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Fig. 3 | Genome Biology

Fig. 3

From: Allele-specific expression reveals genes with recurrent cis-regulatory alterations in high-risk neuroblastoma

Fig. 3

Genes with recurrent allele-specific expression are enriched for stop-gain mutations that cause nonsense-mediated decay. A The number of variants annotated as high-impact by variant effect predictor (VEP) in genes with recurrent allele-specific expression in neuroblastoma (NB-ASE genes) grouped by functional consequence. B NB-ASE genes more frequently carry stop-gain mutations. To create the distributions, we performed 500 sampling iterations and counted the number of unique genes carrying stop-gain mutations each iteration. In each iteration, we sampled 100 genes from three gene sets: a random panel of control genes (random), genes with ASE in both neuroblastoma and normal tissues (normal-ASE), and genes with ASE that is specific to neuroblastoma (NB-ASE). C Overlap between genes with correlated ASE and somatic copy number alteration (SCNA) score and NB-ASE genes which contain at least one stop-gain mutation. D Graphical representation of three categories of neuroblastoma samples we define for a given gene: samples without ASE (non-ASE), samples with ASE and SCNA (ASE_SCNA), and samples with ASE but no SCNA (ASE_non-SCNA). E Samples with ASE in the absence of SCNAs are enriched for stop-gain mutations. The boxplots show the log2 ratio of observed to expected stop-gain mutation rate for the three sample categories. Expected rates are estimated by permuting category labels within each gene; points are observed/expected ratios computed across genes after each permutation. F Spearman’s correlation between ASE (aRNA) and SCNA score for PLEKHG5, a chromosome 1p deletion gene. Two samples have high ASE but low SCNA scores and one of these samples, PAPTCR, carries a premature stop mutation (1:6536019, C>A)

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