ArticleF1000Research2018
False positives in trans-eQTL and co-expression analyses arising from RNA-sequencing alignment errors.
Article in F1000Research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers, 2 of them syntheses that pooled it.
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Who cites it
56 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- A meta-analysis of single-nucleus expression quantitative trait loci linking genetic risk to brain disorders.Nature genetics · 2026Pooled it
- Trans-eQTL mapping prioritises USP18 as a negative regulator of interferon response at a lupus risk locus.Nature communications · 2025Pooled it
- Multiscale structural evolution of proline-rich protein genes shapes primate salivary defenses.Molecular biology and evolution · 2026Article
- Single-nucleus atlas of cell-type specific genetic regulation in the human brain.Nature genetics · 2026Article
- Machine learning and statistical methods for molecular quantitative trait loci.Nature reviews. Genetics · 2026Review
- Genomes From 117 Vertebrate Species Reveal Rapidly Evolving Segmental-Duplication Landscapes.Genome biology and evolution · 2026Article
- NLCD: A method to discover nonlinear causal relations among genes.PLoS computational biology · 2026Article
- Transcriptome analysis in osteoarthritis primary tissues identifies high-confidence effector genes.Nature communications · 2026Article
- Design and interpretation of eQTL-GWAS colocalisation studies: Lessons from a large-scale evaluation.PLoS genetics · 2026Article
- Focus on single-gene effects limits discovery and interpretation of complex-trait-associated variants.American journal of human genetics · 2026Article
- Genetic alternative splicing regulation mapping of cartilage and synovium reveals tissue-specific mechanisms of joint-related traits.Nature communications · 2026Article
- OmiGA for ultra-efficient molecular quantitative trait loci mapping.Nature communications · 2026Article
- Article
- Integration of dilated cardiomyopathy genomics with transcriptomics from the human heart implicates regulatory molecular mechanisms.medRxiv : the preprint server for health sciences · 2026Article
- Read mismapping from segmental duplications drives spuriousbioRxiv : the preprint server for biology · 2025Article
- Functional Role of Single-Nucleotide Polymorphisms on IFNG and IFNGR1 in Humans with Cardiovascular Disease.International journal of molecular sciences · 2025Article
- Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks.Genome research · 2025Article
- Alternative Splicing Regulation in Metabolic Disorders.Obesity reviews : an official journal of the International Association for the Study of Obesity · 2025Review
- Multi-Ancestry Transcriptome-Wide Association Studies of Cognitive Function, White Matter Hyperintensity, and Alzheimer's Disease.International journal of molecular sciences · 2025Article
- The contribution of genetic determinants of blood gene expression and splicing to molecular phenotypes and health outcomes.Nature genetics · 2025Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Sequence similarity among distinct genomic regions can lead to errors in alignment of short reads from next-generation sequencing. While this is well known, the downstream consequences of misalignment have not been fully characterized. We assessed the potential for incorrect alignment of RNA-sequencing reads to cause false positives in both gene expression quantitative trait locus (eQTL) and co-expression analyses. Trans-eQTLs identified from human RNA-sequencing studies appeared to be particularly affected by this phenomenon, even when only uniquely aligned reads are considered. Over 75% of trans-eQTLs using a standard pipeline occurred between regions of sequence similarity and therefore could be due to alignment errors. Further, associations due to mapping errors are likely to misleadingly replicate between studies. To help address this problem, we quantified the potential for "cross-mapping'' to occur between every pair of annotated genes in the human genome. Such cross-mapping data can be used to filter or flag potential false positives in both trans-eQTL and co-expression analyses. Such filtering substantially alters the detection of significant associations and can have an impact on the assessment of false discovery rate, functional enrichment, and replication for RNA-sequencing association studies.
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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.