title: Mapping eQTLs with RNA-seq reveals novel susceptibility genes, non-coding RNAs and alternative-splicing events in systemic lupus erythematosus.
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.
authors.affiliation: Department of Medical & Molecular Genetics, King's College London, London, UK.
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Odhams
authors.affiliation: Department of Medical & Molecular Genetics, King's College London, London, UK.
authors.forename: Andrea
authors.initials: A
authors.lastname: Cortini
authors.affiliation: Department of Medical & Molecular Genetics, King's College London, London, UK.
authors.forename: Lingyan
authors.initials: L
authors.lastname: Chen
authors.affiliation: Department of Medical & Molecular Genetics, King's College London, London, UK.
authors.forename: Amy L
authors.initials: AL
authors.lastname: Roberts
authors.affiliation: Department of Twin Research, King's College London, London, UK.
authors.forename: Ana
authors.initials: A
authors.lastname: Viñuela
authors.forename: Alfonso
authors.initials: A
authors.lastname: Buil
authors.affiliation: Department of Twin Research, King's College London, London, UK.
authors.forename: Kerrin S
authors.initials: KS
authors.lastname: Small
authors.forename: Emmanouil T
authors.initials: ET
authors.lastname: Dermitzakis
authors.affiliation: Department of Medical & Molecular Genetics, King's College London, London, UK.
authors.forename: David L
authors.initials: DL
authors.lastname: Morris
authors.affiliation: Department of Medical & Molecular Genetics, King's College London, London, UK.|Division of Immunology, Infection and Inflammatory Disease, King's College London, London, UK.
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Vyse
authors.affiliation: Department of Medical & Molecular Genetics, King's College London, London, UK.
authors.forename: Deborah S
authors.initials: DS
authors.lastname: Cunninghame Graham
mesh_terms: D017398:Alternative Splicing / Q000235:genetics; D019733:Carbon-Nitrogen Ligases with Glutamine as Amide-N-Donor / Q000096:biosynthesis / Q000235:genetics; D002874:Chromosome Mapping; D005260:Female; D005786:Gene Expression Regulation; D020022:Genetic Predisposition to Disease; D055106:Genome-Wide Association Study; D006239:Haplotypes; D006801:Humans; D008180:Lupus Erythematosus, Systemic / Q000235:genetics* / Q000473:pathology; D008297:Male; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci / Q000235:genetics*; D022661:RNA, Untranslated / Q000235:genetics*; D051822:T Cell Transcription Factor 1 / Q000096:biosynthesis / Q000235:genetics
chemical_list: D022661:RNA, Untranslated; D051822:T Cell Transcription Factor 1; C497576:TCF7 protein, human; D019733:Carbon-Nitrogen Ligases with Glutamine as Amide-N-Donor; C000593321:NADSYN1 protein, human