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<https://discovery.ucl.ac.uk/id/eprint/10203239> <http://purl.org/dc/terms/title> "Inference of clone-specific copy numbers from bulk tumour DNA"^^<http://www.w3.org/2001/XMLSchema#string> .
<https://discovery.ucl.ac.uk/id/eprint/10203239> <http://purl.org/ontology/bibo/abstract> "Cancer is an evolutionary process. During this process, single nucleotide variants (SNVs) and somatic copy-number alterations (SCNAs) accumulate, contributing to clonal evolution. Nevertheless, making accurate inferences about\r\ntheir co-evolution and clone-specific copy numbers from bulk DNA sequencing poses a significant challenge. In this thesis, I present ALPACA (ALlelespecific Phylogenetic Analysis of clone Copy-number Alterations), a computational method which allows inference of clone-specific copy-numbers from bulk\r\nDNA by leveraging phylogenetic trees and SNV cellular frequencies obtained\r\nfrom multi-sample sequencing experiments. I validate this approach with two\r\nsimulated tumour cohorts and with single-cell data, comparing the ALPACA\r\noutput both with the ground truth and with the outputs of two previously\r\npublished methods. I then apply ALPACA to the TRACERx421 (TRAcking\r\nnon-small cell lung Cancer Evolution through therapy Frankell et al. 2023; Al\r\nBakir et al. 2023) cohort and demonstrate that ALPACA can identify loss-ofheterozygosity events and amplifications in minor metastasis seeding clones,\r\nnot detectable on bulk-sample copy-number level. By comparing seeding and\r\nnon-seeding clones within the primary-metastatic matched cohort I observe evidence of increased chromosomal instability in metastasis seeding clones. Using\r\nALPACA’s clone-specific copy-numbers I develop a novel method to quantify\r\nintra-tumour copy-number heterogeneity: clone copy-number diversity (CCD).\r\nUsing this metric I show that patients who later develop a metastatic disease\r\nharbour a higher intra-tumour clone copy number diversity within their primary tumours compared to patients who do not relapse. Lastly, I show an\r\nassociation between CCD and patient survival."^^<http://www.w3.org/2001/XMLSchema#string> .
<https://discovery.ucl.ac.uk/id/eprint/10203239> <http://purl.org/dc/terms/date> "2025-01-28" .
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