ArticlePLoS computational biology2023
Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity.
Article in PLoS computational biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
9 citing papers in PubMed.
- Trial
- Article
- Cancer evolution and multi-omic profile of relapsed colorectal liver metastases after treatment.Genome medicine · 2026Article
- Prospective, multicenter validation of a platform for rapid molecular profiling of central nervous system tumors.Nature medicine · 2025Article
- Article
- Representation of genomic intratumor heterogeneity in multi-region non-small cell lung cancer patient-derived xenograft models.Nature communications · 2024Article
- HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data.Genome biology · 2024Article
- ZygosityPredictor.Bioinformatics advances · 2024Article
- HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data.bioRxiv : the preprint server for biology · 2023Article
Corrections and comments
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Authors and funding
11 authors.
Funding
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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Registered trials
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