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Problem Of Missing Data Of Duplications In Deletion Regions?

Hello.

I have a question and perhaps one of you can help me. I wonder about the generegion around the UGT2B17 gene. It's pretty well known that there are het. and homozygous deletion in all populations around the world. (You can take a look on the region in DGV: UGT2B17). The deletion results from non allelic homologous recombination between two repeats within the segmental duplications. Actually genome wide CNV studies found a loss of sequence in this region (red bars) but they found also duplications. (blue bars). But duplications are so far not described and found in population.

Therefore the question: Have array- (SNP, Oligo) and sequencing-CNV-detection-methods problems in this area? UGT2B15 a gene with high similar sequence identity (94%) is located in the near neighbourhood. So the gain of sequence is a false positive? Perhaps you have an answer? Thanks

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updated by Alex Paciorkowski Alex Paciorkowski • written by romsen • romsen

1 answer

Are you worried that the presence of another gene (UGT2B15) with high sequence homology to UGT2B17 will show up as a dup on array CGH? I think that is your question. First of all, your DGV link takes me somewhere on 7q11.23, not 4q13.2 where UGT2B17 and UGT2B15 are located. If you look at this region in either UCSC or DGV, there are multiple reports of duplications (for example DGV ref # 31177 in 21/30 or so control individuals), so I don't understand what you mean by "duplications are so far not described and found in population". It seems like this region is a good one for NAHR, there are seg dups, and it's actually not all that uncommon to find adjacent genes with high sequence homology in these kinds of regions in the human genome.

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written by Alex Paciorkowski Alex Paciorkowski

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