A dedicated caller for DUX4 rearrangements from whole-genome sequencing data

A dedicated caller for DUX4 rearrangements from whole-genome sequencing data

Abstract Rearrangements involving the DUX4 gene (DUX4-r) define a subtype of paediatric and adult acute lymphoblastic leukaemia (ALL) with a favourable outcome. Currently, there is no ‘standard of care’ diagnostic method for their confident identification. Here, we present an open-source software to...

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Main Authors: Pascal Grobecker, Stefano Berri, John F. Peden, Kai-Jie Chow, Claire Fielding, Ivana Armogida, Helen Northen, David J. McBride, Peter J. Campbell, Jennifer Becq, Sarra L. Ryan, David R. Bentley, Christine J. Harrison, Anthony V. Moorman, Mark T. Ross, Martina Mijuskovic
Format: Article
Language:English
Published: BMC 2025-01-01
Series:BMC Medical Genomics
Subjects:
DUX4
Acute lymphoblastic leukaemia
ALL
Whole-genome sequencing
IGH:DUX4
IGH enhancer hijacking
Online Access:https://doi.org/10.1186/s12920-024-02069-1
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Summary:Abstract Rearrangements involving the DUX4 gene (DUX4-r) define a subtype of paediatric and adult acute lymphoblastic leukaemia (ALL) with a favourable outcome. Currently, there is no ‘standard of care’ diagnostic method for their confident identification. Here, we present an open-source software tool designed to detect DUX4-r from short-read, whole-genome sequencing (WGS) data. Evaluation on a cohort of 210 paediatric ALL cases showed that our method detects all known, as well as previously unidentified, cases of IGH::DUX4 and rearrangements with other partner genes. These findings demonstrate the possibility of robustly detecting DUX4-r using WGS in the routine clinical setting.
ISSN:1755-8794

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