Journal Article

DKFZ-2023-02151

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity.

Watkins, T. B. K. ; Colliver, E. C. ; Huska, M. R. ; Kaufmann, T. L. ; Lim, E. L. ; Duncan, C. B. ; Haase, K.DKFZ* ; Van Loo, P. ; Swanton, C. ; McGranahan, N. ; Schwarz, R. F.

2023
Public Library of Science San Francisco, Calif.

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Please use a persistent id in citations: doi:10.1371/journal.pcbi.1011379

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.

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Contributing Institute(s):

1. DKTK Koordinierungsstelle Berlin (BE01)

Research Program(s):

1. 899 - ohne Topic (POF4-899) (POF4-899)

Appears in the scientific report 2023

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