A community effort to create standards for evaluating tumor subclonal reconstruction

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http://hdl.handle.net/10138/328971

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DREAM SMC-Het Participants , Salcedo , A & Mustonen , V 2020 , ' A community effort to create standards for evaluating tumor subclonal reconstruction ' , Nature Biotechnology , vol. 38 , no. 1 , pp. 97-107 . https://doi.org/10.1038/s41587-019-0364-z

Title: A community effort to create standards for evaluating tumor subclonal reconstruction
Author: DREAM SMC-Het Participants; Salcedo, Adriana; Mustonen, Ville
Contributor: University of Helsinki, Department of Computer Science
Date: 2020-01
Language: eng
Belongs to series: Nature Biotechnology
ISSN: 1087-0156
URI: http://hdl.handle.net/10138/328971
Abstract: Methods for reconstructing tumor evolution are benchmarked in the DREAM Somatic Mutation Calling Tumour Heterogeneity Challenge. Tumor DNA sequencing data can be interpreted by computational methods that analyze genomic heterogeneity to infer evolutionary dynamics. A growing number of studies have used these approaches to link cancer evolution with clinical progression and response to therapy. Although the inference of tumor phylogenies is rapidly becoming standard practice in cancer genome analyses, standards for evaluating them are lacking. To address this need, we systematically assess methods for reconstructing tumor subclonality. First, we elucidate the main algorithmic problems in subclonal reconstruction and develop quantitative metrics for evaluating them. Then we simulate realistic tumor genomes that harbor all known clonal and subclonal mutation types and processes. Finally, we benchmark 580 tumor reconstructions, varying tumor read depth, tumor type and somatic variant detection. Our analysis provides a baseline for the establishment of gold-standard methods to analyze tumor heterogeneity.
Subject: SOMATIC POINT MUTATIONS
GENOME SIMULATION
CANCER
HETEROGENEITY
EVOLUTION
IDENTIFICATION
3122 Cancers
318 Medical biotechnology
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