1
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Jenkins D. How do stochastic processes and genetic threshold effects explain incomplete penetrance and inform causal disease mechanisms? Philos Trans R Soc Lond B Biol Sci 2024; 379:20230045. [PMID: 38432317 PMCID: PMC10909503 DOI: 10.1098/rstb.2023.0045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 01/16/2024] [Indexed: 03/05/2024] Open
Abstract
Incomplete penetrance is the rule rather than the exception in Mendelian disease. In syndromic monogenic disorders, phenotypic variability can be viewed as the combination of incomplete penetrance for each of multiple independent clinical features. Within genetically identical individuals, such as isogenic model organisms, stochastic variation at molecular and cellular levels is the primary cause of incomplete penetrance according to a genetic threshold model. By defining specific probability distributions of causal biological readouts and genetic liability values, stochasticity and incomplete penetrance provide information about threshold values in biological systems. Ascertainment of threshold values has been achieved by simultaneous scoring of relatively simple phenotypes and quantitation of molecular readouts at the level of single cells. However, this is much more challenging for complex morphological phenotypes using experimental and reductionist approaches alone, where cause and effect are separated temporally and across multiple biological modes and scales. Here I consider how causal inference, which integrates observational data with high confidence causal models, might be used to quantify the relative contribution of different sources of stochastic variation to phenotypic diversity. Collectively, these approaches could inform disease mechanisms, improve predictions of clinical outcomes and prioritize gene therapy targets across modes and scales of gene function. This article is part of a discussion meeting issue 'Causes and consequences of stochastic processes in development and disease'.
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Affiliation(s)
- Dagan Jenkins
- Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK
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2
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Fernández-Rhodes L, McArdle CE, Rao H, Wang Y, Martinez-Miller EE, Ward JB, Cai J, Sofer T, Isasi CR, North KE. A Gene-Acculturation Study of Obesity Among US Hispanic/Latinos: The Hispanic Community Health Study/Study of Latinos. Psychosom Med 2023; 85:358-365. [PMID: 36917487 PMCID: PMC10159946 DOI: 10.1097/psy.0000000000001193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
OBJECTIVE In the United States, Hispanic/Latino adults face a high burden of obesity; yet, not all individuals are equally affected, partly due in part to this ethnic group's marked sociocultural diversity. We sought to analyze the modification of body mass index (BMI) genetic effects in Hispanic/Latino adults by their level of acculturation, a complex biosocial phenomenon that remains understudied. METHODS Among 11,747 Hispanic/Latinos adults in the Hispanic Community Health Study/Study of Latinos aged 18 to 76 years from four urban communities (2008-2011), we a) tested our hypothesis that the effect of a genetic risk score (GRS) for increased BMI may be exacerbated by higher levels of acculturation and b) examined if GRS acculturation interactions varied by gender or Hispanic/Latino background group. All genetic modeling controlled for relatedness, age, gender, principal components of ancestry, center, and complex study design within a generalized estimated equation framework. RESULTS We observed a GRS increase of 0.34 kg/m 2 per risk allele in weighted mean BMI. The estimated main effect of GRS on BMI varied both across acculturation level and across gender. The difference between high and low acculturation ranged from 0.03 to 0.23 kg/m 2 per risk allele, but varied across acculturation measure and gender. CONCLUSIONS These results suggest the presence of effect modification by acculturation, with stronger effects on BMI among highly acculturated individuals and female immigrants. Future studies of obesity in the Hispanic/Latino community should account for sociocultural environments and consider their intersection with gender to better target obesity interventions.
