Tri-allelic SNP genotype

Question

[win]

I have a microarray dataset and there are few tri allelic SNP data. I have a SNP for which three different probes show data genotype as AC, CC and TC.

I am not sure which genotype is the correct one that can be used.

Any help appreciated.

Answer 1

[JMR]

Because you are working on a microarray dataset you shouldn't expect to find tri-allelic SNPs. Most platform work only with biallelic SNPs, but you can check the SNP manually using the dbSNP website for example to be sure. Check the manual for your platform as well.

If I had to guess your problem could be due to a genotyping error or contamination.

[win]

But what if it is a custom array with probes for both of the triallelic SNP.

[JMR]

It will depend on your platform. That's why I said to check the manual for your platform.