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Girelli D, Piubelli C, Martinelli N, Corrocher R, Olivieri O. A decade of progress on the genetic basis of coronary artery disease. Practical insights for the internist. Eur J Intern Med 2017; 41:10-17. [PMID: 28395986 DOI: 10.1016/j.ejim.2017.03.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 03/24/2017] [Accepted: 03/27/2017] [Indexed: 12/24/2022]
Abstract
Clinicians are well aware of the importance of a positive family history for coronary artery disease (CAD). Nonetheless, elucidation of the genetic basis of CAD has long proven difficult. The scenario changed in the last decade through the application of modern genomic technologies, like genome-wide association studies (GWAS) and next generation sequencing (NGS). GWAS have discovered over 60 common variants highly associated with CAD. For predictive purposes, such variants have been used to build up Genetic Risk Scores (GRSs), but their incorporation into classical prediction models does not appear substantially outperform the simple addition of family history. To date, the only strong case for the utility of incorporating genetic testing into clinical practice is represented by the diagnosis of Familial Hypercholesterolemia (FH). On the other hand, utilization of genomic techniques has driven formidable advances into the knowledge of CAD pathophysiology, particularly by addressing controversies on the causality of some lipid fractions that had long remained unsolved because of limitations of observational epidemiology. For example, NGS-derived rare variants with strong functional effects on key-genes like ANGPTL4, APOA5, APOC3, LPL, and SCARB1, have proven useful as proxies to demonstrate the causality of triglyceride-rich lipoproteins (TRLs) at variance with HDL-cholesterol concentration, thus contributing to tear down a dogma from classical epidemiology. Moreover, such variants have paved the way for the development of new biologic drugs (i.e. monoclonal antibodies or antisense oligonucleotides) targeting key proteins like PCSK9, Lipoprotein(a), and apolipoprotein C3. Such drugs are currently under active investigation, with first results being extremely promising.
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Affiliation(s)
- Domenico Girelli
- Department of Medicine, Section of Internal Medicine, University of Verona, Italy.
| | - Chiara Piubelli
- Department of Medicine, Section of Internal Medicine, University of Verona, Italy
| | - Nicola Martinelli
- Department of Medicine, Section of Internal Medicine, University of Verona, Italy
| | - Roberto Corrocher
- Department of Medicine, Section of Internal Medicine, University of Verona, Italy
| | - Oliviero Olivieri
- Department of Medicine, Section of Internal Medicine, University of Verona, Italy
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Association of polymorphic variants of PTPN22, TNF and VDR systems in children with lupus nephritis: a study in trios of Colombian families. BIOMEDICA 2017; 37:260-266. [DOI: 10.7705/biomedica.v37i3.3247] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 07/25/2016] [Indexed: 11/21/2022]
Abstract
Introducción. El lupus eritematoso sistémico es una enfermedad autoinmune cuya gravedad varía según la raza, género y edad de aparición. Esta disparidad también se observa en los marcadores genéticos asociados con la enfermedad presentes en los genes PTPN22, VDR y TNF. La estratificación genética que presentan las diferentes poblaciones en el mundo puede estar influyendo dicha variabilidad.Objetivo. Analizar la asociación y heredabilidad de variantes genéticas de los genes PTPN22, VDR y TNF con nefritis lúpica pediátrica (NLp) en familias colombianas.Materiales y métodos. Se realizó un estudio basado en familias con 46 tríos (caso/padre y madre). Se genotipificaron las variantes rs2476601 de PTPN22; rs361525 y rs1800629 de TNF; TaqI [rs731236], ApaI [rs7975232], BsmI [rs1544410] y FokI [rs2228570] de VDR mediante qPCR. Se estimó el efecto de la sobretransmisión del alelo de riesgo de padres a hijos y el desequilibrio de ligamiento de los loci VDR y TNF.Resultados. Se observó que el alelo A de rs2476601 en PTPN22 se distribuyó en el 8,69 % [n=16] de los padres mientras que en los casos es de 19,5 % [n=18] al igual que es sobretransmitido de padres a hijos 17 veces más con relación al alelo G (p=0,028). Los polimorfismos de TNF y VDR no se mostraron en desequilibrio de transmisión. Las variantes TaqI, ApaI y BsmI del VDR se mostraron en desequilibrio de ligamiento.Conclusión. Estos hallazgos muestran una asociación del polimorfismo rs2476601 de PTPN22 con NLp debido a su sobretransmisión en el grupo de familias estudiadas.
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Resolving the Complex Genetic Basis of Phenotypic Variation and Variability of Cellular Growth. Genetics 2017; 206:1645-1657. [PMID: 28495957 DOI: 10.1534/genetics.116.195180] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 05/02/2017] [Indexed: 01/10/2023] Open
Abstract
In all organisms, the majority of traits vary continuously between individuals. Explaining the genetic basis of quantitative trait variation requires comprehensively accounting for genetic and nongenetic factors as well as their interactions. The growth of microbial cells can be characterized by a lag duration, an exponential growth phase, and a stationary phase. Parameters that characterize these growth phases can vary among genotypes (phenotypic variation), environmental conditions (phenotypic plasticity), and among isogenic cells in a given environment (phenotypic variability). We used a high-throughput microscopy assay to map genetic loci determining variation in lag duration and exponential growth rate in growth rate-limiting and nonlimiting glucose concentrations, using segregants from a cross of two natural isolates of the budding yeast, Saccharomyces cerevisiae We find that some quantitative trait loci (QTL) are common between traits and environments whereas some are unique, exhibiting gene-by-environment interactions. Furthermore, whereas variation in the central tendency of growth rate or lag duration is explained by many additive loci, differences in phenotypic variability are primarily the result of genetic interactions. We used bulk segregant mapping to increase QTL resolution by performing whole-genome sequencing of complex mixtures of an advanced intercross mapping population grown in selective conditions using glucose-limited chemostats. We find that sequence variation in the high-affinity glucose transporter HXT7 contributes to variation in growth rate and lag duration. Allele replacements of the entire locus, as well as of a single polymorphic amino acid, reveal that the effect of variation in HXT7 depends on genetic, and allelic, background. Amplifications of HXT7 are frequently selected in experimental evolution in glucose-limited environments, but we find that HXT7 amplifications result in antagonistic pleiotropy that is absent in naturally occurring variants of HXT7 Our study highlights the complex nature of the genotype-to-phenotype map within and between environments.
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Salehe BR, Jones CI, Di Fatta G, McGuffin LJ. RAPIDSNPs: A new computational pipeline for rapidly identifying key genetic variants reveals previously unidentified SNPs that are significantly associated with individual platelet responses. PLoS One 2017; 12:e0175957. [PMID: 28441463 PMCID: PMC5404774 DOI: 10.1371/journal.pone.0175957] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 04/03/2017] [Indexed: 01/14/2023] Open
Abstract
Advances in omics technologies have led to the discovery of genetic markers, or single nucleotide polymorphisms (SNPs), that are associated with particular diseases or complex traits. Although there have been significant improvements in the approaches used to analyse associations of SNPs with disease, further optimised and rapid techniques are needed to keep up with the rate of SNP discovery, which has exacerbated the 'missing heritability' problem. Here, we have devised a novel, integrated, heuristic-based, hybrid analytical computational pipeline, for rapidly detecting novel or key genetic variants that are associated with diseases or complex traits. Our pipeline is particularly useful in genetic association studies where the genotyped SNP data are highly dimensional, and the complex trait phenotype involved is continuous. In particular, the pipeline is more efficient for investigating small sets of genotyped SNPs defined in high dimensional spaces that may be associated with continuous phenotypes, rather than for the investigation of whole genome variants. The pipeline, which employs a consensus approach based on the random forest, was able to rapidly identify previously unseen key SNPs, that are significantly associated with the platelet response phenotype, which was used as our complex trait case study. Several of these SNPs, such as rs6141803 of COMMD7 and rs41316468 in PKT2B, have independently confirmed associations with cardiovascular diseases (CVDs) according to other unrelated studies, suggesting that our pipeline is robust in identifying key genetic variants. Our new pipeline provides an important step towards addressing the problem of 'missing heritability' through enhanced detection of key genetic variants (SNPs) that are associated with continuous complex traits/disease phenotypes.
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Affiliation(s)
| | - Chris Ian Jones
- School of Biological Sciences, University of Reading, Reading, United Kingdom
| | - Giuseppe Di Fatta
- Department of Computer Science, University of Reading, Reading, United Kingdom
| | - Liam James McGuffin
- School of Biological Sciences, University of Reading, Reading, United Kingdom
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Baker LA, Kirkpatrick B, Rosa GJM, Gianola D, Valente B, Sumner JP, Baltzer W, Hao Z, Binversie EE, Volstad N, Piazza A, Sample SJ, Muir P. Genome-wide association analysis in dogs implicates 99 loci as risk variants for anterior cruciate ligament rupture. PLoS One 2017; 12:e0173810. [PMID: 28379989 PMCID: PMC5381864 DOI: 10.1371/journal.pone.0173810] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Accepted: 02/26/2017] [Indexed: 01/28/2023] Open
Abstract
Anterior cruciate ligament (ACL) rupture is a common condition that can be devastating and life changing, particularly in young adults. A non-contact mechanism is typical. Second ACL ruptures through rupture of the contralateral ACL or rupture of a graft repair is also common. Risk of rupture is increased in females. ACL rupture is also common in dogs. Disease prevalence exceeds 5% in several dog breeds, ~100 fold higher than human beings. We provide insight into the genetic etiology of ACL rupture by genome-wide association study (GWAS) in a high-risk breed using 98 case and 139 control Labrador Retrievers. We identified 129 single nucleotide polymorphisms (SNPs) within 99 risk loci. Associated loci (P<5E-04) explained approximately half of phenotypic variance in the ACL rupture trait. Two of these loci were located in uncharacterized or non-coding regions of the genome. A chromosome 24 locus containing nine genes with diverse functions met genome-wide significance (P = 3.63E-0.6). GWAS pathways were enriched for c-type lectins, a gene set that includes aggrecan, a gene set encoding antimicrobial proteins, and a gene set encoding membrane transport proteins with a variety of physiological functions. Genotypic risk estimated for each dog based on the risk contributed by each GWAS locus showed clear separation of ACL rupture cases and controls. Power analysis of the GWAS data set estimated that ~172 loci explain the genetic contribution to ACL rupture in the Labrador Retriever. Heritability was estimated at 0.48. We conclude ACL rupture is a moderately heritable highly polygenic complex trait. Our results implicate c-type lectin pathways in ACL homeostasis.
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Affiliation(s)
- Lauren A. Baker
- Comparative Orthopaedic Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Brian Kirkpatrick
- Department of Animal Sciences, College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Guilherme J. M. Rosa
- Department of Animal Sciences, College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Daniel Gianola
- Department of Animal Sciences, College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Bruno Valente
- Department of Animal Sciences, College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Dairy Sciences, College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Julia P. Sumner
- Department of Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Wendy Baltzer
- Department of Clinical Sciences, College of Veterinary Medicine, Oregon State University, Corvalis, Oregon, United States of America
| | - Zhengling Hao
- Comparative Orthopaedic Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Emily E. Binversie
- Comparative Orthopaedic Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Nicola Volstad
- Comparative Orthopaedic Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Alexander Piazza
- Comparative Orthopaedic Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Susannah J. Sample
- Comparative Orthopaedic Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Peter Muir
- Comparative Orthopaedic Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
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Winkelmann J, Schormair B, Xiong L, Dion PA, Rye DB, Rouleau GA. Genetics of restless legs syndrome. Sleep Med 2017; 31:18-22. [DOI: 10.1016/j.sleep.2016.10.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 10/19/2016] [Accepted: 10/22/2016] [Indexed: 11/25/2022]
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Davegårdh C, Broholm C, Perfilyev A, Henriksen T, García-Calzón S, Peijs L, Hansen NS, Volkov P, Kjøbsted R, Wojtaszewski JFP, Pedersen M, Pedersen BK, Ballak DB, Dinarello CA, Heinhuis B, Joosten LAB, Nilsson E, Vaag A, Scheele C, Ling C. Abnormal epigenetic changes during differentiation of human skeletal muscle stem cells from obese subjects. BMC Med 2017; 15:39. [PMID: 28222718 PMCID: PMC5320752 DOI: 10.1186/s12916-017-0792-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/11/2017] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Human skeletal muscle stem cells are important for muscle regeneration. However, the combined genome-wide DNA methylation and expression changes taking place during adult myogenesis have not been described in detail and novel myogenic factors may be discovered. Additionally, obesity is associated with low relative muscle mass and diminished metabolism. Epigenetic alterations taking place during myogenesis might contribute to these defects. METHODS We used Infinium HumanMethylation450 BeadChip Kit (Illumina) and HumanHT-12 Expression BeadChip (Illumina) to analyze genome-wide DNA methylation and transcription before versus after differentiation of primary human myoblasts from 14 non-obese and 14 obese individuals. Functional follow-up experiments were performed using siRNA mediated gene silencing in primary human myoblasts and a transgenic mouse model. RESULTS We observed genome-wide changes in DNA methylation and expression patterns during differentiation of primary human muscle stem cells (myoblasts). We identified epigenetic and transcriptional changes of myogenic transcription factors (MYOD1, MYOG, MYF5, MYF6, PAX7, MEF2A, MEF2C, and MEF2D), cell cycle regulators, metabolic enzymes and genes previously not linked to myogenesis, including IL32, metallothioneins, and pregnancy-specific beta-1-glycoproteins. Functional studies demonstrated IL-32 as a novel target that regulates human myogenesis, insulin sensitivity and ATP levels in muscle cells. Furthermore, IL32 transgenic mice had reduced insulin response and muscle weight. Remarkably, approximately 3.7 times more methylation changes (147,161 versus 39,572) were observed during differentiation of myoblasts from obese versus non-obese subjects. In accordance, DNMT1 expression increased during myogenesis only in obese subjects. Interestingly, numerous genes implicated in metabolic diseases and epigenetic regulation showed differential methylation and expression during differentiation only in obese subjects. CONCLUSIONS Our study identifies IL-32 as a novel myogenic regulator, provides a comprehensive map of the dynamic epigenome during differentiation of human muscle stem cells and reveals abnormal epigenetic changes in obesity.
