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Related Experiment Video

Updated: Jan 16, 2026

Single-cell RNA Sequencing and Analysis of Human Pancreatic Islets
11:34

Single-cell RNA Sequencing and Analysis of Human Pancreatic Islets

Published on: July 18, 2019

17.0K

Single-cell splicing QTL analysis in pancreatic islets.

Jae-Won Cho1, Jingyi Cao1, Martin Hemberg1

  • 1The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, United States.

Frontiers in Bioinformatics
|September 26, 2025
PubMed
Summary

This study identified 228 cell type-specific splicing quantitative trait loci (sQTLs) in pancreatic islet cells, revealing novel genetic variants impacting gene regulation and cell function. These findings advance our understanding of splicing regulation at a single-cell level.

Keywords:
CDC42alternative splicingpancreatic isletsingle-cell RNA-sequencingsplicing quantitative trait loci

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Last Updated: Jan 16, 2026

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Area of Science:

  • Genomics
  • Molecular Biology
  • Transcriptomics

Background:

  • Alternative splicing (AS) significantly expands transcriptome diversity and is implicated in various diseases.
  • Genetic variants, known as splicing quantitative trait loci (sQTLs), influence AS.
  • Single-cell technologies enable the study of genetic effects at a cell-type-specific resolution.

Purpose of the Study:

  • To identify cell type-specific splicing quantitative trait loci (sQTLs) in pancreatic islet cells.
  • To investigate the genetic regulation of alternative splicing in distinct pancreatic cell types.
  • To explore the functional implications of cell type-specific sQTLs.

Main Methods:

  • Utilized eight full-length single-cell RNA sequencing (scRNA-seq) pancreatic islet datasets.
  • Performed individual genotyping using CTAT and Streka2 pipelines.
  • Quantified isoform expression with RSEM and identified sQTLs using sQTLseeker2.

Main Results:

  • Identified 228 cell type-level sQTLs across 152 genes in alpha and beta cells.
  • Discovered four novel variants affecting CDC42, a gene crucial for cell morphology, not detected in bulk analyses.
  • Demonstrated the feasibility of identifying cell type-specific genetic influences on splicing.

Conclusions:

  • This study provides a proof of concept for identifying cell type-specific sQTLs.
  • Future, larger-scale studies can further elucidate the genetic control of splicing.
  • Cell type-specific sQTL analysis offers deeper insights into disease mechanisms and gene regulation.