Convert (Copy Number Variation) CNV to gene
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3.4 years ago
Saeed • 0

I'm newbie in biology. I have a lot of information about copy number variation for blood cancer and I want convert CNVs to gene? How can i do that?

gene genome copy number variation cnv • 1.3k views
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What do you know of CNVs? CNVs are not comparable to genes, because CNV is a type of mutation and thereby a structural abnormality in DNA and a gene is a functional unit of DNA.

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I agree with the comment above; i.e. we need to know what exactly you mean. Is what you want to say "how can I map the location of each CNV to one or more genes, provided they overlap?"

Second, I would like to ask what kind of data you have (e.g. whole genome sequencing / microarray / multiple / other)?

If you already have the CNVs called and you are confident they are correctly called, then this matters less (but is still good to keep in mind), and it is a pretty simple matter to overlapping them with gene positions.

If your question is "how can I convert raw read counts from WGS to copy number variants in specific genes" that's a lot more complicated...

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Let me jump in and point you to this discussion. If you have confident CNV calls then you can use bedtools to get genes overlapping with CNV segments. Let's say I am fairly confident about the CNV calls. However, I am not sure if mere overlap of genes with CNV segments is enough to assign genes to (Amp/Del) status and visualize this through tools like maftools. Please let me know your opinion about this.

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