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Affiliation(s)
- Cajsa Davegårdh
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Malmö, 205 02, Sweden
| | - Christa Broholm
- Department of Endocrinology, Rigshospitalet, Copenhagen, 2100, Denmark
| | - Alexander Perfilyev
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Malmö, 205 02, Sweden
| | - Tora Henriksen
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Sonia García-Calzón
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Malmö, 205 02, Sweden
| | - Lone Peijs
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | | | - Petr Volkov
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Malmö, 205 02, Sweden
| | - Rasmus Kjøbsted
- Department of Exercise and Sports Sciences, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
| | - Jørgen F P Wojtaszewski
- Department of Exercise and Sports Sciences, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
| | - Maria Pedersen
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Bente Klarlund Pedersen
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Dov B Ballak
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, 80309, USA.,Department of Medicine, University of Colorado, Aurora, CO, 80045, USA
| | - Charles A Dinarello
- Department of Medicine, University of Colorado, Aurora, CO, 80045, USA.,Department of Internal Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Bas Heinhuis
- Department of Internal Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Emma Nilsson
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Malmö, 205 02, Sweden
| | - Allan Vaag
- Department of Endocrinology, Rigshospitalet, Copenhagen, 2100, Denmark.,Early Clinical Development, Translational Medical Unit, AstraZeneca, Mölndal, 431 83, Sweden
| | - Camilla Scheele
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Charlotte Ling
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Malmö, 205 02, Sweden.
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Knief U, Schielzeth H, Backström N, Hemmrich‐Stanisak G, Wittig M, Franke A, Griffith SC, Ellegren H, Kempenaers B, Forstmeier W. Association mapping of morphological traits in wild and captive zebra finches: reliable within, but not between populations. Mol Ecol 2017; 26:1285-1305. [DOI: 10.1111/mec.14009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 12/05/2016] [Accepted: 12/21/2016] [Indexed: 01/17/2023]
Affiliation(s)
- Ulrich Knief
- Department of Behavioural Ecology and Evolutionary Genetics Max Planck Institute for Ornithology 82319 Seewiesen Germany
| | - Holger Schielzeth
- Department of Population Ecology Friedrich Schiller University Jena 07743 Jena Germany
| | - Niclas Backström
- Department of Ecology and Genetics Uppsala University 752 36 Uppsala Sweden
| | | | - Michael Wittig
- Institute of Clinical Molecular Biology Christian‐Albrechts‐University 24105 Kiel Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology Christian‐Albrechts‐University 24105 Kiel Germany
| | - Simon C. Griffith
- Department of Biological Sciences Macquarie University Sydney NSW 2109 Australia
- School of Biological, Earth & Environmental Sciences University of New South Wales Sydney NSW 2057 Australia
| | - Hans Ellegren
- Department of Ecology and Genetics Uppsala University 752 36 Uppsala Sweden
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics Max Planck Institute for Ornithology 82319 Seewiesen Germany
| | - Wolfgang Forstmeier
- Department of Behavioural Ecology and Evolutionary Genetics Max Planck Institute for Ornithology 82319 Seewiesen Germany
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Bagshaw ATM, Horwood LJ, Fergusson DM, Gemmell NJ, Kennedy MA. Microsatellite polymorphisms associated with human behavioural and psychological phenotypes including a gene-environment interaction. BMC MEDICAL GENETICS 2017; 18:12. [PMID: 28158988 PMCID: PMC5291968 DOI: 10.1186/s12881-017-0374-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 01/25/2017] [Indexed: 02/05/2023]
Abstract
Background The genetic and environmental influences on human personality and behaviour are a complex matter of ongoing debate. Accumulating evidence indicates that short tandem repeats (STRs) in regulatory regions are good candidates to explain heritability not accessed by genome-wide association studies. Methods We tested for associations between the genotypes of four selected repeats and 18 traits relating to personality, behaviour, cognitive ability and mental health in a well-studied longitudinal birth cohort (n = 458-589) using one way analysis of variance. The repeats were a highly conserved poly-AC microsatellite in the upstream promoter region of the T-box brain 1 (TBR1) gene and three previously studied STRs in the activating enhancer-binding protein 2-beta (AP2-β) and androgen receptor (AR) genes. Where significance was found we used multiple regression to assess the influence of confounding factors. Results Carriers of the shorter, most common, allele of the AR gene’s GGN microsatellite polymorphism had fewer anxiety-related symptoms, which was consistent with previous studies, but in our study this was not significant following Bonferroni correction. No associations with two repeats in the AP2-β gene withstood this correction. A novel finding was that carriers of the minor allele of the TBR1 AC microsatellite were at higher risk of conduct problems in childhood at age 7-9 (p = 0.0007, which did pass Bonferroni correction). Including maternal smoking during pregnancy (MSDP) in models controlling for potentially confounding influences showed that an interaction between TBR1 genotype and MSDP was a significant predictor of conduct problems in childhood and adolescence (p < 0.001), and of self-reported criminal behaviour up to age 25 years (p ≤ 0.02). This interaction remained significant after controlling for possible confounders including maternal age at birth, socio-economic status and education, and offspring birth weight. Conclusions The potential functional importance of the TBR1 gene’s promoter microsatellite deserves further investigation. Our results suggest that it participates in a gene-environment interaction with MDSP and antisocial behaviour. However, previous evidence that mothers who smoke during pregnancy carry genes for antisocial behaviour suggests that epistasis may influence the interaction. Electronic supplementary material The online version of this article (doi:10.1186/s12881-017-0374-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrew T M Bagshaw
- Department of Pathology, University of Otago, Christchurch, PO Box 4345, Christchurch, New Zealand.
| | - L John Horwood
- Department of Psychological Medicine, University of Otago, Christchurch, New Zealand
| | - David M Fergusson
- Department of Psychological Medicine, University of Otago, Christchurch, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand.,Gravida - National Centre for Growth and Development, University of Otago, Dunedin, New Zealand
| | - Martin A Kennedy
- Department of Pathology, University of Otago, Christchurch, PO Box 4345, Christchurch, New Zealand
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The Genetic Architecture of Gene Expression in Peripheral Blood. Am J Hum Genet 2017; 100:228-237. [PMID: 28065468 DOI: 10.1016/j.ajhg.2016.12.008] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 12/14/2016] [Indexed: 01/28/2023] Open
Abstract
We analyzed the mRNA levels for 36,778 transcript expression traits (probes) from 2,765 individuals to comprehensively investigate the genetic architecture and degree of missing heritability for gene expression in peripheral blood. We identified 11,204 cis and 3,791 trans independent expression quantitative trait loci (eQTL) by using linear mixed models to perform genome-wide association analyses. Furthermore, using information on both closely and distantly related individuals, heritability was estimated for all expression traits. Of the set of expressed probes (15,966), 10,580 (66%) had an estimated narrow-sense heritability (h2) greater than zero with a mean (median) value of 0.192 (0.142). Across these probes, on average the proportion of genetic variance explained by all eQTL (hCOJO2) was 31% (0.060/0.192), meaning that 69% is missing, with the sentinel SNP of the largest eQTL explaining 87% (0.052/0.060) of the variance attributed to all identified cis- and trans-eQTL. For the same set of probes, the genetic variance attributed to genome-wide common (MAF > 0.01) HapMap 3 SNPs (hg2) accounted for on average 48% (0.093/0.192) of h2. Taken together, the evidence suggests that approximately half the genetic variance for gene expression is not tagged by common SNPs, and of the variance that is tagged by common SNPs, a large proportion can be attributed to identifiable eQTL of large effect, typically in cis. Finally, we present evidence that, compared with a meta-analysis, using individual-level data results in an increase of approximately 50% in power to detect eQTL.
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Resende RT, Resende MDV, Silva FF, Azevedo CF, Takahashi EK, Silva-Junior OB, Grattapaglia D. Regional heritability mapping and genome-wide association identify loci for complex growth, wood and disease resistance traits in Eucalyptus. THE NEW PHYTOLOGIST 2017; 213:1287-1300. [PMID: 28079935 DOI: 10.1111/nph.14266] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 09/08/2016] [Indexed: 05/18/2023]
Abstract
Although genome-wide association studies (GWAS) have provided valuable insights into the decoding of the relationships between sequence variation and complex phenotypes, they have explained little heritability. Regional heritability mapping (RHM) provides heritability estimates for genomic segments containing both common and rare allelic effects that individually contribute too little variance to be detected by GWAS. We carried out GWAS and RHM for seven growth, wood and disease resistance traits in a breeding population of 768 Eucalyptus hybrid trees using EuCHIP60K. Total genomic heritabilities accounted for large proportions (64-89%) of pedigree-based trait heritabilities, providing additional evidence that complex traits in eucalypts are controlled by many sequence variants across the frequency spectrum, each with small contributions to the phenotypic variance. RHM detected 26 quantitative trait loci (QTLs) encompassing 2191 single nucleotide polymorphisms (SNPs), whereas GWAS detected 13 single SNP-trait associations. RHM and GWAS QTLs individually explained 5-15% and 4-6% of the genomic heritability, respectively. RHM was superior to GWAS in capturing larger proportions of genomic heritability. Equated to previously mapped QTLs, our results highlighted genomic regions for further examination towards gene discovery. RHM-QTLs bearing a combination of common and rare variants could be useful enhancements to incorporate prior knowledge of the underlying genetic architecture in genomic prediction models.