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Affiliation(s)
- Lindsay Fernández-Rhodes
- Department of Biobehavioral Health, Pennsylvania State University, University Park, PA
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Cristin E. McArdle
- Department of Biobehavioral Health, Pennsylvania State University, University Park, PA
| | - Hridya Rao
- Department of Biobehavioral Health, Pennsylvania State University, University Park, PA
| | - Yujie Wang
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Erline E. Martinez-Miller
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX
| | - Julia B. Ward
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Social & Scientific Systems, a DLH Holdings Company, Durham, NC
| | - Jianwen Cai
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Tamar Sofer
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Carmen R. Isasi
- Departments of Epidemiology & Population Health and Pediatrics, Albert Einstein College of Medicine, Bronx, NY
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC
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3
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Joukhadar R, Thistlethwaite R, Trethowan R, Keeble-Gagnère G, Hayden MJ, Ullah S, Daetwyler HD. Meta-analysis of genome-wide association studies reveal common loci controlling agronomic and quality traits in a wide range of normal and heat stressed environments. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2113-2127. [PMID: 33768282 DOI: 10.1007/s00122-021-03809-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/01/2021] [Indexed: 06/12/2023]
Abstract
Several stable QTL were detected using metaGWAS analysis for different agronomic and quality traits under 26 normal and heat stressed environments. Heat stress, exacerbated by global warming, has a negative influence on wheat production worldwide and climate resilient cultivars can help mitigate these impacts. Selection decisions should therefore depend on multi-environment experiments representing a range of temperatures at critical stages of development. Here, we applied a meta-genome wide association analysis (metaGWAS) approach to detect stable QTL with significant effects across multiple environments. The metaGWAS was applied to 11 traits scored in 26 trials that were sown at optimal or late times of sowing (TOS1 and TOS2, respectively) at five locations. A total of 2571 unique wheat genotypes (13,959 genotypes across all environments) were included and the analysis conducted on TOS1, TOS2 and both times of sowing combined (TOS1&2). The germplasm was genotyped using a 90 k Infinium chip and imputed to exome sequence level, resulting in 341,195 single nucleotide polymorphisms (SNPs). The average accuracy across all imputed SNPs was high (92.4%). The three metaGWAS analyses revealed 107 QTL for the 11 traits, of which 16 were detected in all three analyses and 23 were detected in TOS1&2 only. The remaining QTL were detected in either TOS1 or TOS2 with or without TOS1&2, reflecting the complex interactions between the environments and the detected QTL. Eight QTL were associated with grain yield and seven with multiple traits. The identified QTL provide an important resource for gene enrichment and fine mapping to further understand the mechanisms of gene × environment interaction under both heat stressed and unstressed conditions.
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Affiliation(s)
- Reem Joukhadar
- Agriculture Victoria, Centre for AgriBioscience, AgriBio, Bundoora, VIC, Australia.
| | - Rebecca Thistlethwaite
- School of Life and Environmental Sciences, Plant Breeding Institute, Sydney Institute of Agriculture, The University of Sydney, Narrabri, NSW, Australia
| | - Richard Trethowan
- School of Life and Environmental Sciences, Plant Breeding Institute, Sydney Institute of Agriculture, The University of Sydney, Narrabri, NSW, Australia
- School of Life and Environmental Sciences, Plant Breeding Institute, Sydney Institute of Agriculture, The University of Sydney, Cobbitty, NSW, Australia
| | | | - Matthew J Hayden
- Agriculture Victoria, Centre for AgriBioscience, AgriBio, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Smi Ullah
- School of Life and Environmental Sciences, Plant Breeding Institute, Sydney Institute of Agriculture, The University of Sydney, Narrabri, NSW, Australia
| | - Hans D Daetwyler
- Agriculture Victoria, Centre for AgriBioscience, AgriBio, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
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4
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Tanisawa K, Wang G, Seto J, Verdouka I, Twycross-Lewis R, Karanikolou A, Tanaka M, Borjesson M, Di Luigi L, Dohi M, Wolfarth B, Swart J, Bilzon JLJ, Badtieva V, Papadopoulou T, Casasco M, Geistlinger M, Bachl N, Pigozzi F, Pitsiladis Y. Sport and exercise genomics: the FIMS 2019 consensus statement update. Br J Sports Med 2020; 54:969-975. [PMID: 32201388 PMCID: PMC7418627 DOI: 10.1136/bjsports-2019-101532] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/17/2019] [Indexed: 12/26/2022]
Abstract
