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Benstock SE, Weaver K, Hettema JM, Verhulst B. Using Alternative Definitions of Controls to Increase Statistical Power in GWAS. Behav Genet 2024; 54:353-366. [PMID: 38869698 DOI: 10.1007/s10519-024-10187-w] [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: 01/12/2024] [Accepted: 05/29/2024] [Indexed: 06/14/2024]
Abstract
Genome-wide association studies (GWAS) are often underpowered due to small effect sizes of common single nucleotide polymorphisms (SNPs) on phenotypes and extreme multiple testing thresholds. The most common approach for increasing statistical power is to increase sample size. We propose an alternative strategy of redefining case-control outcomes into ordinal case-subthreshold-asymptomatic variables. While maintaining the clinical case threshold, we subdivide controls into two groups: individuals who are symptomatic but do not meet the clinical criteria for diagnosis (subthreshold) and individuals who are effectively asymptomatic. We conducted a simulation study to examine the impact of effect size, minor allele frequency, population prevalence, and the prevalence of the subthreshold group on statistical power to detect genetic associations in three scenarios: a standard case-control, an ordinal, and a case-asymptomatic control analysis. Our results suggest the ordinal model consistently provides the greatest statistical power while the case-control model the least. Power in the case-asymptomatic control model reflects the case-control or ordinal model depending on the population prevalence and size of the subthreshold category. We then analyzed a major depression phenotype from the UK Biobank to corroborate our simulation results. Overall, the ordinal model improves statistical power in GWAS consistent with increasing the sample size by approximately 10%.
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Affiliation(s)
- Sarah E Benstock
- Department of Psychiatry and Behavioral Sciences, Texas A&M University School of Medicine, College Station, TX, USA
| | - Katherine Weaver
- Department of Psychiatry and Behavioral Sciences, Texas A&M University School of Medicine, College Station, TX, USA
| | - John M Hettema
- Department of Psychiatry and Behavioral Sciences, Texas A&M University School of Medicine, College Station, TX, USA
| | - Brad Verhulst
- Department of Psychiatry and Behavioral Sciences, Texas A&M University School of Medicine, College Station, TX, USA.
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2
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Schwabe I, Jović M, Rimfeld K, Allegrini AG, van den Berg SM. Genotype-Environment Interaction in ADHD: Genetic Predisposition Determines the Extent to Which Environmental Influences Explain Variability in the Symptom Dimensions Hyperactivity and Inattention. Behav Genet 2024; 54:169-180. [PMID: 38270759 PMCID: PMC10861382 DOI: 10.1007/s10519-023-10168-5] [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: 02/16/2023] [Accepted: 11/22/2023] [Indexed: 01/26/2024]
Abstract
Although earlier research has shown that individual differences on the spectrum of attention deficit hyperactivity disorder (ADHD) are highly heritable, emerging evidence suggests that symptoms are associated with complex interactions between genes and environmental influences. This study investigated whether a genetic predisposition [Note that the term 'genetic predisposition' was used in this manuscript to refer to an estimate based on twin modeling (an individual's score on the latent trait that resembles additive genetic influences) in the particular population being examined.] for the symptom dimensions hyperactivity and inattention determines the extent to which unique-environmental influences explain variability in these symptoms. To this purpose, we analysed a sample drawn from the Twins Early Development Study (TEDS) that consisted of item-level scores of 2168 16-year-old twin pairs who completed both the Strengths and Difficulties Questionnaire (SDQ; Goodman, in J Child Psychol Psychiatry 38:581-586, 1997) and the Strength and Weaknesses of ADHD Symptoms and Normal Behavior (SWAN; Swanson, in Paper presented at the meeting of the American Psychological Association, Los Angeles, 1981) questionnaire. To maximize the psychometric information to measure ADHD symptoms, psychometric analyses were performed to investigate whether the items from the two questionnaires could be combined to form two longer subscales. In the estimation of genotype-environment interaction, we corrected for error variance heterogeneity in the measurement of ADHD symptoms through the application of item response theory (IRT) measurement models. A positive interaction was found for both hyperactivity (e.g., [Formula: see text] = 2.20 with 95% highest posterior density interval equal to [1.79;2.65] and effect size equal to 3.00) and inattention (e.g., [Formula: see text] = 2.16 with 95% highest posterior density interval equal to [1.56;2.79] and effect size equal to 3.07). These results indicate that unique-environmental influences were more important in creating individual differences in both hyperactivity and inattention for twins with a genetic predisposition for these symptoms than for twins without such a predisposition.
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Affiliation(s)
- Inga Schwabe
- Department of Methodology and Statistics, Tilburg University, Tilburg, The Netherlands.
| | - Miljan Jović
- Department of Cognition, Data and Education (CODE), University of Twente, Enschede, The Netherlands
| | - Kaili Rimfeld
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Department of Psychology, Royal Holloway, University of London, Egham, UK
| | - Andrea G Allegrini
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Division of Psychology and Language Sciences, Department of Clinical, Educational and Health Psychology, University College London, London, UK
| | - Stéphanie M van den Berg
- Department of Cognition, Data and Education (CODE), University of Twente, Enschede, The Netherlands
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Benstock SE, Weaver K, Hettema J, Verhulst B. Using Alternative Definitions of Controls to Increase Statistical Power in GWAS. RESEARCH SQUARE 2024:rs.3.rs-3858178. [PMID: 38352402 PMCID: PMC10862954 DOI: 10.21203/rs.3.rs-3858178/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Genome-wide association studies (GWAS) are underpowered due to small effect sizes of single nucleotide polymorphisms (SNPs) on phenotypes and extreme multiple testing thresholds. The most common approach for increasing statistical power is to increase sample size. We propose an alternative strategy of redefining case-control outcomes into ordinal case-subthreshold-asymptomatic variables. While maintaining the clinical case threshold, we subdivide controls into two groups: individuals who are symptomatic but do not meet the clinical criteria for diagnosis (subthreshold) and individuals who are effectively asymptomatic. We conducted a simulation study to examine the impact of effect size, minor allele frequency, population prevalence, and the prevalence of the subthreshold group on statistical power to detect genetic associations in three scenarios: a standard case-control, an ordinal, and a case-asymptomatic control analysis. Our results suggest the ordinal model consistently provides the most statistical power while the case-control model the least. Power in the case-asymptomatic control model reflects the case-control or ordinal model depending on the population prevalence and size of the subthreshold category. We then analyzed a major depression phenotype from the UK Biobank to corroborate our simulation results. Overall, the ordinal model improves statistical power in GWAS consistent with increasing the sample size by approximately 10%.
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Tiego J, Thompson K, Arnatkeviciute A, Hawi Z, Finlay A, Sabaroedin K, Johnson B, Bellgrove MA, Fornito A. Dissecting Schizotypy and Its Association With Cognition and Polygenic Risk for Schizophrenia in a Nonclinical Sample. Schizophr Bull 2023; 49:1217-1228. [PMID: 36869759 PMCID: PMC10483465 DOI: 10.1093/schbul/sbac016] [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: 11/13/2022]
Abstract
Schizotypy is a multidimensional construct that captures a continuum of risk for developing schizophrenia-spectrum psychopathology. Existing 3-factor models of schizotypy, consisting of positive, negative, and disorganized dimensions have yielded mixed evidence of genetic continuity with schizophrenia using polygenic risk scores. Here, we propose an approach that involves splitting positive and negative schizotypy into more specific subdimensions that are phenotypically continuous with distinct positive symptoms and negative symptoms recognized in clinical schizophrenia. We used item response theory to derive high-precision estimates of psychometric schizotypy using 251 self-report items obtained from a non-clinical sample of 727 (424 females) adults. These subdimensions were organized hierarchically using structural equation modeling into 3 empirically independent higher-order dimensions enabling associations with polygenic risk for schizophrenia to be examined at different levels of phenotypic generality and specificity. Results revealed that polygenic risk for schizophrenia was associated with variance specific to delusional experiences (γ = 0.093, P = .001) and reduced social interest and engagement (γ = 0.076, P = .020), and these effects were not mediated via the higher-order general, positive, or negative schizotypy factors. We further fractionated general intellectual functioning into fluid and crystallized intelligence in 446 (246 females) participants that underwent onsite cognitive assessment. Polygenic risk scores explained 3.6% of the variance in crystallized intelligence. Our precision phenotyping approach could be used to enhance the etiologic signal in future genetic association studies and improve the detection and prevention of schizophrenia-spectrum psychopathology.
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Affiliation(s)
- Jeggan Tiego
- Turner Institute for Brain and Mental Health, Monash University, Clayton, VIC 3800, Australia
- School of Psychological Sciences, Monash University, Clayton, VIC 3800, Australia
- Monash Biomedical Imaging, Monash University, 770 Blackburn Rd, Clayton, VIC 3800, Australia
| | - Kate Thompson
- Turner Institute for Brain and Mental Health, Monash University, Clayton, VIC 3800, Australia
- School of Psychological Sciences, Monash University, Clayton, VIC 3800, Australia
- Monash Biomedical Imaging, Monash University, 770 Blackburn Rd, Clayton, VIC 3800, Australia
| | - Aurina Arnatkeviciute
- Turner Institute for Brain and Mental Health, Monash University, Clayton, VIC 3800, Australia
- School of Psychological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Ziarih Hawi
- Turner Institute for Brain and Mental Health, Monash University, Clayton, VIC 3800, Australia
- School of Psychological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Amy Finlay
- Turner Institute for Brain and Mental Health, Monash University, Clayton, VIC 3800, Australia
- School of Psychological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Kristina Sabaroedin
- Turner Institute for Brain and Mental Health, Monash University, Clayton, VIC 3800, Australia
- School of Psychological Sciences, Monash University, Clayton, VIC 3800, Australia
- Monash Biomedical Imaging, Monash University, 770 Blackburn Rd, Clayton, VIC 3800, Australia
| | - Beth Johnson
- Turner Institute for Brain and Mental Health, Monash University, Clayton, VIC 3800, Australia
- School of Psychological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Mark A Bellgrove
- Turner Institute for Brain and Mental Health, Monash University, Clayton, VIC 3800, Australia
- School of Psychological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Alex Fornito
- Turner Institute for Brain and Mental Health, Monash University, Clayton, VIC 3800, Australia
- School of Psychological Sciences, Monash University, Clayton, VIC 3800, Australia
- Monash Biomedical Imaging, Monash University, 770 Blackburn Rd, Clayton, VIC 3800, Australia
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Ray NR, Ayodele T, Jean-Francois M, Baez P, Fernandez V, Bradley J, Crane PK, Dalgard CL, Kuzma A, Nicaretta H, Sims R, Williams J, Cuccaro ML, Pericak-Vance MA, Mayeux R, Wang LS, Schellenberg GD, Cruchaga C, Beecham GW, Reitz C. The Early-Onset Alzheimer's Disease Whole-Genome Sequencing Project: Study design and methodology. Alzheimers Dement 2023; 19:4187-4195. [PMID: 37390458 PMCID: PMC10527497 DOI: 10.1002/alz.13370] [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: 02/07/2023] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 07/02/2023]
Abstract
INTRODUCTION Sequencing efforts to identify genetic variants and pathways underlying Alzheimer's disease (AD) have largely focused on late-onset AD although early-onset AD (EOAD), accounting for ∼10% of cases, is largely unexplained by known mutations, resulting in a lack of understanding of its molecular etiology. METHODS Whole-genome sequencing and harmonization of clinical, neuropathological, and biomarker data of over 5000 EOAD cases of diverse ancestries. RESULTS A publicly available genomics resource for EOAD with extensive harmonized phenotypes. Primary analysis will (1) identify novel EOAD risk loci and druggable targets; (2) assess local-ancestry effects; (3) create EOAD prediction models; and (4) assess genetic overlap with cardiovascular and other traits. DISCUSSION This novel resource complements over 50,000 control and late-onset AD samples generated through the Alzheimer's Disease Sequencing Project (ADSP). The harmonized EOAD/ADSP joint call will be available through upcoming ADSP data releases and will allow for additional analyses across the full onset range. HIGHLIGHTS Sequencing efforts to identify genetic variants and pathways underlying Alzheimer's disease (AD) have largely focused on late-onset AD although early-onset AD (EOAD), accounting for ∼10% of cases, is largely unexplained by known mutations. This results in a significant lack of understanding of the molecular etiology of this devastating form of the disease. The Early-Onset Alzheimer's Disease Whole-genome Sequencing Project is a collaborative initiative to generate a large-scale genomics resource for early-onset Alzheimer's disease with extensive harmonized phenotype data. Primary analyses are designed to (1) identify novel EOAD risk and protective loci and druggable targets; (2) assess local-ancestry effects; (3) create EOAD prediction models; and (4) assess genetic overlap with cardiovascular and other traits. The harmonized genomic and phenotypic data from this initiative will be available through NIAGADS.
