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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| Format: | Article |
| Language: | English |
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BMC
2025-01-01
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| Series: | BMC Medical Genomics |
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| Online Access: | https://doi.org/10.1186/s12920-024-02069-1 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Pascal Grobecker |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-9da38a02dd0745d0957a1213590281fe |
| institution | Kabale University |
| issn | 1755-8794 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Medical Genomics |
| spelling | doaj-art-9da38a02dd0745d0957a1213590281fe2025-02-02T12:46:38ZengBMCBMC Medical Genomics1755-87942025-01-0118111110.1186/s12920-024-02069-1A dedicated caller for DUX4 rearrangements from whole-genome sequencing dataPascal Grobecker0Stefano Berri1John F. Peden2Kai-Jie Chow3Claire Fielding4Ivana Armogida5Helen Northen6David J. McBride7Peter J. Campbell8Jennifer Becq9Sarra L. Ryan10David R. Bentley11Christine J. Harrison12Anthony V. Moorman13Mark T. Ross14Martina Mijuskovic15Illumina Cambridge Ltd., Granta Park, Great AbingtonIllumina Cambridge Ltd., Granta Park, Great AbingtonGenpax LtdIllumina Cambridge Ltd., Granta Park, Great AbingtonIllumina Cambridge Ltd., Granta Park, Great AbingtonIllumina Cambridge Ltd., Granta Park, Great AbingtonIllumina Cambridge Ltd., Granta Park, Great AbingtonIllumina Cambridge Ltd., Granta Park, Great AbingtonIllumina Cambridge Ltd., Granta Park, Great AbingtonIllumina Cambridge Ltd., Granta Park, Great AbingtonLeukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University Centre for CancerIllumina Cambridge Ltd., Granta Park, Great AbingtonLeukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University Centre for CancerLeukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University Centre for CancerIllumina Cambridge Ltd., Granta Park, Great AbingtonIllumina Cambridge Ltd., Granta Park, Great AbingtonAbstract 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.https://doi.org/10.1186/s12920-024-02069-1DUX4Acute lymphoblastic leukaemiaALLWhole-genome sequencingIGH:DUX4IGH enhancer hijacking |
| spellingShingle | 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 A dedicated caller for DUX4 rearrangements from whole-genome sequencing data BMC Medical Genomics DUX4 Acute lymphoblastic leukaemia ALL Whole-genome sequencing IGH:DUX4 IGH enhancer hijacking |
| title | A dedicated caller for DUX4 rearrangements from whole-genome sequencing data |
| title_full | A dedicated caller for DUX4 rearrangements from whole-genome sequencing data |
| title_fullStr | A dedicated caller for DUX4 rearrangements from whole-genome sequencing data |
| title_full_unstemmed | A dedicated caller for DUX4 rearrangements from whole-genome sequencing data |
| title_short | A dedicated caller for DUX4 rearrangements from whole-genome sequencing data |
| title_sort | dedicated caller for dux4 rearrangements from whole genome sequencing data |
| topic | DUX4 Acute lymphoblastic leukaemia ALL Whole-genome sequencing IGH:DUX4 IGH enhancer hijacking |
| url | https://doi.org/10.1186/s12920-024-02069-1 |
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