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Rancelis T, Domarkiene I, Ambrozaityte L, Utkus A. Implementing Core Genes and an Omnigenic Model for Behaviour Traits Prediction in Genomics. Genes (Basel) 2023; 14:1630. [PMID: 37628681 PMCID: PMC10454355 DOI: 10.3390/genes14081630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
A high number of genome variants are associated with complex traits, mainly due to genome-wide association studies (GWAS). Using polygenic risk scores (PRSs) is a widely accepted method for calculating an individual's complex trait prognosis using such data. Unlike monogenic traits, the practical implementation of complex traits by applying this method still falls behind. Calculating PRSs from all GWAS data has limited practical usability in behaviour traits due to statistical noise and the small effect size from a high number of genome variants involved. From a behaviour traits perspective, complex traits are explored using the concept of core genes from an omnigenic model, aiming to employ a simplified calculation version. Simplification may reduce the accuracy compared to a complete PRS encompassing all trait-associated variants. Integrating genome data with datasets from various disciplines, such as IT and psychology, could lead to better complex trait prediction. This review elucidates the significance of clear biological pathways in understanding behaviour traits. Specifically, it highlights the essential role of genes related to hormones, enzymes, and neurotransmitters as robust core genes in shaping these traits. Significant variations in core genes are prominently observed in behaviour traits such as stress response, impulsivity, and substance use.
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Affiliation(s)
- Tautvydas Rancelis
- Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariskiu Str. 2, LT-08661 Vilnius, Lithuania; (I.D.); (L.A.); (A.U.)
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Konopka MJ, Sperlich B, Rietjens G, Zeegers MP. Genetics and athletic performance: a systematic SWOT analysis of non-systematic reviews. Front Genet 2023; 14:1232987. [PMID: 37621703 PMCID: PMC10445150 DOI: 10.3389/fgene.2023.1232987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 07/26/2023] [Indexed: 08/26/2023] Open
Abstract
Exercise genetics/genomics is a growing research discipline comprising several Strengths and Opportunities but also deals with Weaknesses and Threats. This "systematic SWOT overview of non-systematic reviews" (sSWOT) aimed to identify the Strengths, Weaknesses, Opportunities, and Threats linked to exercise genetics/genomics. A systematic search was conducted in the Medline and Embase databases for non-systematic reviews to provide a comprehensive overview of the current literature/research area. The extracted data was thematically analyzed, coded, and categorized into SWOT clusters. In the 45 included reviews five Strengths, nine Weaknesses, six Opportunities, and three Threats were identified. The cluster of Strengths included "advances in technology", "empirical evidence", "growing research discipline", the "establishment of consortia", and the "acceptance/accessibility of genetic testing". The Weaknesses were linked to a "low research quality", the "complexity of exercise-related traits", "low generalizability", "high costs", "genotype scores", "reporting bias", "invasive methods", "research progress", and "causality". The Opportunities comprised of "precision exercise", "omics", "multicenter studies", as well as "genetic testing" as "commercial"-, "screening"-, and "anti-doping" detection tool. The Threats were related to "ethical issues", "direct-to-consumer genetic testing companies", and "gene doping". This overview of the present state of the art research in sport genetics/genomics indicates a field with great potential, while also drawing attention to the necessity for additional advancement in methodological and ethical guidance to mitigate the recognized Weaknesses and Threats. The recognized Strengths and Opportunities substantiate the capability of genetics/genomics to make significant contributions to the performance and wellbeing of athletes.
