Single cell mutational profiling and clonal phylogeny in cancer

Abstract

The development of cancer is a dynamic evolutionary process in which intra-clonal, genetic diversity provides a substrate for clonal selection and a source of therapeutic escape. The complexity and topography of intra-clonal genetic architecture has major implications for biopsy-based prognosis and for targeted therapy. High depth, next generation sequencing (NGS) efficiently captures the mutational load of individual tumours or biopsies. But, being a snapshot portrait of total DNA, it disguises the fundamental features of sub-clonal 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 leukaemic cells with known mutational spectra as a tractable model. DNA from flow sorted single cells is screened using multiplex targeted Q-PCR within a micro-fluidic platform allowing unbiased single cell selection, high throughput and comprehensive analysis for all main varieties of genetic abnormalities: chimaeric 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 sub-clonal genetic architectures and phylogenies.