The Gene Team

PlaqueQTL builds a cell-type-resolved eQTL resource for atherosclerotic plaque entirely from public single-cell RNA-seq — no new sequencing, no genotyping array. The key move: donor genotypes are called directly from the RNA reads of published plaque single-cell/single-nucleus datasets using Monopogen, recovering 3,812,318 high-quality variants across 57 donors and all 22 autosomes with zero missingness. Using these de-novo genotypes, we mapped cell-type-specific cis-eQTLs genome-wide (16,902 genes; 118,286 gene×cell-type tests) in diseased human plaque. The method validates cleanly: across 9 cell types it recovers established GTEx artery eGenes in the expected cell type. It then does what bulk tissue cannot — it localizes the known coronary-artery-disease gene GUCY1A1 specifically to the fibroblast compartment (rs7671138, p=8.9×10⁻⁸), and it reveals a distinct class of regulation exemplified by CFDP1: a gene expressed across every cell type whose genetic effect fires only in the smooth-muscle-derived mesenchymal lineage — cell-type specificity invisible to bulk artery. Why it matters: GWAS has found hundreds of CAD loci but rarely resolves the gene and the cell type through which a variant acts, and the standard vascular reference (GTEx) is bulk, non-diseased tissue. PlaqueQTL shows that the thousands of public single-cell datasets are themselves a latent statistical-genetics resource — every one carries recoverable genotypes — offering a low-cost, high-yield route to disease-context, cell-type-resolved regulatory maps.