Overlapping SNPs between two arrays and genotyping choice

Question

[mel22]

Hello, I have genotyping data from Illumina array (460000 SNP) . I will add data from another study but I have only one choice of array : Axium Precision medicine (ThermoFisher, 900000 SNP). The overlopping SNPs between the two arrays are less than 10 % of Illumina (about 40 000 SNPs). Imputing the missing SNPs will it be reliable for GWAS or it's better to use the same Array ?

Any advice is welcome !

Thank you

Answer 1

[Kevin Blighe]

Hey Melania,

You could try to impute the Illumina array using the Axiom Precision Medicine array as the reference panel, if you wished. A much longer solution would be to impute both against 1000 Genomes Phase III, separately, and then merge the 2 imputed datasets together. I have a rough / general pipeline that can help, in these regards: A: genotype imputation pipeline

You could, of course, just proceed with the 40000 that overlap.

Whatever you decide to do, be wary of strand alignment. For example, many of those 40000 that overlap may be genotyping opposite strands, and thus would have to be flipped. Also, if you choose to impute, it would help to have a pre-defined strand definition for each array.

Kevin

[mel22]

Thank you very much Kevin, very useful link ! Yes I think I will impute both of theme separately , I think it's the best solution.