Fig. 1: Overview of the salivary gland basal cell adenoma (BCA) and basal cell adenocarcinoma (BCAC) cohorts.

BCA and BCAC cases are shown to the left and right of the dashed line, respectively. Genes shown in the oncoplot are genes known to be mutated in salivary gland tumours and/or are COSMIC Cancer Gene Census (CGC) genes and mutated in at least 1 BCA or BCAC. Also shown is FBXW11, which is not a CGC gene, but shown in this study to be significantly mutated in BCA. Genes that were mutated exclusively in the dMMR case, PD56546c, are not shown. Genes in the Wnt/β-catenin, NF-κB, PI3K/AKT or HRAS pathways are grouped by colour. PD56541a is a carcinoma of salivary gland type in the lung, with unknown origin. TMB is the tumour mutation burden in mutations per megabase (Mb). Genes are grouped by pathway. TMB was calculated using mutations found in coding exons and 2 bp upstream and downstream of exon boundaries to account for splice site mutations. Fusion genes in red text are those found in the Trinity Cancer Transcriptome Analysis Toolkit human fusion library (see “Methods”). Samples marked as “Discovery set only” did not pass strict criteria for transcriptome sequencing quality control (see “Methods”) and may have a higher false discovery rate as a result. The copy number panel indicates the tumours that had copy number loss of chromosome arms 5q and/or 16q, which was significant in the BCAC cohort. IHC indicates samples that were positive or negative for nuclear β-catenin immunohistochemical staining. BCAC/EMC is differential diagnosis of salivary gland basal cell adenocarcinoma and epithelial-myoepithelial carcinoma. Source data are provided as a Source Data file.