ArticleNature communications2014
Identification of genetic variants associated with alternative splicing using sQTLseekeR.
Article in Nature communications, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers, 2 of them syntheses that pooled it.
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Who cites it
76 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- A resource for integrated genomic analysis of the human liver.Scientific reports · 2022Pooled it
- Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease.Nature genetics · 2017Pooled it
- Co-occurring expression and methylation QTLs allow detection of common causal variants and shared biological mechanisms.Nature communications · 2018Trial
- Beyond the gene: isoform diversity as a key contributor to human brain disorders.Current opinion in genetics & development · 2026Review
- Gene Expression and Alternative Splicing Regulate Phenotypic Plasticity of a Social Wasp.Ecology and evolution · 2026Article
- Distinct genetic architecture of gene and isoform level QTL in the Diversity Outbred (DO) mouse population.bioRxiv : the preprint server for biology · 2026Article
- Full-length transcriptome atlas of porcine skeletal muscle reveals isoform-resolved genetic regulatory mechanisms for muscle growth.BMC genomics · 2026Article
- Analysis of chromatin structure reveals the connection between sQTLs and the splicing of distant genes.Scientific reports · 2025Article
- Genetic variants of LncRNA associated with splicing regulation and their impact on ovarian cancer development.Functional & integrative genomics · 2025Article
- Alternative Splicing Regulation in Metabolic Disorders.Obesity reviews : an official journal of the International Association for the Study of Obesity · 2025Review
- Long-read RNA sequencing atlas of human microglia isoforms elucidates disease-associated genetic regulation of splicing.Nature genetics · 2025Article
- Single-cell splicing QTL analysis in pancreatic islets.Frontiers in bioinformatics · 2025Article
- Regulatory QTLs affecting miRNA-mRNA interactions in cancer: mechanisms, methods, and clinical implications.Frontiers in molecular biosciences · 2025Review
- Identification of candidate causal variants and target genes at 41 breast cancer risk loci through differential allelic expression analysis.Scientific reports · 2024Article
- The impact of genetically controlled splicing on exon inclusion and protein structure.PloS one · 2024Article
- L-type calcium channels and neuropsychiatric diseases: Insights into genetic risk variant-associated genomic regulation and impact on brain development.Channels (Austin, Tex.) · 2023Review
- Long-read RNA-seq atlas of novel microglia isoforms elucidates disease-associated genetic regulation of splicing.medRxiv : the preprint server for health sciences · 2023Article
- A fast non-parametric test of association for multiple traits.Genome biology · 2023Article
- Hidden Genetic Regulation of Human Complex Traits via Brain Isoforms.Phenomics (Cham, Switzerland) · 2023Article
- Integrated analysis of genomic and transcriptomic data for the discovery of splice-associated variants in cancer.Nature communications · 2023Article
16 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
Identification of genetic variants affecting splicing in RNA sequencing population studies is still in its infancy. Splicing phenotype is more complex than gene expression and ought to be treated as a multivariate phenotype to be recapitulated completely. Here we represent the splicing pattern of a gene as the distribution of the relative abundances of a gene's alternative transcript isoforms. We develop a statistical framework that uses a distance-based approach to compute the variability of splicing ratios across observations, and a non-parametric analogue to multivariate analysis of variance. We implement this approach in the R package sQTLseekeR and use it to analyze RNA-Seq data from the Geuvadis project in 465 individuals. We identify hundreds of single nucleotide polymorphisms (SNPs) as splicing QTLs (sQTLs), including some falling in genome-wide association study SNPs. By developing the appropriate metrics, we show that sQTLseekeR compares favorably with existing methods that rely on univariate approaches, predicting variants that behave as expected from mutations affecting splicing.
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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.