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Affiliation(s)
- Nicholas R. Ray
- Gertrude H. Sergievsky Center, Columbia University, New
York, NY 10032, USA
- Taub Institute for Research on Alzheimer’s Disease
and the Aging Brain, Columbia University, New York, NY 10032, USA
| | - Temitope Ayodele
- Gertrude H. Sergievsky Center, Columbia University, New
York, NY 10032, USA
| | - Melissa Jean-Francois
- The John P. Hussman Institute for Human Genomics,
University of Miami, Miami, FL 33136, USA
- Dr. John T. MacDonald Foundation Department of Human
Genetics, University of Miami, Coral Gables, FL 33146, USA
| | - Penelope Baez
- Gertrude H. Sergievsky Center, Columbia University, New
York, NY 10032, USA
| | - Victoria Fernandez
- Department of Psychiatry, Neurology and Genetics,
Washington University School of Medicine, St. Louis, MO 63130, USA
- Neurogenomics and Informatic (NGI) Center, Washington
University School of Medicine, St. Louis, MO 63130, USA
| | - Joseph Bradley
- Department of Psychiatry, Neurology and Genetics,
Washington University School of Medicine, St. Louis, MO 63130, USA
- Neurogenomics and Informatic (NGI) Center, Washington
University School of Medicine, St. Louis, MO 63130, USA
| | - Paul K. Crane
- Division of General Internal Medicine, University of
Washington, Seattle, WA 98195, USA
| | - Clifton L. Dalgard
- Department of Anatomy, Physiology & Genetics,
Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
- The American Genome Center, Uniformed Services University
of the Health Sciences, Bethesda, MD 20814, USA
| | - Amanda Kuzma
- Penn Neurodegeneration Genomics Center, Department of
Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of
Medicine, Philadelphia, PA 19104, USA
| | - Heather Nicaretta
- Penn Neurodegeneration Genomics Center, Department of
Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of
Medicine, Philadelphia, PA 19104, USA
| | - Rebecca Sims
- Division of Psychological Medicine and Clinical
Neurosciences, School of Medicine, Cardiff University, Cardiff CF10 3AT, UK
| | - Julie Williams
- UK Dementia Research Institute, Cardiff University,
Cardiff CF10 3AT, UK
- Division of Psychological Medicine and Clinical
Neurosciences, School of Medicine, Cardiff University, Cardiff CF10 3AT, UK
| | - Michael L. Cuccaro
- The John P. Hussman Institute for Human Genomics,
University of Miami, Miami, FL 33136, USA
- Dr. John T. MacDonald Foundation Department of Human
Genetics, University of Miami, Coral Gables, FL 33146, USA
| | - Margaret A. Pericak-Vance
- The John P. Hussman Institute for Human Genomics,
University of Miami, Miami, FL 33136, USA
- Dr. John T. MacDonald Foundation Department of Human
Genetics, University of Miami, Coral Gables, FL 33146, USA
| | - Richard Mayeux
- Gertrude H. Sergievsky Center, Columbia University, New
York, NY 10032, USA
- Taub Institute for Research on Alzheimer’s Disease
and the Aging Brain, Columbia University, New York, NY 10032, USA
- Department of Neurology, Columbia University, New York, NY
10032, USA
- Department of Epidemiology, Columbia University, New York,
NY 10032, USA
| | - Li-San Wang
- Penn Neurodegeneration Genomics Center, Department of
Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of
Medicine, Philadelphia, PA 19104, USA
| | - Gerard D. Schellenberg
- Penn Neurodegeneration Genomics Center, Department of
Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of
Medicine, Philadelphia, PA 19104, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Neurology and Genetics,
Washington University School of Medicine, St. Louis, MO 63130, USA
- Neurogenomics and Informatic (NGI) Center, Washington
University School of Medicine, St. Louis, MO 63130, USA
| | - Gary W. Beecham
- The John P. Hussman Institute for Human Genomics,
University of Miami, Miami, FL 33136, USA
- Dr. John T. MacDonald Foundation Department of Human
Genetics, University of Miami, Coral Gables, FL 33146, USA
| | - Christiane Reitz
- Gertrude H. Sergievsky Center, Columbia University, New
York, NY 10032, USA
- Taub Institute for Research on Alzheimer’s Disease
and the Aging Brain, Columbia University, New York, NY 10032, USA
- Department of Neurology, Columbia University, New York, NY
10032, USA
- Department of Epidemiology, Columbia University, New York,
NY 10032, USA
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Van Assche E, Hohoff C, Zang J, Knight MJ, Baune BT. Longitudinal early epigenomic signatures inform molecular paths of therapy response and remission in depressed patients. Front Mol Neurosci 2023; 16:1223216. [PMID: 37664245 PMCID: PMC10472456 DOI: 10.3389/fnmol.2023.1223216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/24/2023] [Indexed: 09/05/2023] Open
Abstract
Introduction The etiology of major depressive disorder (MDD) involves the interaction between genes and environment, including treatment. Early molecular signatures for treatment response and remission are relevant in a context of personalized medicine and stratification and reduce the time-to-decision. Therefore, we focused the analyses on patients that responded or remitted following a cognitive intervention of 8 weeks. Methods We used data from a randomized controlled trial (RCT) with MDD patients (N = 112) receiving a cognitive intervention. At baseline and 8 weeks, blood for DNA methylation (Illumina Infinium MethylationEPIC 850k BeadChip) was collected, as well as MADRS. First, responders (N = 24; MADRS-reduction of at least 50%) were compared with non-responders (N = 60). Then, we performed longitudinal within-individual analyses, for response (N = 21) and for remission (N = 18; MADRS smaller or equal to 9 and higher than 9 at baseline), respectively, as well as patients with no change in MADRS over time. At 8 weeks the sample comprised 84 individuals; 73 patients had DNA methylation for both time-points. The RnBeads package (R) was used for data cleaning, quality control, and differential DNA-methylation (limma). The within-individual paired longitudinal analysis was performed using Welch's t-test. Subsequently gene-ontology (GO) pathway analyses were performed. Results No CpG was genome-wide significant CpG (p < 5 × 10-8). The most significant CpG in the differential methylation analysis comparing response versus non-response was in the IQSEC1 gene (cg01601845; p = 1.53 × 10-6), linked to neurotransmission. The most significant GO-terms were linked to telomeres. The longitudinal response analysis returned 67 GO pathways with a p < 0.05. Two of the three most significant pathways were linked to sodium transport. The analysis for remission returned 46 GO terms with a p-value smaller than 0.05 with pathways linked to phosphatase regulation and synaptic functioning. The analysis with stable patients returned mainly GO-terms linked to basic cellular processes. Discussion Our result suggest that DNA methylation can be suitable to capture early signs of treatment response and remission following a cognitive intervention in depression. Despite not being genome-wide significant, the CpG locations and GO-terms returned by our analysis comparing patients with and without cognitive impairment, are in line with prior knowledge on pathways and genes relevant for depression treatment and cognition. Our analysis provides new hypotheses for the understanding of how treatment for depression can act through DNA methylation and induce response and remission.
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Affiliation(s)
| | - Christa Hohoff
- Department of Psychiatry, University of Münster, Münster, Germany
| | - Johannes Zang
- Department of Psychiatry, University of Münster, Münster, Germany
| | - Matthew J. Knight
- Discipline of Psychiatry, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Bernhard T. Baune
- Department of Psychiatry, University of Münster, Münster, Germany
- Department of Psychiatry, Melbourne Medical School, The University of Melbourne, Melbourne, VIC, Australia
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
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Tiego J, Martin EA, DeYoung CG, Hagan K, Cooper SE, Pasion R, Satchell L, Shackman AJ, Bellgrove MA, Fornito A. Precision behavioral phenotyping as a strategy for uncovering the biological correlates of psychopathology. NATURE MENTAL HEALTH 2023; 1:304-315. [PMID: 37251494 PMCID: PMC10210256 DOI: 10.1038/s44220-023-00057-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 03/24/2023] [Indexed: 05/31/2023]
Abstract
Our capacity to measure diverse aspects of human biology has developed rapidly in the past decades, but the rate at which these techniques have generated insights into the biological correlates of psychopathology has lagged far behind. The slow progress is partly due to the poor sensitivity, specificity and replicability of many findings in the literature, which have in turn been attributed to small effect sizes, small sample sizes and inadequate statistical power. A commonly proposed solution is to focus on large, consortia-sized samples. Yet it is abundantly clear that increasing sample sizes will have a limited impact unless a more fundamental issue is addressed: the precision with which target behavioral phenotypes are measured. Here, we discuss challenges, outline several ways forward and provide worked examples to demonstrate key problems and potential solutions. A precision phenotyping approach can enhance the discovery and replicability of associations between biology and psychopathology.
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Affiliation(s)
- Jeggan Tiego
- Turner Institute for Brain and Mental Health and School of Psychological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Elizabeth A. Martin
- Department of Psychological Science, University of California, Irvine, CA, USA
| | - Colin G. DeYoung
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Kelsey Hagan
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | - Samuel E. Cooper
- Department of Psychiatry and Behavioral Sciences, University of Texas at Austin, Austin, TX, USA
| | - Rita Pasion
- HEI-LAB, Lusófona University, Lisbon, Portugal
| | - Liam Satchell
- Department of Psychology, University of Winchester, Winchester, UK
| | | | - Mark A. Bellgrove
- Turner Institute for Brain and Mental Health and School of Psychological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Alex Fornito
- Turner Institute for Brain and Mental Health and School of Psychological Sciences, Monash University, Melbourne, Victoria, Australia
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8
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Mollon J, Almasy L, Jacquemont S, Glahn DC. The contribution of copy number variants to psychiatric symptoms and cognitive ability. Mol Psychiatry 2023; 28:1480-1493. [PMID: 36737482 PMCID: PMC10213133 DOI: 10.1038/s41380-023-01978-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 02/05/2023]
Abstract
Copy number variants (CNVs) are deletions and duplications of DNA sequence. The most frequently studied CNVs, which are described in this review, are recurrent CNVs that occur in the same locations on the genome. These CNVs have been strongly implicated in neurodevelopmental disorders, namely autism spectrum disorder (ASD), intellectual disability (ID), and developmental delay (DD), but also in schizophrenia. More recent work has also shown that CNVs increase risk for other psychiatric disorders, namely, depression, bipolar disorder, and post-traumatic stress disorder. Many of the same CNVs are implicated across all of these disorders, and these neuropsychiatric CNVs are also associated with cognitive ability in the general population, as well as with structural and functional brain alterations. Neuropsychiatric CNVs also show incomplete penetrance, such that carriers do not always develop any psychiatric disorder, and may show only mild symptoms, if any. Variable expressivity, whereby the same CNVs are associated with many different phenotypes of varied severity, also points to highly complex mechanisms underlying disease risk in CNV carriers. Comprehensive and longitudinal phenotyping studies of individual CNVs have provided initial insights into these mechanisms. However, more work is needed to estimate and predict the effect of non-recurrent, ultra-rare CNVs, which also contribute to psychiatric and cognitive outcomes. Moreover, delineating the broader phenotypic landscape of neuropsychiatric CNVs in both clinical and general population cohorts may also offer important mechanistic insights.
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Affiliation(s)
- Josephine Mollon
- Department of Psychiatry, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Laura Almasy
- Department of Genetics, Perelman School of Medicine, Penn-CHOP Lifespan Brain Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Sebastien Jacquemont
- Department of Pediatrics, Université de Montréal, Montreal, QC, Canada
- Center Hospitalier Universitaire Sainte-Justine Research Center, Montreal, QC, Canada
| | - David C Glahn
- Department of Psychiatry, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Olin Neuropsychiatry Research Center, Institute of Living, Hartford, CT, USA
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9
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Jami ES, Hammerschlag AR, Sallis HM, Qiao Z, Andreassen OA, Magnus PM, Njølstad PR, Havdahl A, Pingault JB, Evans DM, Munafò MR, Ystrom E, Bartels M, Middeldorp C. Do environmental effects indexed by parental genetic variation influence common psychiatric symptoms in childhood? Transl Psychiatry 2023; 13:94. [PMID: 36934099 PMCID: PMC10024694 DOI: 10.1038/s41398-023-02348-y] [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] [Received: 03/21/2022] [Revised: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 03/20/2023] Open
Abstract
Parental genes may indirectly influence offspring psychiatric outcomes through the environment that parents create for their children. These indirect genetic effects, also known as genetic nurture, could explain individual differences in common internalising and externalising psychiatric symptoms during childhood. Advanced statistical genetic methods leverage data from families to estimate the overall contribution of parental genetic nurture effects. This study included up to 10,499 children, 5990 mother-child pairs, and 6,222 father-child pairs from the Norwegian Mother Father and Child Study. Genome-based restricted maximum likelihood (GREML) models were applied using software packages GCTA and M-GCTA to estimate variance in maternally reported depressive, disruptive, and attention-deficit hyperactivity disorder (ADHD) symptoms in 8-year-olds that was explained by direct offspring genetic effects and maternal or paternal genetic nurture. There was no strong evidence of genetic nurture in this sample, although a suggestive paternal genetic nurture effect on offspring depressive symptoms (variance explained (V) = 0.098, standard error (SE) = 0.057) and a suggestive maternal genetic nurture effect on ADHD symptoms (V = 0.084, SE = 0.058) was observed. The results indicate that parental genetic nurture effects could be of some relevance in explaining individual differences in childhood psychiatric symptoms. However, robustly estimating their contribution is a challenge for researchers given the current paucity of large-scale samples of genotyped families with information on childhood psychiatric outcomes.
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Affiliation(s)
- Eshim S Jami
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Department of Clinical, Educational and Health Psychology, University College London, London, UK
| | - Anke R Hammerschlag
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Hannah M Sallis
- School of Psychological Science, University of Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Centre for Academic Mental Health, Population Health Sciences, University of Bristol, Bristol, UK
| | - Zhen Qiao
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Australia
| | - Ole A Andreassen
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopment, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Per M Magnus
- Centre of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Pål R Njølstad
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway
| | - Alexandra Havdahl
- Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway
- PROMENTA Research Center, Department of Psychology, University of Oslo, Oslo, Norway
- Nic Waals Institute, Lovisenberg Diakonale Hospital, Oslo, Norway
| | - Jean-Baptiste Pingault
- Department of Clinical, Educational and Health Psychology, University College London, London, UK
| | - David M Evans
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Australia
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Marcus R Munafò
- School of Psychological Science, University of Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- NIHR Biomedical Research Centre at the University Hospitals Bristol NHS Foundation Trust and the University of Bristol, Bristol, UK
| | - Eivind Ystrom
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway
| | - Meike Bartels
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Christel Middeldorp
- Child Health Research Centre, University of Queensland, Brisbane, Australia.
- Child and Youth Mental Health Service, Children's Health Queensland Hospital and Health Service, Brisbane, Australia.
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10
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Dattani S, Sham PC, Jermy BS, Coleman JRI, Howard DM, Lewis CM. Common and rare variant associations with latent traits underlying depression, bipolar disorder, and schizophrenia. Transl Psychiatry 2023; 13:46. [PMID: 36746926 PMCID: PMC9902570 DOI: 10.1038/s41398-023-02324-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/07/2023] [Accepted: 01/18/2023] [Indexed: 02/08/2023] Open
Abstract
Genetic studies in psychiatry have primarily focused on the effects of common genetic variants, but few have investigated the role of rare genetic variants, particularly for major depression. In order to explore the role of rare variants in the gap between estimates of single nucleotide polymorphism (SNP) heritability and twin study heritability, we examined the contribution of common and rare genetic variants to latent traits underlying psychiatric disorders using high-quality imputed genotype data from the UK Biobank. Using a pre-registered analysis, we used items from the UK Biobank Mental Health Questionnaire relevant to three psychiatric disorders: major depression (N = 134,463), bipolar disorder (N = 117,376) and schizophrenia (N = 130,013) and identified a general hierarchical factor for each that described participants' responses. We calculated participants' scores on these latent traits and conducted single-variant genetic association testing (MAF > 0.05%), gene-based burden testing and pathway association testing associations with these latent traits. We tested for enrichment of rare variants (MAF 0.05-1%) in genes that had been previously identified by common variant genome-wide association studies, and genes previously associated with Mendelian disorders having relevant symptoms. We found moderate genetic correlations between the latent traits in our study and case-control phenotypes in previous genome-wide association studies, and identified one common genetic variant (rs72657988, minor allele frequency = 8.23%, p = 1.01 × 10-9) associated with the general factor of schizophrenia, but no other single variants, genes or pathways passed significance thresholds in this analysis, and we did not find enrichment in previously identified genes.
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Affiliation(s)
- Saloni Dattani
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.
- Department of Psychiatry, Li Ka Shing (LKS) Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China.
| | - Pak C Sham
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
- NIHR Maudsley Biomedical Research Centre, South London and Maudsley NHS Trust, London, UK
- Department of Psychiatry, State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong SAR, China
- Centre for PanorOmic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Bradley S Jermy
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
- NIHR Maudsley Biomedical Research Centre, South London and Maudsley NHS Trust, London, UK
| | - Jonathan R I Coleman
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
- NIHR Maudsley Biomedical Research Centre, South London and Maudsley NHS Trust, London, UK
| | - David M Howard
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Cathryn M Lewis
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, UK
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11
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Woodward AA, Urbanowicz RJ, Naj AC, Moore JH. Genetic heterogeneity: Challenges, impacts, and methods through an associative lens. Genet Epidemiol 2022; 46:555-571. [PMID: 35924480 PMCID: PMC9669229 DOI: 10.1002/gepi.22497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/06/2022] [Accepted: 07/19/2022] [Indexed: 01/07/2023]
Abstract
Genetic heterogeneity describes the occurrence of the same or similar phenotypes through different genetic mechanisms in different individuals. Robustly characterizing and accounting for genetic heterogeneity is crucial to pursuing the goals of precision medicine, for discovering novel disease biomarkers, and for identifying targets for treatments. Failure to account for genetic heterogeneity may lead to missed associations and incorrect inferences. Thus, it is critical to review the impact of genetic heterogeneity on the design and analysis of population level genetic studies, aspects that are often overlooked in the literature. In this review, we first contextualize our approach to genetic heterogeneity by proposing a high-level categorization of heterogeneity into "feature," "outcome," and "associative" heterogeneity, drawing on perspectives from epidemiology and machine learning to illustrate distinctions between them. We highlight the unique nature of genetic heterogeneity as a heterogeneous pattern of association that warrants specific methodological considerations. We then focus on the challenges that preclude effective detection and characterization of genetic heterogeneity across a variety of epidemiological contexts. Finally, we discuss systems heterogeneity as an integrated approach to using genetic and other high-dimensional multi-omic data in complex disease research.
