CNV/LOH from RNAseq

Question

[j.f.gutierrez-marcos]

Could I use RNAseq data from healthy and tumour samples to determine chromosome abnormalities?

[Bogdan]

You could use RNA-seq to detect the outliers in gene expression : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4454687/

Regarding the molecular mechanisms that lead to "outlier" gene expression, these could be multiple : either a CNV (AMP) or a SV that bring a super-enhancer near that gene, that determines "super" high gene expression.

Answer 1

[igor]

I actually had a similar question earlier that may give you some ideas: CNV detection from RNA-seq data