Figure 1.

(A) BRAF mutations identified in tumor sequences. BRAF protein is represented here with annotated domains and amino acids (0–766) numbered underneath. Plots were generated (https://github.com/pbnjay/lollipops) with recurrent BRAF mutations (red, missense; green, indel; blue, nonsense) identified in COSMIC (Bamford et al. 2004), with larger dots (not to scale) indicating higher-frequency mutations. Most tumor-associated BRAF variants, including the well-characterized p.V600E and p.V600K and the less frequent p.T599dup variant we report, are within the protein kinase domain, specifically in the conserved glycine motif (G-loop) or in the activation segment (AS) in exon 11 and 15, respectively. (B) Integrated Genomics Viewer (IGV) display of the c.1794_1796dupTAC. Analysis of the tumor DNA revealed a variant allele frequency of ∼8.3% (variant allele present in 5/60 reads). (C) Sanger sequencing of BRAF exon 15 in germline (peripheral blood) and tumor. The arrows indicate the TAC duplication, observed at low frequency, only in the tumor sample. The low peaks seen after the duplication correspond to the offset bases, because of the 3-bp duplication. (D) Schematic representation of Thr599 duplication. The specific TAC duplication is an in-frame variant, which duplicates the threonine residue at amino acid 599.