TY  - JOUR
AU  - Watkins, Thomas B K
AU  - Colliver, Emma C
AU  - Huska, Matthew R
AU  - Kaufmann, Tom L
AU  - Lim, Emilia L
AU  - Duncan, Cody B
AU  - Haase, Kerstin
AU  - Van Loo, Peter
AU  - Swanton, Charles
AU  - McGranahan, Nicholas
AU  - Schwarz, Roland F
TI  - Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity.
JO  - PLoS Computational Biology
VL  - 19
IS  - 10
SN  - 1553-734X
CY  - San Francisco, Calif.
PB  - Public Library of Science
M1  - DKFZ-2023-02151
SP  - e1011379
PY  - 2023
AB  - 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.
LB  - PUB:(DE-HGF)16
C6  - pmid:37871126
DO  - DOI:10.1371/journal.pcbi.1011379
UR  - https://inrepo02.dkfz.de/record/284953
ER  -