Rapid advances in technologies in the field of genomics such as high throughput DNA sequencing, big data processing by machine learning algorithms and gene-editing techniques are expected to make precision medicine and gene-therapy a greater reality. However, this development will raise many important new issues, including ethical, moral, social and privacy issues. The field of exercise genomics has also advanced by incorporating these innovative technologies. There is therefore an urgent need for guiding references for sport and exercise genomics to allow the necessary advancements in this field of sport and exercise medicine, while protecting athletes from any invasion of privacy and misuse of their genomic information. Here, we update a previous consensus and develop a guiding reference for sport and exercise genomics based on a SWOT (Strengths, Weaknesses, Opportunities and Threats) analysis. This SWOT analysis and the developed guiding reference highlight the need for scientists/clinicians to be well-versed in ethics and data protection policy to advance sport and exercise genomics without compromising the privacy of athletes and the efforts of international sports federations. Conducting research based on the present guiding reference will mitigate to a great extent the risks brought about by inappropriate use of genomic information and allow further development of sport and exercise genomics in accordance with best ethical standards and international data protection principles and policies. This guiding reference should regularly be updated on the basis of new information emerging from the area of sport and exercise medicine as well as from the developments and challenges in genomics of health and disease in general in order to best protect the athletes, patients and all other relevant stakeholders.
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Affiliation(s)
- Kumpei Tanisawa
- Faculty of Sport Sciences, Waseda University, Tokorozawa, Japan
| | - Guan Wang
- Collaborating Centre of Sports Medicine, University of Brighton, Eastbourne, UK
| | - Jane Seto
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Ioanna Verdouka
- Collaborating Centre of Sports Medicine, University of Brighton, Eastbourne, UK
| | - Richard Twycross-Lewis
- School of Engineering and Materials Science, Queen Mary University of London, London, UK
| | - Antonia Karanikolou
- Collaborating Centre of Sports Medicine, University of Brighton, Eastbourne, UK
| | - Masashi Tanaka
- Department for Health and Longevity Research, National Institutes of Biomedical Innovation, Health and Nutrition, Tokyo, Japan
| | - Mats Borjesson
- Department of Neuroscience and Physiology, Center for Health and Performance, Goteborg University, Göteborg, Sweden
- Sahlgrenska University Hospital/Ostra, Göteborg, Sweden
| | - Luigi Di Luigi
- Unit of Endocrinology, Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", Rome, Italy
| | - Michiko Dohi
- Sport Medical Center, Japan Institute of Sports Sciences, Tokyo, Japan
| | - Bernd Wolfarth
- Department of Sport Medicine, Humboldt University and Charité University School of Medicine, Berlin, Germany
| | - Jeroen Swart
- UCT Research Unit for Exercise Science and Sports Medicine, Cape Town, South Africa
| | | | - Victoriya Badtieva
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Ministry of Health of Russia, Moscow, Russian Federation
- Moscow Research and Practical Center for Medical Rehabilitation, Restorative and Sports Medicine, Moscow Healthcare Department, Moscow, Russian Federation
| | - Theodora Papadopoulou
- Defence Medical Rehabilitation Centre, Stanford Hall, Loughborough, UK
- British Association of Sport and Exercise Medicine, Doncaster, UK
| | | | - Michael Geistlinger
- Unit of International Law, Department of Constitutional, International and European Law, University of Salzburg, Salzburg, Salzburg, Austria
| | - Norbert Bachl
- Institute of Sports Science, University of Vienna, Vienna, Austria
- Austrian Institute of Sports Medicine, Vienna, Austria
| | - Fabio Pigozzi
- Sport Medicine Unit, Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", Rome, Italy
| | - Yannis Pitsiladis
- Collaborating Centre of Sports Medicine, University of Brighton, Eastbourne, UK
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5
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Claus EB, Cornish AJ, Broderick P, Schildkraut JM, Dobbins SE, Holroyd A, Calvocoressi L, Lu L, Hansen HM, Smirnov I, Walsh KM, Schramm J, Hoffmann P, Nöthen MM, Jöckel KH, Swerdlow A, Larsen SB, Johansen C, Simon M, Bondy M, Wrensch M, Houlston RS, Wiemels JL. Genome-wide association analysis identifies a meningioma risk locus at 11p15.5. Neuro Oncol 2019; 20:1485-1493. [PMID: 29762745 PMCID: PMC6176799 DOI: 10.1093/neuonc/noy077] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Background Meningiomas are adult brain tumors originating in the meningeal coverings of the brain and spinal cord, with significant heritable basis. Genome-wide association studies (GWAS) have previously identified only a single risk locus for meningioma, at 10p12.31. Methods