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Whole-genome sequencing of chronic lymphocytic leukemia identifies subgroups with distinct biological and clinical features

Whole-genome sequencing of chronic lymphocytic leukemia identifies subgroups with distinct biological and clinical features
Whole-genome sequencing of chronic lymphocytic leukemia identifies subgroups with distinct biological and clinical features
The value of genome-wide over targeted driver analyses for predicting clinical outcomes of cancer patients is debated. Here, we report the whole-genome sequencing of 485 chronic lymphocytic leukemia patients enrolled in clinical trials as part of the United Kingdom's 100,000 Genomes Project. We identify an extended catalog of recurrent coding and noncoding genetic mutations that represents a source for future studies and provide the most complete high-resolution map of structural variants, copy number changes and global genome features including telomere length, mutational signatures and genomic complexity. We demonstrate the relationship of these features with clinical outcome and show that integration of 186 distinct recurrent genomic alterations defines five genomic subgroups that associate with response to therapy, refining conventional outcome prediction. While requiring independent validation, our findings highlight the potential of whole-genome sequencing to inform future risk stratification in chronic lymphocytic leukemia.
1061-4036
1675-1689
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Robbe, Pauline, Ridout, Kate E., Vavoulis, Dimitrios V., Dreau, Helene M.P., Kinnersley, Ben, Denny, Nicholas, Chubb, Daniel, Appleby, Niamh, Cutts, Anthony, Cornish, Alex J., Lopez-Pascua, Laura, Clifford, Ruth, Burns, Adam, Stamatopoulos, Basile, Cabes, Maite, Alsolami, Reem, Antoniou, Pavlos, Oates, Melanie, Cavalieri, Doriane, Gibson, Jane, Prabhu, Anika V., Schwessinger, Ron, Jennings, Daisy, James, Terena, Maheswari, Uma, Duran-Ferrer, Martí, Carninci, Piero, Knight, Samantha J.L., Månsson, Robert, Hughes, Jim R., Davies, James, Ross, Mark, Bentley, David, Strefford, Jonathan, Devereux, Stephen, Pettitt, Andrew R., Hillmen, Peter, Caulfield, Mark J., Houlston, Richard S., Martín-Subero, José Ignacio and Schuh, Anna (2022) Whole-genome sequencing of chronic lymphocytic leukemia identifies subgroups with distinct biological and clinical features. Nature Genetics, 54 (11), 1675-1689. (doi:10.1038/s41588-022-01211-y).

Record type: Article

Abstract

The value of genome-wide over targeted driver analyses for predicting clinical outcomes of cancer patients is debated. Here, we report the whole-genome sequencing of 485 chronic lymphocytic leukemia patients enrolled in clinical trials as part of the United Kingdom's 100,000 Genomes Project. We identify an extended catalog of recurrent coding and noncoding genetic mutations that represents a source for future studies and provide the most complete high-resolution map of structural variants, copy number changes and global genome features including telomere length, mutational signatures and genomic complexity. We demonstrate the relationship of these features with clinical outcome and show that integration of 186 distinct recurrent genomic alterations defines five genomic subgroups that associate with response to therapy, refining conventional outcome prediction. While requiring independent validation, our findings highlight the potential of whole-genome sequencing to inform future risk stratification in chronic lymphocytic leukemia.

