Single cell multi-omics technologies enable human immunogenomics monitoring

Abstract Single-cell RNA-seq (scRNAseq) can investigate transcriptomic or targeted gene expression, including V(D)J and surface proteins to provide insights into mechanism discovering and therapeutic monitoring. Multiple scRNAseq technologies have recently been developed and emerged as a major driver of progress in biomedical research. Here we used three scRNAseq platforms, BD Rhapsody, Fluent PIPseq, and Parse Evercode, to monitor immunogenomics variation of certain immune cells from four hematopoietic stem cell transplant recipients. Our results identified major signature genes as potential biomarkers for stem cell transplantation outcomes. We compared an array of metrics from the three platforms in parallel to assess applications, unique advantages, and cost-effectiveness. We conclude that the BD Rhapsody system is the most comprehensive multi-omics platform for immunogenomics analyses of tens of thousands of cells, while Fluent PIPseq & Pasre Evercode have unique features and potential for larger scale single cell multi-omics profiling with Parse enabling up to one million cells per experiment. supported by 5P01CA049605-32 (EHM) from NIH, K00CA245728 (CSB) from NCI, and OPP1113682 (HTM) from the Bill and Melinda Gates Foundation.