Can SNP arrays distinguish 3 different alleles at a certain position?
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9.1 years ago
Dejian ★ 1.3k

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 • 1.8k views
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I think no, but with sequencing data you might have such situation in case of polyploidy.

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9.1 years ago
John 13k

Modern arrays, to my knowledge, have all four combinations per SNP on SNP chips.

https://youtu.be/RtzO7Uk2Ei4

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 :)

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