To identify a susceptibility locus for meningioma, we conducted a meta-analysis of 2 GWAS, imputed using a merged reference panel from the 1000 Genomes Project and UK10K data, with validation in 2 independent sample series totaling 2138 cases and 12081 controls. Results We identified a new susceptibility locus for meningioma at 11p15.5 (rs2686876, odds ratio = 1.44, P = 9.86 × 10–9). A number of genes localize to the region of linkage disequilibrium encompassing rs2686876, including RIC8A, which plays a central role in the development of neural crest-derived structures, such as the meninges. Conclusions This finding advances our understanding of the genetic basis of meningioma development and provides additional support for a polygenic model of meningioma.
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Affiliation(s)
- Elizabeth B Claus
- School of Public Health, Yale University, New Haven, Connecticut, USA.,Department of Neurosurgery, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Alex J Cornish
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Joellen M Schildkraut
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, USA
| | - Sara E Dobbins
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Amy Holroyd
- School of Public Health, Yale University, New Haven, Connecticut, USA.,Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Lisa Calvocoressi
- School of Public Health, Yale University, New Haven, Connecticut, USA
| | - Lingeng Lu
- School of Public Health, Yale University, New Haven, Connecticut, USA
| | - Helen M Hansen
- School of Public Health, Yale University, New Haven, Connecticut, USA.,Division of Neuroepidemiology, Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Ivan Smirnov
- School of Public Health, Yale University, New Haven, Connecticut, USA.,Division of Neuroepidemiology, Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Kyle M Walsh
- School of Public Health, Yale University, New Haven, Connecticut, USA.,Division of Neuroepidemiology, Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Johannes Schramm
- School of Public Health, Yale University, New Haven, Connecticut, USA.,University of Bonn Medical School, Bonn, Germany
| | - Per Hoffmann
- School of Public Health, Yale University, New Haven, Connecticut, USA.,Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland.,Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Markus M Nöthen
- School of Public Health, Yale University, New Haven, Connecticut, USA.,Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany.,Institute of Human Genetics, University of Bonn School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Karl-Heinz Jöckel
- School of Public Health, Yale University, New Haven, Connecticut, USA.,Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK.,Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Signe Benzon Larsen
- Unit of Survivorship, The Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Christoffer Johansen
- Unit of Survivorship, The Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Matthias Simon
- University of Bonn Medical School, Bonn, Germany.,Department of Neurosurgery, Bethel Clinic, Bielefeld, Germany
| | - Melissa Bondy
- Section of Epidemiology and Population Sciences, Department of Medicine and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Margaret Wrensch
- Division of Neuroepidemiology, Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Joseph L Wiemels
- Division of Neuroepidemiology, Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA.,Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, USA
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6
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Zeiler FA, McFadyen C, Newcombe VFJ, Synnot A, Donoghue EL, Ripatti S, Steyerberg EW, Gruen RL, McAllister TW, Rosand J, Palotie A, Maas AIR, Menon DK. Genetic Influences on Patient-Oriented Outcomes in Traumatic Brain Injury: A Living Systematic Review of Non-Apolipoprotein E Single-Nucleotide Polymorphisms. J Neurotrauma 2019; 38:1107-1123. [PMID: 29799308 PMCID: PMC8054522 DOI: 10.1089/neu.2017.5583] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
There is a growing literature on the impact of genetic variation on outcome in traumatic brain injury (TBI). Whereas a substantial proportion of these publications have focused on the apolipoprotein E (APOE) gene, several have explored the influence of other polymorphisms. We undertook a systematic review of the impact of single-nucleotide polymorphisms (SNPs) in non–apolipoprotein E (non-APOE) genes associated with patient outcomes in adult TBI). We searched EMBASE, MEDLINE, CINAHL, and gray literature from inception to the beginning of August 2017 for studies of genetic variance in relation to patient outcomes in adult TBI. Sixty-eight articles were deemed eligible for inclusion into the systematic review. The SNPs described were in the following categories: neurotransmitter (NT) in 23, cytokine in nine, brain-derived neurotrophic factor (BDNF) in 12, mitochondrial genes in three, and miscellaneous SNPs in 21. All studies were based on