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| Item Type: | Article |
|---|---|
| Title: | Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity |
| Creators Name: | Watkins, T.B.K. and Colliver, E.C. and Huska, M.R. and Kaufmann, T.L. and Lim, E.L. and Duncan, C.B. and Haase, K. and Van Loo, P. and Swanton, C. and 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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