Review

. 2024 Dec 11;4(12):100723.

doi: 10.1016/j.xgen.2024.100723.

scTrends: A living review of commercial single-cell and spatial 'omic technologies

Joachim De Jonghe¹, James W Opzoomer², Amaia Vilas-Zornoza³, Benedikt S Nilges⁴, Peter Crane⁵, Marco Vicari⁶, Hower Lee⁷, David Lara-Astiaso⁸, Torsten Gross³, Jörg Morf⁹, Kim Schneider¹⁰, Juliana Cudini³, Lorenzo Ramos-Mucci³, Dylan Mooijman¹¹, Katarína Tiklová¹², Sergio Marco Salas⁷, Christoffer Mattsson Langseth⁷, Nachiket D Kashikar⁴; scTrends Consortium; Denis Schapiro¹³, Joakim Lundeberg⁶, Mats Nilsson¹², Alex K Shalek¹⁴, Adam P Cribbs¹⁵, Jake P Taylor-King¹⁶

Collaborators, Affiliations

Collaborators

scTrends Consortium:
Eli M Carrami, Rebecca McIntyre, Casey Benjamin Swerner, Edith M Hessel, ChantrioInt-Andreas Kapourani, Cristian Regep, Charles E S Roberts

Affiliations

¹ Francis Crick Institute, London, UK.
² Cell Communication Lab, Department of Oncology, University College London Cancer Institute, London, UK; Relation Therapeutics, London, UK.
³ Relation Therapeutics, London, UK.
⁴ OMAPiX GmbH, Langenfeld, Rheinland, Germany.
⁵ Caeruleus Genomics, Oxford, UK.
⁶ Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Solna, Sweden.
⁷ spatialist AB, Stockholm, Sweden; Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 171 65 Solna, Sweden.
⁸ Department of Hematology, University of Cambridge, Cambridge, UK; Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK.
⁹ Skyhawk Therapeutics, Basel, Switzerland.
¹⁰ Roche, Basel, Switzerland.
¹¹ Single Cell Discoveries, Utrecht, the Netherlands.
¹² Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 171 65 Solna, Sweden.
¹³ Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Heidelberg, Germany; Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany; Translational Spatial Profiling Center (TSPC), Heidelberg, Germany.
¹⁴ Relation Therapeutics, London, UK; Institute for Medical Engineering and Science, Department of Chemistry and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.
¹⁵ Caeruleus Genomics, Oxford, UK; Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, UK; Oxford Centre for Translational Myeloma Research University of Oxford, Oxford, UK. Electronic address: adam.cribbs@ndorms.ox.ac.uk.
¹⁶ Relation Therapeutics, London, UK. Electronic address: jake@relationrx.com.

PMID: 39667347
PMCID: PMC11701258
DOI: 10.1016/j.xgen.2024.100723

Review

scTrends: A living review of commercial single-cell and spatial 'omic technologies

Joachim De Jonghe et al. Cell Genom. 2024.

. 2024 Dec 11;4(12):100723.

doi: 10.1016/j.xgen.2024.100723.

Authors

Collaborators

scTrends Consortium:
Eli M Carrami, Rebecca McIntyre, Casey Benjamin Swerner, Edith M Hessel, ChantrioInt-Andreas Kapourani, Cristian Regep, Charles E S Roberts

Affiliations

¹ Francis Crick Institute, London, UK.
² Cell Communication Lab, Department of Oncology, University College London Cancer Institute, London, UK; Relation Therapeutics, London, UK.
³ Relation Therapeutics, London, UK.
⁴ OMAPiX GmbH, Langenfeld, Rheinland, Germany.
⁵ Caeruleus Genomics, Oxford, UK.
⁶ Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Solna, Sweden.
⁷ spatialist AB, Stockholm, Sweden; Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 171 65 Solna, Sweden.
⁸ Department of Hematology, University of Cambridge, Cambridge, UK; Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK.
⁹ Skyhawk Therapeutics, Basel, Switzerland.
¹⁰ Roche, Basel, Switzerland.
¹¹ Single Cell Discoveries, Utrecht, the Netherlands.
¹² Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 171 65 Solna, Sweden.
¹³ Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Heidelberg, Germany; Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany; Translational Spatial Profiling Center (TSPC), Heidelberg, Germany.
¹⁴ Relation Therapeutics, London, UK; Institute for Medical Engineering and Science, Department of Chemistry and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.
¹⁵ Caeruleus Genomics, Oxford, UK; Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, UK; Oxford Centre for Translational Myeloma Research University of Oxford, Oxford, UK. Electronic address: adam.cribbs@ndorms.ox.ac.uk.
¹⁶ Relation Therapeutics, London, UK. Electronic address: jake@relationrx.com.

PMID: 39667347
PMCID: PMC11701258
DOI: 10.1016/j.xgen.2024.100723

Abstract

Understanding the rapidly evolving landscape of single-cell and spatial omic technologies is crucial for advancing biomedical research and drug development. We provide a living review of both mature and emerging commercial platforms, highlighting key methodologies and trends shaping the field. This review spans from foundational single-cell technologies such as microfluidics and plate-based methods to newer approaches like combinatorial indexing; on the spatial side, we consider next-generation sequencing and imaging-based spatial transcriptomics. Finally, we highlight emerging methodologies that may fundamentally expand the scope for data generation within pharmaceutical research, creating opportunities to discover and validate novel drug mechanisms. Overall, this review serves as a critical resource for navigating the commercialization and application of single-cell and spatial omic technologies in pharmaceutical and academic research.

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Conflict of interest statement

Declaration of interests J.D.J., J.W.O., and A.P.C. are inventors on patent applications filed by the University of Cambridge (via Cambridge Enterprise), the University College London Business, and Oxford University Innovations, respectively. J.W.O., A.V.Z., T.G., J.C., L.R.-M., C.E.S.R., A.K.S., and J.P.T.-K. receive compensation from Relation Therapeutics. P.C. and A.P.C. are employees of Caereleus Genomics. B.S.N. and N.D.K. receive compensation from OMAPiX. M.V. and J.L. are scientific consultants for 10× Genomics. J.M. receives compensation from Skyhawk Therapeutics and previously worked as a scientific consultant for Scipio Bioscience. K.S. receives compensation from Roche. D.M. receives compensation from scDiscoveries. H.L., S.M.S., and C.M.L. receive compensation from spatialist. A.K.S. reports compensation for consulting and/or scientific advisory board membership from Honeycomb Biotechnologies, Cellarity, Ochre Bio, Relation Therapeutics, Bio-Rad Laboratories, IntrECate Biotherapeutics, Passkey Therapeutics, Fog Pharma, and Dahlia Biosciences, which are unrelated to this work. D.S. reports funding from Cellzome, a GSK company, and received honorariums from Immunai, Noetik, Alpenglow, and Lunaphore.

Figures

**Figure 1**
Diagram of key biomolecules measurable at single-cell resolution by commercially available solutions in kit format Adapted from figure contained in Peidli et al.

**Figure 2**
Single-cell and spatial omic platform characterization using experimental motifs common to similar technologies

See this image and copyright information in PMC

References

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1. Method of the Year 2019: Single-cell multimodal omics. Nat. Methods. 2020;17:1. doi: 10.1038/s41592-019-0703-5. - DOI - PubMed
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scTrends: A living review of commercial single-cell and spatial 'omic technologies

Collaborators

Affiliations

scTrends: A living review of commercial single-cell and spatial 'omic technologies

Authors

Collaborators

Affiliations

Abstract

Conflict of interest statement

Figures

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources