Hello,

after analyzing exomes with AnnotSV I have some interesting duplications and deletions to validate. I only now how to validate deletions with qPCR and Sybr Green; However this is not the best approach for duplications. These duplicated/deleted genes also are not in ready MRC Holland MLPA probe sets. 

Which method is best for validating duplications and deletions of some exons in genes?

 

 

Thank you!

Could you not just design some primers for your specific genes, do PCR amplification and check on an agarose gel if the sizes are larger/smaller than expected? 

I am not entirely sure if that is the most feasible method, but at least I would assume you could see deletions, and duplications if they happened in the same region (of course if a duplication happened to be present in another chromosomal region, I would expect these to not be visible as the primers wouldn't lead to PCR amplification of 1 long transcript but just 2 equal sized ones, which I suppose you won't detect.

Otherwise, can't you design some MLPA probes? I am not very familiar with qPCR MLPA validation, but if qPCR and sybr Green are used in this manner for duplication and deletion validation (even if it isn't the best way), then might just design the qPCR MLPA probe sets (I am not sure if that is feasible). 

I think you might find some information in: https://bmcmedgenet.biomedcentral.com/articles/10.1186/1471-2350-13-55 

Maybe someone with more knowledge of this particular subject can come along and give you some more useful answers, but I think with that paper and other papers you should find some way ("I searched for deletion and duplication validation of novel genes").

-Dagl