Single-cell genome sequencing: current state of the science

Key Points Single-cell genome sequencing aims to increase our understanding of complex microbial ecosystems and disease in multicellular organisms by isolating the contributions of distinct cellular populations. Acquiring high-quality genotype data after starting from a single molecule of DNA from an individual cell has substantial technical challenges that are continuously being addressed. The three main genome amplification methods have differences in their propensity to produce distinct types of artefacts, which should be carefully considered when designing experiments. The experimental design should also be informed by the questions of the study. Single-cell microorganism sequencing has enabled genome assembly of new phyla and is beginning to provide new biological insights into microbial dark matter. Genetic mosaicism is an area that is beginning to be studied at higher resolution using single-cell genome sequencing. Initial studies have begun to resolve intra-tumour heterogeneity, which have provided new biological insights into tumour formation. Single-cell genome sequencing is rapidly evolving, and the use of these techniques is likely to expand as technologies improve and new discoveries are made. Single-cell genome sequencing can provide detailed insights into the composition of single genomes that are not readily apparent when studying bulk cell populations. This Review discusses the considerable technical challenges of amplifying and interrogating genomes from single cells, emerging innovative solutions and various applications in microbiology and human disease, in particular in cancer. The field of single-cell genomics is advancing rapidly and is generating many new insights into complex biological systems, ranging from the diversity of microbial ecosystems to the genomics of human cancer. In this Review, we provide an overview of the current state of the field of single-cell genome sequencing. First, we focus on the technical challenges of making measurements that start from a single molecule of DNA, and then explore how some of these recent methodological advancements have enabled the discovery of unexpected new biology. Areas highlighted include the application of single-cell genomics to interrogate microbial dark matter and to evaluate the pathogenic roles of genetic mosaicism in multicellular organisms, with a focus on cancer. We then attempt to predict advances we expect to see in the next few years.