Single-cell mutational profiling and clonal phylogeny in cancer
- Nicola E. Potter1,
- Luca Ermini1,
- Elli Papaemmanuil2,
- Giovanni Cazzaniga3,
- Gowri Vijayaraghavan1,
- Ian Titley1,
- Anthony Ford1,
- Peter Campbell2,
- Lyndal Kearney1 and
- Mel Greaves1,4
- 1The Institute of Cancer Research, London, SM2 5NG, United Kingdom;
- 2Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, United Kingdom;
- 3Centro Ricerca Tettamanti, Clinica Pediatrica, Università di Milano Bicocca, Ospedale San Gerardo, 20900 Monza, Italy
Abstract
The development of cancer is a dynamic evolutionary process in which intraclonal, genetic diversity provides a substrate for clonal selection and a source of therapeutic escape. The complexity and topography of intraclonal genetic architectures have major implications for biopsy-based prognosis and for targeted therapy. High-depth, next-generation sequencing (NGS) efficiently captures the mutational load of individual tumors or biopsies. But, being a snapshot portrait of total DNA, it disguises the fundamental features of subclonal variegation of genetic lesions and of clonal phylogeny. Single-cell genetic profiling provides a potential resolution to this problem, but methods developed to date all have limitations. We present a novel solution to this challenge using leukemic cells with known mutational spectra as a tractable model. DNA from flow-sorted single cells is screened using multiplex targeted Q-PCR within a microfluidic platform allowing unbiased single-cell selection, high-throughput, and comprehensive analysis for all main varieties of genetic abnormalities: chimeric gene fusions, copy number alterations, and single-nucleotide variants. We show, in this proof-of-principle study, that the method has a low error rate and can provide detailed subclonal genetic architectures and phylogenies.
Footnotes
-
↵4 Corresponding author
E-mail mel.greaves{at}icr.ac.uk
-
[Supplemental material is available for this article.]
-
Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.159913.113.
- Received May 2, 2013.
- Accepted September 17, 2013.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported), as described at http://creativecommons.org/licenses/by-nc/3.0/.