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| Item Type: | Article |
|---|---|
| Title: | Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity |
| Creators Name: | Watkins, T.B.K., Colliver, E.C., Huska, M.R., Kaufmann, T.L., Lim, E.L., Duncan, C.B., Haase, K., Van Loo, P., Swanton, C., McGranahan, N. and Schwarz, R.F. |
| 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. |
| Keywords: | Algorithms, DNA Copy Number Variations, Haplotypes, Neoplasms |
| Source: | PLoS Computational Biology |
| ISSN: | 1553-734X |
| Publisher: | Public Library of Science |
| Volume: | 19 |
| Number: | 10 |
| Page Range: | e1011379 |
| Date: | 23 October 2023 |
| Official Publication: | https://doi.org/10.1371/journal.pcbi.1011379 |
| PubMed: | View item in PubMed |
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