What can be done with a small set of case/control SNP arrays?

Question

[Adamc]

I'm just getting into working with SNP arrays after a while of working with gene expression data. We've got a small dataset (12 samples) of SNP arrays (Illumina Human Omni 5) which represent disease case and control. We don't have family data. Obviously 12 samples is much too small for a GWAS. I ran PennCNV already, but there has to be more I can look at with this- any suggestions? The data I have available is derived from Illumina "Final Report" files- Allele1-Top, Allele2-Top, and the B-allele frequency and Log R ratio.

Thanks!

[Adamc]

Also, as a secondary question- we don't currently have replicates. Do you usually run replicates (technical in this case) for SNP arrays?

[Adamc]

I know I posted this a little while ago, but it's something I'm still wondering about- has anyone worked with SNP array datasets where 1) you weren't sure what mutation you were looking for and 2) you had less than 15 samples?

Answer 1

[reza.jabal]

I assume this is what DTC genetics companies like 23&me do on a daily basis. I am not sure if it is relevant, but have a look at this:

https://livewello.com/genetics