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Affiliation(s)
| | - Marcos Deon Vilela Resende
- Department of Statistics, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
- EMBRAPA Forestry Research, Colombo, PR, 83411-000, Brazil
| | - Fabyano Fonseca Silva
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
| | | | | | - Orzenil Bonfim Silva-Junior
- EMBRAPA Genetic Resources and Biotechnology - EPqB, 70770-910, Brasilia, DF, Brazil
- Universidade Católica de Brasília - SGAN, 916 modulo B, Brasilia, DF, 70790-160, Brazil
| | - Dario Grattapaglia
- EMBRAPA Genetic Resources and Biotechnology - EPqB, 70770-910, Brasilia, DF, Brazil
- Universidade Católica de Brasília - SGAN, 916 modulo B, Brasilia, DF, 70790-160, Brazil
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A Model of Compound Heterozygous, Loss-of-Function Alleles Is Broadly Consistent with Observations from Complex-Disease GWAS Datasets. PLoS Genet 2017; 13:e1006573. [PMID: 28103232 PMCID: PMC5289629 DOI: 10.1371/journal.pgen.1006573] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 02/02/2017] [Accepted: 01/05/2017] [Indexed: 12/17/2022] Open
Abstract
The genetic component of complex disease risk in humans remains largely unexplained. A corollary is that the allelic spectrum of genetic variants contributing to complex disease risk is unknown. Theoretical models that relate population genetic processes to the maintenance of genetic variation for quantitative traits may suggest profitable avenues for future experimental design. Here we use forward simulation to model a genomic region evolving under a balance between recurrent deleterious mutation and Gaussian stabilizing selection. We consider multiple genetic and demographic models, and several different methods for identifying genomic regions harboring variants associated with complex disease risk. We demonstrate that the model of gene action, relating genotype to phenotype, has a qualitative effect on several relevant aspects of the population genetic architecture of a complex trait. In particular, the genetic model impacts genetic variance component partitioning across the allele frequency spectrum and the power of statistical tests. Models with partial recessivity closely match the minor allele frequency distribution of significant hits from empirical genome-wide association studies without requiring homozygous effect sizes to be small. We highlight a particular gene-based model of incomplete recessivity that is appealing from first principles. Under that model, deleterious mutations in a genomic region partially fail to complement one another. This model of gene-based recessivity predicts the empirically observed inconsistency between twin and SNP based estimated of dominance heritability. Furthermore, this model predicts considerable levels of unexplained variance associated with intralocus epistasis. Our results suggest a need for improved statistical tools for region based genetic association and heritability estimation. Gene action determines how mutations affect phenotype. When placed in an evolutionary context, the details of the genotype-to-phenotype model can impact the maintenance of genetic variation for complex traits. Likewise, non-equilibrium demographic history may affect patterns of genetic variation. Here, we explore the impact of genetic model and population growth on distribution of genetic variance across the allele frequency spectrum underlying risk for a complex disease. Using forward-in-time population genetic simulations, we show that the genetic model has important impacts on the composition of variation for complex disease risk in a population. We explicitly simulate genome-wide association studies (GWAS) and perform heritability estimation on population samples. A particular model of gene-based partial recessivity, based on allelic non-complementation, aligns well with empirical results. This model is congruent with the dominance variance estimates from both SNPs and twins, and the minor allele frequency distribution of GWAS hits.
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63
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Barton NH. How does epistasis influence the response to selection? Heredity (Edinb) 2017; 118:96-109. [PMID: 27901509 PMCID: PMC5176114 DOI: 10.1038/hdy.2016.109] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Revised: 09/19/2016] [Accepted: 09/19/2016] [Indexed: 11/08/2022] Open
Abstract
Much of quantitative genetics is based on the 'infinitesimal model', under which selection has a negligible effect on the genetic variance. This is typically justified by assuming a very large number of loci with additive effects. However, it applies even when genes interact, provided that the number of loci is large enough that selection on each of them is weak relative to random drift. In the long term, directional selection will change allele frequencies, but even then, the effects of epistasis on the ultimate change in trait mean due to selection may be modest. Stabilising selection can maintain many traits close to their optima, even when the underlying alleles are weakly selected. However, the number of traits that can be optimised is apparently limited to ~4Ne by the 'drift load', and this is hard to reconcile with the apparent complexity of many organisms. Just as for the mutation load, this limit can be evaded by a particular form of negative epistasis. A more robust limit is set by the variance in reproductive success. This suggests that selection accumulates information most efficiently in the infinitesimal regime, when selection on individual alleles is weak, and comparable with random drift. A review of evidence on selection strength suggests that although most variance in fitness may be because of alleles with large Nes, substantial amounts of adaptation may be because of alleles in the infinitesimal regime, in which epistasis has modest effects.
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Affiliation(s)
- N H Barton
- Institute of Science and Technology Austria, Klosterneuburg, Austria
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64
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Fahrenkrog AM, Neves LG, Resende MFR, Vazquez AI, de Los Campos G, Dervinis C, Sykes R, Davis M, Davenport R, Barbazuk WB, Kirst M. Genome-wide association study reveals putative regulators of bioenergy traits in Populus deltoides. THE NEW PHYTOLOGIST 2017; 213:799-811. [PMID: 27596807 DOI: 10.1111/nph.14154] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 07/13/2016] [Indexed: 05/18/2023]
Abstract
Genome-wide association studies (GWAS) have been used extensively to dissect the genetic regulation of complex traits in plants. These studies have focused largely on the analysis of common genetic variants despite the abundance of rare polymorphisms in several species, and their potential role in trait variation. Here, we conducted the first GWAS in Populus deltoides, a genetically diverse keystone forest species in North America and an important short rotation woody crop for the bioenergy industry. We searched for associations between eight growth and wood composition traits, and common and low-frequency single-nucleotide polymorphisms detected by targeted resequencing of 18 153 genes in a population of 391 unrelated individuals. To increase power to detect associations with low-frequency variants, multiple-marker association tests were used in combination with single-marker association tests. Significant associations were discovered for all phenotypes and are indicative that low-frequency polymorphisms contribute to phenotypic variance of several bioenergy traits. Our results suggest that both common and low-frequency variants need to be considered for a comprehensive understanding of the genetic regulation of complex traits, particularly in species that carry large numbers of rare polymorphisms. These polymorphisms may be critical for the development of specialized plant feedstocks for bioenergy.
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Affiliation(s)
- Annette M Fahrenkrog
- School of Forest Resources and Conservation, University of Florida, PO Box 110410, Gainesville, FL, 32611, USA
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, PO Box 110690, Gainesville, FL, 32610, USA
| | - Leandro G Neves
- School of Forest Resources and Conservation, University of Florida, PO Box 110410, Gainesville, FL, 32611, USA
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, PO Box 110690, Gainesville, FL, 32610, USA
| | - Márcio F R Resende
- School of Forest Resources and Conservation, University of Florida, PO Box 110410, Gainesville, FL, 32611, USA
- Genetics and Genomics Graduate Program, University of Florida, PO Box 103610, Gainesville, FL, 32610, USA
| | - Ana I Vazquez
- Department of Epidemiology and Biostatistics, Michigan State University, 909 Fee Road, East Lansing, MI, 48824, USA
| | - Gustavo de Los Campos
- Department of Epidemiology and Biostatistics, Michigan State University, 909 Fee Road, East Lansing, MI, 48824, USA
- Statistics Department, Michigan State University, 619 Red Cedar Road, MI, 48824, USA
| | - Christopher Dervinis
- School of Forest Resources and Conservation, University of Florida, PO Box 110410, Gainesville, FL, 32611, USA
| | - Robert Sykes
- National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Mark Davis
- National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Ruth Davenport
- Biology Department, University of Florida, PO Box 118525, Gainesville, FL, 32611, USA
| | - William B Barbazuk
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, PO Box 110690, Gainesville, FL, 32610, USA
- Biology Department, University of Florida, PO Box 118525, Gainesville, FL, 32611, USA
- University of Florida Genetics Institute, University of Florida, PO Box 103610, Gainesville, FL, 32611, USA
| | - Matias Kirst
- School of Forest Resources and Conservation, University of Florida, PO Box 110410, Gainesville, FL, 32611, USA
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, PO Box 110690, Gainesville, FL, 32610, USA
- University of Florida Genetics Institute, University of Florida, PO Box 103610, Gainesville, FL, 32611, USA
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65
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Roshchupkin GV, Adams HHH, Vernooij MW, Hofman A, Van Duijn CM, Ikram MA, Niessen WJ. HASE: Framework for efficient high-dimensional association analyses. Sci Rep 2016; 6:36076. [PMID: 27782180 PMCID: PMC5080584 DOI: 10.1038/srep36076] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 10/10/2016] [Indexed: 12/21/2022] Open
Abstract
High-throughput technology can now provide rich information on a person’s biological makeup and environmental surroundings. Important discoveries have been made by relating these data to various health outcomes in fields such as genomics, proteomics, and medical imaging. However, cross-investigations between several high-throughput technologies remain impractical due to demanding computational requirements (hundreds of years of computing resources) and unsuitability for collaborative settings (terabytes of data to share). Here we introduce the HASE framework that overcomes both of these issues. Our approach dramatically reduces computational time from years to only hours and also requires several gigabytes to be exchanged between collaborators. We implemented a novel meta-analytical method that yields identical power as pooled analyses without the need of sharing individual participant data. The efficiency of the framework is illustrated by associating 9 million genetic variants with 1.5 million brain imaging voxels in three cohorts (total N = 4,034) followed by meta-analysis, on a standard computational infrastructure. These experiments indicate that HASE facilitates high-dimensional association studies enabling large multicenter association studies for future discoveries.
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Affiliation(s)
- G V Roshchupkin
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, Netherlands.,Department of Medical Informatics, Erasmus MC, Rotterdam, Netherlands
| | - H H H Adams
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, Netherlands.,Department of Epidemiology, Erasmus MC, Netherlands
| | - M W Vernooij
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, Netherlands.,Department of Epidemiology, Erasmus MC, Netherlands
| | - A Hofman
- Department of Epidemiology, Erasmus MC, Netherlands
| | | | - M A Ikram
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, Netherlands.,Department of Epidemiology, Erasmus MC, Netherlands.,Department of Neurology, Erasmus MC, Rotterdam, Netherlands
| | - W J Niessen
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, Netherlands.,Department of Medical Informatics, Erasmus MC, Rotterdam, Netherlands.,Faculty of Applied Sciences, Delft University of Technology, Delft, Netherlands
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66
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Hoban S, Kelley JL, Lotterhos KE, Antolin MF, Bradburd G, Lowry DB, Poss ML, Reed LK, Storfer A, Whitlock MC. Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions. Am Nat 2016; 188:379-97. [PMID: 27622873 PMCID: PMC5457800 DOI: 10.1086/688018] [Citation(s) in RCA: 439] [Impact Index Per Article: 54.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Uncovering the genetic and evolutionary basis of local adaptation is a major focus of evolutionary biology. The recent development of cost-effective methods for obtaining high-quality genome-scale data makes it possible to identify some of the loci responsible for adaptive differences among populations. Two basic approaches for identifying putatively locally adaptive loci have been developed and are broadly used: one that identifies loci with unusually high genetic differentiation among populations (differentiation outlier methods) and one that searches for correlations between local population allele frequencies and local environments (genetic-environment association methods). Here, we review the promises and challenges of these genome scan methods, including correcting for the confounding influence of a species' demographic history, biases caused by missing aspects of the genome, matching scales of environmental data with population structure, and other statistical considerations. In each case, we make suggestions for best practices for maximizing the accuracy and efficiency of genome scans to detect the underlying genetic basis of local adaptation. With attention to their current limitations, genome scan methods can be an important tool in finding the genetic basis of adaptive evolutionary change.
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Affiliation(s)
- Sean Hoban
- Morton Arboretum, Lisle, Illinois 60532; and National Institute for Mathematical and Biological Synthesis (NIMBioS), Knoxville, Tennessee 37966
| | - Joanna L. Kelley
- School of Biological Sciences, Washington State University, Pullman, Washington 99164
| | - Katie E. Lotterhos
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, Massachusetts 01908
| | - Michael F. Antolin
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523
| | - Gideon Bradburd
- Museum of Vertebrate Zoology and Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720
| | - David B. Lowry
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Mary L. Poss
- Department of Biology and Veterinary and Biomedical Sciences, Penn State University, University Park, Pennsylvania 16802
| | - Laura K. Reed
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama 35406
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, Washington 99164
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67
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Krapohl E, Euesden J, Zabaneh D, Pingault JB, Rimfeld K, von Stumm S, Dale PS, Breen G, O'Reilly PF, Plomin R. Phenome-wide analysis of genome-wide polygenic scores. Mol Psychiatry 2016; 21:1188-93. [PMID: 26303664 PMCID: PMC4767701 DOI: 10.1038/mp.2015.126] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/06/2015] [Accepted: 07/14/2015] [Indexed: 02/07/2023]
Abstract
Genome-wide polygenic scores (GPS), which aggregate the effects of thousands of DNA variants from genome-wide association studies (GWAS), have the potential to make genetic predictions for individuals. We conducted a systematic investigation of associations between GPS and many behavioral traits, the behavioral phenome. For 3152 unrelated 16-year-old individuals representative of the United Kingdom, we created 13 GPS from the largest GWAS for psychiatric disorders (for example, schizophrenia, depression and dementia) and cognitive traits (for example, intelligence, educational attainment and intracranial volume). The behavioral phenome included 50 traits from the domains of psychopathology, personality, cognitive abilities and educational achievement. We examined phenome-wide profiles of associations for the entire distribution of each GPS and for the extremes of the GPS distributions. The cognitive GPS yielded stronger predictive power than the psychiatric GPS in our UK-representative sample of adolescents. For example, education GPS explained variation in adolescents' behavior problems (~0.6%) and in educational achievement (~2%) but psychiatric GPS were associated with neither. Despite the modest effect sizes of current GPS, quantile analyses illustrate the ability to stratify individuals by GPS and opportunities for research. For example, the highest and lowest septiles for the education GPS yielded a 0.5 s.d. difference in mean math grade and a 0.25 s.d. difference in mean behavior problems. We discuss the usefulness and limitations of GPS based on adult GWAS to predict genetic propensities earlier in development.
