Fig. 2: Using RNA-seq results to verify and prioritize DNA variants.
From: Augmenting precision medicine via targeted RNA-Seq detection of expressed mutations
a The numbers of different types of calls reported by various panels without controlling the FPR. The “true set” was established in our previous study using the same reference samples. Variants not included in the “true set” were categorized as uncharacterized calls. The blue line represents verified true variants that are targeted and sequenced by the specific panels (AGLR or ROCR), meaning they fall within the regions targeted by the probes in the panels. b Comparison of expression levels between two groups of known positive variants: those detected and those missed by targeted RNA-seq across different panels. The number of reads (Y axis) was set to zero if a call was absent in the expression results. A Wilcoxon Rank Sum Test was applied, resulting in a significant p-value of 2.2e-16 for all panels. c Known positive variants missed by targeted RNA-seq data. Not-expressed: not detectably expressed. For example, it may be fairly expressed but the bait performance is poor. Low-VAF: calls were expressed but had a VAF < 2%, Low-DP: expressed calls with VAF ≥ 2% but had a DP < 20, Low-ADP: expressed calls with VAF ≥ 2% and DP ≥ 20, but ADP < 2 (=1). d Comparison of average recall values across panels, considering conditions with non-stringent cutoff versus where the FPR was reduced to 50 per million bases.
