Question: CNV analysis for targeted genomic region
0
gravatar for Sandeep
3.0 years ago by
Sandeep250
Manipal, India
Sandeep250 wrote:

I am currently trying to analyse the presence of CNVs in a targeted sequencing dataset generated from Ion Torrent platform. The data description is as follows.

  • Targeted region is a segment of the genome that spans multiple genes (not limited to exons).
  • Single end reads of variable length.
  • Reads are mapped to the hg19 assembly.
  • The sample are not paired. We have a set of test and control samples.

So far, I have tried analysis using various tools such as CNVkit, CNVSeq, freec, codex. None of them seem to work well with the kind of data that I have in hand.

Can anyone suggest an analysis strategy that I could try with such data?

Thanks.

cnv tools • 1.4k views
ADD COMMENTlink modified 15 months ago by cc10 • written 3.0 years ago by Sandeep250

Also, I would like to know if I am better off using the whole genome approach of analysis by mapping the reads to the segment of the genome in question?

ADD REPLYlink written 3.0 years ago by Sandeep250

You could try to calculate the coverage per gene/exon/target, median normalize over all/within sets, build a reference sample supposed to be copy number of two, calculate the ratio between target and reference sample and perform a cluster analysis for CNV detection per gene/exon/target. This is similar to the tools freely available but I obtain more reliable results using a individualized pipeline for targted NGS results.

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by Jimbou670

Thanks for the suggestion. Can you suggest tools that we could use to perform the above steps?

ADD REPLYlink written 3.0 years ago by Sandeep250
1

I recommend R for this. Additional helpful packages are cn.mops, Gviz or Exomecopy and some more. You can find a comprehensive list in this nice paper: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-S11-S1

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by Jimbou670
1
gravatar for Eric T.
3.0 years ago by
Eric T.2.4k
San Francisco, CA
Eric T.2.4k wrote:

Are your using targeted amplicon capture? If so, there is a program designed specifically for this type of data called OncoCNV: https://oncocnv.curie.fr/

ADD COMMENTlink written 3.0 years ago by Eric T.2.4k

Yes, I have used that already and seems like that is working fine for our kind of data.

ADD REPLYlink written 3.0 years ago by Sandeep250
0
gravatar for cc
15 months ago by
cc10
China/Beijing
cc10 wrote:

Hi,

I just met the same question as you. I got targeted sequencing data (~8M, a continous segment in chr22) for 20 cases and 2 controls, and wanted to detect CNV. I wanna try the oncocnv, but don't have a idea about how and where to get the bed file for amplicon coordinates. How do you prepare the amplicon file?

I also plan to try different softs for detecting CNV, however, no much softs were found to be designed for target sequencing data. What else appropriate software have you tried?

Thanks a lot.

ADD COMMENTlink written 15 months ago by cc10
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