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Affiliation(s)
- Magdalena Johanna Konopka
- Care and Public Health Research Institute, Maastricht University, Maastricht, Netherlands
- Department of Epidemiology, Maastricht University, Maastricht, Netherlands
| | - Billy Sperlich
- Integrative and Experimental Exercise Science and Training, Institute of Sport Science, University of Würzburg, Würzburg, Germany
| | - Gerard Rietjens
- Human Physiology and Sports Physiotherapy Research Group, Vrije Universiteit Brussel, Brussels, Belgium
| | - Maurice Petrus Zeegers
- Care and Public Health Research Institute, Maastricht University, Maastricht, Netherlands
- Department of Epidemiology, Maastricht University, Maastricht, Netherlands
- School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, Netherlands
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Gupta RS, Sehgal S, Wlodarski M, Bilaver LA, Wehbe FH, Spergel JM, Wang J, Ciaccio CE, Nimmagadda SR, Assa'ad A, Mahdavinia M, Wasserman RL, Brown E, Sicherer SH, Bird JA, Roberts B, Sharma HP, Mendez K, Holding EG, Mitchell L, Corbett M, Makhija M, Starren JB. Accelerating Food Allergy Research: Need for a Data Commons. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2023; 11:1063-1067. [PMID: 36796512 DOI: 10.1016/j.jaip.2023.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 02/04/2023] [Indexed: 02/16/2023]
Abstract
Food allergy is a significant health problem affecting approximately 8% of children and 11% of adults in the United States. It exhibits all the characteristics of a "complex" genetic trait; therefore, it is necessary to look at very large numbers of patients, far more than exist at any single organization, to eliminate gaps in the current understanding of this complex chronic disorder. Advances may be achieved by bringing together food allergy data from large numbers of patients into a Data Commons, a secure and efficient platform for researchers, comprising standardized data, available in a common interface for download and/or analysis, in accordance with the FAIR (Findable, Accessible, Interoperable, and Reusable) principles. Prior data commons initiatives indicate that research community consensus and support, formal food allergy ontology, data standards, an accepted platform and data management tools, an agreed upon infrastructure, and trusted governance are the foundation of any successful data commons. In this article, we will present the justification for the creation of a food allergy data commons and describe the core principles that can make it successful and sustainable.
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Affiliation(s)
- Ruchi S Gupta
- Center for Food Allergy and Asthma Research, Institute for Public Health and Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Ill; The Mary Ann & J. Milburn Smith Child Health Outcomes, Research and Evaluation Center, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Ill.
| | - Shruti Sehgal
- Center for Food Allergy and Asthma Research, Institute for Public Health and Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill
| | - Mark Wlodarski
- Center for Food Allergy and Asthma Research, Institute for Public Health and Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill
| | - Lucy A Bilaver
- Center for Food Allergy and Asthma Research, Institute for Public Health and Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Ill
| | - Firas H Wehbe
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill
| | - Jonathan M Spergel
- Division of Allergy and Immunology, Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine at University of Pennsylvania, Philadelphia, Pa
| | - Julie Wang
- Division of Allergy and Immunology, Department of Pediatrics, Jaffe Food Allergy Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Christina E Ciaccio
- Departments of Pediatrics and Medicine, the University of Chicago, Chicago, Ill
| | - Sai R Nimmagadda
- Center for Food Allergy and Asthma Research, Institute for Public Health and Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Ill; Division of Allergy and Immunology, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Ill
| | - Amal Assa'ad
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Mahboobeh Mahdavinia
- Allergy and Immunology Division, Department of Internal Medicine, and Department of Pediatrics, Rush University Medical Center, Chicago, Ill
| | | | | | - Scott H Sicherer
- Division of Allergy and Immunology, Department of Pediatrics, Jaffe Food Allergy Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - J Andrew Bird
- Department of Pediatrics, Division of Allergy and Immunology, University of Texas Southwestern Medical Center, Dallas, Texas
| | | | - Hemant P Sharma
- Division of Allergy and Immunology, Children's National Hospital, Washington, DC
| | | | | | | | - Mark Corbett
- Department of Pediatrics, University of Louisville School of Medicine, Louisville, Ky
| | - Melanie Makhija
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Ill; Division of Allergy and Immunology, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Ill
| | - Justin B Starren
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill
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Mitra S, Kavoor AR, Mahintamani T. The butterflies in the brain-What would it take to understand the genetic basis of psychiatric disorders? Asian J Psychiatr 2018; 31:13-14. [PMID: 29306219 DOI: 10.1016/j.ajp.2017.12.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 12/27/2017] [Accepted: 12/28/2017] [Indexed: 12/01/2022]
Affiliation(s)
- Sayantanava Mitra
- The Accelerator Program for Discovery in Brain disorders using Stem cells, Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bengaluru, India.