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Affiliation(s)
- E Krapohl
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - J Euesden
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - D Zabaneh
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - J-B Pingault
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK,Division of Psychology and Language Sciences, University College London, London, UK
| | - K Rimfeld
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - S von Stumm
- Department of Psychology, Goldsmiths University of London, New Cross, London, UK
| | - P S Dale
- Department of Speech and Hearing Sciences, University of New Mexico, Albuquerque, NM, USA
| | - G Breen
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - P F O'Reilly
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - R Plomin
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK,MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, DeCrespigny Park, Denmark Hill, London SE5 8AF, UK. E-mail:
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68
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Glymour MM, Rudolph KE. Causal inference challenges in social epidemiology: Bias, specificity, and imagination. Soc Sci Med 2016; 166:258-265. [PMID: 27575286 DOI: 10.1016/j.socscimed.2016.07.045] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 07/26/2016] [Accepted: 07/31/2016] [Indexed: 12/16/2022]
Affiliation(s)
- M Maria Glymour
- Department of Epidemiology and Biostatistics, University of California, San Francisco, USA.
| | - Kara E Rudolph
- Center for Health and Community, University of California, San Francisco, USA; School of Public Health, University of California, Berkeley, USA
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69
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A genome-wide analysis of putative functional and exonic variation associated with extremely high intelligence. Mol Psychiatry 2016; 21:1145-51. [PMID: 26239293 PMCID: PMC4650257 DOI: 10.1038/mp.2015.108] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 05/21/2015] [Accepted: 06/16/2015] [Indexed: 02/07/2023]
Abstract
Although individual differences in intelligence (general cognitive ability) are highly heritable, molecular genetic analyses to date have had limited success in identifying specific loci responsible for its heritability. This study is the first to investigate exome variation in individuals of extremely high intelligence. Under the quantitative genetic model, sampling from the high extreme of the distribution should provide increased power to detect associations. We therefore performed a case-control association analysis with 1409 individuals drawn from the top 0.0003 (IQ >170) of the population distribution of intelligence and 3253 unselected population-based controls. Our analysis focused on putative functional exonic variants assayed on the Illumina HumanExome BeadChip. We did not observe any individual protein-altering variants that are reproducibly associated with extremely high intelligence and within the entire distribution of intelligence. Moreover, no significant associations were found for multiple rare alleles within individual genes. However, analyses using genome-wide similarity between unrelated individuals (genome-wide complex trait analysis) indicate that the genotyped functional protein-altering variation yields a heritability estimate of 17.4% (s.e. 1.7%) based on a liability model. In addition, investigation of nominally significant associations revealed fewer rare alleles associated with extremely high intelligence than would be expected under the null hypothesis. This observation is consistent with the hypothesis that rare functional alleles are more frequently detrimental than beneficial to intelligence.
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70
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Abstract
Genes encode components of coevolved and interconnected networks. The effect of genotype on phenotype therefore depends on genotypic context through gene interactions known as epistasis. Epistasis is important in predicting phenotype from genotype for an individual. It is also examined in population studies to identify genetic risk factors in complex traits and to predict evolution under selection. Paradoxically, the effects of genotypic context in individuals and populations are distinct and sometimes contradictory. We argue that predicting genotype from phenotype for individuals based on population studies is difficult and, especially in human genetics, likely to result in underestimating the effects of genotypic context.
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Affiliation(s)
- Timothy B Sackton
- Informatics Group, 38 Oxford Street, Harvard University, Cambridge, MA 02138, USA
| | - Daniel L Hartl
- Department of Organismic and Evolutionary Biology, 16 Divinity Avenue, Harvard University, Cambridge, MA 02138, USA.
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71
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Talas F, Kalih R, Miedaner T, McDonald BA. Genome-Wide Association Study Identifies Novel Candidate Genes for Aggressiveness, Deoxynivalenol Production, and Azole Sensitivity in Natural Field Populations of Fusarium graminearum. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016; 29:417-30. [PMID: 26959837 DOI: 10.1094/mpmi-09-15-0218-r] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Genome-wide association studies can identify novel genomic regions and genes that affect quantitative traits. Fusarium head blight is a destructive disease caused by Fusarium graminearum that exhibits several quantitative traits, including aggressiveness, mycotoxin production, and fungicide resistance. Restriction site-associated DNA sequencing was performed for 220 isolates of F. graminearum. A total of 119 isolates were phenotyped for aggressiveness and deoxynivalenol (DON) production under natural field conditions across four environments. The effective concentration of propiconazole that inhibits isolate growth in vitro by 50% was calculated for 220 strains. Approximately 29,000 single nucleotide polymorphism markers were associated to each trait, resulting in 50, 29, and 74 quantitative trait nucleotides (QTNs) that were significantly associated to aggressiveness, DON production, and propiconazole sensitivity, respectively. Approximately 41% of these QTNs caused nonsynonymous substitutions in predicted exons, while the remainder were synonymous substitutions or located in intergenic regions. Three QTNs associated with propiconazole sensitivity were significant after Bonferroni correction. These QTNs were located in genes not previously associated with azole sensitivity. The majority of the detected QTNs were located in genes with predicted regulatory functions, suggesting that nucleotide variation in regulatory genes plays a major role in the corresponding quantitative trait variation.
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72
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Wei WH, Bowes J, Plant D, Viatte S, Yarwood A, Massey J, Worthington J, Eyre S. Major histocompatibility complex harbors widespread genotypic variability of non-additive risk of rheumatoid arthritis including epistasis. Sci Rep 2016; 6:25014. [PMID: 27109064 PMCID: PMC4842957 DOI: 10.1038/srep25014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 04/08/2016] [Indexed: 11/10/2022] Open
Abstract
Genotypic variability based genome-wide association studies (vGWASs) can identify potentially interacting loci without prior knowledge of the interacting factors. We report a two-stage approach to make vGWAS applicable to diseases: firstly using a mixed model approach to partition dichotomous phenotypes into additive risk and non-additive environmental residuals on the liability scale and secondly using the Levene's (Brown-Forsythe) test to assess equality of the residual variances across genotype groups per marker. We found widespread significant (P < 2.5e-05) vGWAS signals within the major histocompatibility complex (MHC) across all three study cohorts of rheumatoid arthritis. We further identified 10 epistatic interactions between the vGWAS signals independent of the MHC additive effects, each with a weak effect but jointly explained 1.9% of phenotypic variance. PTPN22 was also identified in the discovery cohort but replicated in only one independent cohort. Combining the three cohorts boosted power of vGWAS and additionally identified TYK2 and ANKRD55. Both PTPN22 and TYK2 had evidence of interactions reported elsewhere. We conclude that vGWAS can help discover interacting loci for complex diseases but require large samples to find additional signals.
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Affiliation(s)
- Wen-Hua Wei
- Arthritis Research UK Centre for Genetics and Genomics, Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PT, UK.,Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
| | - John Bowes
- Arthritis Research UK Centre for Genetics and Genomics, Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Darren Plant
- Arthritis Research UK Centre for Genetics and Genomics, Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Sebastien Viatte
- Arthritis Research UK Centre for Genetics and Genomics, Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Annie Yarwood
- Arthritis Research UK Centre for Genetics and Genomics, Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Jonathan Massey
- Arthritis Research UK Centre for Genetics and Genomics, Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Jane Worthington
- Arthritis Research UK Centre for Genetics and Genomics, Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PT, UK.,NIHR Manchester Musculoskeletal Biomedical Research Unit, Central Manchester NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Stephen Eyre
- Arthritis Research UK Centre for Genetics and Genomics, Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PT, UK.,NIHR Manchester Musculoskeletal Biomedical Research Unit, Central Manchester NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
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73
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Abstract
Genome-wide association studies (GWAS) have associated many single variants with complex disease, yet the better part of heritable complex disease risk remains unexplained. Analytical tools designed to work under specific population genetic models are needed. Rare variants are increasingly shown to be important in human complex disease, but most existing GWAS data do not cover rare variants. Explicit population genetic models predict that genes contributing to complex traits and experiencing recurrent, unconditionally deleterious, mutation will harbor multiple rare, causative mutations of subtle effect. It is difficult to identify genes harboring rare variants of large effect that contribute to complex disease risk via the single marker association tests typically used in GWAS. Gene/region-based association tests may have the power detect associations by combining information from multiple markers, but have yielded limited success in practice. This is partially because many methods have not been widely applied. Here, we empirically demonstrate the utility of a procedure based on the rank truncated product (RTP) method, filtered to reduce the effects of linkage disequilibrium. We apply the procedure to the Wellcome Trust Case Control Consortium (WTCCC) data set, and uncover previously unidentified associations, some of which have been replicated in much larger studies. We show that, in the absence of significant rare variant coverage, RTP based methods still have the power to detect associated genes. We recommend that RTP-based methods be applied to all existing GWAS data to maximize the usefulness of those data. For this, we provide efficient software implementing our procedure.
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74
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Fareed M, Afzal M. Increased cardiovascular risks associated with familial inbreeding: a population-based study of adolescent cohort. Ann Epidemiol 2016; 26:283-92. [PMID: 27084548 DOI: 10.1016/j.annepidem.2016.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 03/15/2016] [Accepted: 03/16/2016] [Indexed: 01/03/2023]
Abstract
PURPOSE Cardiovascular diseases are the leading cause of mortality and morbidity among humans worldwide. We aimed to estimate the effect of familial inbreeding on cardiovascular risks. METHODS The study was conducted during April 2014 through June 2014, and a total of 587 adolescent subjects (male = 270, female = 317; 11-18 years of age) were recruited from five Muslim populations viz., Gujjar and Bakarwal (n = 130), Mughal (n = 111), Malik (n = 114), Syed (n = 108), and Khan (n = 124). Wright's path relationship method was used for calculating the coefficient of inbreeding (F). Anthropometric and physiological parameters were estimated using standard methods. RESULTS We observed higher mean values for major physiological traits among the inbred subjects in comparison with the non-inbred groups of five different populations. Our study suggests that inbreeding and sex are the key factors affecting cardiovascular profile. Multivariate analysis of covariance revealed inbreeding as a major source of variation for cardiovascular risks, dominating over other factors causing greater variability in the physiological traits. The magnitude of cardiovascular risks shows an increase with the increase in the values of coefficient of inbreeding (i.e., from F = 0.00 to F = 0.125). The abnormal levels of systolic blood pressure (SBP; range 140-159 mm Hg) and fasting blood glucose (FBG; range 101-126 mg per dL) show persuasive increase with an upsurge in the homozygosity level (i.e., coefficient of inbreeding). CONCLUSIONS Our comprehensive assessment presents the deleterious consequence of inbreeding on cardiovascular profile. This study can be used as fact-sheet for framing the heath policies and hence can play a vital role in genetic counseling strategies for transforming the public opinion regarding the practice of consanguinity and its associated risks.
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Affiliation(s)
- Mohd Fareed
- Human Genetics and Toxicology Laboratory, Section of Genetics, Department of Zoology, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India.
| | - Mohammad Afzal
- Human Genetics and Toxicology Laboratory, Section of Genetics, Department of Zoology, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India.
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75
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Vrablik M, Zlatohlavek L, Stulc T, Adamkova V, Prusikova M, Schwarzova L, Hubacek JA, Ceska R. Statin-associated myopathy: from genetic predisposition to clinical management. Physiol Res 2016; 63:S327-34. [PMID: 25428737 DOI: 10.33549/physiolres.932865] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Statin-associated myopathy (SAM) represents a broad spectrum of disorders from insignificant myalgia to fatal rhabdomyolysis. Its frequency ranges from 1-5 % in clinical trials to 15-20 % in everyday clinical practice. To a large extent, these variations can be explained by the definition used. Thus, we propose a scoring system to classify statin-induced myopathy according to clinical and biochemical criteria as 1) possible, 2) probable or 3) definite. The etiology of this disorder remains poorly understood. Most probably, an underlying genetic cause is necessary for overt SAM to develop. Variants in a few gene groups that encode proteins involved in: i) statin metabolism and distribution (e.g. membrane transporters and enzymes; OATP1B1, ABCA1, MRP, CYP3A4), ii) coenzyme Q10 production (e.g. COQ10A and B), iii) energy metabolism of muscle tissue (e.g. PYGM, GAA, CPT2) and several others have been proposed as candidates which can predispose to SAM. Pharmacological properties of individual statin molecules (e.g. lipophilicity, excretion pathways) and patients´ characteristics influence the likelihood of SAM development. This review summarizes current data as well as our own results.
