Target enrichment and CNV analysis

[gendxdoc]

Is it possible to derive exon-size deletion/duplication information from target-enriched (array or in-solution), paired-end sequencing data ?

I'm working with a set of genes that frequently undergo partial and whole gene deletion duplications and would be grateful if I could derive this information from the sequencing data without having to also perform high-density CGH of each of the genes.

Is anyone working on a strategy for this ?

Thanks much !

[krobison]

How much do you know about the flanking sequences? Add those to the target set & it should be doable if you can recognize the junction sequences from a deleted exon/gene.

One paper showed finding rearrangements this way.