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Affiliation(s)
- Alexa A. Woodward
- Department of Biostatistics, Epidemiology and InformaticsUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Ryan J. Urbanowicz
- Department of Computational BiomedicineCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA
| | - Adam C. Naj
- Department of Biostatistics, Epidemiology and InformaticsUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Jason H. Moore
- Department of Computational BiomedicineCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA
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12
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Tan VY, Timpson NJ. The UK Biobank: A Shining Example of Genome-Wide Association Study Science with the Power to Detect the Murky Complications of Real-World Epidemiology. Annu Rev Genomics Hum Genet 2022; 23:569-589. [PMID: 35508184 DOI: 10.1146/annurev-genom-121321-093606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genome-wide association studies (GWASs) have successfully identified thousands of genetic variants that are reliably associated with human traits. Although GWASs are restricted to certain variant frequencies, they have improved our understanding of the genetic architecture of complex traits and diseases. The UK Biobank (UKBB) has brought substantial analytical opportunity and performance to association studies. The dramatic expansion of many GWAS sample sizes afforded by the inclusion of UKBB data has improved the power of estimation of effect sizes but, critically, has done so in a context where phenotypic depth and precision enable outcome dissection and the application of epidemiological approaches. However, at the same time, the availability of such a large, well-curated, and deeply measured population-based collection has the capacity to increase our exposure to the many complications and inferential complexities associated with GWASs and other analyses. In this review, we discuss the impact that UKBB has had in the GWAS era, some of the opportunities that it brings, and exemplar challenges that illustrate the reality of using data from this world-leading resource.
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Affiliation(s)
- Vanessa Y Tan
- Medical Research Council (MRC) Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom;
- Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Nicholas J Timpson
- Medical Research Council (MRC) Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom;
- Bristol Medical School, University of Bristol, Bristol, United Kingdom
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13
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Dattani S, Howard DM, Lewis CM, Sham PC. Clarifying the causes of consistent and inconsistent findings in genetics. Genet Epidemiol 2022; 46:372-389. [PMID: 35652173 PMCID: PMC9544854 DOI: 10.1002/gepi.22459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/12/2022] [Accepted: 04/22/2022] [Indexed: 11/29/2022]
Abstract
As research in genetics has advanced, some findings have been unexpected or shown to be inconsistent between studies or datasets. The reasons these inconsistencies arise are complex. Results from genetic studies can be affected by various factors including statistical power, linkage disequilibrium, quality control, confounding and selection bias, as well as real differences from interactions and effect modifiers, which may be informative about the mechanisms of traits and disease. Statistical artefacts can manifest as differences between results but they can also conceal underlying differences, which implies that their critical examination is important for understanding the underpinnings of traits. In this review, we examine these factors and outline how they can be identified and conceptualised with structural causal models. We explain the consequences they have on genetic estimates, such as genetic associations, polygenic scores, family‐ and genome‐wide heritability, and describe methods to address them to aid in the estimation of true effects of genetic variation. Clarifying these factors can help researchers anticipate when results are likely to diverge and aid researchers' understanding of causal relationships between genes and complex traits.
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Affiliation(s)
- Saloni Dattani
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.,Department of Psychiatry, Li Ka Shing (LKS) Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - David M Howard
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.,Division of Psychiatry, Royal Edinburgh Hospital, University of Edinburgh, Edinburgh, UK
| | - Cathryn M Lewis
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.,Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Pak C Sham
- Department of Psychiatry, State Key Laboratory of Brain and Cognitive Sciences, and Centre for Panoromic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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14
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Genetically Adjusted Propensity Score Matching: A Comparison to Discordant MZ Twin Models. Twin Res Hum Genet 2022; 25:24-39. [PMID: 35506340 DOI: 10.1017/thg.2022.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Discordant monozygotic (MZ) twin methodologies are considered one of the foremost statistical approaches for estimating the influence of environmental factors on phenotypic variance. Limitations associated with the discordant MZ twin approach generates an inability to estimate particular relationships and adjust estimates for the confounding influence of gene-nonshared environment interactions. Recent advancements in molecular genetics, however, can provide the opportunity to address these limitations. The current study reviews an alternative technique, genetically adjusted propensity scores (GAPS) matching, that integrates observed genetic and environmental information to adjust for the confounding of these factors in nonkin individuals. Simulations and a real data example were used to compare the GAPS matching approach to the discordant MZ twin method. Although the results of the simulated comparisons demonstrated that the discordant MZ twin approach remains the more robust statistical technique to adjust for shared environmental and genetic factors, GAPS matching - under certain conditions - could represent a viable alternative when MZ twin samples are unavailable. Overall, the findings suggest that GAPS matching can potentially provide an alternative to the discordant MZ twin approach when limited variation exists between identical twin pairs. Moreover, the ability to adjust for gene-nonshared environment interactions represents a potential advancement associated with the GAPS approach. The limitations of the approach, as well as polygenic risk scores, are also discussed.
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15
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Alotaibi RN, Howe BJ, Moreno Uribe LM, Sanchez C, Deleyiannis FW, Padilla C, Poletta FA, Orioli IM, Buxó CJ, Wehby GL, Vieira AR, Murray J, Valencia-Ramírez C, Restrepo Muñeton CP, Long RE, Shaffer JR, Reis SE, Weinberg SM, Neiswanger K, McNeil DW, Marazita ML. Genetic Analyses of Enamel Hypoplasia in Multiethnic Cohorts. Hum Hered 2022; 87:000522642. [PMID: 35172313 PMCID: PMC9378791 DOI: 10.1159/000522642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 02/09/2022] [Indexed: 11/19/2022] Open
Abstract
Enamel hypoplasia causes reduction in the thickness of affected enamel and is one of the most common dental anomalies. This defect is caused by environmental and/or genetic factors that interfere with tooth formation, emphasizing the importance of investigating enamel hypoplasia on an epidemiological and genetic level. A genome-wide association of enamel hypoplasia was performed in multiple cohorts, overall comprising 7,159 individuals ranging in age from 7-82 years. Mixed-models were used to test for genetic association while simultaneously accounting for relatedness and genetic population structure. Meta-analysis was then performed. More than 5 million single-nucleotide polymorphisms were tested in individual cohorts. Analyses of the individual cohorts and meta-analysis identified association signals close to genome-wide significance (P < 510-8), and many suggestive association signals (510-8 < P < 510-6) near genes with plausible roles in tooth/enamel development. The strongest association signal (P = 1.5710-9) was observed near BMP2K in one of the individual cohorts. Additional suggestive signals were observed near genes with plausible roles in tooth development in the meta-analysis, such as SLC4A4 which can influence enamel hypoplasia. Additional human genetic studies are needed to replicate these results and functional studies in model systems are needed to validate our findings.
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Affiliation(s)
- Rasha N. Alotaibi
- Dental Health Department, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Brian J. Howe
- Department of Family Dentistry, College of Dentistry, University of Iowa, Iowa City, Iowa, USA
| | - Lina M. Moreno Uribe
- The Iowa Institute for Oral Health Research, College of Dentistry, University of Iowa, Iowa City, Iowa, USA
- Department of Orthodontics, School of Dentistry, University of Iowa, Iowa City, Iowa, USA
| | - Carla Sanchez
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | - Carmencita Padilla
- Department of Pediatrics, College of Medicine, University of the Philippines, Manila, Philippines
| | - Fernando A. Poletta
- ECLAMC/INAGEMP CEMIC, Dirección de Investigación A. Galván, Buenos Aires, Argentina
| | - Ieda M. Orioli
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carmen J. Buxó
- School of Dental Medicine, University of Puerto Rico, San Juan, Puerto Rico
| | - George L. Wehby
- Department of Health Management and Policy, College of Public Health, University of Iowa, Iowa City, Iowa, USA
| | - Alexandre R. Vieira
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jeffrey Murray
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, USA
| | | | | | - Ross E. Long
- Lancaster Cleft Palate Clinic, Lancaster, Pennsylvania, USA
| | - John R. Shaffer
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Steven E. Reis
- Clinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Seth M. Weinberg
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Katherine Neiswanger
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Daniel W. McNeil
- Department of Psychology, Eberly College of Arts and Sciences, West Virginia University, Morgantown, West Virginia, USA
- Department of Dental Practice and Rural Health, School of Dentistry, West Virginia University, Morgantown, West Virginia, USA
| | - Mary L. Marazita
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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16
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Basavaraju P, Balasubramani R, Kathiresan DS, Devaraj I, Babu K, Alagarsamy V, Puthamohan VM. Genetic Regulatory Networks of Apolipoproteins and Associated Medical Risks. Front Cardiovasc Med 2022; 8:788852. [PMID: 35071357 PMCID: PMC8770923 DOI: 10.3389/fcvm.2021.788852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 11/22/2021] [Indexed: 12/22/2022] Open
Abstract
Apolipoproteins (APO proteins) are the lipoprotein family proteins that play key roles in transporting lipoproteins all over the body. There are nearly more than twenty members reported in the APO protein family, among which the A, B, C, E, and L play major roles in contributing genetic risks to several disorders. Among these genetic risks, the single nucleotide polymorphisms (SNPs), involving the variation of single nucleotide base pairs, and their contributing polymorphisms play crucial roles in the apolipoprotein family and its concordant disease heterogeneity that have predominantly recurred through the years. In this review, we have contributed a handful of information on such genetic polymorphisms that include APOE, ApoA1/B ratio, and A1/C3/A4/A5 gene cluster-based population genetic studies carried throughout the world, to elaborately discuss the effects of various genetic polymorphisms in imparting various medical conditions, such as obesity, cardiovascular, stroke, Alzheimer's disease, diabetes, vascular complications, and other associated risks.
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Affiliation(s)
- Preethi Basavaraju
- Biomaterials and Nano-Medicine Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore, India
| | - Rubadevi Balasubramani
- Biomaterials and Nano-Medicine Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore, India
| | - Divya Sri Kathiresan
- Biomaterials and Nano-Medicine Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore, India
| | - Ilakkiyapavai Devaraj
- Biomaterials and Nano-Medicine Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore, India
| | - Kavipriya Babu
- Biomaterials and Nano-Medicine Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore, India
| | - Vasanthakumar Alagarsamy
- Biomaterials and Nano-Medicine Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore, India
| | - Vinayaga Moorthi Puthamohan
- Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore, India
- *Correspondence: Vinayaga Moorthi Puthamohan
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17
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Working memory and reaction time variability mediate the relationship between polygenic risk and ADHD traits in a general population sample. Mol Psychiatry 2022; 27:5028-5037. [PMID: 36151456 PMCID: PMC9763105 DOI: 10.1038/s41380-022-01775-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/19/2022] [Accepted: 09/02/2022] [Indexed: 01/14/2023]
Abstract
Endophenotypes are heritable and quantifiable traits indexing genetic liability for a disorder. Here, we examined three potential endophenotypes, working memory function, response inhibition, and reaction time variability, for attention-deficit hyperactivity disorder (ADHD) measured as a dimensional latent trait in a large general population sample derived from the Adolescent Brain Cognitive DevelopmentSM Study. The genetic risk for ADHD was estimated using polygenic risk scores (PRS) whereas ADHD traits were quantified as a dimensional continuum using Bartlett factor score estimates, derived from Attention Problems items from the Child Behaviour Checklist and Effortful Control items from the Early Adolescent Temperament Questionnaire-Revised. The three candidate cognitive endophenotypes were quantified using task-based performance measures. Higher ADHD PRSs were associated with higher ADHD traits, as well as poorer working memory performance and increased reaction time variability. Lower working memory performance, poorer response inhibition, and increased reaction time variability were associated with more pronounced ADHD traits. Working memory and reaction time variability partially statistically mediated the relationship between ADHD PRS and ADHD traits, explaining 14% and 16% of the association, respectively. The mediation effect was specific to the genetic risk for ADHD and did not generalise to genetic risk for four other major psychiatric disorders. Together, these findings provide robust evidence from a large general population sample that working memory and reaction time variability can be considered endophenotypes for ADHD that mediate the relationship between ADHD PRS and ADHD traits.
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18
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van der Meer D, Kaufmann T, Shadrin AA, Makowski C, Frei O, Roelfs D, Monereo-Sánchez J, Linden DEJ, Rokicki J, Alnæs D, de Leeuw C, Thompson WK, Loughnan R, Fan CC, Westlye LT, Andreassen OA, Dale AM. The genetic architecture of human cortical folding. SCIENCE ADVANCES 2021; 7:eabj9446. [PMID: 34910505 PMCID: PMC8673767 DOI: 10.1126/sciadv.abj9446] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 10/27/2021] [Indexed: 05/04/2023]
Abstract
The folding of the human cerebral cortex is a highly genetically regulated process that allows for a much larger surface area to fit into the cranial vault and optimizes functional organization. Sulcal depth is a robust yet understudied measure of localized folding, previously associated with multiple neurodevelopmental disorders. Here, we report the first genome-wide association study of sulcal depth. Through the multivariate omnibus statistical test (MOSTest) applied to vertex-wise measures from 33,748 U.K. Biobank participants (mean age, 64.3 years; 52.0% female), we identified 856 genome-wide significant loci (P < 5 × 10−8). Comparisons with cortical thickness and surface area indicated that sulcal depth has higher locus yield, heritability, and effective sample size. There was a large amount of genetic overlap between these traits, with gene-based analyses indicating strong associations with neurodevelopmental processes. Our findings demonstrate sulcal depth is a promising neuroimaging phenotype that may enhance our understanding of cortical morphology.
