Other - Bioinformatics
Kee Thai Yeo, MD CM (McGill U, Canada), Diplomate of the American Board of Pediatrics (General Pediatrics, Neonatal-Perinatal Medicine, Pediatric Infectious Diseases)
Translational Immunology Institute/ SingHealth Duke-NUS Academic Medical Centre
Mass cytometry (CyTOF) measures the expression of many proteins (currently up to 40) in single cells. TII applies CyTOF to characterise cellular diversity of the immune system in peripheral blood and other tissues. Our version of the immune atlas, called EPIC (Extended Poly-dimensional Immunome characterisation) is built on a growing collection of CyTOF data acquired from blood of clinically and demographically diverse human subjects. The core components of the atlas are ‘immune maps’, which comprise CyTOF data of samples labeled with identical antibody panels and grouped according to a common biological theme. Besides protein expression patterns, immune maps contain contain clinical and demographic metadata, as well as phenotypic information inferred from clustering and cell type annotation. To intuitively analyse these complex multi-dimensional data, we developed a Shiny/R web application that has two main objectives. First, clients can explore the immunome at different levels of details using a wide range of interactive visualisation methods, such as bar charts comparing the abundance of all or subsets of immune cell types in different age groups, or tSNE/UMAP scatter plots providing global perspectives of expression domains. Second, users can upload their own CyTOF data and, through pattern matching, obtain instant estimates about the abundance of selected immune cell populations in their own samples. We tested our system using immune maps constructed from healthy paediatric samples. We will provide updates on the data analytics pipeline and software development.