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New tool brings clarity and quality to cutting-edge tissue mapping technique

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Researchers at The Ottawa Hospital and the University of Ottawa played a key role in developing a new open-access resource that could greatly advance the use of a powerful tissue mapping technique called spatial transcriptomics. This cutting-edge technique allows researchers to understand the organization and activity of the various cells that make up a tissue. 

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“Spatial transcriptomics can be incredibly powerful for understanding complex biological systems like tumours or developing organs, but until now, there haven’t been shared standards to judge and compare data generated in different labs,” said Dr. David Cook

“Spatial transcriptomics can be incredibly powerful for understanding complex biological systems like tumours or developing organs, but until now, there haven’t been shared standards to judge and compare data generated in different labs,” said Dr. David Cook, scientist at The Ottawa Hospital and assistant professor at the University of Ottawa. “We developed this resource to make spatial transcriptomics data more consistent, reliable, and easier to use across different labs, so scientists can trust their findings and build on each other’s work.”

The new tool was developed through the international Spatial Touchstone project, co-led by Dr. Cook, along with colleagues from St. Jude Children’s Research Hospital, Weill Cornell Medicine and the University of Adelaide. It is published in Nature Biotechnology. 

The Spatial Touchstone project includes: 

  • A large, high quality collection of spatial transcriptomics data from multiple tissue types.
  • Standard protocols that labs can follow so experiments are done the same way everywhere.
  • Free software tools that let scientists check the quality of their own data and compare it against the reference dataset.
  • A user-friendly online portal where researchers can upload their initial samples and see if they meet quality standards before spending a lot of time and money on full analysis. 
     
Authors:

Plummer JT, Dezem FS, Cook DP, Park J, Zhang L, Liu Y, Marção M, DuBose H, Wani A, Wise K, Roach M, Harvey K, Wang T, Jensen KB, Morosini N, De Gregorio R, Alonso A, Houlihan SL, Schwartz RE, Hissong E, Snopkowski C, Wrana JL, Ryan N, Butler LM, Church G, Swarbrick A, Mason CE, Martelotto LG.

Funding:

South Australian immune GENomics Cancer Institute (SAiGENCI), Ovarian Cancer Research Alliance, Chan Zuckerburg Foundation, Breast Cancer Research Foundation, National Health and Medical Research Council, National Breast Cancer Foundation, Cancer Council NSW, WorldQuant and GI Research Foundation (GIRF), NASA, National Institutes of Health, UK Cancer Grand Challenges (SAMBAI), Blood Cancer United, Boryung and Bumrungrad International Hospital.

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The Ottawa Hospital is a leading academic health, research and learning hospital proudly affiliated with the University of Ottawa and supported by The Ottawa Hospital Foundation.