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Affiliation(s)
- Dennis van der Meer
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, Netherlands
| | - Tobias Kaufmann
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Psychiatry and Psychotherapy, University of Tübingen, Tübingen, Germany
| | - Alexey A. Shadrin
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Carolina Makowski
- Center for Multimodal Imaging and Genetics, University of California at San Diego, La Jolla, CA 92037, USA
| | - Oleksandr Frei
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Daniel Roelfs
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Jennifer Monereo-Sánchez
- School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, Netherlands
| | - David E. J. Linden
- School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, Netherlands
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Jaroslav Rokicki
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Psychology, University of Oslo, Oslo, Norway
| | - Dag Alnæs
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Bjørknes College, Oslo, Norway
| | - Christiaan de Leeuw
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Wesley K. Thompson
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California at San Diego, La Jolla, CA 92037, USA
| | - Robert Loughnan
- Center for Multimodal Imaging and Genetics, University of California at San Diego, La Jolla, CA 92037, USA
| | - Chun Chieh Fan
- Center for Multimodal Imaging and Genetics, University of California at San Diego, La Jolla, CA 92037, USA
| | - Lars T. Westlye
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Psychology, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway
| | - Ole A. Andreassen
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway
| | - Anders M. Dale
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Center for Multimodal Imaging and Genetics, University of California at San Diego, La Jolla, CA 92037, USA
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19
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Measurement Issues in Tests of the Socioecological Complexity Hypothesis. EVOLUTIONARY PSYCHOLOGICAL SCIENCE 2021. [DOI: 10.1007/s40806-021-00301-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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20
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Knott R, Johnson BP, Tiego J, Mellahn O, Finlay A, Kallady K, Kouspos M, Mohanakumar Sindhu VP, Hawi Z, Arnatkeviciute A, Chau T, Maron D, Mercieca EC, Furley K, Harris K, Williams K, Ure A, Fornito A, Gray K, Coghill D, Nicholson A, Phung D, Loth E, Mason L, Murphy D, Buitelaar J, Bellgrove MA. The Monash Autism-ADHD genetics and neurodevelopment (MAGNET) project design and methodologies: a dimensional approach to understanding neurobiological and genetic aetiology. Mol Autism 2021; 12:55. [PMID: 34353377 PMCID: PMC8340366 DOI: 10.1186/s13229-021-00457-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 07/05/2021] [Indexed: 11/20/2022] Open
Abstract
Background ASD and ADHD are prevalent neurodevelopmental disorders that frequently co-occur and have strong evidence for a degree of shared genetic aetiology. Behavioural and neurocognitive heterogeneity in ASD and ADHD has hampered attempts to map the underlying genetics and neurobiology, predict intervention response, and improve diagnostic accuracy. Moving away from categorical conceptualisations of psychopathology to a dimensional approach is anticipated to facilitate discovery of data-driven clusters and enhance our understanding of the neurobiological and genetic aetiology of these conditions. The Monash Autism-ADHD genetics and neurodevelopment (MAGNET) project is one of the first large-scale, family-based studies to take a truly transdiagnostic approach to ASD and ADHD. Using a comprehensive phenotyping protocol capturing dimensional traits central to ASD and ADHD, the MAGNET project aims to identify data-driven clusters across ADHD-ASD spectra using deep phenotyping of symptoms and behaviours; investigate the degree of familiality for different dimensional ASD-ADHD phenotypes and clusters; and map the neurocognitive, brain imaging, and genetic correlates of these data-driven symptom-based clusters. Methods The MAGNET project will recruit 1,200 families with children who are either typically developing, or who display elevated ASD, ADHD, or ASD-ADHD traits, in addition to affected and unaffected biological siblings of probands, and parents. All children will be comprehensively phenotyped for behavioural symptoms, comorbidities, neurocognitive and neuroimaging traits and genetics. Conclusion The MAGNET project will be the first large-scale family study to take a transdiagnostic approach to ASD-ADHD, utilising deep phenotyping across behavioural, neurocognitive, brain imaging and genetic measures. Supplementary Information The online version contains supplementary material available at 10.1186/s13229-021-00457-3.
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Affiliation(s)
- Rachael Knott
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, 18 Innovation Walk, Melbourne, VIC, 3800, Australia.
| | - Beth P Johnson
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, 18 Innovation Walk, Melbourne, VIC, 3800, Australia
| | - Jeggan Tiego
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, 18 Innovation Walk, Melbourne, VIC, 3800, Australia
| | - Olivia Mellahn
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, 18 Innovation Walk, Melbourne, VIC, 3800, Australia
| | - Amy Finlay
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, 18 Innovation Walk, Melbourne, VIC, 3800, Australia
| | - Kathryn Kallady
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, 18 Innovation Walk, Melbourne, VIC, 3800, Australia
| | - Maria Kouspos
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, 18 Innovation Walk, Melbourne, VIC, 3800, Australia
| | - Vishnu Priya Mohanakumar Sindhu
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, 18 Innovation Walk, Melbourne, VIC, 3800, Australia
| | - Ziarih Hawi
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, 18 Innovation Walk, Melbourne, VIC, 3800, Australia
| | - Aurina Arnatkeviciute
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, 18 Innovation Walk, Melbourne, VIC, 3800, Australia
| | - Tracey Chau
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, 18 Innovation Walk, Melbourne, VIC, 3800, Australia
| | - Dalia Maron
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, 18 Innovation Walk, Melbourne, VIC, 3800, Australia
| | - Emily-Clare Mercieca
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, 18 Innovation Walk, Melbourne, VIC, 3800, Australia
| | - Kirsten Furley
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, 18 Innovation Walk, Melbourne, VIC, 3800, Australia
| | - Katrina Harris
- Department of Paediatrics, Monash University, Melbourne, VIC, 3800, Australia.,Department of Developmental Paediatrics, Monash Children's Hospital, 246 Clayton Rd, Clayton, VIC, 3168, Australia
| | - Katrina Williams
- Department of Paediatrics, Monash University, Melbourne, VIC, 3800, Australia.,Department of Developmental Paediatrics, Monash Children's Hospital, 246 Clayton Rd, Clayton, VIC, 3168, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, 50 Flemington Rd, Parkville, VIC, 3052, Australia.,Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, Royal Children's Hospital, 50 Flemington Road, Parkville, VIC, 3052, Australia
| | - Alexandra Ure
- Department of Paediatrics, Monash University, Melbourne, VIC, 3800, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, 50 Flemington Rd, Parkville, VIC, 3052, Australia.,Department of Mental Health, Royal Children's Hospital, 50 Flemington Rd, Parkville, VIC, 3052, Australia.,Neurodevelopment and Disability Research, Murdoch Children's Research Institute, Royal Children's Hospital, 50 Flemington Rd, Parkville, VIC, 3052, Australia
| | - Alex Fornito
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, 18 Innovation Walk, Melbourne, VIC, 3800, Australia
| | - Kylie Gray
- Centre for Educational Development, Appraisal, and Research, University of Warwick, Coventry, CV4 7AL, UK.,Department of Psychiatry, School of Clinical Sciences, Monash University, 246 Clayton Rd, Melbourne, VIC, 3168, Australia
| | - David Coghill
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, Royal Children's Hospital, 50 Flemington Road, Parkville, VIC, 3052, Australia.,Department of Mental Health, Royal Children's Hospital, 50 Flemington Rd, Parkville, VIC, 3052, Australia.,Neurodevelopment and Disability Research, Murdoch Children's Research Institute, Royal Children's Hospital, 50 Flemington Rd, Parkville, VIC, 3052, Australia
| | - Ann Nicholson
- Faculty of Information and Technology, Monash University, Melbourne, VIC, 3800, Australia
| | - Dinh Phung
- Faculty of Information and Technology, Monash University, Melbourne, VIC, 3800, Australia
| | - Eva Loth
- Sackler Institute for Translational Neurodevelopment, Institute of Psychiatry, Psychology and Neuroscience, King's College London, De Crespigny Park, Denmark Hill, London, SE5 8AF, UK.,Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology and Neuroscience, King's College London, De Crespigny Park, Denmark Hill, London, SE5 8AF, UK
| | - Luke Mason
- Centre for Brain and Cognitive Development, Birkbeck, University of London, Henry Welcome Building, Malet Street, London, WC1E 7HX, UK
| | - Declan Murphy
- Sackler Institute for Translational Neurodevelopment, Institute of Psychiatry, Psychology and Neuroscience, King's College London, De Crespigny Park, Denmark Hill, London, SE5 8AF, UK.,Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology and Neuroscience, King's College London, De Crespigny Park, Denmark Hill, London, SE5 8AF, UK
| | - Jan Buitelaar
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Medical Centre, Kapittelweg 29, 6525 EN, Nijmegen, The Netherlands
| | - Mark A Bellgrove
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, 18 Innovation Walk, Melbourne, VIC, 3800, Australia
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21
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De Leon D, Nishitani S, Walum H, McCormack KM, Wilson ME, Smith AK, Young LJ, Sanchez MM. Methylation of OXT and OXTR genes, central oxytocin, and social behavior in female macaques. Horm Behav 2020; 126:104856. [PMID: 32979349 PMCID: PMC7725942 DOI: 10.1016/j.yhbeh.2020.104856] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/01/2020] [Accepted: 08/14/2020] [Indexed: 12/24/2022]
Abstract
Oxytocin (OXT) and its receptor (OXTR) are encoded by OXT and OXTR, respectively. Variable methylation of these genes has been linked to variability in sociability and neuroendophenotypes. Here we examine whether OXTR or OXT methylation in blood predicts concentrations of OXT in cerebrospinal fluid (CSF) (n = 166) and social behavior (n = 207) in socially-housed female rhesus macaques. We report a similarity between human and rhesus CpG sites for OXT and OXTR and a putative negative association between methylation of two OXTR CpG units with aggressive behavior (both P = 0.003), though this finding does not survive the most stringent correction for multiple comparison testing. We did not detect a statistically significant association between methylation of any CpG sites and CSF OXT concentrations, either. Because none of the tested associations survived statistical corrections, if there is any relationship between blood-derived methylation of these genes and the behavioral and physiological outcomes measured here, the effect size is too small to be detected reliably with this sample size. These results do not support the hypothesis that blood methylation of OXT or OXTR is robustly associated with CSF OXT concentration or social behavior in rhesus. It is possible, though, that methylation of these loci in the brain or in cheek epithelia may be associated with central OXT release and behavior. Finally, we consider the limitations of this exploratory study in the context of statistical power.
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Affiliation(s)
- Desirée De Leon
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States of America; Silvio O. Conte Center for Oxytocin and Social Cognition, Emory University, Atlanta, GA, United States of America; Center for Translational Social Neuroscience, Emory University, Atlanta, GA, United States of America
| | - Shota Nishitani
- Dept. of Gynecology and Obstetrics, Emory School of Medicine, Emory University, Atlanta, GA, United States of America; Research Center for Child Mental Development, University of Fukui, Fukui, Japan; Dept. of Psychiatry & Behavioral Sciences, Emory School of Medicine, Emory University, Atlanta, GA, United States of America
| | - Hasse Walum
- Silvio O. Conte Center for Oxytocin and Social Cognition, Emory University, Atlanta, GA, United States of America
| | - Kai M McCormack
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States of America; Dept. of Psychology, Spelman College, Atlanta, GA, United States of America
| | - Mark E Wilson
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States of America; Dept. of Psychiatry & Behavioral Sciences, Emory School of Medicine, Emory University, Atlanta, GA, United States of America
| | - Alicia K Smith
- Dept. of Gynecology and Obstetrics, Emory School of Medicine, Emory University, Atlanta, GA, United States of America; Dept. of Psychiatry & Behavioral Sciences, Emory School of Medicine, Emory University, Atlanta, GA, United States of America
| | - Larry J Young
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States of America; Silvio O. Conte Center for Oxytocin and Social Cognition, Emory University, Atlanta, GA, United States of America; Center for Translational Social Neuroscience, Emory University, Atlanta, GA, United States of America; Dept. of Psychiatry & Behavioral Sciences, Emory School of Medicine, Emory University, Atlanta, GA, United States of America
| | - Mar M Sanchez
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States of America; Silvio O. Conte Center for Oxytocin and Social Cognition, Emory University, Atlanta, GA, United States of America; Center for Translational Social Neuroscience, Emory University, Atlanta, GA, United States of America; Dept. of Psychiatry & Behavioral Sciences, Emory School of Medicine, Emory University, Atlanta, GA, United States of America.
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22
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Van Someren EJW. Brain mechanisms of insomnia: new perspectives on causes and consequences. Physiol Rev 2020; 101:995-1046. [PMID: 32790576 DOI: 10.1152/physrev.00046.2019] [Citation(s) in RCA: 154] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
While insomnia is the second most common mental disorder, progress in our understanding of underlying neurobiological mechanisms has been limited. The present review addresses the definition and prevalence of insomnia and explores its subjective and objective characteristics across the 24-hour day. Subsequently, the review extensively addresses how the vulnerability to develop insomnia is affected by genetic variants, early life stress, major life events, and brain structure and function. Further supported by the clear mental health risks conveyed by insomnia, the integrated findings suggest that the vulnerability to develop insomnia could rather be found in brain circuits regulating emotion and arousal than in circuits involved in circadian and homeostatic sleep regulation. Finally, a testable model is presented. The model proposes that in people with a vulnerability to develop insomnia, the locus coeruleus is more sensitive to-or receives more input from-the salience network and related circuits, even during rapid eye movement sleep, when it should normally be sound asleep. This vulnerability may ignite a downward spiral of insufficient overnight adaptation to distress, resulting in accumulating hyperarousal, which, in turn, impedes restful sleep and moreover increases the risk of other mental health adversity. Sensitized brain circuits are likely to be subjectively experienced as "sleeping with one eye open". The proposed model opens up the possibility for novel intervention studies and animal studies, thus accelerating the ignition of a neuroscience of insomnia, which is direly needed for better treatment.
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Affiliation(s)
- Eus J W Van Someren
- Department of Sleep and Cognition, Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands; Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit University Amsterdam, Amsterdam, The Netherlands; and Amsterdam UMC, Vrije Universiteit, Psychiatry, Amsterdam Neuroscience, Amsterdam, The Netherlands
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23
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van der Meer D, Frei O, Kaufmann T, Shadrin AA, Devor A, Smeland OB, Thompson WK, Fan CC, Holland D, Westlye LT, Andreassen OA, Dale AM. Understanding the genetic determinants of the brain with MOSTest. Nat Commun 2020; 11:3512. [PMID: 32665545 PMCID: PMC7360598 DOI: 10.1038/s41467-020-17368-1] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 06/22/2020] [Indexed: 12/11/2022] Open
Abstract
Regional brain morphology has a complex genetic architecture, consisting of many common polymorphisms with small individual effects. This has proven challenging for genome-wide association studies (GWAS). Due to the distributed nature of genetic signal across brain regions, multivariate analysis of regional measures may enhance discovery of genetic variants. Current multivariate approaches to GWAS are ill-suited for complex, large-scale data of this kind. Here, we introduce the Multivariate Omnibus Statistical Test (MOSTest), with an efficient computational design enabling rapid and reliable inference, and apply it to 171 regional brain morphology measures from 26,502 UK Biobank participants. At the conventional genome-wide significance threshold of α = 5 × 10-8, MOSTest identifies 347 genomic loci associated with regional brain morphology, more than any previous study, improving upon the discovery of established GWAS approaches more than threefold. Our findings implicate more than 5% of all protein-coding genes and provide evidence for gene sets involved in neuron development and differentiation.
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Affiliation(s)
- Dennis van der Meer
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
- School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands.
| | - Oleksandr Frei
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Tobias Kaufmann
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Alexey A Shadrin
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Anna Devor
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Departments of Neurosciences and Radiology, University of California at San Diego, La Jolla, CA, 92037, USA
- Martinos Center for Biomedical Imaging, MGH/HMS, Charlestown, MA, 02129, USA
| | - Olav B Smeland
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Wesley K Thompson
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Family Medicine and Public Health, University of California at San Diego, La Jolla, CA, 92037, USA
| | - Chun Chieh Fan
- Center for Multimodal Imaging and Genetics, University of California at San Diego, La Jolla, CA, 92037, USA
| | - Dominic Holland
- Departments of Neurosciences and Radiology, University of California at San Diego, La Jolla, CA, 92037, USA
- Center for Multimodal Imaging and Genetics, University of California at San Diego, La Jolla, CA, 92037, USA
| | - Lars T Westlye
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Psychology, University of Oslo, Oslo, Norway
| | - Ole A Andreassen
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Anders M Dale
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
- Center for Multimodal Imaging and Genetics, University of California at San Diego, La Jolla, CA, 92037, USA.
