Gene annotation.

Genes wholly or partially present within genomic intervals covered by CNVs to a specified depth within different subsets of tumours. Interval coordinates are presented, and “Depth” represents the cumulative coverage across the interval in CNV gains or losses (specified in “Type”). The CNV IDs of associated CNVs are shown (S3 Table). The “COSMIC” and “COSMIC summary” columns annotate genes within intervals that are included in the COSMIC Cancer Gene Census [61] (accessed 18 November 2019), as well as COSMIC annotation for these genes. (A) DFT1 biopsies (DFT1 cell lines excluded), genomic intervals covered by at least 3 gain CNVs or at least 3 loss CNVs. HMGA2 is not annotated in the reference genome Devil7.1, but its presence is inferred in interval 5:17100000–18299999 is based on alignment with other species’ genomes. (B) DFT1 cell lines, genomic intervals covered by at least 3 gain CNVs or at least 3 loss CNVs. (C) DFT2, genomic intervals covered by at least 2 gain CNVs or at least 2 loss CNVs. (D) Non-DFTD tumours, genomic intervals covered by at least 2 gain CNVs or at least 2 loss CNVs. (XLSX)