I have basic question on CNV that when can we call a CNV as novel one? I am working on arab population genetic data. I find a CNV in the region chr7:128470838-128508839 in arabs. In DGV I could see few CNVs in the same region of genome. However, the CNV that I have is different in terms of genomic coordinate/breakpoints (I mean start and end site of this CNV is different than what is there in DGV already). Now given this difference of genome coordinate and population, can we call this as novel CNV?
Thanking you in anticipation.
Regards,
Prashantha
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hebbar.prashanth •
If you can't find any other mention of this CNV anywhere then it's novel, by definition.
The only problem that I see is 1) uncertainty in coordinates (as described by karl.stamm in the comments), 2) I am afraid human genome is almost fully "covered" with CNVs (hopefully not in housekeeping genes but idk) - due to [presumably] low quality of submissions accepted to DGV
You can use CNVbase to decide, the database of human genomic copy number variation (CNV) and an online tool to identify novel CNV. Here is the link: http://database.gdg-fudan.org/DB_HTML/DataSub.html
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The breakpoints are often uncertain; most CNV have not been resolved to the single basepair level. When microarray is used to detect CNV, the segment is labeled as the nearest probes, which can be several kilobases distant. So when you see others in the same area, consider it the same, or investigate how it was discovered.