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24
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Pralle RS, Schultz NE, White HM, Weigel KA. Hyperketonemia GWAS and parity-dependent SNP associations in Holstein dairy cows intensively sampled for blood β-hydroxybutyrate concentration. Physiol Genomics 2020; 52:347-357. [PMID: 32628084 DOI: 10.1152/physiolgenomics.00016.2020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Hyperketonemia (HYK) is a metabolic disorder that affects early postpartum dairy cows; however, there has been limited success in identifying genomic variants contributing to HYK susceptibility. We conducted a genome-wide association study (GWAS) using HYK phenotypes based on an intensive screening protocol, interrogated genotype interactions with parity group (GWIS), and evaluated the enrichment of annotated metabolic pathways. Holstein cows were enrolled into the experiment after parturition, and blood samples were collected at four timepoints between 5 and 18 days postpartum. Concentration of blood β-hydroxybutyrate (BHB) was quantified cow-side via a handheld BHB meter. Cows were labeled as a HYK case when at least one blood sample had BHB ≥ 1.2 mmol/L, and all other cows were considered non-HYK controls. After quality control procedures, 1,710 cows and 58,699 genotypes were available for further analysis. The GWAS and GWIS were performed using the forward feature select linear mixed model method. There was evidence for an association between ARS-BFGL-NGS-91238 and HYK susceptibility, as well as parity-dependent associations to HYK for BovineHD0600024247 and BovineHD1400023753. Candidate genes annotated to these single nuclear polymorphism associations have been previously associated with obesity, diabetes, insulin resistance, and fatty liver in humans and rodent models. Enrichment analysis revealed focal adhesion and axon guidance as metabolic pathways contributing to HYK etiology, while genetic variation in pathways related to insulin secretion and sensitivity may affect HYK susceptibility in a parity-dependent matter. In conclusion, the present work proposes several novel marker associations and metabolic pathways contributing to genetic risk for HYK susceptibility.
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Affiliation(s)
- Ryan S Pralle
- Department of Dairy Science, University of Wisconsin-Madison, Madison, Wisconsin
| | - Nichol E Schultz
- Department of Dairy Science, University of Wisconsin-Madison, Madison, Wisconsin
| | - Heather M White
- Department of Dairy Science, University of Wisconsin-Madison, Madison, Wisconsin
| | - Kent A Weigel
- Department of Dairy Science, University of Wisconsin-Madison, Madison, Wisconsin
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25
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Genetic and epigenetic analyses of panic disorder in the post-GWAS era. J Neural Transm (Vienna) 2020; 127:1517-1526. [PMID: 32388794 PMCID: PMC7578165 DOI: 10.1007/s00702-020-02205-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 05/03/2020] [Indexed: 02/07/2023]
Abstract
Panic disorder (PD) is a common and debilitating neuropsychiatric disorder characterized by panic attacks coupled with excessive anxiety. Both genetic factors and environmental factors play an important role in PD pathogenesis and response to treatment. However, PD is clinically heterogeneous and genetically complex, and the exact genetic or environmental causes of this disorder remain unclear. Various approaches for detecting disease-causing genes have recently been made available. In particular, genome-wide association studies (GWAS) have attracted attention for the identification of disease-associated loci of multifactorial disorders. This review introduces GWAS of PD, followed by a discussion about the limitations of GWAS and the major challenges facing geneticists in the post-GWAS era. Alternative strategies to address these challenges are then proposed, such as epigenome-wide association studies (EWAS) and rare variant association studies (RVAS) using next-generation sequencing. To date, however, few reports have described these analyses, and the evidence remains insufficient to confidently identify or exclude rare variants or epigenetic changes in PD. Further analyses are therefore required, using sample sizes in the tens of thousands, extensive functional annotations, and highly targeted hypothesis testing.
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26
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Shafquat A, Crystal RG, Mezey JG. Identifying novel associations in GWAS by hierarchical Bayesian latent variable detection of differentially misclassified phenotypes. BMC Bioinformatics 2020; 21:178. [PMID: 32381021 PMCID: PMC7204256 DOI: 10.1186/s12859-020-3387-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 01/24/2020] [Indexed: 12/22/2022] Open
Abstract
Background Heterogeneity in the definition and measurement of complex diseases in Genome-Wide Association Studies (GWAS) may lead to misdiagnoses and misclassification errors that can significantly impact discovery of disease loci. While well appreciated, almost all analyses of GWAS data consider reported disease phenotype values as is without accounting for potential misclassification. Results Here, we introduce Phenotype Latent variable Extraction of disease misdiagnosis (PheLEx), a GWAS analysis framework that learns and corrects misclassified phenotypes using structured genotype associations within a dataset. PheLEx consists of a hierarchical Bayesian latent variable model, where inference of differential misclassification is accomplished using filtered genotypes while implementing a full mixed model to account for population structure and genetic relatedness in study populations. Through simulations, we show that the PheLEx framework dramatically improves recovery of the correct disease state when considering realistic allele effect sizes compared to existing methodologies designed for Bayesian recovery of disease phenotypes. We also demonstrate the potential of PheLEx for extracting new potential loci from existing GWAS data by analyzing bipolar disorder and epilepsy phenotypes available from the UK Biobank. From the PheLEx analysis of these data, we identified new candidate disease loci not previously reported for these datasets that have value for supplemental hypothesis generation. Conclusion PheLEx shows promise in reanalyzing GWAS datasets to provide supplemental candidate loci that are ignored by traditional GWAS analysis methodologies.
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Affiliation(s)
- Afrah Shafquat
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Ronald G Crystal
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA.,Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jason G Mezey
- Department of Computational Biology, Cornell University, Ithaca, NY, USA. .,Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA.
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27
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Yu C, Ni G, van der Werf J, Lee SH. Detecting Genotype-Population Interaction Effects by Ancestry Principal Components. Front Genet 2020; 11:379. [PMID: 32373165 PMCID: PMC7186421 DOI: 10.3389/fgene.2020.00379] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/27/2020] [Indexed: 01/22/2023] Open
Abstract
Heterogeneity in the phenotypic mean and variance across populations is often observed for complex traits. One way to understand heterogeneous phenotypes lies in uncovering heterogeneity in genetic effects. Previous studies on genetic heterogeneity across populations were typically based on discrete groups in populations stratified by different countries or cohorts, which ignored the difference of population characteristics for the individuals within each group and resulted in loss of information. Here, we introduce a novel concept of genotype-by-population (G × P) interaction where population is defined by the first and second ancestry principal components (PCs), which are less likely to be confounded with country/cohort-specific factors. We applied a reaction norm model fitting each of 70 complex traits with significant SNP-heritability and the PCs as covariates to examine G × P interactions across diverse populations including white British and other white Europeans from the UK Biobank (N = 22,229). Our results demonstrated a significant population genetic heterogeneity for behavioral traits such as age at first sexual intercourse and academic qualification. Our approach may shed light on the latent genetic architecture of complex traits that underlies the modulation of genetic effects across different populations.
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Affiliation(s)
- Chenglong Yu
- Australian Centre for Precision Health, University of South Australia Cancer Research Institute, University of South Australia, Adelaide, SA, Australia
- College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Guiyan Ni
- Australian Centre for Precision Health, University of South Australia Cancer Research Institute, University of South Australia, Adelaide, SA, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - Julius van der Werf
- School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - S. Hong Lee
- Australian Centre for Precision Health, University of South Australia Cancer Research Institute, University of South Australia, Adelaide, SA, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
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28
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Cheesman R, Coleman J, Rayner C, Purves KL, Morneau-Vaillancourt G, Glanville K, Choi SW, Breen G, Eley TC. Familial Influences on Neuroticism and Education in the UK Biobank. Behav Genet 2020; 50:84-93. [PMID: 31802328 PMCID: PMC7028797 DOI: 10.1007/s10519-019-09984-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 11/20/2019] [Indexed: 01/22/2023]
Abstract
Genome-wide studies often exclude family members, even though they are a valuable source of information. We identified parent-offspring pairs, siblings and couples in the UK Biobank and implemented a family-based DNA-derived heritability method to capture additional genetic effects and multiple sources of environmental influence on neuroticism and years of education. Compared to estimates from unrelated individuals, total heritability increased from 10 to 27% and from 17 to 56% for neuroticism and education respectively by including family-based genetic effects. We detected no family environmental influences on neuroticism. The couple similarity variance component explained 35% of the variation in years of education, probably reflecting assortative mating. Overall, our genetic and environmental estimates closely replicate previous findings from an independent sample. However, more research is required to dissect contributions to the additional heritability by rare and structural genetic effects, assortative mating, and residual environmental confounding. The latter is especially relevant for years of education, a highly socially contingent variable, for which our heritability estimate is at the upper end of twin estimates in the literature. Family-based genetic effects could be harnessed to improve polygenic prediction.
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Affiliation(s)
- R Cheesman
- Social Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, 16 de Crespigny Park, Denmark Hill, London, SE5 8AF, UK.
| | - J Coleman
- Social Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, 16 de Crespigny Park, Denmark Hill, London, SE5 8AF, UK
- NIHR Biomedical Research Centre for Mental Health, South London and Maudsley NHS Trust, London, UK
| | - C Rayner
- Social Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, 16 de Crespigny Park, Denmark Hill, London, SE5 8AF, UK
| | - K L Purves
- Social Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, 16 de Crespigny Park, Denmark Hill, London, SE5 8AF, UK
| | - G Morneau-Vaillancourt
- Research Unit on Child Psychosocial Maladjustment, Laval University, Quebec City, Canada
| | - K Glanville
- Social Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, 16 de Crespigny Park, Denmark Hill, London, SE5 8AF, UK
| | - S W Choi
- Social Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, 16 de Crespigny Park, Denmark Hill, London, SE5 8AF, UK
| | - G Breen
- Social Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, 16 de Crespigny Park, Denmark Hill, London, SE5 8AF, UK
- NIHR Biomedical Research Centre for Mental Health, South London and Maudsley NHS Trust, London, UK
| | - T C Eley
- Social Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, 16 de Crespigny Park, Denmark Hill, London, SE5 8AF, UK.
- NIHR Biomedical Research Centre for Mental Health, South London and Maudsley NHS Trust, London, UK.
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29
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Agler CS, Divaris K. Sources of bias in genomics research of oral and dental traits. COMMUNITY DENTAL HEALTH 2020; 37:102-106. [PMID: 32031351 PMCID: PMC7316399 DOI: 10.1922/cdh_specialissue_divaris05] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Evidence regarding the genomic basis of oral/dental traits and diseases is a fundamental pillar of the emerging notion of precision health. During the last decade, technological advances have improved the feasibility and affordability of conducting genome-wide association studies (GWAS) and studying the associations of emanating data with both common and rare oral conditions. Most evidence thus far emanates from GWAS of dental caries and periodontal disease that have tested the associations of several million single nucleotide polymorphisms (SNPs) with typically binary, health vs. disease phenotypes. GWAS offer advantages over the previous candidate-gene studies, mainly owing to their agnostic (i.e., unbiased, or hypothesis-free) nature. Nevertheless, GWAS are prone to virtually all sources of random and systematic error. Here, we review common sources of bias in genomics research with focus on GWAS including: type I and II errors, population stratification and heterogeneity, selection bias, adjustment for heritable covariates, appropriate reference panels for imputation, and gene annotation. We argue that valid and precise phenotype measurement is a key requirement, as GWAS sample sizes and thus statistical power increase. Finally, we stress that the lack of diversity of populations with phenotypes and genotypes is a major limitation for the generalizability and ultimate translation of the emerging genomics evidence-base into oral health promotion for all.
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Affiliation(s)
- Cary S Agler
- Adams School of Dentistry, University of North Carolina Chapel Hill, Chapel Hill, NC, United States
| | - Kimon Divaris
- Adams School of Dentistry, University of North Carolina Chapel Hill, Chapel Hill, NC, United States
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30
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Long EC, Kaneva R, Vasilev G, Moeller FG, Vassileva J. Neurocognitive and Psychiatric Markers for Addiction: Common vs. Specific Endophenotypes for Heroin and Amphetamine Dependence. Curr Top Med Chem 2020; 20:585-597. [PMID: 32003694 DOI: 10.2174/1568026620666200131124608] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 12/05/2019] [Accepted: 12/12/2019] [Indexed: 01/27/2023]
Abstract
BACKGROUND The differential utility of neurocognitive impulsivity and externalizing/ internalizing traits as putative endophenotypes for dependence on heroin vs. amphetamine is unclear. OBJECTIVE This exploratory study aims to determine: (1) whether neurocognitive impulsivity dimensions and externalizing/internalizing traits are correlated between siblings discordant for heroin and amphetamine dependence; and (2) which of these associations are common across substances and which are substance- specific. METHODS Pearson correlations between individuals with 'pure' heroin and amphetamine dependence and their unaffected biological siblings (n = 37 heroin sibling pairs; n = 30 amphetamine sibling pairs) were run on 10 neurocognitive measures, 6 externalizing measures, and 5 internalizing measures. Sibling pair effects were further examined using regression. RESULTS Siblings discordant for heroin dependence were significantly correlated on delay aversion on the Cambridge Gambling Task, risk-taking on the Balloon Analogue Risk Task, sensation seeking, and hopelessness. Siblings discordant for amphetamine dependence were significantly correlated on the quality of decision-making on the Cambridge Gambling Task, discriminability on the Immediate Memory Task, commission errors on the Go/No Go Task, trait impulsivity, ADHD and anxiety sensitivity. CONCLUSION Dimensions of impulsivity and externalizing/internalizing traits appear to aggregate among siblings discordant for substance dependence. Risk-taking propensity, sensation seeking and hopelessness were specific for heroin sibling pairs. Motor/action impulsivity, trait impulsivity, and anxiety sensitivity were specific to amphetamine sibling pairs. Decisional/choice impulsivity was common across both heroin and amphetamine sibling pairs. These findings provide preliminary evidence for the utility of neurocognitive impulsivity and externalizing/ internalizing traits as candidate endophenotypes for substance dependence in general and for substance-specific dependencies.
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Affiliation(s)
- Elizabeth C Long
- Edna Bennett Pierce Prevention Research Center, Pennsylvania State University, University Park, Pennsylvania PA, United States
| | - Radka Kaneva
- Department of Medical Chemistry and Biochemistry, Sofia Medical University, Sofia, Bulgaria
| | | | - F Gerard Moeller
- Institute for Drug and Alcohol Studies, Virginia Commonwealth University, Richmond, VA, United States.,Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, United States
| | - Jasmin Vassileva
- Institute for Drug and Alcohol Studies, Virginia Commonwealth University, Richmond, VA, United States.,Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, United States
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31
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Waszczuk MA, Eaton NR, Krueger RF, Shackman AJ, Waldman ID, Zald DH, Lahey BB, Patrick CJ, Conway CC, Ormel J, Hyman SE, Fried EI, Forbes MK, Docherty AR, Althoff RR, Bach B, Chmielewski M, DeYoung CG, Forbush KT, Hallquist M, Hopwood CJ, Ivanova MY, Jonas KG, Latzman RD, Markon KE, Mullins-Sweatt SN, Pincus AL, Reininghaus U, South SC, Tackett JL, Watson D, Wright AGC, Kotov R. Redefining phenotypes to advance psychiatric genetics: Implications from hierarchical taxonomy of psychopathology. JOURNAL OF ABNORMAL PSYCHOLOGY 2020; 129:143-161. [PMID: 31804095 PMCID: PMC6980897 DOI: 10.1037/abn0000486] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Genetic discovery in psychiatry and clinical psychology is hindered by suboptimal phenotypic definitions. We argue that the hierarchical, dimensional, and data-driven classification system proposed by the Hierarchical Taxonomy of Psychopathology (HiTOP) consortium provides a more effective approach to identifying genes that underlie mental disorders, and to studying psychiatric etiology, than current diagnostic categories. Specifically, genes are expected to operate at different levels of the HiTOP hierarchy, with some highly pleiotropic genes influencing higher order psychopathology (e.g., the general factor), whereas other genes conferring more specific risk for individual spectra (e.g., internalizing), subfactors (e.g., fear disorders), or narrow symptoms (e.g., mood instability). We propose that the HiTOP model aligns well with the current understanding of the higher order genetic structure of psychopathology that has emerged from a large body of family and twin studies. We also discuss the convergence between the HiTOP model and findings from recent molecular studies of psychopathology indicating broad genetic pleiotropy, such as cross-disorder SNP-based shared genetic covariance and polygenic risk scores, and we highlight molecular genetic studies that have successfully redefined phenotypes to enhance precision and statistical power. Finally, we suggest how to integrate a HiTOP approach into future molecular genetic research, including quantitative and hierarchical assessment tools for future data-collection and recommendations concerning phenotypic analyses. (PsycINFO Database Record (c) 2020 APA, all rights reserved).
