1.
PLoS Comput Biol
; 19(10): e1011379, 2023 Oct.
Article
in English
| MEDLINE
| ID: mdl-37871126
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.
Subject(s)
DNA Copy Number Variations , Neoplasms , Humans , DNA Copy Number Variations/genetics , Haplotypes/genetics , Neoplasms/genetics , Neoplasms/pathology , Algorithms
2.
Pediatr Pathol
; 3(2-4): 375-6, 1985.
Article
in English
| MEDLINE
| ID: mdl-4095030