Introducing scTrends
A Living Review of Commercial Single Cell and Spatial Omic Technologies
We are now in the single cell era of biomedical research. The last 5 years has been marked by numerous use cases, from the identification of rare cell populations; to inferring the regulatory consequences of SNPs; the perturbation of cells using drugs, cytokines, and CRISPR (including variations thereof); the simultaneous measurement of multiple -omic modalities; and the spatial organization of tissue.
We are launching scTrends.org as a living review to continually monitor emerging single cell and spatial omic technologies, identify key industry players and trends, and eventually, rigorously benchmark these protocols against one another in our own labs.
What is a living review?
Whilst the nomenclature is not yet settled, we are referring to a new type of review article wherein the central thrust of the manuscript is continually updated on a semi-regular basis. In a similar manner to open source software projects, whereby contributors leave and join the project as time affords, we expect scTrends to have the same ethos with regular version updates every ~6-18 months across a range of formats (blogs, more formal manuscripts etc).
Our first commentary was published in the July 2024 edition of Nature Biotechnology.
What kinds of topics are you interested in?
Mapping the space of commercial single cell protocols, in particular:
Historical context for the company
Molecular basis of the platform
What are the standard variations on the platform? E.g., CRISPR, 5’ seq, BCR etc.
What are the relative strengths/weaknesses (throughput, biases, economics)?
How established are the methods? Have challenging clinical samples been attempted, or use of functional genomics?
Associated computational pipelines and infrastructure?
The broader commentary on industry trends:
Engineering and computational pipelines
Emerging technologies from academia
Business aspects, including legal and public markets.
Why are you doing this?
Whilst there is no single reason, a key problem with reviewing a particular field is that knowledge needs to be constantly updated. Review articles typically take months to write and, were it permitted, >70% of your review could have been largely quoted directly from a similar article a few years earlier.
In addition, we’re expecting to see a tidal change in available single cell technologies, from CRISPR screens being more widely available than ever, to off-the-shelf kits not requiring complex microfluidic devices, and large multimodal cohort studies, often powered for statistical genetics.
Single cell technology appears to be a good test bed for the living review concept because:
The technology is developing very quickly, such that its hard to keep up with current developments, except at an abstract level (i.e., this review will be useful!),
A plethora start ups are interested in using single cell technologies but can’t weigh the relative merits/demerits of a particular technology.
Single cell experiments are expensive, and therefore being cost effective in your aims to answer a specific question is a sensible idea.
Who are you? Can I get involved?
Currently, we’re a group of friends, colleagues and scientists who share informal hints on what is happening within the single cell community. However, we see no reason that this should be a closed shop. In which case, drop me an email at jake@relationrx.com and please detail what you would want to contribute to scTrends.
Conflicts of interest?
We also note that we welcome contributors from single cell technology developers providing they declare conflicts of interests upfront.
We will also endeavour to be data-driven and avoid value judgements where possible. One possible exception to this is speaking of “ease of use”, in which case we will resort to consensus opinion with clear justifications thereof.
As an immediate disclaimer, I am a cofounder of Relation Therapeutics. At Relation, we’re committed to using the latest and greatest single cell technologies; however, we have no commitment to using one particular technology over another. Therefore, keeping track of emerging trends in an unbiased manner is of strategic interest.