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Affiliation(s)
- M Vrablik
- Third Department of Internal Medicine, First Faculty of Medicine, Charles University, Prague, Czech Republic.
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76
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Dai X, Wiernek S, Evans JP, Runge MS. Genetics of coronary artery disease and myocardial infarction. World J Cardiol 2016; 8:1-23. [PMID: 26839654 PMCID: PMC4728103 DOI: 10.4330/wjc.v8.i1.1] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Revised: 10/18/2015] [Accepted: 11/10/2015] [Indexed: 02/06/2023] Open
Abstract
Atherosclerotic coronary artery disease (CAD) comprises a broad spectrum of clinical entities that include asymptomatic subclinical atherosclerosis and its clinical complications, such as angina pectoris, myocardial infarction (MI) and sudden cardiac death. CAD continues to be the leading cause of death in industrialized society. The long-recognized familial clustering of CAD suggests that genetics plays a central role in its development, with the heritability of CAD and MI estimated at approximately 50% to 60%. Understanding the genetic architecture of CAD and MI has proven to be difficult and costly due to the heterogeneity of clinical CAD and the underlying multi-decade complex pathophysiological processes that involve both genetic and environmental interactions. This review describes the clinical heterogeneity of CAD and MI to clarify the disease spectrum in genetic studies, provides a brief overview of the historical understanding and estimation of the heritability of CAD and MI, recounts major gene discoveries of potential causal mutations in familial CAD and MI, summarizes CAD and MI-associated genetic variants identified using candidate gene approaches and genome-wide association studies (GWAS), and summarizes the current status of the construction and validations of genetic risk scores for lifetime risk prediction and guidance for preventive strategies. Potential protective genetic factors against the development of CAD and MI are also discussed. Finally, GWAS have identified multiple genetic factors associated with an increased risk of in-stent restenosis following stent placement for obstructive CAD. This review will also address genetic factors associated with in-stent restenosis, which may ultimately guide clinical decision-making regarding revascularization strategies for patients with CAD and MI.
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Affiliation(s)
- Xuming Dai
- Xuming Dai, Szymon Wiernek, Marschall S Runge, Division of Cardiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Szymon Wiernek
- Xuming Dai, Szymon Wiernek, Marschall S Runge, Division of Cardiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - James P Evans
- Xuming Dai, Szymon Wiernek, Marschall S Runge, Division of Cardiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Marschall S Runge
- Xuming Dai, Szymon Wiernek, Marschall S Runge, Division of Cardiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
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77
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Kagale S, Koh C, Clarke WE, Bollina V, Parkin IAP, Sharpe AG. Analysis of Genotyping-by-Sequencing (GBS) Data. Methods Mol Biol 2016; 1374:269-284. [PMID: 26519412 DOI: 10.1007/978-1-4939-3167-5_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The development of genotyping-by-sequencing (GBS) to rapidly detect nucleotide variation at the whole genome level, in many individuals simultaneously, has provided a transformative genetic profiling technique. GBS can be carried out in species with or without reference genome sequences yields huge amounts of potentially informative data. One limitation with the approach is the paucity of tools to transform the raw data into a format that can be easily interrogated at the genetic level. In this chapter we describe bioinformatics tools developed to address this shortfall together with experimental design considerations to fully leverage the power of GBS for genetic analysis.
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Affiliation(s)
- Sateesh Kagale
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, Canada, S7N 0W9
| | - Chushin Koh
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, Canada, S7N 0W9
| | - Wayne E Clarke
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada, S7N 0X2
| | - Venkatesh Bollina
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada, S7N 0X2
| | - Isobel A P Parkin
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada, S7N 0X2
| | - Andrew G Sharpe
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, Canada, S7N 0W9.
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78
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ZHOU YING, CHENG YANGYANG, ZHU WENSHENG, ZHOU QIAN. A nonparametric method to test for associations between rare variants and multiple traits. Genet Res (Camb) 2016; 98:e1. [PMID: 27159928 PMCID: PMC6865163 DOI: 10.1017/s0016672315000269] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 09/18/2015] [Accepted: 12/08/2015] [Indexed: 11/06/2022] Open
Abstract
More and more rare genetic variants are being detected in the human genome, and it is believed that besides common variants, some rare variants also explain part of the phenotypic variance for human diseases. Due to the importance of rare variants, many statistical methods have been proposed to test for associations between rare variants and human traits. However, in existing studies, most methods only test for associations between multiple loci and one trait; therefore, the joint information of multiple traits has not been considered simultaneously and sufficiently. In this article, we present a study of testing for associations between rare variants and multiple traits, where trait value can be binary, ordinal, quantitative and/or any mixture of them. Based on the method of generalized Kendall’s τ, a nonparametric method called NM-RV is proposed. A new kernel function for U-statistic, which could incorporate the information of each rare variant itself, is also presented and is expected to enhance the power of rare variant analysis. We further consider the asymptotic distribution of the proposed association test statistic. Our simulation work suggests that the proposed method is more powerful and robust than existing methods in testing for associations between rare variants and multiple traits,especially for multivariate ordinal traits.
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Affiliation(s)
- YING ZHOU
- Key Laboratory for Applied Statistics of MOE, School of Mathematics and Statistics, Northeast Normal University, Changchun 130024, China
- School of Mathematical Sciences, Heilongjiang University, Harbin 150080, China
| | - YANGYANG CHENG
- Key Laboratory for Applied Statistics of MOE, School of Mathematics and Statistics, Northeast Normal University, Changchun 130024, China
| | - WENSHENG ZHU
- Key Laboratory for Applied Statistics of MOE, School of Mathematics and Statistics, Northeast Normal University, Changchun 130024, China
| | - QIAN ZHOU
- Department of Humanities, Mianyang Vocational and Technical College, Mianyang 621000, China
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79
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Plomin R, DeFries JC, Knopik VS, Neiderhiser JM. Top 10 Replicated Findings From Behavioral Genetics. PERSPECTIVES ON PSYCHOLOGICAL SCIENCE 2016; 11:3-23. [PMID: 26817721 PMCID: PMC4739500 DOI: 10.1177/1745691615617439] [Citation(s) in RCA: 188] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In the context of current concerns about replication in psychological science, we describe 10 findings from behavioral genetic research that have replicated robustly. These are "big" findings, both in terms of effect size and potential impact on psychological science, such as linearly increasing heritability of intelligence from infancy (20%) through adulthood (60%). Four of our top 10 findings involve the environment, discoveries that could have been found only with genetically sensitive research designs. We also consider reasons specific to behavioral genetics that might explain why these findings replicate.
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Affiliation(s)
- Robert Plomin
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London
| | - John C DeFries
- Institute for Behavioral Genetics, University of Colorado
| | - Valerie S Knopik
- Department of Psychiatry, Rhode Island Hospital, Providence, Rhode Island, and Departments of Psychiatry and Human Behavior and Behavioral and Social Sciences, Brown University
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80
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Hirbo J, Eidem H, Rokas A, Abbot P. Integrating Diverse Types of Genomic Data to Identify Genes that Underlie Adverse Pregnancy Phenotypes. PLoS One 2015; 10:e0144155. [PMID: 26641094 PMCID: PMC4671692 DOI: 10.1371/journal.pone.0144155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 11/14/2015] [Indexed: 11/18/2022] Open
Abstract
Progress in understanding complex genetic diseases has been bolstered by synthetic approaches that overlay diverse data types and analyses to identify functionally important genes. Pre-term birth (PTB), a major complication of pregnancy, is a leading cause of infant mortality worldwide. A major obstacle in addressing PTB is that the mechanisms controlling parturition and birth timing remain poorly understood. Integrative approaches that overlay datasets derived from comparative genomics with function-derived ones have potential to advance our understanding of the genetics of birth timing, and thus provide insights into the genes that may contribute to PTB. We intersected data from fast evolving coding and non-coding gene regions in the human and primate lineage with data from genes expressed in the placenta, from genes that show enriched expression only in the placenta, as well as from genes that are differentially expressed in four distinct PTB clinical subtypes. A large fraction of genes that are expressed in placenta, and differentially expressed in PTB clinical subtypes (23–34%) are fast evolving, and are associated with functions that include adhesion neurodevelopmental and immune processes. Functional categories of genes that express fast evolution in coding regions differ from those linked to fast evolution in non-coding regions. Finally, there is a surprising lack of overlap between fast evolving genes that are differentially expressed in four PTB clinical subtypes. Integrative approaches, especially those that incorporate evolutionary perspectives, can be successful in identifying potential genetic contributions to complex genetic diseases, such as PTB.
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Affiliation(s)
- Jibril Hirbo
- Department of Biological Sciences, Vanderbilt University, Box 35164 Station B, Nashville, TN, 37235–1634, United States of America
| | - Haley Eidem
- Department of Biological Sciences, Vanderbilt University, Box 35164 Station B, Nashville, TN, 37235–1634, United States of America
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Box 35164 Station B, Nashville, TN, 37235–1634, United States of America
| | - Patrick Abbot
- Department of Biological Sciences, Vanderbilt University, Box 35164 Station B, Nashville, TN, 37235–1634, United States of America
- * E-mail:
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81
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Goes FS, McGrath J, Avramopoulos D, Wolyniec P, Pirooznia M, Ruczinski I, Nestadt G, Kenny EE, Vacic V, Peters I, Lencz T, Darvasi A, Mulle JG, Warren ST, Pulver AE. Genome-wide association study of schizophrenia in Ashkenazi Jews. Am J Med Genet B Neuropsychiatr Genet 2015. [PMID: 26198764 DOI: 10.1002/ajmg.b.32349] [Citation(s) in RCA: 149] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Schizophrenia is a common, clinically heterogeneous disorder associated with lifelong morbidity and early mortality. Several genetic variants associated with schizophrenia have been identified, but the majority of the heritability remains unknown. In this study, we report on a case-control sample of Ashkenazi Jews (AJ), a founder population that may provide additional insights into genetic etiology of schizophrenia. We performed a genome-wide association analysis (GWAS) of 592 cases and 505 controls of AJ ancestry ascertained in the US. Subsequently, we performed a meta-analysis with an Israeli AJ sample of 913 cases and 1640 controls, followed by a meta-analysis and polygenic risk scoring using summary results from Psychiatric GWAS Consortium 2 schizophrenia study. The U.S. AJ sample showed strong evidence of polygenic inheritance (pseudo-R(2) ∼9.7%) and a SNP-heritability estimate of 0.39 (P = 0.00046). We found no genome-wide significant associations in the U.S. sample or in the combined US/Israeli AJ meta-analysis of 1505 cases and 2145 controls. The strongest AJ specific associations (P-values in 10(-6) -10(-7) range) were in the 22q 11.2 deletion region and included the genes TBX1, GLN1, and COMT. Supportive evidence (meta P < 1 × 10(-4) ) was also found for several previously identified genome-wide significant findings, including the HLA region, CNTN4, IMMP2L, and GRIN2A. The meta-analysis of the U.S. sample with the PGC2 results provided initial genome-wide significant evidence for six new loci. Among the novel potential susceptibility genes is PEPD, a gene involved in proline metabolism, which is associated with a Mendelian disorder characterized by developmental delay and cognitive deficits.
