Landscape of BRAF transcript variants in human cancer.

ABSTRACT: The BRAFV600E mutant kinase is widely studied as a cancer driver and therapeutic target. Here, we investigated how the annotation of the BRAF-reference (ref) and BRAF-X1 variants has evolved in public databases and addressed challenges posed by their discrimination and quantification from short-read sequencing. We built IsoWorm, a bioinformatic pipeline tailored to discriminate and quantify BRAF variants, and employed it to analyze > 600 cancer cell lines and > 1000 cancer tissue samples. Using FLIBase, we reanalyzed TCGA data from > 9000 cancer tissue samples. We consistently found that BRAF-X1 (now BRAF-204) is very abundant in human cancer and its expression is 1.5-75 times greater than that of BRAF-ref (now BRAF-220). Crucially, we identified KIRP-kidney renal papillary cell carcinoma

SUBMITTER: Podda MS 

PROVIDER: S-EPMC12420348 | biostudies-literature | 2025 Sep

REPOSITORIES: biostudies-literature