Expert view: The future of single-cell sequencing

With current technology, standard taxonomy studies are a great fit, but to gain a more advanced functional understanding involving pathway analysis, this technology still poses a challenge. At the moment, we really don’t know how much of the single-cell transcriptome we are capturing. With current single-cell methods, is there 25% more we can capture, or 250% more we can capture? The method of obtaining the cells also creates a stumbling block. There is no standard protocol to dissociate tissue without often sacrificing viability or causing transcriptome changes due to cell stress.

A challenge remains in identifying very rare low abundance cell populations that may have important implications in clonal evolution. To detect extremely rare populations, it is simply not economical to sequence the required number of cells to the necessary depth.

Despite the current challenges, droplet-based single-cell sequencing has enjoyed overwhelming success in recent years due to a couple of key innovations. First, the ability to robustly isolate single cells in droplets paired with captured oligos has led to unprecedented cell scalability – researchers can now look at tens of thousands of individual cells per sample. Second, more recently, is the ability to assay not only cytoplasmic mRNA transcripts, but also nuclear mRNA transcripts, genome accessibility (ATAC-Seq), and protein conjugation (CITE-Seq). This is leading to novel ways of looking at cell state and epigenetic markers.

Many of the early adopters, mostly core labs, are performing single-cell analysis for their research and customers. However, we are seeing individual labs bringing single-cell sequencing in-house, signalling that single-cell analysis is becoming a routine research tool. Looking to the future, single-cell sequencing technology will play a major part in projects such as The Human Cell Atlas, which, once the first draft is completed in the next few years, will offer unprecedented opportunities to influence a broad range of applications.