DOI: 10.1101/518316Jan 14, 2019Paper

ScaR - A tool for sensitive detection of known fusion transcripts: Establishing prevalence of fusions in testicular germ cell tumors

BioRxiv : the Preprint Server for Biology
Sen ZhaoRolf I Skotheim

Abstract

Bioinformatics tools for fusion transcript detection from RNA-sequencing data are in general developed for identification of novel fusions, which demands a high number of supporting reads and strict filters to avoid false discoveries. As our knowledge of bona-fide fusion genes becomes more saturated, there is a need to establish their prevalence with high sensitivity. We present ScaR, a tool that uses a scaffold realignment approach for sensitive fusion detection in RNA-seq data. ScaR detects a set of 50 synthetic fusion transcripts from simulated data at a higher sensitivity compared to established fusion finders. Applied to fusion transcripts potentially involved in testicular germ cell tumors (TGCTs), ScaR detects the fusions RCC1-ABHD12B and CLEC6A-CLEC4D in 9% and 28% of 150 TGCTs, respectively. The fusions were not detected in any of 198 normal testis tissues. Thus, we demonstrate high prevalence of RCC1-ABHD12B and CLEC6A-CLEC4D in TGCTs, and their cancer specific features. Further, we find that RCC1-ABHD12B and CLEC6A-CLEC4D are predominantly expressed in the seminoma and embryonal carcinoma histological subtypes of TGCTs, respectively. In conclusion, ScaR is useful for establishing the frequency of known fusion transcr...Continue Reading

Related Concepts

Malignant Neoplasms
Genes
Membrane Fusion
Neoplasms
Seminoma
Fusion protein
Embryonal Carcinoma
Subtype (Attribute)
Sequence Determinations, RNA
Bio-Informatics

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