An optimized workflow to improve reliability of detection of KIAA1549:BRAF fusions from RNA sequencing data

摘要

Total read count of 22 fresh-frozen pediatric PA tumor samples sequenced by RNA-Seq. The five samples in which the fusion was missed were re-sequenced, increasing their total read number and allowing detection of the fusion in one additional sample (although still in the ‘discarded’ list). Mean ± SD. Relative frequency of reported, discarded and missed fusions in the initial RNA-Seq data and after re-sequencing. Chi-square test on the underlying absolute values. Immune score calculated by ESTIMATE as an indicator of immune cell content in samples with a missed or detected fusion. Mean ± SD. Unpaired test. Expression of in samples with a missed or detected fusion as well as expression of the upstream fusion partner in alternative fusion variants (see main text). Mean ± SD. One-way ANOVA followed by Tukey multiple comparisons test. Relative frequency of reported, discarded and missed fusions after workflow optimization. Relative frequency of reported and missed fusions in an independent diagnostic cohort in comparison to FusionCatcher and STAR-Fusion as the previous standard analysis tools. Fisher's exact test on the underlying absolute values. For all panels: *  p p p