Overview
Many applications of scRNA-seq are focused on cell type identification, gene regulatory networks, or biomarker discovery. These applications often do not require surveying the whole transcriptome (WT), but
rather require the interrogation of specific sets of well-characterized genes. In these cases, sequencing the entire transcriptome may be adding unnecessary costs. To increase throughput and minimize
sequencing costs, the development of a targeted gene enrichment method is required. Here, we demonstrate an approach to combine split-pool combinatorial barcoding with enrichment of 1000 genes
(Immune1000 panel) representing immune cell markers and pathways. We use this gene panel to characterize 730,000 human bone marrow mononuclear cells (BMMCs) from four leukemia and four healthy
donors. We found that enrichment with the Immune1000 Panel enabled the characterization of all major immune cell types at low sequencing depth and allowed for the detection of known leukemia-associated
shifts in cell type proportions. Moreover, our targeted sequencing method enabled the detection of a rare (~0.35%), leukemia-specific T cell population that showed highly proliferative and cytotoxic potential.
Overall, we demonstrate our modular enrichment strategy preserves biological structure and allows for deep characterization of rare disease-relevant cell types and gene signatures with less sequencing.
