Functional phenotyping of genomic variants using joint multiomic single-cell DNA-RNA sequencing

Genetic variants (both coding and noncoding) can impact gene function and expression, driving disease mechanisms such as cancer progression. The systematic study of endogenous genetic variants is hindered by inefficient precision editing tools, combined with technical limitations in confidently linking genotypes to gene expression at single-cell resolution. We developed single-cell DNA-RNA sequencing (SDR-seq) to simultaneously profile up to 480 genomic DNA loci and genes in thousands of single cells, enabling accurate determination of coding and noncoding variant zygosity alongside associated gene expression changes. Using SDR-seq, we associate coding and noncoding variants with distinct gene expression in human induced pluripotent stem cells. Furthermore, we demonstrate that in primary B cell lymphoma samples, cells with a higher mutational burden exhibit elevated B cell receptor signaling and tumorigenic gene expression. SDR-seq provides a powerful platform to dissect regulatory mechanisms encoded by genetic variants, advancing our understanding of gene expression regulation and its implications for disease. Several experiments were performed in this study. Proof-of-concept (01_POP) experiment test two different fixation conditions (PFA, glyoxal). Panel size experiment tested different tested different panels sizes of gDNA and RNA targets (02_Panel_size). Size of the panel is indicated in sample Title. CRISPRi experiment (03_CRISPRi) aimed to perturb TSS sites completely with a CROP-seq vector. PE experiment (04_PE) aimed to install eQTLs and STOP controls variants that have an impact on gene expression. BE experiment (05_BE) aimed to install eQTLs that have an impact on gene expression. (07_Species_Mix) tested cross-contamination of gDNA and RNA using SDR-seq.