| | - Anjana Rao Kavoor
- Department of Mental and Behavioural Sciences, Fortis Healthcare, Bengaluru, India
| | - Tathagata Mahintamani
- Department of Psychiatry, Vidyasagar Institute of Mental Health, Government Mental Hospital, Amritsar, Punjab, India
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Mirkovic B, Laurent C, Podlipski MA, Frebourg T, Cohen D, Gerardin P. Genetic Association Studies of Suicidal Behavior: A Review of the Past 10 Years, Progress, Limitations, and Future Directions. Front Psychiatry 2016; 7:158. [PMID: 27721799 PMCID: PMC5034008 DOI: 10.3389/fpsyt.2016.00158] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 08/31/2016] [Indexed: 12/21/2022] Open
Abstract
Suicidal behaviors (SBs), which range from suicidal ideation to suicide attempts and completed suicide, represent a fatal dimension of mental ill-health. The involvement of genetic risk factors in SB is supported by family, twin, and adoption studies. The aim of this paper is to review recent genetic association studies in SBs including (i) case-control studies, (ii) family-based association studies, and (iii) genome-wide association studies (GWAS). Various studies on genetic associations have tended to suggest that a number of genes [e.g., tryptophan hydroxylase, serotonin receptors and transporters, or brain-derived neurotrophic factors (BDNFs)] are linked to SBs, but these findings are not consistently supported by the results obtained. Although the candidate-gene approach is useful, it is hampered by the present state of knowledge concerning the pathophysiology of diseases. Interpretations of GWAS results are mostly hindered by a lack of annotation describing the functions of most variation throughout the genome. Association studies have addressed a wide range of single-nucleotide polymorphisms in numerous genes. We have included 104 such studies, of which 10 are family-based association studies and 11 are GWAS. Numerous meta-analyses of case-control studies have shown significant associations of SB with variants in the serotonin transporter gene (5-HTT or SLC6A4) and the tryptophan hydroxylase 1 gene (TPH1), but others report contradictory results. The gene encoding BDNF and its receptor (NTRK2) are also promising candidates. Only two of the GWAS showed any significant associations. Several pathways are mentioned in an attempt to understand the lack of reproducibility and the disappointing results. Consequently, we review and discuss here the following aspects: (i) sample characteristics and confounding factors; (ii) statistical limits; (iii) gene-gene interactions; (iv) gene, environment, and by time interactions; and (v) technological and theoretical limits.
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Affiliation(s)
- Bojan Mirkovic
- Department of Child and Adolescent Psychiatry, CHU Charles Nicolle, Rouen, France; INSERM Unit U1079, Genetics of Cancer and Neurogenetics, University of Rouen, Rouen, France; Department of Child and Adolescent Psychiatry, Hôpital Pitié-Salpêtrière, Paris, France
| | - Claudine Laurent
- Department of Child and Adolescent Psychiatry, Hôpital Pitié-Salpêtrière, Paris, France; ICM - Brain and Spine Institute, Hôpital Pitié-Salpêtrière - University Pierre and Marie Curie, Paris, France
| | | | - Thierry Frebourg
- INSERM Unit U1079, Genetics of Cancer and Neurogenetics, University of Rouen, Rouen, France; Department of Genetics, CHU Charles Nicolle, Rouen, France
| | - David Cohen
- Department of Child and Adolescent Psychiatry, Hôpital Pitié-Salpêtrière, Paris, France; UMR 7222, Institute for Intelligent Systems and Robotics, University Pierre and Marie Curie, Paris, France
| | - Priscille Gerardin
- Department of Child and Adolescent Psychiatry, CHU Charles Nicolle, Rouen, France; Laboratoire Psy-NCA-EA-4700, University of Rouen, Rouen, France
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Sokolowski M, Wasserman J, Wasserman D. Genome-wide association studies of suicidal behaviors: a review. Eur Neuropsychopharmacol 2014; 24:1567-77. [PMID: 25219938 DOI: 10.1016/j.euroneuro.2014.08.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 07/24/2014] [Accepted: 08/10/2014] [Indexed: 11/17/2022]
Abstract
Suicidal behaviors represent a fatal dimension of mental ill-health, involving both environmental and heritable (genetic) influences. The putative genetic components of suicidal behaviors have until recent years been mainly investigated by hypothesis-driven research (of "candidate genes"). But technological progress in genotyping has opened the possibilities towards (hypothesis-generating) genomic screens and novel opportunities to explore polygenetic perspectives, now spanning a wide array of possible analyses falling under the term Genome-Wide Association Study (GWAS). Here we introduce and discuss broadly some apparent limitations but also certain developing opportunities of GWAS. We summarize the results from all the eight GWAS conducted up to date focused on suicidality outcomes; treatment emergent suicidal ideation (3 studies), suicide attempts (4 studies) and completed suicides (1 study). Clearly, there are few (if any) genome-wide significant and reproducible findings yet to be demonstrated. We then discuss and pinpoint certain future considerations in relation to sample sizes, the units of genetic associations used, study designs and outcome definitions, psychiatric diagnoses or biological measures, as well as the use of genomic sequencing. We conclude that GWAS should have a lot more potential to show in the case of suicidal outcomes, than what has yet been realized.
