Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues.

Huan Wang¹, Ruixu Huang², Jack Nelson¹, Ce Gao³, Miles Tran³, Anna Yeaton^1,4, Sachi Krishna¹, Kristen Felt⁵, Kathleen L Pfaff⁶, Teri Bowman⁷, Scott J Rodig^6,7, Kevin Wei^8,9, Brittany A Goods¹⁰, Samouil L Farhi¹¹

¹Spatial Technology Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.

²Thayer School of Engineering, Molecular and Systems Biology and Program in Quantitative Biomedical Sciences at Dartmouth College, Hanover, NH, USA.

³Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital at Harvard Medical School, Boston, MA, USA.

⁴Immunai, New York, NY, USA.

⁵ImmunoProfile, Brigham & Women's Hospital and Dana-Farber Cancer Institute, Boston, MA, USA.

⁶Center for Immuno-Oncology, Tissue Biomarker Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA.

⁷Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.

⁸Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital at Harvard Medical School, Boston, MA, USA. kwei@bwh.harvard.edu.

⁹Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA. kwei@bwh.harvard.edu.

¹⁰Thayer School of Engineering, Molecular and Systems Biology and Program in Quantitative Biomedical Sciences at Dartmouth College, Hanover, NH, USA. Britt.Anne.Goods@dartmouth.edu.

¹¹Spatial Technology Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA. sfarhi@broadinstitute.org.

PubMed PMC DOI PDF

Abstract

Emerging imaging spatial transcriptomics (iST) platforms and coupled analytical methods can recover cell-to-cell interactions, groups of spatially covarying genes, and gene signatures associated with pathological features, and are thus particularly well-suited for applications in formalin fixed paraffin embedded (FFPE) tissues. Here, we benchmark the performance of three commercial iST platforms-1…

Create a free account to keep reading

Free members get 10 full research views every month across publications, clinical trials, FDA clearances, adverse events, and NIH grants. No credit card required.

Create Free Account Sign In

Want unlimited research access? See Pro plans

Data Accuracy Notice: Research intelligence on Health AI Central is aggregated from public sources (PubMed, ClinicalTrials.gov, FDA, NIH, CMS, and others) and refreshed nightly. Classifications and derived metrics are produced by automated methods described in our Methodology. We recommend verifying critical data points against the primary sources before making decisions.