ArticleGenome biology2021
Single cell eQTL analysis identifies cell type-specific genetic control of gene expression in fibroblasts and reprogrammed induced pluripotent stem cells.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers, 1 of them a synthesis that pooled it.
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Who cites it
68 citing papers in PubMed, 1 synthesis or guideline pooled it, 116 citations in OpenAlex.
- Integrating cell-type-specific gene expression and genome-wide associations identifies risk genes for schizophrenia.Molecular psychiatry · 2026Pooled it
- Data-intensive immune network modelling for One Health.Briefings in bioinformatics · 2026Review
- A scalable framework for single-cell eQTL mapping uncovers genetic regulators of meat production traits in pigs.Journal of animal science and biotechnology · 2026Article
- A novel machine learning-based algorithm for eQTL identification reveals complex pleiotropic effects in the MHC region.Briefings in bioinformatics · 2026Article
- eQTL analysis: A bridge from genome to mechanism.Genes & diseases · 2026Review
- Lessons from single cell omics: admixed American ancestry and sex confer cardiometabolic disease risk in Mexicans.Genome medicine · 2026Article
- Article
- Single-cell eQTL mapping reveals cell-type-specific genetic regulation in lung cancer.Cell genomics · 2026Article
- Generation of Donor-Specific iPSC for Modelling Lysosomal Storage Disorders.Methods in molecular biology (Clifton, N.J.) · 2026Article
- distQTL: distribution quantitative trait loci identification by population-scale single-cell data.NAR genomics and bioinformatics · 2025Article
- Cell type-specific eQTL analysis of COVID-19 based on single-cell transcriptomic data.NAR genomics and bioinformatics · 2025Article
- distQTL: Distribution Quantitative Trait Loci Identification by Population-Scale Single-Cell Data.bioRxiv : the preprint server for biology · 2025Article
- Article
- scQTLtools: An R/Bioconductor Package for Comprehensive Identification and Visualization of Single-Cell eQTLs.Biology · 2025Article
- Single-cell eQTL mapping reveals cell-type-specific genes associated with the risk of gastric cancer.Cell genomics · 2025Article
- Article
- The impact of ambient contamination on demultiplexing methods for single-nucleus multiome experiments.Research square · 2025Article
- The impact of ambient contamination on demultiplexing methods for single-nucleus multiome experiments.bioRxiv : the preprint server for biology · 2025Article
- Haplotype rather than single causal variants effects contribute to regulatory gene expression associations in human myeloid cells.bioRxiv : the preprint server for biology · 2025Article
- A multi-omics Mendelian randomization study identifies new therapeutic targets for alcohol use disorder and problem drinking.Nature human behaviour · 2025Article
8 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
17 authors at 5 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe discovery that somatic cells can be reprogrammed to induced pluripotent stem cells (iPSCs) has provided a foundation for in vitro human disease modelling, drug development and population genetics studies. Gene expression plays a critical role in complex disease risk and therapeutic response. However, while the genetic background of reprogrammed cell lines has been shown to strongly influence gene expression, the effect has not been evaluated at the level of individual cells which would provide significant resolution. By integrating single cell RNA-sequencing (scRNA-seq) and population genetics, we apply a framework in which to evaluate cell type-specific effects of genetic variation on gene expression.
resultsHere, we perform scRNA-seq on 64,018 fibroblasts from 79 donors and map expression quantitative trait loci (eQTLs) at the level of individual cell types. We demonstrate that the majority of eQTLs detected in fibroblasts are specific to an individual cell subtype. To address if the allelic effects on gene expression are maintained following cell reprogramming, we generate scRNA-seq data in 19,967 iPSCs from 31 reprogramed donor lines. We again identify highly cell type-specific eQTLs in iPSCs and show that the eQTLs in fibroblasts almost entirely disappear during reprogramming.
conclusionsThis work provides an atlas of how genetic variation influences gene expression across cell subtypes and provides evidence for patterns of genetic architecture that lead to cell type-specific eQTL effects.
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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.