Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity.
other · Level V
Where this comes from
- Record sourced from PubMed, PMID 37871126.
- Also identified by DOI 10.1371/journal.pcbi.1011379 and PMC identifier 10621967.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
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.
Medical subject headings
- DNA Copy Number Variations
- Neoplasms