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Bo Bach
- Centre of Excellence on Personality Disorder
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Luningham JM, McArtor DB, Hendriks AM, van Beijsterveldt CEM, Lichtenstein P, Lundström S, Larsson H, Bartels M, Boomsma DI, Lubke GH. Data Integration Methods for Phenotype Harmonization in Multi-Cohort Genome-Wide Association Studies With Behavioral Outcomes. Front Genet 2020; 10:1227. [PMID: 31921287 PMCID: PMC6914843 DOI: 10.3389/fgene.2019.01227] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 11/05/2019] [Indexed: 01/03/2023] Open
Abstract
Parallel meta-analysis is a popular approach for increasing the power to detect genetic effects in genome-wide association studies across multiple cohorts. Consortia studying the genetics of behavioral phenotypes are oftentimes faced with systematic differences in phenotype measurement across cohorts, introducing heterogeneity into the meta-analysis and reducing statistical power. This study investigated integrative data analysis (IDA) as an approach for jointly modeling the phenotype across multiple datasets. We put forth a bi-factor integration model (BFIM) that provides a single common phenotype score and accounts for sources of study-specific variability in the phenotype. In order to capitalize on this modeling strategy, a phenotype reference panel was utilized as a supplemental sample with complete data on all behavioral measures. A simulation study showed that a mega-analysis of genetic variant effects in a BFIM were more powerful than meta-analysis of genetic effects on a cohort-specific sum score of items. Saving the factor scores from the BFIM and using those as the outcome in meta-analysis was also more powerful than the sum score in most simulation conditions, but a small degree of bias was introduced by this approach. The reference panel was necessary to realize these power gains. An empirical demonstration used the BFIM to harmonize aggression scores in 9-year old children across the Netherlands Twin Register and the Child and Adolescent Twin Study in Sweden, providing a template for application of the BFIM to a range of different phenotypes. A supplemental data collection in the Netherlands Twin Register served as a reference panel for phenotype modeling across both cohorts. Our results indicate that model-based harmonization for the study of complex traits is a useful step within genetic consortia.
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Affiliation(s)
- Justin M Luningham
- Department of Psychology, University of Notre Dame, Notre Dame, IN, United States
| | - Daniel B McArtor
- Department of Psychology, University of Notre Dame, Notre Dame, IN, United States
| | - Anne M Hendriks
- Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, Netherlands.,Faculty of Behavioural and Movement Sciences, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Catharina E M van Beijsterveldt
- Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, Netherlands.,Faculty of Behavioural and Movement Sciences, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Paul Lichtenstein
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Sebastian Lundström
- Gillberg Neuropsychiatry Centre, University of Gothenburg, Gothenburg, Sweden
| | - Henrik Larsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,School of Medical Sciences, Örebro University, Örebro, Sweden
| | - Meike Bartels
- Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, Netherlands.,Faculty of Behavioural and Movement Sciences, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, Netherlands.,Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, Netherlands
| | - Dorret I Boomsma
- Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, Netherlands.,Faculty of Behavioural and Movement Sciences, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, Netherlands.,Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, Netherlands
| | - Gitta H Lubke
- Department of Psychology, University of Notre Dame, Notre Dame, IN, United States
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33
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Mataix-Cols D, Hansen B, Mattheisen M, Karlsson EK, Addington AM, Boberg J, Djurfeldt DR, Halvorsen M, Lichtenstein P, Solem S, Lindblad-Toh K, Haavik J, Kvale G, Rück C, Crowley JJ. Nordic OCD & Related Disorders Consortium: Rationale, design, and methods. Am J Med Genet B Neuropsychiatr Genet 2020; 183:38-50. [PMID: 31424634 PMCID: PMC6898732 DOI: 10.1002/ajmg.b.32756] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 07/19/2019] [Accepted: 07/29/2019] [Indexed: 12/23/2022]
Abstract
Obsessive-compulsive disorder (OCD) is a debilitating psychiatric disorder, yet its etiology is unknown and treatment outcomes could be improved if biological targets could be identified. Unfortunately, genetic findings for OCD are lagging behind other psychiatric disorders. Thus, there is a pressing need to understand the causal mechanisms implicated in OCD in order to improve clinical outcomes and to reduce morbidity and societal costs. Specifically, there is a need for a large-scale, etiologically informative genetic study integrating genetic and environmental factors that presumably interact to cause the condition. The Nordic countries provide fertile ground for such a study, given their detailed population registers, national healthcare systems and active specialist clinics for OCD. We thus formed the Nordic OCD and Related Disorders Consortium (NORDiC, www.crowleylab.org/nordic), and with the support of NIMH and the Swedish Research Council, have begun to collect a large, richly phenotyped and genotyped sample of OCD cases. Our specific aims are geared toward answering a number of key questions regarding the biology, etiology, and treatment of OCD. This article describes and discusses the rationale, design, and methodology of NORDiC, including details on clinical measures and planned genomic analyses.
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Affiliation(s)
- David Mataix-Cols
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden,Stockholm Health Care Services, Stockholm, Sweden
| | - Bjarne Hansen
- Haukeland University Hospital, OCD-team, Bergen, Norway,Department of Clinical Psychology, University of Bergen, Bergen, Norway
| | - Manuel Mattheisen
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany,Institute of Human Genetics, University of Bonn, Bonn, Germany,Center for Integrative Sequencing, iSEQ, Department of Biomedicine, Aarhus University, Denmark,Department of Psychiatry, Psychosomatics, and Psychotherapy, University of Würzburg, Germany
| | - Elinor K. Karlsson
- Broad Institute of MIT and Harvard, Cambridge, MA, USA,Program in Bioinformatics & Integrative Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Anjené M. Addington
- Genomics Research Branch, National Institute of Mental Health in Bethesda, Bethesda, Maryland, USA
| | - Julia Boberg
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden,Stockholm Health Care Services, Stockholm, Sweden
| | - Diana R. Djurfeldt
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden,Stockholm Health Care Services, Stockholm, Sweden
| | - Matthew Halvorsen
- Department of Genetics, University of North Carolina at Chapel Hill, NC, USA
| | - Paul Lichtenstein
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Stian Solem
- Haukeland University Hospital, OCD-team, Bergen, Norway,Department of Psychology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA, USA,Science for Life Laboratory, IMBIM, Uppsala University, Uppsala, Sweden
| | | | - Jan Haavik
- Department of Biomedicine, University of Bergen, Bergen, Norway,Division of Psychiatry, Haukeland University Hospital, Bergen, Norway
| | - Gerd Kvale
- Haukeland University Hospital, OCD-team, Bergen, Norway,Department of Clinical Psychology, University of Bergen, Bergen, Norway
| | - Christian Rück
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden,Stockholm Health Care Services, Stockholm, Sweden
| | - James J. Crowley
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden,Department of Genetics, University of North Carolina at Chapel Hill, NC, USA,Department of Psychiatry, University of North Carolina at Chapel Hill, NC, USA
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Schwabe I, Milaneschi Y, Gerring Z, Sullivan PF, Schulte E, Suppli NP, Thorp JG, Derks EM, Middeldorp CM. Unraveling the genetic architecture of major depressive disorder: merits and pitfalls of the approaches used in genome-wide association studies. Psychol Med 2019; 49:2646-2656. [PMID: 31559935 PMCID: PMC6877467 DOI: 10.1017/s0033291719002502] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 07/23/2019] [Accepted: 08/23/2019] [Indexed: 11/27/2022]
Abstract
To identify genetic risk loci for major depressive disorder (MDD), two broad study design approaches have been applied: (1) to maximize sample size by combining data from different phenotype assessment modalities (e.g. clinical interview, self-report questionnaires) and (2) to reduce phenotypic heterogeneity through selecting more homogenous MDD subtypes. The value of these strategies has been debated. In this review, we summarize the most recent findings of large genomic studies that applied these approaches, and we highlight the merits and pitfalls of both approaches with particular attention to methodological and psychometric issues. We also discuss the results of analyses that investigated the heterogeneity of MDD. We conclude that both study designs are essential for further research. So far, increasing sample size has led to the identification of a relatively high number of genomic loci linked to depression. However, part of the identified variants may be related to a phenotype common to internalizing disorders and related traits. As such, samples containing detailed clinical information are needed to dissect depression heterogeneity and enable the potential identification of variants specific to a more restricted MDD phenotype. A balanced portfolio reconciling both study design approaches is the optimal approach to progress further in unraveling the genetic architecture of depression.
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Affiliation(s)
- I. Schwabe
- Department of Methodology and Statistics, Tilburg University, Tilburg, The Netherlands
- Translational Neurogenomics Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Y. Milaneschi
- Department of Psychiatry, Amsterdam Neuroscience and Amsterdam Public Health Research Institute, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Z. Gerring
- Translational Neurogenomics Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - P. F. Sullivan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA
| | - E. Schulte
- Medical Centre of the University of Munich, Munich, Germany
| | - N. P. Suppli
- Mental Health Centre Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
| | - J. G. Thorp
- Translational Neurogenomics Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - E. M. Derks
- Translational Neurogenomics Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - C. M. Middeldorp
- Child Health Research Centre, University of Queensland, Brisbane, Australia
- Child and Youth Mental Health Service, Children's Health Queensland Hospital and Health Service, Brisbane, Australia
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
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35
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Smith-Woolley E, Selzam S, Plomin R. Polygenic score for educational attainment captures DNA variants shared between personality traits and educational achievement. J Pers Soc Psychol 2019; 117:1145-1163. [PMID: 30920283 PMCID: PMC6902055 DOI: 10.1037/pspp0000241] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Genome-wide polygenic scores (GPS) can be used to predict individual genetic risk and resilience. For example, a GPS for years of education (EduYears) explains substantial variance in cognitive traits such as general cognitive ability and educational achievement. Personality traits are also known to contribute to individual differences in educational achievement. However, the association between EduYears GPS and personality traits remains largely unexplored. Here, we test the relation between GPS for EduYears, neuroticism, and well-being, and 6 personality and motivation domains: Academic Motivation, Extraversion, Openness, Conscientiousness, Neuroticism, and Agreeableness. The sample was drawn from a U.K.-representative sample of up to 8,322 individuals assessed at age 16. We find that EduYears GPS was positively associated with Openness, Conscientiousness, Agreeableness, and Academic Motivation, predicting between 0.6% and 3% of the variance. In addition, we find that EduYears GPS explains between 8% and 16% of the association between personality domains and educational achievement at the end of compulsory education. In contrast, both the neuroticism and well-being GPS significantly accounted for between 0.3% and 0.7% of the variance in a subset of personality domains. Furthermore, they did not significantly account for any of the covariance between the personality domains and achievement, with the exception of the neuroticism GPS explaining 5% of the covariance between Neuroticism and achievement. These results demonstrate that the genetic effects of educational attainment relate to personality traits, highlighting the multifaceted nature of EduYears GPS. (PsycINFO Database Record (c) 2019 APA, all rights reserved).
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Affiliation(s)
- Emily Smith-Woolley
- King’s College London, MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, London. SE5 8AF, UK
| | - Saskia Selzam
- King’s College London, MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, London. SE5 8AF, UK
| | - Robert Plomin
- King’s College London, MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, London. SE5 8AF, UK
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36
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Ponzi E, Keller LF, Muff S. The simulation extrapolation technique meets ecology and evolution: A general and intuitive method to account for measurement error. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13255] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Erica Ponzi
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
- Department of Biostatistics, Epidemiology, Biostatistics and Prevention Institute University of Zurich Zurich Switzerland
| | - Lukas F. Keller
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
- Zoological Museum University of Zurich Zurich Switzerland
| | - Stefanie Muff
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
- Department of Biostatistics, Epidemiology, Biostatistics and Prevention Institute University of Zurich Zurich Switzerland
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37
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Ong JS, Law MH, An J, Han X, Gharahkhani P, Whiteman DC, Neale RE, MacGregor S. Association between coffee consumption and overall risk of being diagnosed with or dying from cancer among >300 000 UK Biobank participants in a large-scale Mendelian randomization study. Int J Epidemiol 2019; 48:1447-1456. [PMID: 31412118 DOI: 10.1093/ije/dyz144] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Previous observational studies have suggested that coffee intake may be associated with a reduction in cancer risk. Mendelian randomization (MR) studies can help clarify whether the observed associations are likely to be causal. Here we evaluated whether coffee intake is associated with: (i) overall risk of being diagnosed with/dying from any cancer; and (ii) risk of individual cancers. METHODS We identified 46 155 cases (of which 6998 were fatal) and 270 342 controls of White British ancestry from the UK Biobank cohort (UKB), based on ICD10 diagnoses. Individuals with benign tumours were excluded. Coffee intake was self-reported and recorded based on cup/day consumption. We conducted both observational and summary data MR analyses. RESULTS There was no observational association between coffee intake and overall cancer risk [odds ratio (OR) per one cup/day increase = 0.99, 95% confidence interval (CI) 0.98, 1.00] or cancer death (OR = 1.01, 0.99, 1.03); the estimated OR from MR is 1.01 (0.94, 1.08) for overall cancer risk and 1.11 (0.95, 1.31) for cancer death. The relationship between coffee intake and individual cancer risks were consistent with a null effect, with most cancers showing little or no associations with coffee. Meta-analysis of our MR findings with publicly available summary data on various cancers do not support a strong causal relationship between coffee and risk of breast, ovarian, lung or prostate cancer, upon correction for multiple testing. CONCLUSIONS Taken together, coffee intake is not associated with overall risk of being diagnosed with or dying from cancer in UKB. For individual cancers, our findings were not statistically inconsistent with earlier observational studies, although for these we were unable to rule out a small effect on specific types of cancer.
