identify disease related variants with RNA-seq

Question

[wenhui]

Hi,

Is it possible to detemine disease related variants with RNA-seq data only?

I have identify variants with RNA-seq data of disease and normal samples using GATK best pratice. What could I do to narrow down the list of variants and determine those highly related to disease?

Any advice would be appreciated.

Answer 1

[Brice Sarver]

There are a number of third-party databases that provide information on the clinical impact of various types of short and gross germline mutations. Consider starting with HGMD, ClinVar, and/or OMIM. Information can be accessed via API or, in some cases, as databases, delimited files, or VCFs.

If you are specifically interested in somatic mutations, COSMIC or TCGA are good starting points. Be aware that somatic variant classification procedures are less characterized than those recommended for germline variant classification, especially in the clinical space. There are a number of factors to consider, e.g., tumor heterogeneity, mutational burden, algorithm performance, driver vs. passenger, etc.