Question: When can we call a CNV as Novel CNV?
1
gravatar for hebbar.prashanth
6.6 years ago by
Kuwait
hebbar.prashanth10 wrote:

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

cnv • 1.7k views
ADD COMMENTlink modified 14 months ago by sevcanatay10 • written 6.6 years ago by hebbar.prashanth10
1

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.

ADD REPLYlink written 6.6 years ago by karl.stamm3.9k
1
gravatar for Devon Ryan
6.6 years ago by
Devon Ryan98k
Freiburg, Germany
Devon Ryan98k wrote:

If you can't find any other mention of this CNV anywhere then it's novel, by definition.

ADD COMMENTlink written 6.6 years ago by Devon Ryan98k

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

ADD REPLYlink written 14 months ago by German.M.Demidov1.9k
1
gravatar for sevcanatay
14 months ago by
sevcanatay10
sevcanatay10 wrote:

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

ADD COMMENTlink written 14 months ago by sevcanatay10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1407 users visited in the last hour
_