Efficient count-based models improve power and robustness for large-scale single-cell eQTL mapping

Population-scale single-cell transcriptomic technologies (scRNA-seq) enable characterizing variant effects on gene regulation at the cellular level (e.g., single-cell eQTLs; sc-eQTLs). However, existing sc-eQTL mapping approaches are either not designed for analyzing sparse counts in scRNA-seq data or can become intractable in extremely large datasets. Here, we propose jaxQTL, a flexible and efficient sc-eQTL mapping framework using highly efficient count-based models given pseudobulk data. Using extensive simulations, we demonstrated that jaxQTL with a negative binomial model outperformed other models in identifying sc-eQTLs, while maintaining a calibrated type I error. We applied jaxQTL across 14 cell types of OneK1K scRNA-seq data (N=982), and identified 11-16% more eGenes compared with existing approaches, primarily driven by jaxQTL ability to identify lowly expressed eGenes. We observed that fine-mapped sc-eQTLs were further from transcription starting site (TSS) than fine-mapped eQTLs identified in all cells (bulk-eQTLs; P=1x10-4) and more enriched in cell-type-specific enhancers (P=3x10-10), suggesting that sc-eQTLs improve our ability to identify distal eQTLs that are missed in bulk tissues. Overall, the genetic effect of fine-mapped sc-eQTLs were largely shared across cell types, with cell-type-specificity increasing with distance to TSS. Lastly, we observed that sc-eQTLs explain more SNP-heritability (h2) than bulk-eQTLs (9.90 {+/-} 0.88% vs. 6.10 {+/-} 0.76% when meta-analyzed across 16 blood and immune-related traits), improving but not closing the missing link between GWAS and eQTLs. As an example, we highlight that sc-eQTLs in T cells (unlike bulk-eQTLs) can successfully nominate IL6ST as a candidate gene for rheumatoid arthritis. Overall, jaxQTL provides an efficient and powerful approach using count-based models to identify missing disease-associated eQTLs.