Figure 3: Analysis of loss of heterozygosity in rare truncation and missense variants.
From: Patterns and functional implications of rare germline variants across 12 cancer types
(a) Bar plot shows individual truncations from nine genes (FDR shown) with lengths representing ratios of tumour-to-normal variant allele fractions (that is, the fraction of reads containing the variant allele). Statistically significant events, defined as FDR≤5%, are shaded boldly, while non-significant events are muted, with colours corresponding to genes. Cancer source of each truncation is shown underneath, for example, most BRCA1 variants occur in ovarian and breast cancers and all BAP1 variants in KIRC. (b) Bar plot for individual missense variants from four genes having elevated frequencies of such variants that show very significant LOH, that is, at the 1% FDR level. (c) Dot plot shows individual missense variants where abscissa and ordinate are amino acid positions and the ratio of tumour-to-normal variant allele fraction, respectively. Blue and red indicate significant (FDR ≤5%) and non-significant events, respectively, with size of dots proportional to negative log of the FDR. Annotated domains from the PFAM database are aligned with position, while shaded areas indicate ‘hotspot’ regions where variants having significant LOH cluster more than the rate explainable by chance. Plots are shown for ATM, BRCA1, BRCA2, FANCA and FANCM.
