Watkins, Thomas BK;
Colliver, Emma C;
Huska, Matthew R;
Kaufmann, Tom L;
Lim, Emilia L;
Duncan, Cody B;
Haase, Kerstin;
... Schwarz, Roland F; + view all
(2023)
Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity.
PLoS Computational Biology
, 19
(10)
, Article e1011379. 10.1371/journal.pcbi.1011379.
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Abstract
Most computational methods that infer somatic copy number alterations (SCNAs) from bulk sequencing of DNA analyse tumour samples individually. However, the sequencing of multiple tumour samples from a patient’s disease is an increasingly common practice. We introduce Refphase, an algorithm that leverages this multi-sampling approach to infer haplotype-specific copy numbers through multi-sample phasing. We demonstrate Refphase’s ability to infer haplotype-specific SCNAs and characterise their intra-tumour heterogeneity, to uncover previously undetected allelic imbalance in low purity samples, and to identify parallel evolution in the context of whole genome doubling in a pan-cancer cohort of 336 samples from 99 tumours.
| Type: | Article |
|---|---|
| Title: | Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity |
| Location: | United States |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1371/journal.pcbi.1011379 |
| Publisher version: | https://doi.org/10.1371/journal.pcbi.1011379 |
| Language: | English |
| Additional information: | Copyright © 2023 Watkins et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, https://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute > Research Department of Oncology |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10181788 |
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