Does CNV-Seq run with DNA-seq or RNA-seq?

[louis7781x]

Hi,

Does anyone has experience to use CNV-seq to detect copy number variation?

I want to know that CNV-Seq run with DNA-seq or RNA-seq?

Because I have RNA-seq of tumor paired-end from illumina ,can I use it to run CNV-seq?

Thanks!!

[arcolombo698]

the manual says both. read their paper it is on page 1

[dpryan]

If a CNV affects an entire gene then you will never be able to detect it with RNAseq. Further, even if it affects only a part of a gene your ability to detect it in tumor-normal pairs is near zero. Their paper says nothing about using RNA for CNV detection (in fact, the word "RNA" only appears once in the paper and only in the context of mentioning other uses of high-throughput sequencing).

[arcolombo698]

I stand corrected. thank you.

RNAseq uses cDNA, not quite the same as DNA from Whole Genome.

Basically there are two types of data used for CNV analysis WGS (whole genome DNA sequencing) and WES (whole exome sequencing data)

CNV-seq uses WGS that uses Read Depth basis which uses statistical models estimating window lengths. This is in contrast to model based algorithms which use Hidden Markov models, Mean Shift Based models...or paired end mapping to calculate CNVs/SNVs.

so the answer is : WGS or WES is used. not RNAseq. thank you