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This may not be the correct place for such a question, but I see people are posting regarding CNV so I may get some help.
I believe that particular alleles of a gene I am studying may display CNV. Simply, this is related to consistent variances in depth acquired per allele between genotypes (as well as other lines of evidence).
However, it was commented that if a particular allele was duplicated multiple times, we would expect to see them in the form of closely related haplotypes which have slightly diverged. This is assuming the duplications are ancient. If this was always the case then I can see that identifying paralogs would be easy. However, multiple recent studies have identified CNV based on total sequencing depth of a sequence/region of the genome. I am assuming then that all of the paralogs are identical, as a result of recent duplication or strong concerted evolution?
So can someone with experience please tell me if you expect/identify duplicated alleles which are identical?
(note that I am only looking at a 200bp amplicon of the functional region of a coding sequence, maybe paraloges may appear identical where polymorphisms exists outside of the amplicon?)
I believe that particular alleles of a gene I am studying may display CNV. Simply, this is related to consistent variances in depth acquired per allele between genotypes (as well as other lines of evidence).
However, it was commented that if a particular allele was duplicated multiple times, we would expect to see them in the form of closely related haplotypes which have slightly diverged. This is assuming the duplications are ancient. If this was always the case then I can see that identifying paralogs would be easy. However, multiple recent studies have identified CNV based on total sequencing depth of a sequence/region of the genome. I am assuming then that all of the paralogs are identical, as a result of recent duplication or strong concerted evolution?
So can someone with experience please tell me if you expect/identify duplicated alleles which are identical?
(note that I am only looking at a 200bp amplicon of the functional region of a coding sequence, maybe paraloges may appear identical where polymorphisms exists outside of the amplicon?)