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Updated: Jul 15, 2025
Rare Event Detection Using Error-corrected DNA and RNA Sequencing
Published on: August 3, 2018
Toblerone: detecting exon deletion events in cancer using RNA-seq
Andrew Lonsdale1,2,3, Andreas Halman1,3, Lauren Brown2,4,5
1Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, 3010, Australia.
Abstract:
Cancer is driven by mutations of the genome that can result in the activation of oncogenes or repression of tumour suppressor genes. In acute lymphoblastic leukemia (ALL) focal deletions in IKAROS family zinc finger 1 (IKZF1) result in the loss of zinc-finger DNA-binding domains and a dominant negative isoform that is associated with higher rates of relapse and poorer patient outcomes. Clinically, the presence of IKZF1 deletions informs prognosis and treatment options. In this work we developed a method for detecting exon deletions in genes using RNA-seq with application to IKZF1. We developed a pipeline that first uses a custom transcriptome reference consisting of transcripts with exon deletions. Next, RNA-seq reads are mapped using a pseudoalignment algorithm to identify reads that uniquely support deletions. These are then evaluated for evidence of the deletion with respect to gene expression and other samples. We applied the algorithm, named Toblerone, to a cohort of 99 B-ALL paediatric samples including validated IKZF1 deletions. Furthermore, we developed a graphical desktop app for non-bioinformatics users that can quickly and easily identify and report deletions in IKZF1 from RNA-seq data with informative graphical outputs.
Insights
This study introduces Toblerone, a novel method using RNA-seq to detect gene exon deletions, specifically applied to IKZF1 deletions in acute lymphoblastic leukemia (ALL) for improved patient outcome prediction.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Cancer arises from genomic mutations, including oncogene activation and tumor suppressor gene repression.
- IKZF1 gene deletions in acute lymphoblastic leukemia (ALL) correlate with poor patient prognosis and increased relapse rates.
- Accurate detection of IKZF1 deletions is crucial for informing ALL treatment strategies.
Purpose of the Study:
- To develop and validate a method for detecting exon deletions in genes using RNA-sequencing (RNA-seq) data.
- To apply this method to identify IKZF1 deletions in pediatric B-ALL samples.
- To create a user-friendly application for non-bioinformaticians to analyze RNA-seq data for IKZF1 deletions.
Main Methods:
- Developed a bioinformatics pipeline utilizing a custom transcriptome reference with known exon deletions.
- Employed a pseudoalignment algorithm to map RNA-seq reads and identify those supporting deletions.
- Integrated gene expression analysis and cohort-wide comparisons to validate deletion evidence.
Main Results:
- Successfully applied the Toblerone algorithm to a cohort of 99 pediatric B-ALL samples.
- Identified and validated IKZF1 deletions within the studied cohort.
- Developed a graphical desktop application for accessible deletion analysis.
Conclusions:
- The Toblerone method provides an effective means for detecting gene exon deletions from RNA-seq data.
- This approach, particularly for IKZF1 deletions in ALL, can aid in prognostic assessment and treatment decisions.
- The accompanying graphical application democratizes the analysis of RNA-seq data for clinical applications.
