Applications of Single-Cell DNA Sequencing

Abstract

Over the past decade, genomic analyses of single cells-the fundamental units of life-have become possible. Single-cell DNA sequencing has shed light on biological questions that were previously inaccessible across diverse fields of research, including somatic mutagenesis, organismal development, genome function, and microbiology. Single-cell DNA sequencing also promises significant future biomedical and clinical impact, spanning oncology, fertility, and beyond. While single-cell approaches that profile RNA and protein have greatly expanded our understanding of cellular diversity, many fundamental questions in biology and important biomedical applications require analysis of the DNA of single cells. Here, we review the applications and biological questions for which single-cell DNA sequencing is uniquely suited or required. We include a discussion of the fields that will be impacted by single-cell DNA sequencing as the technology continues to advance.

Keywords: DNA modifications; germ cells; lineage tracing; organismal development; single-cell DNA sequencing; single-cell genomics.

Figure 1.. The three core capabilities of single-cell DNA sequencing and application requirements of throughput versus genome coverage.

A-C: The three core capabilities of single-cell DNA sequencing (Adapted from ref. (42)). A, Fidelity: In bulk sequencing, very low-level mosaic mutations cannot be distinguished from sequencing library and sequencing error artifacts. In contrast, in single-cell sequencing, the distribution of read depths is the same for somatic mutations and germline (inherited) heterozygous mutations. This enables detection of somatic mutations regardless of mosaicism, albeit it requires the same total sequencing costs as a hypothetical bulk sequencing method with perfect fidelity due to the need to sequence many single cells. Additionally, single-cell sequencing generally has an increased level of artifacts due to the single-cell amplification process. B, Co-presence: Single-cell sequencing preserves information regarding which somatic mutations are present together in the same cells. This enables reconstruction of lineage trees. C, Single-cell sequencing, when combined with simultaneous cell phenotyping (multi-omic scDNA-seq), preserves information regarding which somatic mutations are present in which cell types. This enables deconvolution of cell types or species in heterogenous samples and annotation of lineage trees with cell phenotypes. D, Schematic of approximate application-specific requirements and current technological capabilities in terms of throughput (number of single cells per experiment or project) versus genome coverage. Low/High-cvg WGS, Low/high-coverage whole genome sequencing.