ArticleNature genetics2022
Identifying disease-critical cell types and cellular processes by integrating single-cell RNA-sequencing and human genetics.
Article in Nature genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 149 papers, 4 of them syntheses that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
149 citing papers in PubMed, 4 syntheses or guidelines pooled it, 228 citations in OpenAlex.
- GWAS meta-analysis of psoriasis identifies new susceptibility alleles impacting disease mechanisms and therapeutic targets.Nature communications · 2025Pooled it
- Single-cell transcriptome landscape of circulating CD4Cell genomics · 2024Pooled it
- Integrating leiomyoma genetics, epigenomics, and single-cell transcriptomics reveals causal genetic variants, genes, and cell types.Nature communications · 2024Pooled it
- Oxidative stress gene expression, DNA methylation, and gut microbiota interaction trigger Crohn's disease: a multi-omics Mendelian randomization study.BMC medicine · 2023Pooled it
- CausalCellInfer: Prioritizing Cell-Type-Specific Disease Associations From Genetically Predicted Transcriptomes in Biobank Cohorts.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Genetic susceptibility, risk prediction, and druggable targets for oropharyngeal cancer: a UK Biobank study.European archives of oto-rhino-laryngology : official journal of the European Federation of Oto-Rhino-Laryngological Societies (EUFOS) : affiliated with the German Society for Oto-Rhino-Laryngology - Head and Neck Surgery · 2026Article
- Identifying independent causal cell types for human diseases and risk variants.Cell genomics · 2026Article
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- High-resolution promoter interaction analysis implicates genes involved in activation of type 3 innate lymphoid cells in immune disease risk.Nature genetics · 2026Article
- Genetic influences on haematopoiesis.Nature reviews. Genetics · 2026Review
- Mapping mesenchymal diversity in the human small intestine and organoids.Nature cell biology · 2026Article
- Parvalbumin interneuron activation rescues both seizures and impaired social novelty in digenic absence epilepsy mice.Science advances · 2026Article
- Ribo-ITP enables identification of translons from limited input samples.Nature communications · 2026Article
- Human genetics across levels of biological organization.Nature reviews. Genetics · 2026Review
- cellGeometry: ultra-fast single-cell deconvolution of bulk RNA-Seq using a geometric solution.Nature communications · 2026Article
- Multi-tissue analyses of allele-specific chromatin accessibility nominate likely functional variants for type 2 diabetes.medRxiv : the preprint server for health sciences · 2026Article
- From GWAS Signals to Molecular Mechanisms: Explainable AI for Causal Gene Prioritization and Biomolecular Target Interpretation.Biomolecules · 2026Review
- Microbiome-metabolite signaling networks in gastrointestinal disease: systems biology, network rewiring, and precision therapeutics.Archives of microbiology · 2026Review
- Translating genome-wide association studies at multiple scales: Drug target prioritization, cellular architectures, and organ imaging.Cell genomics · 2026Review
89 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors at 2 institutions in 1 country.
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Abstract
Genome-wide association studies provide a powerful means of identifying loci and genes contributing to disease, but in many cases, the related cell types/states through which genes confer disease risk remain unknown. Deciphering such relationships is important for identifying pathogenic processes and developing therapeutics. In the present study, we introduce sc-linker, a framework for integrating single-cell RNA-sequencing, epigenomic SNP-to-gene maps and genome-wide association study summary statistics to infer the underlying cell types and processes by which genetic variants influence disease. The inferred disease enrichments recapitulated known biology and highlighted notable cell-disease relationships, including γ-aminobutyric acid-ergic neurons in major depressive disorder, a disease-dependent M-cell program in ulcerative colitis and a disease-specific complement cascade process in multiple sclerosis. In autoimmune disease, both healthy and disease-dependent immune cell-type programs were associated, whereas only disease-dependent epithelial cell programs were prominent, suggesting a role in disease response rather than initiation. Our framework provides a powerful approach for identifying the cell types and cellular processes by which genetic variants influence disease.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.