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Affiliation(s)
- Marcus Sokolowski
- National Centre for Suicide Research and Prevention of Mental Ill-Health (NASP), Karolinska Institute (KI), S-171 77 Stockholm, Sweden.
| | - Jerzy Wasserman
- National Centre for Suicide Research and Prevention of Mental Ill-Health (NASP), Karolinska Institute (KI), S-171 77 Stockholm, Sweden
| | - Danuta Wasserman
- National Centre for Suicide Research and Prevention of Mental Ill-Health (NASP), Karolinska Institute (KI), S-171 77 Stockholm, Sweden
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Tan YT, McPherson GE, Peretz I, Berkovic SF, Wilson SJ. The genetic basis of music ability. Front Psychol 2014; 5:658. [PMID: 25018744 PMCID: PMC4073543 DOI: 10.3389/fpsyg.2014.00658] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Accepted: 06/08/2014] [Indexed: 01/18/2023] Open
Abstract
Music is an integral part of the cultural heritage of all known human societies, with the capacity for music perception and production present in most people. Researchers generally agree that both genetic and environmental factors contribute to the broader realization of music ability, with the degree of music aptitude varying, not only from individual to individual, but across various components of music ability within the same individual. While environmental factors influencing music development and expertise have been well investigated in the psychological and music literature, the interrogation of possible genetic influences has not progressed at the same rate. Recent advances in genetic research offer fertile ground for exploring the genetic basis of music ability. This paper begins with a brief overview of behavioral and molecular genetic approaches commonly used in human genetic analyses, and then critically reviews the key findings of genetic investigations of the components of music ability. Some promising and converging findings have emerged, with several loci on chromosome 4 implicated in singing and music perception, and certain loci on chromosome 8q implicated in absolute pitch and music perception. The gene AVPR1A on chromosome 12q has also been implicated in music perception, music memory, and music listening, whereas SLC6A4 on chromosome 17q has been associated with music memory and choir participation. Replication of these results in alternate populations and with larger samples is warranted to confirm the findings. Through increased research efforts, a clearer picture of the genetic mechanisms underpinning music ability will hopefully emerge.
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Affiliation(s)
- Yi Ting Tan
- Melbourne Conservatorium of Music, University of Melbourne Parkville, VIC, Australia
| | - Gary E McPherson
- Melbourne Conservatorium of Music, University of Melbourne Parkville, VIC, Australia
| | - Isabelle Peretz
- International Laboratory for Brain, Music and Sound Research and Department of Psychology, Université de Montréal Montreal, QC, Canada
| | - Samuel F Berkovic
- Department of Medicine, Epilepsy Research Centre, University of Melbourne Heidelberg, VIC, Australia
| | - Sarah J Wilson
- Department of Medicine, Epilepsy Research Centre, University of Melbourne Heidelberg, VIC, Australia ; Melbourne School of Psychological Sciences, University of Melbourne Parkville, VIC, Australia
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Affiliation(s)
- Alessandro Serretti
- Department of Biomedical and NeuroMotor Sciences, University of Bologna, Bologna 40123, Italy.
| | - Chiara Fabbri
- Department of Biomedical and NeuroMotor Sciences, University of Bologna, Bologna 40123, Italy
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Tenesa A, Haley CS. The heritability of human disease: estimation, uses and abuses. Nat Rev Genet 2013; 14:139-49. [PMID: 23329114 DOI: 10.1038/nrg3377] [Citation(s) in RCA: 176] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Relatives provide the basic material for the study of inheritance of human disease. However, the methodologies for the estimation of heritability and the interpretation of the results have been controversial. The debate arises from the plethora of methods used, the validity of the methodological assumptions and the inconsistent and sometimes erroneous genetic interpretations made. We will discuss how to estimate disease heritability, how to interpret it, how biases in heritability estimates arise and how heritability relates to other measures of familial disease aggregation.
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Affiliation(s)
- Albert Tenesa
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK.
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