# The Gene Team

- **Event:** [Built with Claude: Life Sciences](https://cerebralvalley.ai/e/built-with-claude-life-sciences)
- **When:** Jul 7 at 12:00 PM – Jul 14 at 12:00 AM (EDT)
- **Where:** Online
- **Team:** [James Hilser](https://cerebralvalley.ai/u/JRH)
- **GitHub:** https://github.com/thegeneteam/PlaqueQTL
- **Demo video:** https://www.youtube.com/watch?v=_d9BmmTHEOg
- **Gallery:** https://cerebralvalley.ai/e/built-with-claude-life-sciences/hackathon/gallery
- **Page:** https://cerebralvalley.ai/e/built-with-claude-life-sciences/hackathon/gallery/72

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.

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Markdown version of https://cerebralvalley.ai/e/built-with-claude-life-sciences/hackathon/gallery/72. Site index for agents: https://cerebralvalley.ai/llms.txt · full text: https://cerebralvalley.ai/llms-full.txt