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Affiliation(s)
- Fernando S Goes
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - John McGrath
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Dimitrios Avramopoulos
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Paula Wolyniec
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Mehdi Pirooznia
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ingo Ruczinski
- Department of Biostatistics, Bloomberg School of Public Health, Baltimore, Maryland
| | - Gerald Nestadt
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Eimear E Kenny
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, New York.,Department of Genetics and Genome Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York.,Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York City, New York.,Center of Statistical Genetics, Icahn School of Medicine at Mount Sinai, New York City, New York
| | | | - Inga Peters
- Department of Genetics and Genome Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York
| | - Todd Lencz
- Division of Research, Department of Psychiatry, The Zucker Hillside Hospital Division of the North Shore-Long Island Jewish Health System, Glen Oaks, New York.,Center for Psychiatric Neuroscience, The Feinstein Institute for Medical Research, Manhasset, New York.,Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York.,Department of Psychiatry, Hofstra University School of Medicine, Hempstead, New York.,Department of Molecular Medicine, Hofstra University School of Medicine, Hempstead, New York
| | - Ariel Darvasi
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Jennifer G Mulle
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Stephen T Warren
- Departments of Human Genetics, Pediatrics and Biochemistry, Emory University, Atlanta, Georgia
| | - Ann E Pulver
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
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82
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Hamzić E, Buitenhuis B, Hérault F, Hawken R, Abrahamsen MS, Servin B, Elsen JM, Pinard-van der Laan MH, Bed'Hom B. Genome-wide association study and biological pathway analysis of the Eimeria maxima response in broilers. Genet Sel Evol 2015; 47:91. [PMID: 26607727 PMCID: PMC4659166 DOI: 10.1186/s12711-015-0170-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Accepted: 11/05/2015] [Indexed: 02/22/2023] Open
Abstract
Background Coccidiosis is the most common and costly disease in the poultry industry and is caused by protozoans of the Eimeria genus. The current control of coccidiosis, based on the use of anticoccidial drugs and vaccination, faces serious obstacles such as drug resistance and the high costs for the development of efficient vaccines, respectively. Therefore, the current control programs must be expanded with complementary approaches such as the use of genetics to improve the host response to Eimeria infections. Recently, we have performed a large-scale challenge study on Cobb500 broilers using E. maxima for which we investigated variability among animals in response to the challenge. As a follow-up to this challenge study, we performed a genome-wide association study (GWAS) to identify genomic regions underlying variability of the measured traits in the response to Eimeria maxima in broilers. Furthermore, we conducted a post-GWAS functional analysis to increase our biological understanding of the underlying response to Eimeria maxima challenge. Results In total, we identified 22 single nucleotide polymorphisms (SNPs) with q value <0.1 distributed across five chromosomes. The highly significant SNPs were associated with body weight gain (three SNPs on GGA5, one SNP on GGA1 and one SNP on GGA3), plasma coloration measured as optical density at wavelengths in the range 465–510 nm (10 SNPs and all on GGA10) and the percentage of β2-globulin in blood plasma (15 SNPs on GGA1 and one SNP on GGA2). Biological pathways related to metabolic processes, cell proliferation, and primary innate immune processes were among the most frequent significantly enriched biological pathways. Furthermore, the network-based analysis produced two networks of high confidence, with one centered on large tumor suppressor kinase 1 (LATS1) and 2 (LATS2) and the second involving the myosin heavy chain 6 (MYH6). Conclusions We identified several strong candidate genes and genomic regions associated with traits measured in response to Eimeria maxima in broilers. Furthermore, the post-GWAS functional analysis indicates that biological pathways and networks involved in tissue proliferation and repair along with the primary innate immune response may play the most important role during the early stage of Eimeria maxima infection in broilers. Electronic supplementary material The online version of this article (doi:10.1186/s12711-015-0170-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Edin Hamzić
- UMR1313 Animal Genetics and Integrative Biology Unit, AgroParisTech, 16 rue Claude Bernard, 75005, Paris, France. .,UMR1313 Animal Genetics and Integrative Biology Unit, INRA, Domaine de Vilvert, 78350, Jouy-en-Josas, France. .,Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Blichers Allé 20, P.O. Box 50, 8830, Tjele, Denmark.
| | - Bart Buitenhuis
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Blichers Allé 20, P.O. Box 50, 8830, Tjele, Denmark.
| | - Frédéric Hérault
- UMR1348 Physiology, Environment and Genetics for the Animal and Livestock Systems Unit, INRA, Domaine de la Prise, 35590, Saint Gilles, France.
| | | | | | - Bertrand Servin
- UMR1388 Genetics, Physiology and Breeding Systems, INRA, 24 chemin de Borde-Rouge, 31326, Castanet-Tolosan, France.
| | - Jean-Michel Elsen
- UMR1388 Genetics, Physiology and Breeding Systems, INRA, 24 chemin de Borde-Rouge, 31326, Castanet-Tolosan, France.
| | - Marie-Hélène Pinard-van der Laan
- UMR1313 Animal Genetics and Integrative Biology Unit, AgroParisTech, 16 rue Claude Bernard, 75005, Paris, France. .,UMR1313 Animal Genetics and Integrative Biology Unit, INRA, Domaine de Vilvert, 78350, Jouy-en-Josas, France.
| | - Bertrand Bed'Hom
- UMR1313 Animal Genetics and Integrative Biology Unit, AgroParisTech, 16 rue Claude Bernard, 75005, Paris, France. .,UMR1313 Animal Genetics and Integrative Biology Unit, INRA, Domaine de Vilvert, 78350, Jouy-en-Josas, France.
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83
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Hussain S. A new conceptual framework for investigating complex genetic disease. Front Genet 2015; 6:327. [PMID: 26583033 PMCID: PMC4631989 DOI: 10.3389/fgene.2015.00327] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 10/21/2015] [Indexed: 01/17/2023] Open
Abstract
Some common diseases are known to have an inherited component, however, their population- and familial-incidence patterns do not conform to any known monogenic Mendelian pattern of inheritance and instead they are currently much better explained if an underlying polygenic architecture is posited. Studies that have attempted to identify the causative genetic factors have been designed on this polygenic framework, but so far the yield has been largely unsatisfactory. Based on accumulating recent observations concerning the roles of somatic mosaicism in disease, in this article a second framework which posits a single gene-two hit model which can be modulated by a mutator/anti-mutator genetic background is suggested. I discuss whether such a model can be considered a viable alternative based on current knowledge, its advantages over the current polygenic framework, and describe practical routes via which the new framework can be investigated.
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Affiliation(s)
- Shobbir Hussain
- Department of Biology and Biochemistry, University of BathBath, UK
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84
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Robinson MR, Hemani G, Medina-Gomez C, Mezzavilla M, Esko T, Shakhbazov K, Powell JE, Vinkhuyzen A, Berndt SI, Gustafsson S, Justice AE, Kahali B, Locke AE, Pers TH, Vedantam S, Wood AR, van Rheenen W, Andreassen OA, Gasparini P, Metspalu A, Berg LHVD, Veldink JH, Rivadeneira F, Werge TM, Abecasis GR, Boomsma DI, Chasman DI, de Geus EJC, Frayling TM, Hirschhorn JN, Hottenga JJ, Ingelsson E, Loos RJF, Magnusson PKE, Martin NG, Montgomery GW, North KE, Pedersen NL, Spector TD, Speliotes EK, Goddard ME, Yang J, Visscher PM. Population genetic differentiation of height and body mass index across Europe. Nat Genet 2015; 47:1357-62. [PMID: 26366552 PMCID: PMC4984852 DOI: 10.1038/ng.3401] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/19/2015] [Indexed: 12/13/2022]
Abstract
Across-nation differences in the mean values for complex traits are common, but the reasons for these differences are unknown. Here we find that many independent loci contribute to population genetic differences in height and body mass index (BMI) in 9,416 individuals across 14 European countries. Using discovery data on over 250,000 individuals and unbiased effect size estimates from 17,500 sibling pairs, we estimate that 24% (95% credible interval (CI) = 9%, 41%) and 8% (95% CI = 4%, 16%) of the captured additive genetic variance for height and BMI, respectively, reflect population genetic differences. Population genetic divergence differed significantly from that in a null model (height, P < 3.94 × 10(-8); BMI, P < 5.95 × 10(-4)), and we find an among-population genetic correlation for tall and slender individuals (r = -0.80, 95% CI = -0.95, -0.60), consistent with correlated selection for both phenotypes. Observed differences in height among populations reflected the predicted genetic means (r = 0.51; P < 0.001), but environmental differences across Europe masked genetic differentiation for BMI (P < 0.58).
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Affiliation(s)
- Matthew R Robinson
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Gibran Hemani
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Carolina Medina-Gomez
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Massimo Mezzavilla
- Institute for Maternal and Child Health, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) 'Burlo Garofolo', Trieste, Italy
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Tonu Esko
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Konstantin Shakhbazov
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Joseph E Powell
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
- University of Queensland Diamantina Institute, University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Anna Vinkhuyzen
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institutes of Health, Bethesda, Maryland, USA
| | - Stefan Gustafsson
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anne E Justice
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Bratati Kahali
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Adam E Locke
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
| | - Tune H Pers
- Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Sailaja Vedantam
- Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Andrew R Wood
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Wouter van Rheenen
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Ole A Andreassen
- Norwegian Centre for Mental Disorders Research (NORMENT), KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Paolo Gasparini
- Institute for Maternal and Child Health, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) 'Burlo Garofolo', Trieste, Italy
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | | | - Leonard H van den Berg
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jan H Veldink
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Thomas M Werge
- Institute of Biological Psychiatry, MHC Sct. Hans, Mental Health Devices Copenhagen, Roskilde, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Lundbeck Foundation Initiative for Integrative Psychiatric Research, (iPSYCH), Aarhus, Denmark
| | - Goncalo R Abecasis
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
| | - Dorret I Boomsma
- Neuroscience Campus Amsterdam, VU University Medical Center, Amsterdam, the Netherlands
- EMGO+ Institute for Health and Care Research, VU University Medical Center, Amsterdam, the Netherlands
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, the Netherlands
| | - Daniel I Chasman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Eco J C de Geus
- Neuroscience Campus Amsterdam, VU University Medical Center, Amsterdam, the Netherlands
- EMGO+ Institute for Health and Care Research, VU University Medical Center, Amsterdam, the Netherlands
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, the Netherlands
| | - Timothy M Frayling
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Joel N Hirschhorn
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Jouke Jan Hottenga
- Neuroscience Campus Amsterdam, VU University Medical Center, Amsterdam, the Netherlands
- EMGO+ Institute for Health and Care Research, VU University Medical Center, Amsterdam, the Netherlands
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, the Netherlands
| | - Erik Ingelsson
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ruth J F Loos
- Medical Research Council (MRC) Epidemiology Unit, University of Cambridge, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Patrik K E Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Nicholas G Martin
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Grant W Montgomery
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Kari E North
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, St. Thomas' Hospital, London, UK
| | - Elizabeth K Speliotes
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
| | - Michael E Goddard
- Biosciences Research Division, Department of Primary Industries, Melbourne, Victoria, Australia
- Department of Food and Agricultural Systems, University of Melbourne, Melbourne, Victoria, Australia
| | - Jian Yang
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
- University of Queensland Diamantina Institute, University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Peter M Visscher
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
- University of Queensland Diamantina Institute, University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
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Cheng HH, Perumbakkam S, Pyrkosz AB, Dunn JR, Legarra A, Muir WM. Fine mapping of QTL and genomic prediction using allele-specific expression SNPs demonstrates that the complex trait of genetic resistance to Marek's disease is predominantly determined by transcriptional regulation. BMC Genomics 2015; 16:816. [PMID: 26481588 PMCID: PMC4617451 DOI: 10.1186/s12864-015-2016-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 10/04/2015] [Indexed: 11/30/2022] Open
Abstract
Background Marek’s disease (MD) is a lymphoproliferative disease of poultry induced by Marek’s disease virus (MDV), a highly oncogenic alphaherpesvirus. Identifying the underlying genes conferring MD genetic resistance is desired for more efficacious control measures including genomic selection, which requires accurately identified genetic markers throughout the chicken genome. Methods Hypothesizing that variants located in transcriptional regulatory regions are the main mechanism underlying this complex trait, a genome-wide association study was conducted by genotyping a ~1,000 bird MD resource population derived from experimental inbred layers with SNPs containing 1,824 previously identified allele-specific expression (ASE) SNPs in response to MDV infection as well as 3,097 random SNPs equally spaced throughout the chicken genome. Based on the calculated associations, genomic predictions were determined for 200 roosters and selected sires had their progeny tested for Marek’s disease incidence. Results Our analyses indicate that these ASE SNPs account for more than 83 % of the genetic variance and exhibit nearly all the highest associations. To validate these findings, 200 roosters had their genetic merit predicted from the ASE SNPs only, and the top 30 and bottom 30 ranked roosters were reciprocally mated to random hens. The resulting progeny showed that after only one generation of bidirectional selection, there was a 22 % difference in MD incidence and this approach gave a 125 % increase in accuracy compared to current pedigree-based estimates. Conclusions We conclude that variation in transcriptional regulation is the major driving cause for genetic resistance to MD, and ASE SNPs identify the underlying genes and are sufficiently linked to the causative polymorphisms that they can be used for accurate genomic prediction as well as help define the underlying molecular basis. Furthermore, this approach should be applicable to other complex traits. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2016-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hans H Cheng
- USDA, ARS, Avian Disease and Oncology Laboratory, East Lansing, MI, 48823, USA.
| | - Sudeep Perumbakkam
- USDA, ARS, Avian Disease and Oncology Laboratory, East Lansing, MI, 48823, USA.,Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | | | - John R Dunn
- USDA, ARS, Avian Disease and Oncology Laboratory, East Lansing, MI, 48823, USA
| | - Andres Legarra
- INRA, Animal Genetics, GenPhySE, Castanet Tolosan, 31326, France
| | - William M Muir
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA
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86
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Abstract
Language is a defining characteristic of the human species, but its foundations remain mysterious. Heritable disorders offer a gateway into biological underpinnings, as illustrated by the discovery that FOXP2 disruptions cause a rare form of speech and language impairment. The genetic architecture underlying language-related disorders is complex, and although some progress has been made, it has proved challenging to pinpoint additional relevant genes with confidence. Next-generation sequencing and genome-wide association studies are revolutionizing understanding of the genetic bases of other neurodevelopmental disorders, like autism and schizophrenia, and providing fundamental insights into the molecular networks crucial for typical brain development. We discuss how a similar genomic perspective, brought to the investigation of language-related phenotypes, promises to yield equally informative discoveries. Moreover, we outline how follow-up studies of genetic findings using cellular systems and animal models can help to elucidate the biological mechanisms involved in the development of brain circuits supporting language.