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Affiliation(s)
- Jue-Sheng Ong
- Statistical Genetics, Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Matthew H Law
- Statistical Genetics, Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Jiyuan An
- Statistical Genetics, Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Xikun Han
- Statistical Genetics, Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Puya Gharahkhani
- Statistical Genetics, Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - David C Whiteman
- Cancer Control, Department of Population Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Rachel E Neale
- Cancer Aetiology and Prevention, Department of Population Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Stuart MacGregor
- Statistical Genetics, Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
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38
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Holleman AM, Broadaway KA, Duncan R, Todor A, Almli LM, Bradley B, Ressler KJ, Ghosh D, Mulle JG, Epstein MP. Powerful and Efficient Strategies for Genetic Association Testing of Symptom and Questionnaire Data in Psychiatric Genetic Studies. Sci Rep 2019; 9:7523. [PMID: 31101869 PMCID: PMC6525248 DOI: 10.1038/s41598-019-44046-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 05/01/2019] [Indexed: 11/09/2022] Open
Abstract
Genetic studies of psychiatric disorders often deal with phenotypes that are not directly measurable. Instead, researchers rely on multivariate symptom data from questionnaires and surveys like the PTSD Symptom Scale (PSS) and Beck Depression Inventory (BDI) to indirectly assess a latent phenotype of interest. Researchers subsequently collapse such multivariate questionnaire data into a univariate outcome to represent a surrogate for the latent phenotype. However, when a causal variant is only associated with a subset of collapsed symptoms, the effect will be challenging to detect using the univariate outcome. We describe a more powerful strategy for genetic association testing in this situation that jointly analyzes the original multivariate symptom data collectively using a statistical framework that compares similarity in multivariate symptom-scale data from questionnaires to similarity in common genetic variants across a gene. We use simulated data to demonstrate this strategy provides substantially increased power over standard approaches that collapse questionnaire data into a single surrogate outcome. We also illustrate our approach using GWAS data from the Grady Trauma Project and identify genes associated with BDI not identified using standard univariate techniques. The approach is computationally efficient, scales to genome-wide studies, and is applicable to correlated symptom data of arbitrary dimension.
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Affiliation(s)
- Aaron M Holleman
- Department of Epidemiology, Emory University, Atlanta, GA, USA.,Center for Computational and Quantitative Genetics, Emory University, Atlanta, GA, USA
| | | | - Richard Duncan
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Andrei Todor
- Center for Computational and Quantitative Genetics, Emory University, Atlanta, GA, USA.,Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Lynn M Almli
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Bekh Bradley
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA.,Clinical Psychologist, Mental Health Service Line, Department of Veterans Affairs Medical Center, Atlanta, GA, USA
| | - Kerry J Ressler
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, MA, USA
| | - Debashis Ghosh
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO, USA
| | - Jennifer G Mulle
- Center for Computational and Quantitative Genetics, Emory University, Atlanta, GA, USA.,Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Michael P Epstein
- Center for Computational and Quantitative Genetics, Emory University, Atlanta, GA, USA. .,Department of Human Genetics, Emory University, Atlanta, GA, USA.
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Mishra A, Chauhan G, Violleau MH, Vojinovic D, Jian X, Bis JC, Li S, Saba Y, Grenier-Boley B, Yang Q, Bartz TM, Hofer E, Soumaré A, Peng F, Duperron MG, Foglio M, Mosley TH, Schmidt R, Psaty BM, Launer LJ, Boerwinkle E, Zhu Y, Mazoyer B, Lathrop M, Bellenguez C, Van Duijn CM, Ikram MA, Schmidt H, Longstreth WT, Fornage M, Seshadri S, Joutel A, Tzourio C, Debette S. Association of variants in HTRA1 and NOTCH3 with MRI-defined extremes of cerebral small vessel disease in older subjects. Brain 2019; 142:1009-1023. [PMID: 30859180 PMCID: PMC6439324 DOI: 10.1093/brain/awz024] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 11/30/2018] [Accepted: 12/21/2018] [Indexed: 12/20/2022] Open
Abstract
We report a composite extreme phenotype design using distribution of white matter hyperintensities and brain infarcts in a population-based cohort of older persons for gene-mapping of cerebral small vessel disease. We demonstrate its application in the 3C-Dijon whole exome sequencing (WES) study (n = 1924, nWESextremes = 512), with both single variant and gene-based association tests. We used other population-based cohort studies participating in the CHARGE consortium for replication, using whole exome sequencing (nWES = 2,868, nWESextremes = 956) and genome-wide genotypes (nGW = 9924, nGWextremes = 3308). We restricted our study to candidate genes known to harbour mutations for Mendelian small vessel disease: NOTCH3, HTRA1, COL4A1, COL4A2 and TREX1. We identified significant associations of a common intronic variant in HTRA1, rs2293871 using single variant association testing (Pdiscovery = 8.21 × 10-5, Preplication = 5.25 × 10-3, Pcombined = 4.72 × 10-5) and of NOTCH3 using gene-based tests (Pdiscovery = 1.61 × 10-2, Preplication = 3.99 × 10-2, Pcombined = 5.31 × 10-3). Follow-up analysis identified significant association of rs2293871 with small vessel ischaemic stroke, and two blood expression quantitative trait loci of HTRA1 in linkage disequilibrium. Additionally, we identified two participants in the 3C-Dijon cohort (0.4%) carrying heterozygote genotypes at known pathogenic variants for familial small vessel disease within NOTCH3 and HTRA1. In conclusion, our proof-of-concept study provides strong evidence that using a novel composite MRI-derived phenotype for extremes of small vessel disease can facilitate the identification of genetic variants underlying small vessel disease, both common variants and those with rare and low frequency. The findings demonstrate shared mechanisms and a continuum between genes underlying Mendelian small vessel disease and those contributing to the common, multifactorial form of the disease.
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Affiliation(s)
- Aniket Mishra
- University of Bordeaux, Inserm, Bordeaux Population Health Research Center, team VINTAGE, UMR 1219, F-33000 Bordeaux, France
| | - Ganesh Chauhan
- University of Bordeaux, Inserm, Bordeaux Population Health Research Center, team VINTAGE, UMR 1219, F-33000 Bordeaux, France
- Centre for Brain Research, Indian Institute of Science, Bangalore, India
| | - Marie-Helene Violleau
- University of Bordeaux, Inserm, Bordeaux Population Health Research Center, team VINTAGE, UMR 1219, F-33000 Bordeaux, France
| | - Dina Vojinovic
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Xueqiu Jian
- The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Joshua C Bis
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Shuo Li
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Yasaman Saba
- Gottfried Schatz Research Center, Department of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Benjamin Grenier-Boley
- Inserm, U1167, RID-AGE - Risk factors and molecular determinants of aging-related diseases, F-59000 Lille, France
- Institut Pasteur de Lille, F-59000 Lille, France
- Univ. Lille, U1167 - Excellence Laboratory LabEx DISTALZ, F-59000 Lille, France
| | - Qiong Yang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Traci M Bartz
- Cardiovascular Health Research Unit, Departments of Biostatistics and Medicine, University of Washington, Seattle, WA, USA
| | - Edith Hofer
- Clinical Division of Neurogeriatrics, Department of Neurology, Medical University of Graz, Austria
- Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Austria
| | - Aïcha Soumaré
- University of Bordeaux, Inserm, Bordeaux Population Health Research Center, team VINTAGE, UMR 1219, F-33000 Bordeaux, France
| | - Fen Peng
- The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Marie-Gabrielle Duperron
- University of Bordeaux, Inserm, Bordeaux Population Health Research Center, team VINTAGE, UMR 1219, F-33000 Bordeaux, France
| | - Mario Foglio
- University of McGill Genome Center, Montreal, Canada
| | - Thomas H Mosley
- Division of Geriatrics, School of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
- Memory Impairment and Neurodegenerative Dementia Center, University of Mississippi Medical Center, Jackson, MS, USA
| | - Reinhold Schmidt
- Clinical Division of Neurogeriatrics, Department of Neurology, Medical University of Graz, Austria
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Health Services, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Lenore J Launer
- Intramural Research Program, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Eric Boerwinkle
- The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Yicheng Zhu
- Department of Neurology, Peking Union Medical College Hospital, Beijing, China
| | - Bernard Mazoyer
- University of Bordeaux, Institut des Maladies Neurodégénératives, CNRS-CEA UMR 5293, France
| | - Mark Lathrop
- University of McGill Genome Center, Montreal, Canada
| | - Celine Bellenguez
- Inserm, U1167, RID-AGE - Risk factors and molecular determinants of aging-related diseases, F-59000 Lille, France
- Institut Pasteur de Lille, F-59000 Lille, France
- Univ. Lille, U1167 - Excellence Laboratory LabEx DISTALZ, F-59000 Lille, France
| | - Cornelia M Van Duijn
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
- Department of Radiology and Nuclear Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Helena Schmidt
- Gottfried Schatz Research Center, Department of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - W T Longstreth
- Department of Neurology and Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Myriam Fornage
- The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Sudha Seshadri
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health Sciences Center, San Antonio, Texas, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Anne Joutel
- Institute of Psychiatry and Neurosciences of Paris, Inserm, University Paris Descartes, DHU NeuroVasc, Sorbonne Paris Cité, Paris, France
| | - Christophe Tzourio
- University of Bordeaux, Inserm, Bordeaux Population Health Research Center, team VINTAGE, UMR 1219, F-33000 Bordeaux, France
- CHU de Bordeaux, Pole de santé publique, Service d’information médicale, F-33000 Bordeaux, France
| | - Stephanie Debette
- University of Bordeaux, Inserm, Bordeaux Population Health Research Center, team VINTAGE, UMR 1219, F-33000 Bordeaux, France
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- CHU de Bordeaux, Department of Neurology, F-33000 Bordeaux, France
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Langevin S, Mascheretti S, Côté SM, Vitaro F, Boivin M, Turecki G, Tremblay RE, Ouellet-Morin I. Cumulative risk and protection effect of serotonergic genes on male antisocial behaviour: results from a prospective cohort assessed in adolescence and early adulthood. Br J Psychiatry 2019; 214:137-145. [PMID: 30774060 DOI: 10.1192/bjp.2018.251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
BACKGROUND Heritability of antisocial behaviour is estimated at approximately 50% and involves multiple genes.AimsTo investigate the cumulative genetic effects of 116 single nucleotide polymorphisms mapping to 11 candidate serotonergic genes and antisocial behaviours, in adolescence and in early adulthood. METHOD Participants were 410 male members of the Quebec Longitudinal Study of Kindergarten Children, a population-based cohort followed up prospectively from age 6 to age 23. The serotonergic genes were selected based on known physiological processes and prior associations with antisocial behaviours. Antisocial behaviours were self-reported and assessed by using semi-structured interviews in adolescence and in adulthood. RESULTS Cumulative, haplotype-based contributions of serotonergic genes conferring risk and protection for antisocial behaviours were detected by using multilocus genetic profile risk scores (MGPRSs) and multilocus genetic profile protection scores (MGPPSs). Cumulatively, haplotype-based MGPRSs and MGPPSs contributed to 9.6, 8.5 and 15.2% of the variance in general delinquency in adolescence, property/violent crimes in early adulthood and physical partner violence in early adulthood, respectively. CONCLUSIONS This study extends previous research by showing a cumulative effect of multiple haplotypes conferring risk and protection to antisocial behaviours in adolescence and early adulthood. The findings further support the relevance of concomitantly considering multiple serotonergic polymorphisms to better understand the genetic aetiology of antisocial behaviours. Future studies should investigate the interplay between risk and protective haplotype-based multilocus genetic profile scores with the environment. DECLARATION OF INTEREST I.O.-M. holds a Canada Research Chair in the developmental origins of vulnerability and resilience.
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Affiliation(s)
- Stephanie Langevin
- School of Criminology,University of Montreal and The Montreal Mental Health University Institute,Canada
| | - Sara Mascheretti
- Centre-affiliated Researcher,Child Psychopathology Unit,Scientific Institute, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Eugenio Medea,Italy
| | - Sylvana M Côté
- Full Professor,School of Public Health, University of Montreal, Canada and Bordeaux Population Health Inserm 1219, University of Bordeaux,France
| | - Frank Vitaro
- Full Professor,School of Psychoeducation,University of Montreal,Canada
| | - Michel Boivin
- Full Professor,School of Psychology, Laval University,Canada
| | - Gustavo Turecki
- Full Professor,McGill Group for Suicide Studies,Douglas Mental Health University Institute and McGill University,Canada
| | - Richard E Tremblay
- Emeritus Professor,Psychology Department,University of Montreal,Canadaand School of Public Health,University College Dublin,Ireland
| | - Isabelle Ouellet-Morin
- Associate Professor,School of Criminology,University of Montreal and The Montreal Mental Health University Institute,Canada
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41
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Kievit RA, Brandmaier AM, Ziegler G, van Harmelen AL, de Mooij SMM, Moutoussis M, Goodyer IM, Bullmore E, Jones PB, Fonagy P, Lindenberger U, Dolan RJ. Developmental cognitive neuroscience using latent change score models: A tutorial and applications. Dev Cogn Neurosci 2018; 33:99-117. [PMID: 29325701 PMCID: PMC6614039 DOI: 10.1016/j.dcn.2017.11.007] [Citation(s) in RCA: 229] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 10/17/2017] [Accepted: 11/17/2017] [Indexed: 12/14/2022] Open
Abstract
Assessing and analysing individual differences in change over time is of central scientific importance to developmental neuroscience. However, the literature is based largely on cross-sectional comparisons, which reflect a variety of influences and cannot directly represent change. We advocate using latent change score (LCS) models in longitudinal samples as a statistical framework to tease apart the complex processes underlying lifespan development in brain and behaviour using longitudinal data. LCS models provide a flexible framework that naturally accommodates key developmental questions as model parameters and can even be used, with some limitations, in cases with only two measurement occasions. We illustrate the use of LCS models with two empirical examples. In a lifespan cognitive training study (COGITO, N = 204 (N = 32 imaging) on two waves) we observe correlated change in brain and behaviour in the context of a high-intensity training intervention. In an adolescent development cohort (NSPN, N = 176, two waves) we find greater variability in cortical thinning in males than in females. To facilitate the adoption of LCS by the developmental community, we provide analysis code that can be adapted by other researchers and basic primers in two freely available SEM software packages (lavaan and Ωnyx).