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Accepted/In Press date: 16 September 2022
Published date: 4 November 2022
Additional Information: Funding Information: In the past five years, A.S. has received in-kind contributions from Illumina and Oxford Nanopore Technology and is a shareholder of Illumina. She is a company director and shareholder of SERENOx Ltd. A.S. has received honoraria from Exact Sciences, Janssen, Astra Zeneca, Abbvie and Beigene, non-restricted research grants from Janssen and Astra Zeneca and an educational grant from Abbvie. A.R.P. receives research funding from Celgene/BMS, Gilead, Napp and Roche. N.A. received speaker fees from Gilead. P.A., T.J., U.M., M.R. and D.B. are employees of Illumina, a public company that develops and markets systems for genetic analysis. The remaining authors declare no competing interests. Funding Information: Patient material was obtained from the UK CLL Biobank, University of Liverpool, which is funded by Blood Cancer UK. This work was supported by the Genomics England Research Consortium and the CLL pilot consortium (full list of Individual consortia authors are listed in the ). This research was made possible through access to the data and findings generated by the 100,000 Genomes Project. The 100,000 Genomes Project is managed by Genomics England Limited (a wholly owned company of the Department of Health and Social Care). The 100,000 Genomes Project is funded by the National Institute for Health Research and NHS England. The Wellcome Trust, Cancer Research UK and the Medical Research Council also funded research infrastructure. The 100,000 Genomes Project uses data provided by patients and collected by the National Health Service as part of their care and support. This work was supported by the National Institute for Health Research Oxford Biomedical Research Centre (A.S., D.V. and K.R.). The views expressed in this publication are those of the authors and not necessarily those of the Department of Health. The work of P.R. was supported by the Japan Society for the Promotion of Science Postdoctoral standard program. The work of R.S.H. is supported Wellcome Trust (214388) and Cancer Research UK (C124388) grants. The work of A.R.P. and S.D. was supported by Blood Cancer UK. A.B. received D.Phil. funding from Health Education England and Genomics England. J.I.M.-S. is funded by the European Research Council under the European Union’s Horizon 2020 research and innovation program (Project BCLLATLAS, grant agreement 810287). J.C.S. is funded by Cancer Research UK (ECRIN-M3 accelerator award C42023/A29370, Southampton Experimental Cancer Medicine Centre grant C24563/A15581, Cancer Research UK Southampton Centre grant C34999/A18087 and program C2750/A23669). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript. Funding Information: Patient material was obtained from the UK CLL Biobank, University of Liverpool, which is funded by Blood Cancer UK. This work was supported by the Genomics England Research Consortium and the CLL pilot consortium (full list of Individual consortia authors are listed in the Supplementary Material). This research was made possible through access to the data and findings generated by the 100,000 Genomes Project. The 100,000 Genomes Project is managed by Genomics England Limited (a wholly owned company of the Department of Health and Social Care). The 100,000 Genomes Project is funded by the National Institute for Health Research and NHS England. The Wellcome Trust, Cancer Research UK and the Medical Research Council also funded research infrastructure. The 100,000 Genomes Project uses data provided by patients and collected by the National Health Service as part of their care and support. This work was supported by the National Institute for Health Research Oxford Biomedical Research Centre (A.S., D.V. and K.R.). The views expressed in this publication are those of the authors and not necessarily those of the Department of Health. The work of P.R. was supported by the Japan Society for the Promotion of Science Postdoctoral standard program. The work of R.S.H. is supported Wellcome Trust (214388) and Cancer Research UK (C124388) grants. The work of A.R.P. and S.D. was supported by Blood Cancer UK. A.B. received D.Phil. funding from Health Education England and Genomics England. J.I.M.-S. is funded by the European Research Council under the European Union’s Horizon 2020 research and innovation program (Project BCLLATLAS, grant agreement 810287). J.C.S. is funded by Cancer Research UK (ECRIN-M3 accelerator award C42023/A29370, Southampton Experimental Cancer Medicine Centre grant C24563/A15581, Cancer Research UK Southampton Centre grant C34999/A18087 and program C2750/A23669). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript. Publisher Copyright: © 2022, The Author(s).

Identifiers

Local EPrints ID: 472511
URI: http://eprints.soton.ac.uk/id/eprint/472511
ISSN: 1061-4036
PURE UUID: 51cba57f-f16e-4a08-a918-3721daa4b367
ORCID for Jane Gibson: ORCID iD orcid.org/0000-0002-0973-8285
ORCID for Jonathan Strefford: ORCID iD orcid.org/0000-0002-0972-2881

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Date deposited: 07 Dec 2022 17:42
Last modified: 17 Mar 2024 02:59

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Contributors

Author: Pauline Robbe
Author: Kate E. Ridout
Author: Dimitrios V. Vavoulis
Author: Helene M.P. Dreau
Author: Ben Kinnersley
Author: Nicholas Denny
Author: Daniel Chubb
Author: Niamh Appleby
Author: Anthony Cutts
Author: Alex J. Cornish
Author: Laura Lopez-Pascua
Author: Ruth Clifford
Author: Adam Burns
Author: Basile Stamatopoulos
Author: Maite Cabes
Author: Reem Alsolami
Author: Pavlos Antoniou
Author: Melanie Oates
Author: Doriane Cavalieri
Author: Jane Gibson ORCID iD
Author: Anika V. Prabhu
Author: Ron Schwessinger
Author: Daisy Jennings
Author: Terena James
Author: Uma Maheswari
Author: Martí Duran-Ferrer
Author: Piero Carninci
Author: Samantha J.L. Knight
Author: Robert Månsson
Author: Jim R. Hughes
Author: James Davies
Author: Mark Ross
Author: David Bentley
Author: Stephen Devereux
Author: Andrew R. Pettitt
Author: Peter Hillmen
Author: Mark J. Caulfield
Author: Richard S. Houlston
Author: José Ignacio Martín-Subero
Author: Anna Schuh

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