small patient cohorts and suffered from potential bias. A range of SNPs associated with genes coding for monoamine NTs, BDNF, cytokines, and mitochondrial proteins have been reported to be associated with variation in global, neuropsychiatric, and behavioral outcomes. An analysis of the tissue, cellular, and subcellular location of the genes that harbored the SNPs studied showed that they could be clustered into blood–brain barrier associated, neuroprotective/regulatory, and neuropsychiatric/degenerative groups. Several small studies report that various NT, cytokine, and BDNF-related SNPs are associated with variations in global outcome at 6–12 months post-TBI. The association of these SNPs with neuropsychiatric and behavioral outcomes is less clear. A definitive assessment of role and effect size of genetic variation in these genes on outcome remains uncertain, but could be clarified by an adequately powered genome-wide association study with appropriate recording of outcomes.
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Affiliation(s)
- Frederick A Zeiler
- Division of Anaesthesia, University of Cambridge, Cambridge, United Kingdom.,Section of Neurosurgery, Department of Surgery, University of Manitoba, Winnipeg, Manitoba, Canada.,Clinician Investigator Program, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Charles McFadyen
- Division of Anaesthesia, University of Cambridge, Cambridge, United Kingdom
| | | | - Anneliese Synnot
- Centre for Excellence in Traumatic Brain Injury Research, National Trauma Research Institute, Monash University, The Alfred Hospital, Melbourne, Australia and Cochrane Consumers and Communication Review Group, Centre for Health Communication and Participation, School of Psychology and Public Health, La Trobe University, Melbourne, Australia
| | - Emma L Donoghue
- Australian and New Zealand Intensive Care Research Centre, School of Public Health and Preventive Medicine and Cochrane Australia, Monash University, Melbourne, Australia
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM) and Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ewout W Steyerberg
- Department of Public Health, Erasmus MC-University Medical Center Rotterdam, Rotterdam, the Netherlands and Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
| | - Russel L Gruen
- Central Clinical School, Monash University, Melbourne, Australia and Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Thomas W McAllister
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, Indiana
| | - Jonathan Rosand
- Division of Neurocritical Care and Emergency Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, and Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Aarno Palotie
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland; Psychiatric and Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts; Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts
| | - Andrew I R Maas
- Department of Neurosurgery, Antwerp University Hospital and University of Antwerp, Edegem, Belgium
| | - David K Menon
- Division of Anaesthesia, University of Cambridge, Cambridge, United Kingdom
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7
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Gupta V, Walia GK. Genomics of Type 2 Diabetes Mellitus and Glycemic Traits. INT J HUM GENET 2017. [DOI: 10.1080/09723757.2017.1383655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Vipin Gupta
- Department of Anthropology, University of Delhi, Delhi 110 007, India
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8
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Ahn K, An SS, Shugart YY, Rapoport JL. Common polygenic variation and risk for childhood-onset schizophrenia. Mol Psychiatry 2016; 21:94-6. [PMID: 25510512 DOI: 10.1038/mp.2014.158] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 10/02/2014] [Accepted: 10/09/2014] [Indexed: 12/16/2022]
Abstract
Childhood-onset schizophrenia (COS) is a rare and severe form of the disorder, with more striking abnormalities with respect to prepsychotic developmental disorders and abnormities in the brain development compared with later-onset schizophrenia. We previously documented that COS patients, compared with their healthy siblings and with adult-onset patients (AOS), carry significantly more rare chromosomal copy number variations, spanning large genomic regions (>100 kb) (Ahn et al. 2014). Here, we interrogated the contribution of common polygenic variation to the genetic susceptibility for schizophrenia. We examined the association between a direct measure of genetic risk of schizophrenia in 130 COS probands and 103 healthy siblings. Using data from the schizophrenia and autism GWAS of the Psychiatric Genomic Consortia, we selected three risk-related sets of single nucleotide polymorphisms from which we conducted polygenic risk score comparisons for COS probands and their healthy siblings. COS probands had higher genetic risk scores of both schizophrenia and autism than their siblings (P<0.05). Given the small sample size, these findings suggest that COS patients have more salient genetic risk than do AOS.
