Run of homozigosity on multiple imputed chips

Question

[giovanni.birolo]

Dear all, we are doing a study on the possible association between ROH and disease. We have SNP-chip data from three different chips, which have been imputed with the Haplotype Reference Consortium data. We have not yet been able to distinguish which SNPs are imputed and which ones are from the original chip. So it would be easier to just compute ROH (using plink) on the imputed data. From my understanding of imputation, this should produce more or less the same result as ROH from the original chip data, since ROH in the original chip will be ROH also after imputation, regardless of imputation accurancy.

Can we reasonalby compute ROH from the imputed data or should we try harder to reconstruct the original data?

Thanks!

Answer 1

[Kevin Blighe]

Just continue with the imputed data - no problem. When you aim to publish, your reviewers will have further comments (or, possibly, not) with regards to this.

Kevin