Copy Number Variation Map and Analysis

Question

[caspase8mach]

Hi all,

I am new to this community and hope to get a good solution to my query.

1) How can one generate Copy Number Variation (CNV) map from online data, for example say for TCGA data, etc?

2) Once such a map is generated, can one use it to predict disease associated with a particular CNV?

I have some basic understanding of R and hence would be able to use it if the solution requires understanding of R.

Thanks a lot, Akhil

[WouterDeCoster]

What exactly do you mean by a CNV "map"? Perhaps I'm not sufficiently aware of terminology, but I'm not sure what you aim for.

[caspase8mach]

I have chromosome co-ordinates for amplifications and deletions. I would like to plot these in the form of a heat-map.

For example:

Donor Chromosome Chromosome_Start Chromosome_End Mean 0001 1 100000 120000 2 0001 2 500000 620000 -2 0001 3 20000 100000 -0.73 0002 2 100000 120000 0.23 0002 3 500000 620000 5 0002 6 20000 100000 -3.73 0003 5 100000 120000 2.4 0003 7 500000 620000 -4 0003 X 20000 100000 2.73

Answer 1

[natasha.sernova]

There are some papers, some maybe helpful:

A copy number variation map of the human genome

http://www.nature.com.sci-hub.cc/nrg/journal/v16/n3/abs/nrg3871.html

Software description:

CONAN: copy number variation analysis software for genome-wide association studies

http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-318

Genome-Wide Mapping of Copy Number Variation in Humans: Comparative Analysis of High Resolution Array Platforms

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0027859

Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-S11-S1