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Affiliation(s)
- Sarah A Graham
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, The Netherlands;
| | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, The Netherlands; .,Donders Institute for Brain, Cognition and Behavior, Radboud University, 6525 EN Nijmegen, The Netherlands;
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87
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Palla L, Dudbridge F. A Fast Method that Uses Polygenic Scores to Estimate the Variance Explained by Genome-wide Marker Panels and the Proportion of Variants Affecting a Trait. Am J Hum Genet 2015; 97:250-9. [PMID: 26189816 DOI: 10.1016/j.ajhg.2015.06.005] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 06/09/2015] [Indexed: 01/05/2023] Open
Abstract
Several methods have been proposed to estimate the variance in disease liability explained by large sets of genetic markers. However, current methods do not scale up well to large sample sizes. Linear mixed models require solving high-dimensional matrix equations, and methods that use polygenic scores are very computationally intensive. Here we propose a fast analytic method that uses polygenic scores, based on the formula for the non-centrality parameter of the association test of the score. We estimate model parameters from the results of multiple polygenic score tests based on markers with p values in different intervals. We estimate parameters by maximum likelihood and use profile likelihood to compute confidence intervals. We compare various options for constructing polygenic scores, based on nested or disjoint intervals of p values, weighted or unweighted effect sizes, and different numbers of intervals, in estimating the variance explained by a set of markers, the proportion of markers with effects, and the genetic covariance between a pair of traits. Our method provides nearly unbiased estimates and confidence intervals with good coverage, although estimation of the variance is less reliable when jointly estimated with the covariance. We find that disjoint p value intervals perform better than nested intervals, but the weighting did not affect our results. A particular advantage of our method is that it can be applied to summary statistics from single markers, and so can be quickly applied to large consortium datasets. Our method, named AVENGEME (Additive Variance Explained and Number of Genetic Effects Method of Estimation), is implemented in R software.
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88
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Toro R, Poline JB, Huguet G, Loth E, Frouin V, Banaschewski T, Barker GJ, Bokde A, Büchel C, Carvalho FM, Conrod P, Fauth-Bühler M, Flor H, Gallinat J, Garavan H, Gowland P, Heinz A, Ittermann B, Lawrence C, Lemaître H, Mann K, Nees F, Paus T, Pausova Z, Rietschel M, Robbins T, Smolka MN, Ströhle A, Schumann G, Bourgeron T. Genomic architecture of human neuroanatomical diversity. Mol Psychiatry 2015; 20:1011-6. [PMID: 25224261 DOI: 10.1038/mp.2014.99] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 06/02/2014] [Accepted: 07/14/2014] [Indexed: 02/06/2023]
Abstract
Human brain anatomy is strikingly diverse and highly inheritable: genetic factors may explain up to 80% of its variability. Prior studies have tried to detect genetic variants with a large effect on neuroanatomical diversity, but those currently identified account for <5% of the variance. Here, based on our analyses of neuroimaging and whole-genome genotyping data from 1765 subjects, we show that up to 54% of this heritability is captured by large numbers of single-nucleotide polymorphisms of small-effect spread throughout the genome, especially within genes and close regulatory regions. The genetic bases of neuroanatomical diversity appear to be relatively independent of those of body size (height), but shared with those of verbal intelligence scores. The study of this genomic architecture should help us better understand brain evolution and disease.
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Affiliation(s)
- R Toro
- 1] Human Genetics and Cognitive Functions, Neuroscience Department, Institut Pasteur, Paris, France [2] CNRS URA 2182 'Genes, synapses and cognition', Paris, France [3] Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France
| | - J-B Poline
- 1] Henry H. Wheeler, Jr. Brain Imaging Center, University of California at Berkeley, Berkeley, CA, USA [2] Neurospin, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Paris, France
| | - G Huguet
- 1] Human Genetics and Cognitive Functions, Neuroscience Department, Institut Pasteur, Paris, France [2] CNRS URA 2182 'Genes, synapses and cognition', Paris, France [3] Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France
| | - E Loth
- 1] Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, King's College London, London, UK [2] MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, London, UK
| | - V Frouin
- Henry H. Wheeler, Jr. Brain Imaging Center, University of California at Berkeley, Berkeley, CA, USA
| | - T Banaschewski
- Department of Child and Adolescent Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - G J Barker
- Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, King's College London, London, UK
| | - A Bokde
- Discipline of Psychiatry, School of Medicine and Trinity College Institute of Neurosciences, Trinity College Dublin, Dublin, Ireland
| | - C Büchel
- University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - F M Carvalho
- 1] Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, King's College London, London, UK [2] MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, London, UK
| | - P Conrod
- 1] Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, King's College London, London, UK [2] Department of Psychiatry, Université de Montreal, CHU Ste Justine Hospital, Montreal, QC, Canada
| | - M Fauth-Bühler
- Department of Addictive Behaviour and Addiction Medicine, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - H Flor
- Department of Cognitive and Clinical Neuroscience, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - J Gallinat
- Department of Psychiatry and Psychotherapy, Campus Charité Mitte, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - H Garavan
- 1] Discipline of Psychiatry, School of Medicine and Trinity College Institute of Neurosciences, Trinity College Dublin, Dublin, Ireland [2] Departments of Psychiatry and Psychology, University of Vermont, Burlington, VT, USA
| | - P Gowland
- Departments of Psychiatry and Psychology, University of Vermont, Burlington, VT, USA
| | - A Heinz
- Department of Psychiatry and Psychotherapy, Campus Charité Mitte, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - B Ittermann
- Physikalisch-Technische Bundesanstalt, Berlin, Germany
| | - C Lawrence
- School of Psychology, University of Nottingham, Nottingham, UK
| | - H Lemaître
- 1] Institut National de la Santé et de la Recherche Medicale, INSERM CEA Unit 1000, 'Imaging & Psychiatry', University Paris Sud, Orsay, France [2] Department of Adolescent Psychopathology and Medicine, Assistance Publique Hôpitaux de Paris, Maison de Solenn, Université Paris Descartes, Paris, France
| | - K Mann
- Department of Addictive Behaviour and Addiction Medicine, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - F Nees
- Department of Cognitive and Clinical Neuroscience, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - T Paus
- 1] School of Psychology, University of Nottingham, Nottingham, UK [2] Psychology and Psychiatry Department, Rotman Research Institute, University of Toronto, Toronto, ON, Canada [3] Department of Psychiatry, Université de Montreal, CHU Ste Justine Hospital, Montreal, QC, Canada
| | - Z Pausova
- The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - M Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - T Robbins
- Department of Psychology and Behavioural and Clinical Neuroscience Institute, University of Cambridge, Cambridge, UK
| | - M N Smolka
- 1] Department of Psychiatry and Psychotherapy, Technische Universität Dresden, Dresden, Germany [2] Department of Psychology, Neuroimaging Center, Technische Universität Dresden, Dresden, Germany
| | - A Ströhle
- Department of Psychiatry and Psychotherapy, Campus Charité Mitte, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - G Schumann
- 1] Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, King's College London, London, UK [2] MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, London, UK [3] Fondamental Foundation, Créteil, France
| | - T Bourgeron
- 1] Human Genetics and Cognitive Functions, Neuroscience Department, Institut Pasteur, Paris, France [2] CNRS URA 2182 'Genes, synapses and cognition', Paris, France [3] Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France [4] Fondamental Foundation, Créteil, France
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Multiscale modelling of palisade formation in gliobastoma multiforme. J Theor Biol 2015; 383:145-56. [PMID: 26235287 DOI: 10.1016/j.jtbi.2015.07.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 06/14/2015] [Accepted: 07/18/2015] [Indexed: 01/01/2023]
Abstract
Palisades are characteristic tissue aberrations that arise in glioblastomas. Observation of palisades is considered as a clinical indicator of the transition from a noninvasive to an invasive tumour. In this paper we propose a computational model to study the influence of the hypoxic switch in palisade formation. For this we produced three-dimensional realistic simulations, based on a multiscale hybrid model, coupling the evolution of tumour cells and the oxygen diffusion in tissue, that depict the shape of palisades during its formation. Our results can be summarized as follows: (1) the presented simulations can provide clinicians and biologists with a better understanding of three-dimensional structure of palisades as well as of glioblastomas growth dynamics; (2) we show that heterogeneity in cell response to hypoxia is a relevant factor in palisade and pseudopalisade formation; (3) we show how selective processes based on the hypoxia switch influence the tumour proliferation.
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90
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Buchner DA, Nadeau JH. Contrasting genetic architectures in different mouse reference populations used for studying complex traits. Genome Res 2015; 25:775-91. [PMID: 25953951 PMCID: PMC4448675 DOI: 10.1101/gr.187450.114] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 03/31/2015] [Indexed: 01/14/2023]
Abstract
Quantitative trait loci (QTLs) are being used to study genetic networks, protein functions, and systems properties that underlie phenotypic variation and disease risk in humans, model organisms, agricultural species, and natural populations. The challenges are many, beginning with the seemingly simple tasks of mapping QTLs and identifying their underlying genetic determinants. Various specialized resources have been developed to study complex traits in many model organisms. In the mouse, remarkably different pictures of genetic architectures are emerging. Chromosome Substitution Strains (CSSs) reveal many QTLs, large phenotypic effects, pervasive epistasis, and readily identified genetic variants. In contrast, other resources as well as genome-wide association studies (GWAS) in humans and other species reveal genetic architectures dominated with a relatively modest number of QTLs that have small individual and combined phenotypic effects. These contrasting architectures are the result of intrinsic differences in the study designs underlying different resources. The CSSs examine context-dependent phenotypic effects independently among individual genotypes, whereas with GWAS and other mouse resources, the average effect of each QTL is assessed among many individuals with heterogeneous genetic backgrounds. We argue that variation of genetic architectures among individuals is as important as population averages. Each of these important resources has particular merits and specific applications for these individual and population perspectives. Collectively, these resources together with high-throughput genotyping, sequencing and genetic engineering technologies, and information repositories highlight the power of the mouse for genetic, functional, and systems studies of complex traits and disease models.
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Affiliation(s)
- David A Buchner
- Department of Genetics and Genome Sciences, Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Joseph H Nadeau
- Pacific Northwest Diabetes Research Institute, Seattle, Washington 98122, USA
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91
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Abstract
Obesity-related morbidity and mortality are related to fat accumulation and fat distribution in humans. Two large-scale meta-analyses recently published in Nature by Shungin et al. (2015) and Locke et al. (2015) report novel genetic associations for central and overall obesity; these greatly advance our understanding of the biology of obesity.
