title: eQTL mapping identifies insertion- and deletion-specific eQTLs in multiple tissues.
abstract: Genome-wide gene expression quantitative trait loci (eQTL) mapping have been focused on single-nucleotide polymorphisms and have helped interpret findings from diseases mapping studies. The functional effect of structure variants, especially short insertions and deletions (indel) has not been well investigated. Here we impute 1,380,133 indels based on the latest 1,000 Genomes Project panel into three eQTL data sets from multiple tissues. Imputation of indels increased 9.9% power and identifies indel-specific eQTLs for 325 genes. We find introns and vicinities of UTRs are more enriched of indel eQTLs and 3.6 (single-tissue)-9.2%(multi-tissue) of previous identified eSNPs were taggers of eindels. Functional analyses identifies epigenetics marks, gene ontology categories and disease GWAS loci affected by SNPs and indels eQTLs showing tissue-consistent or tissue-specific effects. This study provides new insights into the underlying genetic architecture of gene expression across tissues and new resource to interpret function of diseases and traits associated structure variants.
authors.affiliation: 1] State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China [2] Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts 02115, USA.
authors.forename: Jinyan
authors.initials: J
authors.lastname: Huang
authors.affiliation: 1] Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts 02115, USA [2] Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota 55905, USA.
authors.forename: Jun
authors.initials: J
authors.lastname: Chen
authors.affiliation: Max-Delbrück-Center for Molecular Medicine, Berlin 13092, Germany.
authors.forename: Jorge
authors.initials: J
authors.lastname: Esparza
authors.affiliation: Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA.
authors.forename: Jun
authors.initials: J
authors.lastname: Ding
authors.affiliation: 1] Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA [2] Ann Arbor Veterans Affairs Hospital, Ann Arbor, Michigan 48105, USA.
authors.forename: James T
authors.initials: JT
authors.lastname: Elder
authors.affiliation: Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA.
authors.forename: Goncalo R
authors.initials: GR
authors.lastname: Abecasis
authors.affiliation: Max-Delbrück-Center for Molecular Medicine, Berlin 13092, Germany.
authors.forename: Young-Ae
authors.initials: YA
authors.lastname: Lee
authors.affiliation: Department of Human and Medical Genetics, McGill University and Génome Québec Innovation Centre, Montréal, Canada H3A 0G1.
authors.forename: G
authors.initials: G
authors.lastname: Mark Lathrop
authors.affiliation: National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.
authors.forename: Miriam F
authors.initials: MF
authors.lastname: Moffatt
authors.affiliation: National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.
authors.forename: William O C
authors.initials: WO
authors.lastname: Cookson
authors.affiliation: 1] Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts 02115, USA [2] Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts 02115, USA.
authors.forename: Liming
authors.initials: L
authors.lastname: Liang
mesh_terms: D002648:Child; D002874:Chromosome Mapping; D044127:Epigenesis, Genetic; D056726:Genetic Association Studies; D055106:Genome-Wide Association Study; D006801:Humans; D054643:INDEL Mutation / Q000235:genetics*; D015201:Meta-Analysis as Topic; D009928:Organ Specificity / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci / Q000235:genetics*