Journal article
Completing a genomic characterisation of microscopic tumour samples with copy number
- Abstract:
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Background: Genomic insights in settings where tumour sample sizes are limited to just hundreds or even tens of cells hold great clinical potential, but also present significant technical challenges. We previously developed the DigiPico sequencing platform to accurately identify somatic mutations from such samples.
Results: Here, we complete this genomic characterisation with copy number. We present a novel protocol, PicoCNV, to call allele-specific somatic copy number alterations from picogram quantities of tumour DNA. We find that PicoCNV provides exactly accurate copy number in 84% of the genome for even the smallest samples, and demonstrate its clinical potential in maintenance therapy.
Conclusions: PicoCNV complements our existing platform, allowing for accurate and comprehensive genomic characterisations of cancers in settings where only microscopic samples are available.
- Publication status:
- Published
- Peer review status:
- Peer reviewed
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(Preview, Other, pdf, 652.7KB, Terms of use)
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(Preview, Version of record, pdf, 1.7MB, Terms of use)
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- Publisher copy:
- 10.1186/s12859-023-05576-7
Authors
- Publisher:
- BioMed Central
- Journal:
- BMC Bioinformatics More from this journal
- Volume:
- 24
- Issue:
- 1
- Article number:
- 453
- Place of publication:
- England
- Publication date:
- 2023-11-30
- Acceptance date:
- 2023-11-21
- DOI:
- EISSN:
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1471-2105
- ISSN:
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1471-2105
- Pmid:
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38036971
- Language:
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English
- Keywords:
- Pubs id:
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1575681
- Local pid:
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pubs:1575681
- Deposit date:
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2025-01-16
- ARK identifier:
Terms of use
- Copyright holder:
- Nulsen et al
- Copyright date:
- 2023
- Rights statement:
- © The Author(s) 2023, corrected publication 2024. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http:// creat iveco mmons. org/ licen ses/ by/4. 0/. The Creative Commons Public Domain Dedication waiver (http:// creat iveco mmons. org/ publi cdoma in/ zero/1. 0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
- Notes:
- A correction to this article is available online from BioMed Central at: https://doi.org/10.1186/s12859-024-05642-8
- Licence:
- CC Attribution (CC BY)
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