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Loucoubar C, Grant AV, Bureau JF, Casademont I, Bar NA, Bar-Hen A, Diop M, Faye J, Sarr FD, Badiane A, Tall A, Trape JF, Cliquet F, Schwikowski B, Lathrop M, Paul RE, Sakuntabhai A. Detecting multi-way epistasis in family-based association studies. Brief Bioinform 2017; 18:394-402. [PMID: 27178992 DOI: 10.1093/bib/bbw039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Indexed: 11/13/2022] Open
Abstract
The era of genome-wide association studies (GWAS) has led to the discovery of numerous genetic variants associated with disease. Better understanding of whether these or other variants interact leading to differential risk compared with individual marker effects will increase our understanding of the genetic architecture of disease, which may be investigated using the family-based study design. We present M-TDT (the multi-locus transmission disequilibrium test), a tool for detecting family-based multi-locus multi-allelic effects for qualitative or quantitative traits, extended from the original transmission disequilibrium test (TDT). Tests to handle the comparison between additive and epistatic models, lack of independence between markers and multiple offspring are described. Performance of M-TDT is compared with a multifactor dimensionality reduction (MDR) approach designed for investigating families in the hypothesis-free genome-wide setting (the multifactor dimensionality reduction pedigree disequilibrium test, MDR-PDT). Other methods derived from the TDT or MDR to investigate genetic interaction in the family-based design are also discussed. The case of three independent biallelic loci is illustrated using simulations for one- to three-locus alternative hypotheses. M-TDT identified joint-locus effects and distinguished effectively between additive and epistatic models. We showed a practical example of M-TDT based on three genes already known to be implicated in malaria susceptibility. Our findings demonstrate the value of M-TDT in a hypothesis-driven context to test for multi-way epistasis underlying common disease etiology, whereas MDR-PDT-based methods are more appropriate in a hypothesis-free genome-wide setting.
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Mascheretti S, Trezzi V, Giorda R, Boivin M, Plourde V, Vitaro F, Brendgen M, Dionne G, Marino C. Complex effects of dyslexia risk factors account for ADHD traits: evidence from two independent samples. J Child Psychol Psychiatry 2017; 58:75-82. [PMID: 27501527 DOI: 10.1111/jcpp.12612] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/13/2016] [Indexed: 01/01/2023]
Abstract
BACKGROUND Developmental dyslexia (DD) and attention deficit/hyperactivity disorder (ADHD) are among the most common neurodevelopmental disorders, whose etiology involves multiple risk factors. DD and ADHD co-occur in the same individuals much more often than would be expected by chance. Several studies have found significant bivariate heritability, and specific genes associated with either DD or ADHD have been investigated for association in the other disorder. Moreover, there are likely to be gene-by-gene and gene-by-environment interaction effects (G × G and G × E, respectively) underlying the comorbidity between DD and ADHD. We investigated the pleiotropic effects of 19 SNPs spanning five DD genes (DYX1C1, DCDC2, KIAA0319, ROBO1, and GRIN2B) and seven DD environmental factors (smoke, miscarriage, birth weight, breastfeeding, parental age, socioeconomic status, and parental education) for main, either (a) genetic or (b) environmental, (c) G × G, and (d) G × E upon inattention and hyperactivity/impulsivity. We then attempted replication of these findings in an independent twin cohort. METHODS Marker-trait association was analyzed by implementing the Quantitative Transmission Disequilibrium Test (QTDT). Environmental associations were tested by partial correlations. G × G were investigated by a general linear model equation and a family-based association test. G × E were analyzed through a general test for G × E in sib pair-based association analysis of quantitative traits. RESULTS DCDC2-rs793862 was associated with hyperactivity/impulsivity via G × G (KIAA0319) and G × E (miscarriage). Smoke was significantly correlated with hyperactivity/impulsivity. We replicated the DCDC2 × KIAA0319 interaction upon hyperactivity/impulsivity in the twin cohort. CONCLUSIONS DD genetic (DCDC2) and environmental factors (smoke and miscarriage) underlie ADHD traits supporting a potential pleiotropic effect.
