Shared genetic origin of asthma, hay fever and eczema elucidates allergic disease biology
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Pinart, M. et al. Comorbidity of eczema, rhinitis, and asthma in IgE-sensitised and non-IgE-sensitised children in MeDALL: a population-based cohort study. Lancet Respir. Med. 2, 131–140 (2014).
Thomsen, S.F. et al. Findings on the atopic triad from a Danish twin registry. Int. J. Tuberc. Lung Dis. 10, 1268–1272 (2006).
van Beijsterveldt, C.E. & Boomsma, D.I. Genetics of parentally reported asthma, eczema and rhinitis in 5-yr-old twins. Eur. Respir. J. 29, 516–521 (2007).
Loh, P.R. et al. Contrasting genetic architectures of schizophrenia and other complex diseases using fast variance-components analysis. Nat. Genet. 47, 1385–1392 (2015).
Yang, J. et al. Conditional and joint multiple-SNP analysis of GWAS summary statistics identifies additional variants influencing complex traits. Nat. Genet. 44, 369–375, S1–S3 (2012).
Ferreira, M.A. Improving the power to detect risk variants for allergic disease by defining case–control status based on both asthma and hay fever. Twin Res. Hum. Genet. 17, 505–511 (2014).
Bulik-Sullivan, B.K. et al. LD Score regression distinguishes confounding from polygenicity in genome-wide association studies. Nat. Genet. 47, 291–295 (2015).
GTEx Consortium. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science 348, 648–660 (2015).
Wells, A. et al. The anatomical distribution of genetic associations. Nucleic Acids Res. 43, 10804–10820 (2015).
Finucane, H.K. et al. Partitioning heritability by functional annotation using genome-wide association summary statistics. Nat. Genet. 47, 1228–1235 (2015).
Farh, K.K. et al. Genetic and epigenetic fine mapping of causal autoimmune disease variants. Nature 518, 337–343 (2015).
Fehrmann, R.S. et al. Gene expression analysis identifies global gene dosage sensitivity in cancer. Nat. Genet. 47, 115–125 (2015).
Thomsen, S.F., Kyvik, K.O. & Backer, V. Etiological relationships in atopy: a review of twin studies. Twin Res. Hum. Genet. 11, 112–120 (2008).
Sanseau, P. et al. Use of genome-wide association studies for drug repositioning. Nat. Biotechnol. 30, 317–320 (2012).
Bonder, M.J. et al. Disease variants alter transcription factor levels and methylation of their binding sites. Nat. Genet. 49, 131–138 (2017).
Joehanes, R. et al. Epigenetic signatures of cigarette smoking. Circ Cardiovasc Genet 9, 436–447 (2016).
Lev, S. et al. Identification of a novel family of targets of PYK2 related to Drosophila retinal degeneration B (rdgB) protein. Mol. Cell. Biol. 19, 2278–2288 (1999).
Yan, S.R. & Novak, M.J. β2 integrin–dependent phosphorylation of protein-tyrosine kinase Pyk2 stimulated by tumor necrosis factor α and fMLP in human neutrophils adherent to fibrinogen. FEBS Lett. 451, 33–38 (1999).
Kamen, L.A., Schlessinger, J. & Lowell, C.A. Pyk2 is required for neutrophil degranulation and host defense responses to bacterial infection. J. Immunol. 186, 1656–1665 (2011).
Willer, C.J., Li, Y. & Abecasis, G.R. METAL: fast and efficient meta-analysis of genomewide association scans. Bioinformatics 26, 2190–2191 (2010).
Fadista, J., Manning, A.K., Florez, J.C. & Groop, L. The (in)famous GWAS P-value threshold revisited and updated for low-frequency variants. Eur. J. Hum. Genet. 24, 1202–1205 (2016).
Gough, H. et al. Allergic multimorbidity of asthma, rhinitis and eczema over 20 years in the German birth cohort MAS. Pediatr. Allergy Immunol. 26, 431–437 (2015).
