Assessing Intratumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-generation Sequencing

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 2016 Aug 31

PMID 27573852

Citations 118

Authors

Yuchao Jiang

Yu Qiu

Andy J Minn

Nancy R Zhang

Affiliations

Soon will be listed here.

Abstract

Cancer is a disease driven by evolutionary selection on somatic genetic and epigenetic alterations. Here, we propose Canopy, a method for inferring the evolutionary phylogeny of a tumor using both somatic copy number alterations and single-nucleotide alterations from one or more samples derived from a single patient. Canopy is applied to bulk sequencing datasets of both longitudinal and spatial experimental designs and to a transplantable metastasis model derived from human cancer cell line MDA-MB-231. Canopy successfully identifies cell populations and infers phylogenies that are in concordance with existing knowledge and ground truth. Through simulations, we explore the effects of key parameters on deconvolution accuracy and compare against existing methods. Canopy is an open-source R package available at https://cran.r-project.org/web/packages/Canopy/.

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