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Affiliation(s)
- Rogier A Kievit
- Max Planck Centre for Computational Psychiatry and Ageing Research, London/Berlin; MRC Cognition and Brain Sciences Unit University of Cambridge, Cambridge, 15 Chaucer Rd, Cambridge CB2 7EF.
| | - Andreas M Brandmaier
- Max Planck Centre for Computational Psychiatry and Ageing Research, London/Berlin; Center for Lifespan Psychology, Max Planck Institute for Human Development, Berlin, Germany
| | - Gabriel Ziegler
- Institute of Cognitive Neurology and Dementia Research, Otto-von-Guericke-University Magdeburg, Germany; German Center for Neurodegenerative Diseases (DZNE), Magdeburg, Germany
| | | | | | - Michael Moutoussis
- Max Planck Centre for Computational Psychiatry and Ageing Research, London/Berlin; The Wellcome Centre for Human Neuroimaging, University College London, London WC1N 3BG, United Kingdom
| | - Ian M Goodyer
- Department of Psychiatry, University of Cambridge, United Kingdom
| | - Ed Bullmore
- Department of Psychiatry, University of Cambridge, United Kingdom; Cambridgeshire and Peterborough National Health Service Foundation Trust, Cambridge, CB21 5EF, United Kingdom; ImmunoPsychiatry, GlaxoSmithKline Research and Development, Stevenage SG1 2NY, United Kingdom; Medical Research Council/Wellcome Trust Behavioural and Clinical Neuroscience Institute, University of Cambridge
| | - Peter B Jones
- Department of Psychiatry, University of Cambridge, United Kingdom; Cambridgeshire and Peterborough National Health Service Foundation Trust, Cambridge, CB21 5EF, United Kingdom
| | - Peter Fonagy
- Research Department of Clinical, Educational and Health Psychology, University College London
| | - Ulman Lindenberger
- Max Planck Centre for Computational Psychiatry and Ageing Research, London/Berlin; Center for Lifespan Psychology, Max Planck Institute for Human Development, Berlin, Germany; European University Institute, San Domenico di Fiesole (FI), Italy
| | - Raymond J Dolan
- Max Planck Centre for Computational Psychiatry and Ageing Research, London/Berlin; The Wellcome Centre for Human Neuroimaging, University College London, London WC1N 3BG, United Kingdom
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Ponzi E, Keller LF, Bonnet T, Muff S. Heritability, selection, and the response to selection in the presence of phenotypic measurement error: Effects, cures, and the role of repeated measurements. Evolution 2018; 72:1992-2004. [DOI: 10.1111/evo.13573] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 07/12/2018] [Accepted: 07/12/2018] [Indexed: 02/02/2023]
Affiliation(s)
- Erica Ponzi
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZürichWinterthurerstrasse 190 8057 Zürich Switzerland
- Department of Biostatistics, Epidemiology, Biostatistics and Prevention InstituteUniversity of ZürichHirschengraben 84 8001 Zürich Switzerland
| | - Lukas F. Keller
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZürichWinterthurerstrasse 190 8057 Zürich Switzerland
- Zoological MuseumUniversity of ZürichKarl‐Schmid‐Strasse 4 8006 Zürich Switzerland
| | - Timothée Bonnet
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZürichWinterthurerstrasse 190 8057 Zürich Switzerland
- Division of Ecology and Evolution, Research School of BiologyThe Australian National UniversityActon Canberra ACT 2601 Australia
| | - Stefanie Muff
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZürichWinterthurerstrasse 190 8057 Zürich Switzerland
- Department of Biostatistics, Epidemiology, Biostatistics and Prevention InstituteUniversity of ZürichHirschengraben 84 8001 Zürich Switzerland
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43
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Investigation of the CADM2 polymorphism rs17518584 in memory and executive functions measures in a cohort of young healthy individuals. Neurobiol Learn Mem 2018; 155:330-336. [PMID: 30125698 DOI: 10.1016/j.nlm.2018.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 07/04/2018] [Accepted: 08/02/2018] [Indexed: 11/22/2022]
Abstract
The common polymorphism rs17518584, near the cell adhesion molecule 2 gene (CADM2), was previously identified as playing a role in information processing speed in a genome-wide association study of executive functions and processing speed performed in a cohort of non-demented older adults. In this study, we investigated this polymorphism in a younger population cohort (≤30 years old, median age 19 years), with no known memory or psychiatric disorders, for which we had phenotyped all participants for memory function (n = 514), and a subset of the participants for executive functions (n = 338), using a battery of tests measuring visuo-spatial memory, working memory, verbal memory, and frontal lobe functions (visual scanning, graphomotor speed, and cognitive flexibility). The polymorphism rs17518584 was genotyped by a restriction fragment length polymorphism assay and analysis indicated that the CADM2 polymorphism showed evidence of association with information processing speed as inferred from scores from the Stroop Word, Colour, and Colour-Word Tests (p = 0.005, p = 0.04, and p = 0.028, respectively, in a dominant inheritance model), as well as Trail Making Test Part A (p = 0.005 in an additive model). Significant associations of rs17518584 with scores from other tests of memory subtypes were not detected. The findings of this study provide further support for a role of CADM2 in aspects of cognitive function, in particular reading and information processing speed, and suggest that this role extends to younger individuals.
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Nagel M, Watanabe K, Stringer S, Posthuma D, van der Sluis S. Item-level analyses reveal genetic heterogeneity in neuroticism. Nat Commun 2018; 9:905. [PMID: 29500382 PMCID: PMC5834468 DOI: 10.1038/s41467-018-03242-8] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 01/29/2018] [Indexed: 12/23/2022] Open
Abstract
Genome-wide association studies (GWAS) of psychological traits are generally conducted on (dichotomized) sums of items or symptoms (e.g., case-control status), and not on the individual items or symptoms themselves. We conduct large-scale GWAS on 12 neuroticism items and observe notable and replicable variation in genetic signal between items. Within samples, genetic correlations among the items range between 0.38 and 0.91 (mean rg = .63), indicating genetic heterogeneity in the full item set. Meta-analyzing the two samples, we identify 255 genome-wide significant independent genomic regions, of which 138 are item-specific. Genetic analyses and genetic correlations with 33 external traits support genetic differences between the items. Hierarchical clustering analysis identifies two genetically homogeneous item clusters denoted depressed affect and worry. We conclude that the items used to measure neuroticism are genetically heterogeneous, and that biological understanding can be gained by studying them in genetically more homogeneous clusters.
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Affiliation(s)
- Mats Nagel
- Department of Clinical Genetics, Section Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU Medical Centre, Amsterdam, 1081 HV, The Netherlands
| | - Kyoko Watanabe
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, 1081 HV, The Netherlands
| | - Sven Stringer
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, 1081 HV, The Netherlands
| | - Danielle Posthuma
- Department of Clinical Genetics, Section Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU Medical Centre, Amsterdam, 1081 HV, The Netherlands.
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, 1081 HV, The Netherlands.
| | - Sophie van der Sluis
- Department of Clinical Genetics, Section Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU Medical Centre, Amsterdam, 1081 HV, The Netherlands.
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Abstract
Does general intelligence exist across species, and has it been a target of natural selection? These questions can be addressed with genomic data, which can rule out artifacts by demonstrating that distinct cognitive abilities are genetically correlated and thus share a biological substrate. This work has begun with data from humans and can be extended to other species; it should focus not only on general intelligence but also specific capacities like language and spatial ability.
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46
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Cheesman R, Selzam S, Ronald A, Dale PS, McAdams TA, Eley TC, Plomin R. Childhood behaviour problems show the greatest gap between DNA-based and twin heritability. Transl Psychiatry 2017; 7:1284. [PMID: 29234009 PMCID: PMC5802501 DOI: 10.1038/s41398-017-0046-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 09/07/2017] [Accepted: 09/13/2017] [Indexed: 12/22/2022] Open
Abstract
For most complex traits, DNA-based heritability ('SNP heritability') is roughly half that of twin-based heritability. A previous report from the Twins Early Development Study suggested that this heritability gap is much greater for childhood behaviour problems than for other domains. If true, this finding is important because SNP heritability, not twin heritability, is the ceiling for genome-wide association studies. With twice the sample size as the previous report, we estimated SNP heritabilities (N up to 4653 unrelated individuals) and compared them with twin heritabilities from the same sample (N up to 4724 twin pairs) for diverse domains of childhood behaviour problems as rated by parents, teachers, and children themselves at ages 12 and 16. For 37 behaviour problem measures, the average twin heritability was 0.52, whereas the average SNP heritability was just 0.06. In contrast, results for cognitive and anthropometric traits were more typical (average twin and SNP heritabilities were 0.58 and 0.28, respectively). Future research should continue to investigate the reasons why SNP heritabilities for childhood behaviour problems are so low compared with twin estimates, and find ways to maximise SNP heritability for genome-wide association studies.
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Affiliation(s)
- Rosa Cheesman
- King's College London, Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, London, UK.
| | - Saskia Selzam
- King's College London, Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Angelica Ronald
- Department of Psychological Sciences, Birkbeck, University of London, London, UK
| | - Philip S Dale
- Department of Speech and Hearing Sciences, University of New Mexico, Albuquerque, NM, USA
| | - Tom A McAdams
- King's College London, Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Thalia C Eley
- King's College London, Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Robert Plomin
- King's College London, Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, London, UK
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47
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Bearden CE, Glahn DC. Cognitive genomics: Searching for the genetic roots of neuropsychological functioning. Neuropsychology 2017; 31:1003-1019. [PMID: 29376674 PMCID: PMC5791763 DOI: 10.1037/neu0000412] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
OBJECTIVE Human cognition has long been known to be under substantial genetic control. With the complete mapping of the human genome, genome-wide association studies for many complex traits have proliferated; however, the highly polygenic nature of intelligence has made the identification of the precise genes that influence both global and specific cognitive abilities more difficult than anticipated. METHOD Here, we review the latest developments in the genomics of cognition, including a discussion of methodological advances in the genetic analysis of complex traits, and shared genetic contributions to cognitive abilities and neuropsychiatric disorders. RESULTS A wealth of twin and family studies have provided compelling evidence for a strong heritable component of both global and specific cognitive abilities, and for the existence of "generalist genes" responsible for a large portion of the variance in diverse cognitive abilities. Increasingly sophisticated analytic tools and ever-larger sample sizes are now facilitating the identification of specific genetic and molecular underpinnings of cognitive abilities, leading to optimism regarding possibilities for novel treatments for illnesses related to cognitive function. CONCLUSIONS We conclude with a set of future directions for the field, which will further accelerate discoveries regarding the biological pathways relevant to cognitive abilities. These, in turn, may be further interrogated in order to link biological mechanisms to behavior. (PsycINFO Database Record
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Affiliation(s)
- Carrie E Bearden
- Department of Psychiatry, University of California at Los Angeles
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48
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Xu MK, Gaysina D, Tsonaka R, Morin AJS, Croudace TJ, Barnett JH, Houwing-Duistermaat J, Richards M, Jones PB. Monoamine Oxidase A ( MAOA) Gene and Personality Traits from Late Adolescence through Early Adulthood: A Latent Variable Investigation. Front Psychol 2017; 8:1736. [PMID: 29075213 PMCID: PMC5641687 DOI: 10.3389/fpsyg.2017.01736] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 09/20/2017] [Indexed: 11/13/2022] Open
Abstract
Very few molecular genetic studies of personality traits have used longitudinal phenotypic data, therefore molecular basis for developmental change and stability of personality remains to be explored. We examined the role of the monoamine oxidase A gene (MAOA) on extraversion and neuroticism from adolescence to adulthood, using modern latent variable methods. A sample of 1,160 male and 1,180 female participants with complete genotyping data was drawn from a British national birth cohort, the MRC National Survey of Health and Development (NSHD). The predictor variable was based on a latent variable representing genetic variations of the MAOA gene measured by three SNPs (rs3788862, rs5906957, and rs979606). Latent phenotype variables were constructed using psychometric methods to represent cross-sectional and longitudinal phenotypes of extraversion and neuroticism measured at ages 16 and 26. In males, the MAOA genetic latent variable (AAG) was associated with lower extraversion score at age 16 (β = −0.167; CI: −0.289, −0.045; p = 0.007, FDRp = 0.042), as well as greater increase in extraversion score from 16 to 26 years (β = 0.197; CI: 0.067, 0.328; p = 0.003, FDRp = 0.036). No genetic association was found for neuroticism after adjustment for multiple testing. Although, we did not find statistically significant associations after multiple testing correction in females, this result needs to be interpreted with caution due to issues related to x-inactivation in females. The latent variable method is an effective way of modeling phenotype- and genetic-based variances and may therefore improve the methodology of molecular genetic studies of complex psychological traits.
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Affiliation(s)
- Man K Xu
- Faculty of Psychology and Educational Sciences, Welten Institute, Open University of the Netherlands, Heerlen, Netherlands.,Department of Medical Statistics and Bioinformatics, Leiden University Medical Centre, Leiden, Netherlands.,Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom.,Department of Psychology, Education, and Child Studies, Erasmus University Rotterdam, Rotterdam, Netherlands
| | - Darya Gaysina
- EDGE Lab, School of Psychology, University of Sussex, Brighton, United Kingdom
| | - Roula Tsonaka
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Centre, Leiden, Netherlands
| | - Alexandre J S Morin
- Substantive-Methodological Synergy Research Laboratory, Department of Psychology, Concordia University, Montreal, QC, Canada
| | - Tim J Croudace
- School of Nursing and Health Sciences, University of Dundee, Dundee, United Kingdom
| | | | | | - Marcus Richards
- MRC Unit for Lifelong Health and Ageing at UCL, London, United Kingdom
| | - Peter B Jones
- Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
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Alzheimer's Disease Sequencing Project discovery and replication criteria for cases and controls: Data from a community-based prospective cohort study with autopsy follow-up. Alzheimers Dement 2017; 13:1410-1413. [PMID: 29055816 DOI: 10.1016/j.jalz.2017.09.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 05/30/2017] [Accepted: 09/20/2017] [Indexed: 11/23/2022]
Abstract
INTRODUCTION The Alzheimer's Disease Sequencing Project (ADSP) used different criteria for assigning case and control status from the discovery and replication phases of the project. We considered data from a community-based prospective cohort study with autopsy follow-up where participants could be categorized as case, control, or neither by both definitions and compared the two sets of criteria. METHODS We used data from the Adult Changes in Thought (ACT) study including Diagnostic and Statistical Manual-IV criteria for dementia status, McKhann et al. criteria for clinical Alzheimer's disease, and Braak and Consortium to Establish a Registry for AD findings on neurofibrillary tangles and neuritic plaques to categorize the 621 ACT participants of European ancestry who died and came to autopsy. We applied ADSP discovery and replication definitions to identify controls, cases, and people who were neither controls nor cases. RESULTS There was some agreement between the discovery and replication definitions. Major areas of discrepancy included the finding that only 40% of the discovery sample controls had sufficiently low levels of neurofibrillary tangles and neuritic plaques to be considered controls by the replication criteria and the finding that 16% of the replication phase cases were diagnosed with non-AD dementia during life and thus were excluded as cases for the discovery phase. CONCLUSIONS These findings should inform interpretation of genetic association findings from the ADSP. Differences in genetic association findings between the two phases of the study may reflect these different phenotype definitions from the discovery and replication phase of the ADSP.
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Genome-wide analysis of health-related biomarkers in the UK Household Longitudinal Study reveals novel associations. Sci Rep 2017; 7:11008. [PMID: 28887542 PMCID: PMC5591265 DOI: 10.1038/s41598-017-10812-1] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/08/2017] [Indexed: 11/24/2022] Open
Abstract
Serum biomarker levels are associated with the risk of complex diseases. Here, we aimed to gain insights into the genetic architecture of biomarker traits which can reflect health status. We performed genome-wide association analyses for twenty serum biomarkers involved in organ function and reproductive health. 9,961 individuals from the UK Household Longitudinal Study were genotyped using the Illumina HumanCoreExome array and variants imputed to the 1000 Genomes Project and UK10K haplotypes. We establish a polygenic heritability for all biomarkers, confirm associations of fifty-four established loci, and identify five novel, replicating associations at genome-wide significance. A low-frequency variant, rs28929474, (beta = 0.04, P = 2 × 10−10) was associated with levels of alanine transaminase, an indicator of liver damage. The variant is located in the gene encoding serine protease inhibitor, low levels of which are associated with alpha-1 antitrypsin deficiency which leads to liver disease. We identified novel associations (rs78900934, beta = 0.05, P = 6 × 10−12; rs2911280, beta = 0.09, P = 6 × 10−10) for dihydroepiandrosterone sulphate, a precursor to major sex-hormones, and for glycated haemoglobin (rs12819124, beta = −0.03, P = 4 × 10−9; rs761772, beta = 0.05, P = 5 × 10−9). rs12819124 is nominally associated with risk of type 2 diabetes. Our study offers insights into the genetic architecture of well-known and less well-studied biomarkers.
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