Cnv Analysis Related Inquiry

Question

[Abdo]

Dear Sir/Madam

I have sent some samples the AGRF to be analysed by Human omni 2.5 .. However, I need to assess the CNV by using CNV partition plugins with genomestudio and I have some inquiry regarding the CNV detection parameter. Actually , I have designed my experiment to detect the genomic difference between the sample from patient diagnosed with cancer and his sequential samples after treatment .My concerns that I don’t have normal control sample from the patient and Its required that I get alteration related to the disease progression. In addition , I don’t have background in bioinformatics that enable me to get accurate analysis for my samples. I got some information from the genome studio manual that I have to create project , assess my data by CNV analysis function and visualize my data on Illumina genome viewer(IGV )and to exclude the normal CNV available in the CNV database. So , I need to get your advice about the CNV algorithm threshold and could you please help me to understand the important things that I have to consider when analyse my data.

Regards,

abdo PhD Student

[Sean Davis]

I suggest you find a bioinformatics collaborator.

Answer 1

[Vikas Bansal]

For CNV analysis, there are some algorithms and tools available.

Here are some questions in my profile which I discussed here. There are some normalization steps needs to be carried out (GC content and segment duplication regions in genome).

Some of the tools I know are readdepth (R package by Miller et. al.), ExomeCNV, CNVnator, exomeCopy, Varscan, CNAseg, CNV-seq etc.

You can also have look at this question.

Also I will recommend these papers -> Yoon et. al, Nord et. al., Alkan et. al..

Can you tell me little bit more about your data, so that I can suggest something more if aforementioned will not be helpful for your data.