ▴ 60

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!

SNPs • 273 views
ADD COMMENT
1
Entering edit mode
7 weeks ago

What did you not understand about the other answer?

ADD COMMENT
0
Entering edit mode

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?

ADD REPLY
1
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 1727 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6