Question: Can SNP arrays distinguish 3 different alleles at a certain position?
1
gravatar for Dejian
4.1 years ago by
Dejian1.3k
United States
Dejian1.3k wrote:

I notice that people usually use two allele-specific oligonucleotide probes (ASO) on SNP arrays to distinguish two alleles for a certain SNP position. I wonder if there is a SNP array platform that can distinguish more than two alleles for a certain position (in dbSNP, there are 3 alleles for some SNP positions). Thanks!

 
snp • 1.0k views
ADD COMMENTlink modified 4.1 years ago by John12k • written 4.1 years ago by Dejian1.3k

I think no, but with sequencing data you might have such situation in case of polyploidy.

ADD REPLYlink written 4.1 years ago by kumar.vinod81280
0
gravatar for John
4.1 years ago by
John12k
Germany
John12k wrote:

Modern arrays, to my knowledge, have all four combinations per SNP on SNP chips.
https://youtu.be/RtzO7Uk2Ei4?t=359

But they're kind of going out of fashion these days in favour of Seq.
Arguably the best chip on the market, Affy's 6.0 chip: http://www.affymetrix.com/estore/catalog/131533/AFFY/Genome-Wide+Human+SNP+Array+6.0#1_1
Your best bet is to fire them an e-mail and ask :)

ADD COMMENTlink written 4.1 years ago by John12k
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