Related Experiment Video
Updated: Jan 18, 2026

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies
Published on: April 11, 2016
Landscape of BRAF transcript variants in human cancer
Maurizio S Podda1,2,3,4, Danilo Tatoni3,4, Gianluca Mattei5
1Institute of Clinical Physiology (IFC), CNR, Pisa, Italy.
None:
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 as a cancer subtype in which a high BRAF-204/BRAF-220 ratio is an independent prognostic factor of poor outcome. Our in silico analyses establish BRAF as a mix of two protein-coding transcript variants, with BRAF-204 being more highly expressed than BRAF-220. These findings prompt us to undertake the systematic benchmarking of BRAF-204 against BRAF-220 in terms of molecular mechanisms, biological activities, druggability, and clinical relevance.
More Related Videos
07:49Characterize Disease-related Mutants of RAF Family Kinases by Using a Set of Practical and Feasible Methods
Published on: July 17, 2019
10:16Employing Digital Droplet PCR to Detect BRAF V600E Mutations in Formalin-fixed Paraffin-embedded Reference Standard Cell Lines
Published on: October 8, 2015
Related Concept Videos
The Ras Gene
Ras is a...
The Retinoblastoma Gene
The first-ever tumor suppressor gene called Rb was identified in retinoblastoma - a rare eye tumor in children. In inherited forms of the disease, a child inherits one defective copy of the Rb gene, which predisposes them to retinoblastoma. However,...
Cancer-Critical Genes II: Tumor Suppressor Genes
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
Such genes that act...
Non-LTR Retrotransposons
Cancer-Critical Genes I: Proto-oncogenes
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
Such genes that act...
RNA Splicing