ArticleHuman molecular genetics2017
Mapping eQTLs with RNA-seq reveals novel susceptibility genes, non-coding RNAs and alternative-splicing events in systemic lupus erythematosus.
Article in Human molecular genetics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers, 1 of them a synthesis that pooled it.
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Who cites it
27 citing papers in PubMed, 1 synthesis or guideline pooled it, 51 citations in OpenAlex.
- Omics-based integrated analysis identified IKZF2 as a biomarker associated with lupus nephritis.Scientific reports · 2022Pooled it
- A scoping review of statistical methods to investigate colocalization between genetic associations and microRNA expression in osteoarthritis.Osteoarthritis and cartilage open · 2024Article
- Autoimmunity-Associated SNP rs3024505 Disrupts STAT3 Binding in B Cells, Leading to IL10 Dysregulation.International journal of molecular sciences · 2024Article
- Get Spliced: Uniting Alternative Splicing and Arthritis.International journal of molecular sciences · 2024Review
- Extensive Alternative Splicing Patterns in Systemic Lupus Erythematosus Highlight Sexual Differences.Cells · 2023Article
- Evaluating the Contribution of Cell Type-Specific Alternative Splicing to Variation in Lipid Levels.Circulation. Genomic and precision medicine · 2023Article
- High throughput sequencing revealed enhanced cell cycle signaling in SLE patients.Scientific reports · 2023Article
- Sequencing technology as a major impetus in the advancement of studies into rheumatism: A bibliometric study.Frontiers in immunology · 2023Article
- Cross-species transcriptome analysis for early detection and specific therapeutic targeting of human lupus nephritis.Annals of the rheumatic diseases · 2022Article
- Integrative epigenomics in Sjögren´s syndrome reveals novel pathways and a strong interaction between the HLA, autoantibodies and the interferon signature.Scientific reports · 2021Article
- Harnessing natural variation to identify cis regulators of sex-biased gene expression in a multi-strain mouse liver model.PLoS genetics · 2021Article
- Article
- Calcineurin and Systemic Lupus Erythematosus: The Rationale for Using Calcineurin Inhibitors in the Treatment of Lupus Nephritis.International journal of molecular sciences · 2021Review
- Variant to Gene Mapping to Discover New Targets for Immune Tolerance.Frontiers in immunology · 2021Article
- Mapping effector genes at lupus GWAS loci using promoter Capture-C in follicular helper T cells.Nature communications · 2020Article
- ReQTL: identifying correlations between expressed SNVs and gene expression using RNA-sequencing data.Bioinformatics (Oxford, England) · 2020Article
- Combined genetic and transcriptome analysis of patients with SLE: distinct, targetable signatures for susceptibility and severity.Annals of the rheumatic diseases · 2019Article
- TCF1 and LEF1 Control Treg Competitive Survival and Tfr Development to Prevent Autoimmune Diseases.Cell reports · 2019Article
- Exome-wide search and functional annotation of genes associated in patients with severe tick-borne encephalitis in a Russian population.BMC medical genomics · 2019Article
- Interferon inducible X-linked gene CXorf21 may contribute to sexual dimorphism in Systemic Lupus Erythematosus.Nature communications · 2019Article
Corrections and comments
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Authors and funding
11 authors at 1 institution in 1 country.
Funding
Abstract
Studies attempting to functionally interpret complex-disease susceptibility loci by GWAS and eQTL integration have predominantly employed microarrays to quantify gene-expression. RNA-Seq has the potential to discover a more comprehensive set of eQTLs and illuminate the underlying molecular consequence. We examine the functional outcome of 39 variants associated with Systemic Lupus Erythematosus (SLE) through the integration of GWAS and eQTL data from the TwinsUK microarray and RNA-Seq cohort in lymphoblastoid cell lines. We use conditional analysis and a Bayesian colocalisation method to provide evidence of a shared causal-variant, then compare the ability of each quantification type to detect disease relevant eQTLs and eGenes. We discovered the greatest frequency of candidate-causal eQTLs using exon-level RNA-Seq, and identified novel SLE susceptibility genes (e.g. NADSYN1 and TCF7) that were concealed using microarrays, including four non-coding RNAs. Many of these eQTLs were found to influence the expression of several genes, supporting the notion that risk haplotypes may harbour multiple functional effects. Novel SLE associated splicing events were identified in the T-reg restricted transcription factor, IKZF2, and other candidate genes (e.g. WDFY4) through asQTL mapping using the Geuvadis cohort. We have significantly increased our understanding of the genetic control of gene-expression in SLE by maximising the leverage of RNA-Seq and performing integrative GWAS-eQTL analysis against gene, exon, and splice-junction quantifications. We conclude that to better understand the true functional consequence of regulatory variants, quantification by RNA-Seq should be performed at the exon-level as a minimum, and run in parallel with gene and splice-junction level quantification.
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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.