Integrated Single-Cell Detection of Genotype and Phenotype in SF3B1-Mutated Chronic Lymphocytic Leukemia Cells

Cancer cell phenotype is controlled by both genetic composition and gene expression. Recent large-scale cancer sequencing studies have revealed extensive intratumoral genetic heterogeneity and have demonstrated its potential impact on clonal evolution and clinical outcome. The most direct approach to uncovering the impact of genetic heterogeneity on cellular phenotype requires integration of genetic and transcriptomic profiles of single cells. Currently, however, RNA and DNA cannot be reliably isolated from the same cell. Here, we demonstrate the feasibility for linking single-cell somatic mutation data with cellular transcriptional heterogeneity through a targeted RNA-based approach. By leveraging a microfluidic platform (Fluidigm BioMarkTMHD system) to perform multiplexed targeted amplification of RNA derived from hundreds of single cells, we have generated a versatile approach for the integrated detection of somatic mutations in relation to specific gene transcripts.