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      Epistasis between FLG and IL4R Genes on the Risk of Allergic Sensitization: Results from Two Population-Based Birth Cohort Studies

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          Abstract

          Immune-specific genes as well as genes responsible for the formation and integrity of the epidermal barrier have been implicated in the pathogeneses of allergic sensitization. This study sought to determine whether an epistatic effect (gene-gene interaction) between genetic variants within interleukin 4 receptor ( IL4R) and filaggrin ( FLG) genes predispose to the development of allergic sensitization. Data from two birth cohort studies were analyzed, namely the Isle of Wight (IOW; n = 1,456) and the Manchester Asthma and Allergy Study (MAAS; n = 1,058). In the IOW study, one interaction term ( IL4R rs3024676 ×  FLG variants) showed statistical significance (interaction term: P = 0.003). To illustrate the observed epistasis, stratified analyses were performed, which showed that FLG variants were associated with allergic sensitization only among IL4R rs3024676 homozygotes (OR, 1.97; 95% CI, 1.27–3.05; P = 0.003). In contrast, FLG variants effect was masked among IL4R rs3024676 heterozygotes (OR, 0.53; 95% CI, 0.22–1.32; P = 0.175). Similar results were demonstrated in the MAAS study. Epistasis between immune ( IL4R) and skin ( FLG) regulatory genes exist in the pathogenesis of allergic sensitization. Hence, genetic susceptibility towards defective epidermal barrier and deviated immune responses could work together in the development of allergic sensitization.

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          Common loss-of-function variants of the epidermal barrier protein filaggrin are a major predisposing factor for atopic dermatitis.

          Atopic disease, including atopic dermatitis (eczema), allergy and asthma, has increased in frequency in recent decades and now affects approximately 20% of the population in the developed world. Twin and family studies have shown that predisposition to atopic disease is highly heritable. Although most genetic studies have focused on immunological mechanisms, a primary epithelial barrier defect has been anticipated. Filaggrin is a key protein that facilitates terminal differentiation of the epidermis and formation of the skin barrier. Here we show that two independent loss-of-function genetic variants (R510X and 2282del4) in the gene encoding filaggrin (FLG) are very strong predisposing factors for atopic dermatitis. These variants are carried by approximately 9% of people of European origin. These variants also show highly significant association with asthma occurring in the context of atopic dermatitis. This work establishes a key role for impaired skin barrier function in the development of atopic disease.
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            The mystery of missing heritability: Genetic interactions create phantom heritability.

            Human genetics has been haunted by the mystery of "missing heritability" of common traits. Although studies have discovered >1,200 variants associated with common diseases and traits, these variants typically appear to explain only a minority of the heritability. The proportion of heritability explained by a set of variants is the ratio of (i) the heritability due to these variants (numerator), estimated directly from their observed effects, to (ii) the total heritability (denominator), inferred indirectly from population data. The prevailing view has been that the explanation for missing heritability lies in the numerator--that is, in as-yet undiscovered variants. While many variants surely remain to be found, we show here that a substantial portion of missing heritability could arise from overestimation of the denominator, creating "phantom heritability." Specifically, (i) estimates of total heritability implicitly assume the trait involves no genetic interactions (epistasis) among loci; (ii) this assumption is not justified, because models with interactions are also consistent with observable data; and (iii) under such models, the total heritability may be much smaller and thus the proportion of heritability explained much larger. For example, 80% of the currently missing heritability for Crohn's disease could be due to genetic interactions, if the disease involves interaction among three pathways. In short, missing heritability need not directly correspond to missing variants, because current estimates of total heritability may be significantly inflated by genetic interactions. Finally, we describe a method for estimating heritability from isolated populations that is not inflated by genetic interactions.
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              Longitudinal Data Analysis for Discrete and Continuous Outcomes

              Longitudinal data sets are comprised of repeated observations of an outcome and a set of covariates for each of many subjects. One objective of statistical analysis is to describe the marginal expectation of the outcome variable as a function of the covariates while accounting for the correlation among the repeated observations for a given subject. This paper proposes a unifying approach to such analysis for a variety of discrete and continuous outcomes. A class of generalized estimating equations (GEEs) for the regression parameters is proposed. The equations are extensions of those used in quasi-likelihood (Wedderburn, 1974, Biometrika 61, 439-447) methods. The GEEs have solutions which are consistent and asymptotically Gaussian even when the time dependence is misspecified as we often expect. A consistent variance estimate is presented. We illustrate the use of the GEE approach with longitudinal data from a study of the effect of mothers' stress on children's morbidity.
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                Author and article information

                Contributors
                aziyab@hsc.edu.kw
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                19 February 2018
                19 February 2018
                2018
                : 8
                : 3221
                Affiliations
                [1 ]ISNI 0000 0001 1240 3921, GRID grid.411196.a, Department of Community Medicine and Behavioral Sciences, Faculty of Medicine, , Kuwait University, ; Kuwait City, Kuwait
                [2 ]ISNI 0000000121662407, GRID grid.5379.8, Division of Infection, Immunity and Respiratory Medicine, Manchester Academic Health Science Centre, , The University of Manchester, Manchester University NHS Foundation Trust, ; Manchester, UK
                [3 ]ISNI 0000 0001 2150 1785, GRID grid.17088.36, College of Veterinary Medicine, , Michigan State University, ; East Lansing, Michigan USA
                [4 ]ISNI 0000 0000 9025 8099, GRID grid.239573.9, Division of Allergy and Immunology, , Cincinnati Children’s Hospital, ; Cincinnati, OH USA
                [5 ]ISNI 0000000121662407, GRID grid.5379.8, Centre for Respiratory Medicine and Allergy, Institute of Inflammation and Repair, , University of Manchester, University Hospital of South Manchester NHS Foundation Trust, ; Manchester, UK
                [6 ]ISNI 0000 0000 9560 654X, GRID grid.56061.34, Division of Epidemiology, Biostatistics and Environmental Health, , School of Public Health, University of Memphis, ; Memphis, TN USA
                [7 ]ISNI 0000 0001 2113 8111, GRID grid.7445.2, Department of Paediatrics, , Imperial College London, ; London, UK
                [8 ]ISNI 0000 0004 0641 2620, GRID grid.416523.7, David Hide Asthma and Allergy Research Centre, , St Mary’s Hospital, ; Isle of Wight, UK
                [9 ]ISNI 0000 0004 1936 9297, GRID grid.5491.9, Clinical and Experimental Sciences Academic Unit, Faculty of Medicine, , University of Southampton, ; Southampton, UK
                Author information
                http://orcid.org/0000-0003-3099-4424
                http://orcid.org/0000-0001-5069-7190
                Article
                21459
                10.1038/s41598-018-21459-x
                5818621
                29459738
                74dcee84-ed43-4e30-87a1-02d432f73782
                © The Author(s) 2018

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 9 August 2017
                : 5 February 2018
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