Clinker: visualizing fusion genes detected in RNA-seq data

Abstract

BackgroundGenomic profiling efforts have revealed a rich diversity of oncogenic fusion genes. While there are many methods for identifying fusion genes from RNA-sequencing (RNA-seq) data, visualizing these transcripts and their supporting reads remains challenging.FindingsClinker is a bioinformatics tool written in Python, R, and Bpipe that leverages the superTranscript method to visualize fusion genes. We demonstrate the use of Clinker to obtain interpretable visualizations of the RNA-seq data that lead to fusion calls. In addition, we use Clinker to explore multiple fusion transcripts with novel breakpoints within the P2RY8-CRLF2 fusion gene in B-cell acute lymphoblastic leukemia.ConclusionsClinker is freely available software that allows visualization of fusion genes and the RNA-seq data used in their discovery.

Targeted therapy and disease monitoring in CNTRL‐FGFR1‐driven leukaemia

“…In both instances, the precise identity of the FGFR1 fusion was definitively established using RNA‐Seq. The full details of the RNA‐Seq protocol and bioinformatics analyses are provided in Supporting Information “Methods.” We identified fusion transcripts with the JAFFA pipeline in direct mode, and Clinker, a fusion visualisation program (Figure , Figure S1). The malignant cells from Patient 1 expressed two CNTRL‐FGFR1 isoforms, distinguished by alternative splicing of exon 40 of CNTRL (Figure , Figure S2).…”

Integration of whole-exome and anchored PCR-based next generation sequencing significantly increases detection of actionable alterations in precision oncology

“…AGFusion was used to annotate and visualize the protein domain architecture [25] . We used Clinker software to visualize selected fusions and its supporting reads, and circos plot for showing the detected fusions [26 , 27] .…”

FUNGI: FUsioN Gene Integration toolset

“…FusionVisualizer’s breakpoint-mode, recreating the exact fusion and mapping against it, provides useful information for manual inspection of the fusion and helps determine if it is an artifact or not. The main purpose of FusionVisualizer is to aid in rapid inspection of fusions in genome browsers and supervised fusion calling, but it is not intended to replace more sophisticated visualization tools such as Clinker ( Schmidt et al, 2018 ) and INTEGRATE-Vis ( Zhang et al, 2017 ).…”