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
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written
by
caspase8mach •
1 answer
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
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Tool: Anntools - Annotation Toolkit For Snps, Insertions/Deletions, And Copy Number Variations
written by Malachi Griffith
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.
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