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Affiliation(s)
- K Ahn
- Childhood Psychiatry Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - S S An
- Department of Environmental Health Sciences, Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, USA
| | - Y Y Shugart
- Unit of Statistical Genomics, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - J L Rapoport
- Childhood Psychiatry Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
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9
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Statistical and Computational Methods for Genetic Diseases: An Overview. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2015; 2015:954598. [PMID: 26106440 PMCID: PMC4464008 DOI: 10.1155/2015/954598] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 04/23/2015] [Indexed: 12/19/2022]
Abstract
The identification of causes of genetic diseases has been carried out by several approaches with increasing complexity. Innovation of genetic methodologies leads to the production of large amounts of data that needs the support of statistical and computational methods to be correctly processed. The aim of the paper is to provide an overview of statistical and computational methods paying attention to methods for the sequence analysis and complex diseases.
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10
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Detecting a weak association by testing its multiple perturbations: a data mining approach. Sci Rep 2014; 4:5081. [PMID: 24866319 PMCID: PMC4035575 DOI: 10.1038/srep05081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 05/07/2014] [Indexed: 01/09/2023] Open
Abstract
Many risk factors/interventions in epidemiologic/biomedical studies are of minuscule effects. To detect such weak associations, one needs a study with a very large sample size (the number of subjects, n). The n of a study can be increased but unfortunately only to an extent. Here, we propose a novel method which hinges on increasing sample size in a different direction–the total number of variables (p). We construct a p-based ‘multiple perturbation test', and conduct power calculations and computer simulations to show that it can achieve a very high power to detect weak associations when p can be made very large. As a demonstration, we apply the method to analyze a genome-wide association study on age-related macular degeneration and identify two novel genetic variants that are significantly associated with the disease. The p-based method may set a stage for a new paradigm of statistical tests.
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11
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Evangelou E, Ioannidis JPA. Meta-analysis methods for genome-wide association studies and beyond. Nat Rev Genet 2013; 14:379-89. [PMID: 23657481 DOI: 10.1038/nrg3472] [Citation(s) in RCA: 382] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Meta-analysis of genome-wide association studies (GWASs) has become a popular method for discovering genetic risk variants. Here, we overview both widely applied and newer statistical methods for GWAS meta-analysis, including issues of interpretation and assessment of sources of heterogeneity. We also discuss extensions of these meta-analysis methods to complex data. Where possible, we provide guidelines for researchers who are planning to use these methods. Furthermore, we address special issues that may arise for meta-analysis of sequencing data and rare variants. Finally, we discuss challenges and solutions surrounding the goals of making meta-analysis data publicly available and building powerful consortia.