Mortz, C.G., Andersen, K.E., Dellgren, C., Barington, T. & Bindslev-Jensen, C. Atopic dermatitis from adolescence to adulthood in the TOACS cohort: prevalence, persistence and comorbidities. Allergy 70, 836–845 (2015).
Sarnowski, C. et al. Identification of a new locus at 16q12 associated with time to asthma onset. J. Allergy Clin. Immunol. 138, 1071–1080 (2016).
Chang, X. & Wang, K. wANNOVAR: annotating genetic variants for personal genomes via the web. J. Med. Genet. 49, 433–436 (2012).
1000 Genomes Project Consortium. An integrated map of genetic variation from 1,092 human genomes. Nature 491, 56–65 (2012).
Rebhan, M., Chalifa-Caspi, V., Prilusky, J. & Lancet, D. GeneCards: integrating information about genes, proteins and diseases. Trends Genet. 13, 163 (1997).
Davis, J.R. et al. An efficient multiple-testing adjustment for eQTL studies that accounts for linkage disequilibrium between variants. Am. J. Hum. Genet. 98, 216–224 (2016).
Montgomery, S.B. et al. Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464, 773–777 (2010).
Lappalainen, T. et al. Transcriptome and genome sequencing uncovers functional variation in humans. Nature 501, 506–511 (2013).
Westra, H.J. et al. Systematic identification of trans eQTLs as putative drivers of known disease associations. Nat. Genet. 45, 1238–1243 (2013).
Chun, S. et al. Limited statistical evidence for shared genetic effects of eQTLs and autoimmune-disease-associated loci in three major immune-cell types. Nat. Genet. 49, 600–605 (2017).
Sanyal, A., Lajoie, B.R., Jain, G. & Dekker, J. The long-range interaction landscape of gene promoters. Nature 489, 109–113 (2012).
Mifsud, B. et al. Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C. Nat. Genet. 47, 598–606 (2015).
Li, G. et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell 148, 84–98 (2012).
Rao, S.S. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665–1680 (2014).
Corradin, O. et al. Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits. Genome Res. 24, 1–13 (2014).
Hnisz, D. et al. Super-enhancers in the control of cell identity and disease. Cell 155, 934–947 (2013).
He, B., Chen, C., Teng, L. & Tan, K. Global view of enhancer–promoter interactome in human cells. Proc. Natl. Acad. Sci. USA 111, E2191–E2199 (2014).
Andersson, R. et al. An atlas of active enhancers across human cell types and tissues. Nature 507, 455–461 (2014).
Welter, D. et al. The NHGRI GWAS Catalog, a curated resource of SNP–trait associations. Nucleic Acids Res. 42, D1001–D1006 (2014).
Astle, W.J. et al. The allelic landscape of human blood cell trait variation and links to common complex disease. Cell 167, 1415–1429.e19 (2016).
Zheng, J. et al. LD Hub: a centralized database and web interface to perform LD score regression that maximizes the potential of summary level GWAS data for SNP heritability and genetic correlation analysis. Bioinformatics 33, 272–279 (2017).
Fairfax, B.P. et al. Genetics of gene expression in primary immune cells identifies cell type–specific master regulators and roles of HLA alleles. Nat. Genet. 44, 502–510 (2012).
Fairfax, B.P. et al. Innate immune activity conditions the effect of regulatory variants upon monocyte gene expression. Science 343, 1246949 (2014).
Fu, J. et al. Unraveling the regulatory mechanisms underlying tissue-dependent genetic variation of gene expression. PLoS Genet. 8, e1002431 (2012).
Zhernakova, D.V. et al. Identification of context-dependent expression quantitative trait loci in whole blood. Nat. Genet. 49, 139–145 (2017).
Willemsen, G. et al. The Netherlands Twin Register biobank: a resource for genetic epidemiological studies. Twin Res. Hum. Genet. 13, 231–245 (2010).