Can SNP arrays distinguish 3 different alleles at a certain position? · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

Can SNP arrays distinguish 3 different alleles at a certain position?

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

• 2,398 views • link

updated 3.5 years ago by Ram

• written 11.3 years ago by Dejian

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

• 0 views • link

written 11.3 years ago by kumar.vinod81

1 answer

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 :)

• 0 views • link

updated 3.5 years ago by Ram

• written 11.3 years ago by John

Log in to answer this question.

More posts like this

Snp array intensity
written 6.7 years ago by German.M.Demidov

Dear all, I am validating CNV calls using micro arrays. For now I use only CNV probes, but using SNP probes will increase the resolution …
Normalization of allele specific counts in RNA-seq
written 7.0 years ago by Ankit

Hi everyone, I am performing an allele-specific RNA-seq analysis. Basically, I used SNP positions between two alleles of a mouse hybrid strain to separate reads …
Do we need to filter out control probes and low expressed probes (as given in LIMMA user guide 2016…
written 7.3 years ago by anandprem1792 •

I am analyzing a GEO dataset of platform (GPL17077) Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray. I followed the steps given in LIMMA user …
How to change ID of SNP in one file to adjust to the other file?
written 8.2 years ago by khn

Hello, I am merging two datasets from different platforms. The gene builds are the same for both datasets (h37, p13), but each chromosome has multiple …
how are alleles represented in the sequenced reads?
written 8.8 years ago by lait

Suppose the following: 1. there exists gene X on chromosome Y. The wild type allele is 'A' and the recessive allele is 'a' 2. Allele …
Difference of CN probes and SNP probes on genotyping microchip arrays
written 9.1 years ago by Jimbou

Is there a difference between copy number (CN) probes compared to SNP probes on SNP arrays such as the Affymetrix 6.0 SNP array? Physically there …
Do multiple double peaks surely indicate both alleles of my PCR product are sequenced? (Sanger)
written 9.9 years ago by michael.nagle

I sequenced PCR products with primers expected to amplify both alleles of a hybrid. I see double peaks and believe these indicate positions where there …
A simple question about Affymetrix SNP platform
written 10.2 years ago by Na Sed

In [this paper][1] , section "Affymetrix platform", the below paragraph has been written: *Affymetrix was the first to commercially produce SNP arrays, nearly a decade …
Different ancestral alleles for same snp ID coming from different batch ID, same build
written 10.6 years ago by Mr Locuace

Hello, I am new in the evolutionary genomics field. For getting ancestral alleles I have followed the instructions given here: http://www.ncbi.nlm.nih.gov/sites/books/NBK44409/ However, when looking into …
How To Find Major And Minor Alleles From Dbsnp ?
written 13.9 years ago by thecuriousbiologist

<p>I am new to SNPs and the dbSNP database. I am not quite sure if I understand how to find major and minor alleles for …