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Affiliation(s)
- Evangelos Evangelou
- Clinical and Molecular Epidemiology Unit, Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina 45110, Greece
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Rotondi MA, Bull SB. Cumulative meta-analysis for genetic association: when is a new study worthwhile? Hum Hered 2012; 74:61-70. [PMID: 23258221 DOI: 10.1159/000345604] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 10/30/2012] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES In this paper, we address the questions: how large a sample size would be required to show genome-wide significance between a single nucleotide polymorphism (SNP) and a genetic trait in a meta-analysis of a newly planned study together with the existing ones? Or alternatively: will a planned study of size n be able to provide evidence of a genetic association when this study is combined with a current meta-analysis? METHODS We examine the potential impact of a newly planned genetic study on an existing meta-analysis through the use of a simulation-based algorithm. The proposed approach provides an empirical estimate of the power of the updated meta-analysis to detect genome-wide significance (p<5.0×10(-8)) of a complex trait and each of a set of specific SNPs of interest or the expected p value of the updated meta-analysis including the current and proposed studies. RESULTS This technique is illustrated in the context of an updated meta-analysis of case-control studies in Paget's disease. A second example illustrates the impact of adding a newly planned study to a large meta-analysis of SNP associations with human height. CONCLUSIONS The proposed algorithm is particularly useful for the design of studies to assess a selected set of high-priority SNP associations that are 'nearly' significant in meta-analysis of existing studies. The results may help investigators decide whether an updated meta-analysis is likely to achieve genome-wide significance.
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Affiliation(s)
- Michael A Rotondi
- School of Kinesiology and Health Science, York University, and Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.
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Mtiraoui N, Turki A, Nemr R, Echtay A, Izzidi I, Al-Zaben GS, Irani-Hakime N, Keleshian SH, Mahjoub T, Almawi WY. Contribution of common variants of ENPP1, IGF2BP2, KCNJ11, MLXIPL, PPARγ, SLC30A8 and TCF7L2 to the risk of type 2 diabetes in Lebanese and Tunisian Arabs. DIABETES & METABOLISM 2012; 38:444-9. [PMID: 22749234 DOI: 10.1016/j.diabet.2012.05.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 05/07/2012] [Accepted: 05/07/2012] [Indexed: 12/15/2022]
Abstract
BACKGROUND While several type 2 diabetes mellitus (T2DM) susceptibility loci identified through genome-wide association studies (GWAS) have been replicated in many populations, their association in Arabs has not been reported. For this reason, the present study looked at the contribution of ENNP1 (rs1044498), IGF2BP2 (rs1470579), KCNJ11 (rs5219), MLXIPL (rs7800944), PPARγ (rs1801282), SLC30A8 (rs13266634) and TCF7L2 (rs7903146) SNPs to the risk of T2DM in Lebanese and Tunisian Arabs. METHODS Study subjects (case/controls) were Lebanese (751/918) and Tunisians (1470/838). Genotyping was carried out by the allelic discrimination method. RESULTS In Lebanese and Tunisians, neither ENNP1 nor MLXIPL was associated with T2DM, whereas TCF7L2 was significantly associated with an increased risk of T2DM in both the Lebanese [P < 0.001; OR (95% CI): 1.38 (1.20-1.59)] and Tunisians [P < 0.001; OR (95% CI): 1.36 (1.18-1.56)]. Differential associations of IGF2BP2, KCNJ11, PPARγ and SLC30A8 with T2DM were noted in the two populations. IGF2BP2 [P = 1.3 × 10(-5); OR (95% CI): 1.66 (1.42-1.94)] and PPARγ [P = 0.005; OR (95% CI): 1.41 (1.10-1.80)] were associated with T2DM in the Lebanese, but not Tunisians, while KCNJ11 [P = 8.0 × 10(-4); OR (95% CI): 1.27 (1.09-1.47)] and SLC30A8 [P = 1.6 × 10(-5); OR (95% CI): 1.37 (1.15-1.62)] were associated with T2DM in the Tunisians, but not Lebanese, after adjusting for gender and body mass index. CONCLUSION T2DM susceptibility loci SNPs identified through GWAS showed differential associations with T2DM in two Arab populations, thus further confirming the ethnic contributions of these variants to T2DM susceptibility.
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Affiliation(s)
- N Mtiraoui
- Research Unit of Biology and Genetics of Hematological and Autoimmune diseases, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
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