REFLEX, a Novel Immune Profiling Assay, Combining TCR Repertoire and Multiome at Massively Scalable Single-cell...

Single-cell profiling of T cell state with immune repertoire is critical for understanding heterogenous T cell phenotypes and responses to antigen, however, existing technologies struggle to generate this information at sufficient throughput to match biological complexity. We present "REFLEX", a novel single-cell method enabling highly scalable, cost-efficient, multiomic profiling with paired-chain TCR sequencing. REFLEX utilizes in-situ reverse transcription with integrated sample multiplexing barcodes in a way that merges seamlessly with the commonly used 10x FLEX platform to allow capture of TCR sequences at unprecedented scale and depth. We profile >2 million cells from CMV-peptide-pulsed T cell expansions, capturing TCR sequences and rich multiomic information from 1.4M T cells, identifying many putative novel CMV reactive clonotypes and illustrating the scale and transformative impact on our understanding of T cell mediated adaptive immunity achievable with REFLEX.