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Affiliation(s)
- Sara Mascheretti
- Child Psychopathology Unit, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Italy
| | - Vittoria Trezzi
- Child Psychopathology Unit, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Italy
| | - Roberto Giorda
- Molecular Biology Lab, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Italy
| | - Michel Boivin
- Research Unit on Children's Psychosocial Maladjustment, Montréal, QC, Canada.,Ecole de Psychologie, Laval University, Québec, QC, Canada.,Institute of Genetic, Neurobiological, and Social Foundations of Child Development, Tomsk State University, Tomsk, Russian Federation
| | - Vickie Plourde
- Research Unit on Children's Psychosocial Maladjustment, Montréal, QC, Canada.,Ecole de Psychologie, Laval University, Québec, QC, Canada
| | - Frank Vitaro
- Research Unit on Children's Psychosocial Maladjustment, Montréal, QC, Canada.,Department of Psycho-Education, GRIP, University of Montreal, Montreal, QC, Canada
| | - Mara Brendgen
- Research Unit on Children's Psychosocial Maladjustment, Montréal, QC, Canada.,Department of Psychology, Université du Québec à Montréal, Montreal, QC, Canada
| | - Ginette Dionne
- Research Unit on Children's Psychosocial Maladjustment, Montréal, QC, Canada.,Ecole de Psychologie, Laval University, Québec, QC, Canada
| | - Cecilia Marino
- Child Psychopathology Unit, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Italy.,Centre for Addiction and Mental Health, University of Toronto, Toronto, ON, Canada
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Gola D, Mahachie John JM, van Steen K, König IR. A roadmap to multifactor dimensionality reduction methods. Brief Bioinform 2015; 17:293-308. [PMID: 26108231 PMCID: PMC4793893 DOI: 10.1093/bib/bbv038] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Indexed: 02/02/2023] Open
Abstract
Complex diseases are defined to be determined by multiple genetic and environmental factors alone as well as in interactions. To analyze interactions in genetic data, many statistical methods have been suggested, with most of them relying on statistical regression models. Given the known limitations of classical methods, approaches from the machine-learning community have also become attractive. From this latter family, a fast-growing collection of methods emerged that are based on the Multifactor Dimensionality Reduction (MDR) approach. Since its first introduction, MDR has enjoyed great popularity in applications and has been extended and modified multiple times. Based on a literature search, we here provide a systematic and comprehensive overview of these suggested methods. The methods are described in detail, and the availability of implementations is listed. Most recent approaches offer to deal with large-scale data sets and rare variants, which is why we expect these methods to even gain in popularity.
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Lee Y, Ghosh D, Zhang Y. Association testing to detect gene-gene interactions on sex chromosomes in trio data. Front Genet 2013; 4:239. [PMID: 24312118 PMCID: PMC3826485 DOI: 10.3389/fgene.2013.00239] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 10/24/2013] [Indexed: 11/13/2022] Open
Abstract
Autism Spectrum Disorder (ASD) occurs more often among males than females in a 4:1 ratio. Among theories used to explain the causes of ASD, the X chromosome and the Y chromosome theories attribute ASD to the X-linked mutation and the male-limited gene expressions on the Y chromosome, respectively. Despite the rationale of the theory, studies have failed to attribute the sex-biased ratio to the significant linkage or association on the regions of interest on X chromosome. We further study the gender biased ratio by examining the possible interaction effects between two genes in the sex chromosomes. We propose a logistic regression model with mixed effects to detect gene–gene interactions on sex chromosomes. We investigated the power and type I error rates of the approach for a range of minor allele frequencies and varying linkage disequilibrium between markers and QTLs. We also evaluated the robustness of the model to population stratification. We applied the model to a trio-family data set with an ASD affected male child to study gene–gene interactions on sex chromosomes.
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Affiliation(s)
- Yeonok Lee
- Department of Statistics, Penn State University, University Park PA, USA
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