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Affiliation(s)
- Jingyuan Fu
- Molecular Genetics Section, Department of Pediatrics, University of Groningen, University Medical Center Groningen, 9712 CP Groningen, The Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, 9712 CP Groningen, The Netherlands.
| | - Marten Hofker
- Molecular Genetics Section, Department of Pediatrics, University of Groningen, University Medical Center Groningen, 9712 CP Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9712 CP Groningen, The Netherlands
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92
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93
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Mesbah-Uddin M, Elango R, Banaganapalli B, Shaik NA, Al-Abbasi FA. In-silico analysis of inflammatory bowel disease (IBD) GWAS loci to novel connections. PLoS One 2015; 10:e0119420. [PMID: 25786114 PMCID: PMC4364731 DOI: 10.1371/journal.pone.0119420] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 01/13/2015] [Indexed: 12/19/2022] Open
Abstract
Genome-wide association studies (GWASs) for many complex diseases, including inflammatory bowel disease (IBD), produced hundreds of disease-associated loci—the majority of which are noncoding. The number of GWAS loci is increasing very rapidly, but the process of translating single nucleotide polymorphisms (SNPs) from these loci to genomic medicine is lagging. In this study, we investigated 4,734 variants from 152 IBD associated GWAS loci (IBD associated 152 lead noncoding SNPs identified from pooled GWAS results + 4,582 variants in strong linkage-disequilibrium (LD) (r2 ≥0.8) for EUR population of 1K Genomes Project) using four publicly available bioinformatics tools, e.g. dbPSHP, CADD, GWAVA, and RegulomeDB, to annotate and prioritize putative regulatory variants. Of the 152 lead noncoding SNPs, around 11% are under strong negative selection (GERP++ RS ≥2); and ~30% are under balancing selection (Tajima’s D score >2) in CEU population (1K Genomes Project)—though these regions are positively selected (GERP++ RS <0) in mammalian evolution. The analysis of 4,734 variants using three integrative annotation tools produced 929 putative functional SNPs, of which 18 SNPs (from 15 GWAS loci) are in concordance with all three classifiers. These prioritized noncoding SNPs may contribute to IBD pathogenesis by dysregulating the expression of nearby genes. This study showed the usefulness of integrative annotation for prioritizing fewer functional variants from a large number of GWAS markers.
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Affiliation(s)
- Md. Mesbah-Uddin
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- * E-mail: (MMU); (FAA)
| | - Ramu Elango
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Babajan Banaganapalli
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Noor Ahmad Shaik
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Fahad A. Al-Abbasi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- * E-mail: (MMU); (FAA)
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94
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Hawi Z, Cummins TDR, Tong J, Johnson B, Lau R, Samarrai W, Bellgrove MA. The molecular genetic architecture of attention deficit hyperactivity disorder. Mol Psychiatry 2015; 20:289-97. [PMID: 25600112 DOI: 10.1038/mp.2014.183] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 11/14/2014] [Accepted: 11/19/2014] [Indexed: 12/27/2022]
Abstract
Attention deficit hyperactivity disorder (ADHD) is a common childhood behavioral condition which affects 2-10% of school age children worldwide. Although the underlying molecular mechanism for the disorder is poorly understood, familial, twin and adoption studies suggest a strong genetic component. Here we provide a state-of-the-art review of the molecular genetics of ADHD incorporating evidence from candidate gene and linkage designs, as well as genome-wide association (GWA) studies of common single-nucleotide polymorphisms (SNPs) and rare copy number variations (CNVs). Bioinformatic methods such as functional enrichment analysis and protein-protein network analysis are used to highlight biological processes of likely relevance to the aetiology of ADHD. Candidate gene associations of minor effect size have been replicated across a number of genes including SLC6A3, DRD5, DRD4, SLC6A4, LPHN3, SNAP-25, HTR1B, NOS1 and GIT1. Although case-control SNP-GWAS have had limited success in identifying common genetic variants for ADHD that surpass critical significance thresholds, quantitative trait designs suggest promising associations with Cadherin13 and glucose-fructose oxidoreductase domain 1 genes. Further, CNVs mapped to glutamate receptor genes (GRM1, GRM5, GRM7 and GRM8) have been implicated in the aetiology of the disorder and overlap with bioinformatic predictions based on ADHD GWAS SNP data regarding enriched pathways. Although increases in sample size across multi-center cohorts will likely yield important new results, we advocate that this must occur in parallel with a shift away from categorical case-control approaches that view ADHD as a unitary construct, towards dimensional approaches that incorporate endophenotypes and statistical classification methods.
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Affiliation(s)
- Z Hawi
- School of Psychological Sciences, Monash University, Melbourne, VIC, Australia
| | - T D R Cummins
- School of Psychological Sciences, Monash University, Melbourne, VIC, Australia
| | - J Tong
- School of Psychological Sciences, Monash University, Melbourne, VIC, Australia
| | - B Johnson
- School of Psychological Sciences, Monash University, Melbourne, VIC, Australia
| | - R Lau
- School of Psychological Sciences, Monash University, Melbourne, VIC, Australia
| | - W Samarrai
- New York City College of Technology, City University of New York, New York, NY, USA
| | - M A Bellgrove
- School of Psychological Sciences, Monash University, Melbourne, VIC, Australia
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Shafer AB, Wolf JB, Alves PC, Bergström L, Bruford MW, Brännström I, Colling G, Dalén L, De Meester L, Ekblom R, Fawcett KD, Fior S, Hajibabaei M, Hill JA, Hoezel AR, Höglund J, Jensen EL, Krause J, Kristensen TN, Krützen M, McKay JK, Norman AJ, Ogden R, Österling EM, Ouborg NJ, Piccolo J, Popović D, Primmer CR, Reed FA, Roumet M, Salmona J, Schenekar T, Schwartz MK, Segelbacher G, Senn H, Thaulow J, Valtonen M, Veale A, Vergeer P, Vijay N, Vilà C, Weissensteiner M, Wennerström L, Wheat CW, Zieliński P. Genomics and the challenging translation into conservation practice. Trends Ecol Evol 2015; 30:78-87. [DOI: 10.1016/j.tree.2014.11.009] [Citation(s) in RCA: 278] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 11/20/2014] [Accepted: 11/21/2014] [Indexed: 10/24/2022]
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96
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Ogura T, Busch W. From phenotypes to causal sequences: using genome wide association studies to dissect the sequence basis for variation of plant development. CURRENT OPINION IN PLANT BIOLOGY 2015; 23:98-108. [PMID: 25449733 DOI: 10.1016/j.pbi.2014.11.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 11/04/2014] [Accepted: 11/05/2014] [Indexed: 05/20/2023]
Abstract
Tremendous natural variation of growth and development exists within species. Uncovering the molecular mechanisms that tune growth and development promises to shed light on a broad set of biological issues including genotype to phenotype relations, regulatory mechanisms of biological processes and evolutionary questions. Recent progress in sequencing and data processing capabilities has enabled Genome Wide Association Studies (GWASs) to identify DNA sequence polymorphisms that underlie the variation of biological traits. In the last years, GWASs have proven powerful in revealing the complex genetic bases of many phenotypes in various plant species. Here we highlight successful recent GWASs that uncovered mechanistic and sequence bases of trait variation related to plant growth and development and discuss important considerations for conducting successful GWASs.
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Affiliation(s)
- Takehiko Ogura
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Wolfgang Busch
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
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Kim YS, Leventhal BL. Genetic epidemiology and insights into interactive genetic and environmental effects in autism spectrum disorders. Biol Psychiatry 2015; 77:66-74. [PMID: 25483344 PMCID: PMC4260177 DOI: 10.1016/j.biopsych.2014.11.001] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 10/31/2014] [Accepted: 11/02/2014] [Indexed: 12/27/2022]
Abstract
Understanding the pathogenesis of neurodevelopmental disorders has proven to be challenging. Using autism spectrum disorder (ASD) as a paradigmatic neurodevelopmental disorder, this article reviews the existing literature on the etiological substrates of ASD and explores how genetic epidemiology approaches including gene-environment interactions (G×E) can play a role in identifying factors associated with ASD etiology. New genetic and bioinformatics strategies have yielded important clues to ASD genetic substrates. The next steps for understanding ASD pathogenesis require significant effort to focus on how genes and environment interact with one another in typical development and its perturbations. Along with larger sample sizes, future study designs should include sample ascertainment that is epidemiologic and population-based to capture the entire ASD spectrum with both categorical and dimensional phenotypic characterization; environmental measurements with accuracy, validity, and biomarkers; statistical methods to address population stratification, multiple comparisons, and G×E of rare variants; animal models to test hypotheses; and new methods to broaden the capacity to search for G×E, including genome-wide and environment-wide association studies, precise estimation of heritability using dense genetic markers, and consideration of G×E both as the disease cause and a disease course modifier. Although examination of G×E appears to be a daunting task, tremendous recent progress in gene discovery has opened new horizons for advancing our understanding of the role of G×E in the pathogenesis of ASD and ultimately identifying the causes, treatments, and even preventive measures for ASD and other neurodevelopmental disorders.
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Affiliation(s)
- Young Shin Kim
- Department of Psychiatry, University of California, San Francisco, San Francisco, California..
| | - Bennett L Leventhal
- Department of Psychiatry, Yonsei University College of Medicine, Seoul, South Korea
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Moon SW, Dinov ID, Kim J, Zamanyan A, Hobel S, Thompson PM, Toga AW. Structural Neuroimaging Genetics Interactions in Alzheimer's Disease. J Alzheimers Dis 2015; 48:1051-63. [PMID: 26444770 PMCID: PMC4730943 DOI: 10.3233/jad-150335] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This article investigates late-onset cognitive impairment using neuroimaging and genetics biomarkers for Alzheimer's Disease Neuroimaging Initiative (ADNI) participants. Eight-hundred and eight ADNI subjects were identified and divided into three groups: 200 subjects with Alzheimer's disease (AD), 383 subjects with mild cognitive impairment (MCI), and 225 asymptomatic normal controls (NC). Their structural magnetic resonance imaging (MRI) data were parcellated using BrainParser, and the 80 most important neuroimaging biomarkers were extracted using the global shape analysis Pipeline workflow. Using Plink via the Pipeline environment, we obtained 80 SNPs highly-associated with the imaging biomarkers. In the AD cohort, rs2137962 was significantly associated bilaterally with changes in the hippocampi and the parahippocampal gyri, and rs1498853, rs288503, and rs288496 were associated with the left and right hippocampi, the right parahippocampal gyrus, and the left inferior temporal gyrus. In the MCI cohort, rs17028008 and rs17027976 were significantly associated with the right caudate and right fusiform gyrus, rs2075650 (TOMM40) was associated with the right caudate, and rs1334496 and rs4829605 were significantly associated with the right inferior temporal gyrus. In the NC cohort, Chromosome 15 [rs734854 (STOML1), rs11072463 (PML), rs4886844 (PML), and rs1052242 (PML)] was significantly associated with both hippocampi and both insular cortices, and rs4899412 (RGS6) was significantly associated with the caudate. We observed significant correlations between genetic and neuroimaging phenotypes in the 808 ADNI subjects. These results suggest that differences between AD, MCI, and NC cohorts may be examined by using powerful joint models of morphometric, imaging and genotypic data.
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Affiliation(s)
- Seok Woo Moon
- Department of Psychiatry, Konkuk University School of Medicine, Seoul, Republic of Korea
| | - Ivo D. Dinov
- Laboratory of Neuro Imaging, Institute for Neuroimaging and Informatics, Keck School of Medicine of USC, University of Southern California, Los Angeles, California, United States of America
- University of Michigan, School of Nursing, Ann Arbor, Michigan, United States of America
| | - Jaebum Kim
- Department of Animal Biotechnology, Konkuk University, Seoul, Republic of Korea
| | - Alen Zamanyan
- Laboratory of Neuro Imaging, Institute for Neuroimaging and Informatics, Keck School of Medicine of USC, University of Southern California, Los Angeles, California, United States of America
| | - Sam Hobel
- Laboratory of Neuro Imaging, Institute for Neuroimaging and Informatics, Keck School of Medicine of USC, University of Southern California, Los Angeles, California, United States of America
| | - Paul M. Thompson
- Laboratory of Neuro Imaging, Institute for Neuroimaging and Informatics, Keck School of Medicine of USC, University of Southern California, Los Angeles, California, United States of America
| | - Arthur W. Toga
- Laboratory of Neuro Imaging, Institute for Neuroimaging and Informatics, Keck School of Medicine of USC, University of Southern California, Los Angeles, California, United States of America
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