Fig. 3: Splicing profiling can detect mis-splicing in individuals carrying germline likely pathogenic/pathogenic variants. | npj Precision Oncology

Fig. 3: Splicing profiling can detect mis-splicing in individuals carrying germline likely pathogenic/pathogenic variants.

From: Splicing profile by capture RNA-seq identifies pathogenic germline variants in tumor suppressor genes

Fig. 3

a Plot comparing PSI of alternative splicing event associated with the given pathogenic (red) or variant likely pathogenic (VLP; blue) germline DNA variant obtained from proband against median PSI and interquartile range for that splicing event in controls, excluding samples in which the splicing event was not detected (black boxplot; outlier points are not shown). If the event was not found in controls, only the proband PSI was plotted. All PSI values were significantly higher than the mean control PSI (one-sample two-sided t test, p < 1 × 10−55). For CDH1 r.1055_1137del, the PSI values of 20 and 27 were observed in individuals with the pathogenic variant c.1137 + 1delG and the PSI value of 33 was observed in an individual with the VLP c.1057G > A. b–g Sashimi plot indicating reads supporting alternative splicing obtained via CloneSeq for HBOC (b, c), HNPCC (d, e), and HDGC (hereditary diffuse gastric cancer)/FAP (f, g) variants. b Partial skipping of CDS6 in PALB2. c Partial skipping of CDS2 in ATM. d Full skipping of CDS18 in MLH1. e Partial retention of intron 7 in MSH2. f Full skipping of CDS2 in APC. g Partial skipping of CDS16 in CDH1.

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