SNP array - Affy data analysis

Question

[David_emir]

Hi All,

I have got .dat and .cell from Affymetrix 2.0 platform. It's a Custom Array-based genotyping experiment, it is designed to perform deep replication to establish disease signals and fine mapping of GWAS loci. Now my Question is how to perform an analysis so that the highly frequent genes and their respective SNPs related to a Disease can be found. It would be really helpful if you can share the analysis steps/pipeline involved or any other tutorials in this respect.

Thanks a lot for your kind help,

Regards, dave

P.S: I have around 2000 samples (Disease and normal)

Answer 1

[Kevin Blighe]

Human Mapping 10K 2.0? - that is an old platform. The easiest way (point and click) is the Genotyping Console.

In R, you can use Aroma.

Kevin

[David_emir]

Thanks a lot Kevin, Its of great help me me, also is it possible to come up with other genes that has secondary association to a perticular disease and also how to identify the most frequent genes associated with a disease at a very early stage with this GWAS? Thanks again for your kind help. Sincerely, Dave

[Kevin Blighe]

Just to clarify, what is 'secondary association' in your mind?

[David_emir]

Thanks a lot for your kind reply! it means a lot. Here Secondary association means - genes that have the secondary association to Myocardial Infraction associated genes or in Myocardial Infraction development.

[Kevin Blighe]

I do not know the background to your study. MI (myocardial infarction) is one of the most well-studied ailments in humans. OMIM stores known susceptibility genes:

• MYOCARDIAL INFARCTION, SUSCEPTIBILITY TO
• MYOCARDIAL INFARCTION, SUSCEPTIBILITY TO, 2