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Yuan L, Li D, Tian Y, Sun Y. Greenness, Genetic Predisposition, and Tinnitus. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306706. [PMID: 38445888 PMCID: PMC11077638 DOI: 10.1002/advs.202306706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/19/2024] [Indexed: 03/07/2024]
Abstract
This study aimed to investigate the association between residential greenness and tinnitus and the potential interaction between greenness and genetic predisposition to tinnitus. The normalized difference vegetation index (NDVI) is used to measure residential greenness. The tinnitus is defined based on self-reported. In the cross-sectional analyses, logistic regression models are used for the baseline sample of the United Kingdom Biobank cohort. In the secondary analysis, a Cox proportional hazard model is used for a subsample of participants who completed the tinnitus questionnaire at follow-up. In the cross-sectional analysis including 106471 participants, higher residential greenness is associated with lower odds of tinnitus for each interquartile range increase in continuous NDVI, with an adjusted odds ratio of 0.97 (95% confidence interval: 0.95 to 0.99) for tinnitus. A similar association is observed in the longitudinal analysis, with an adjusted hazard ratio of 0.92 (95% confidence interval: 0.86 to 0.98) for the association of NDVI increased per interquartile range with incident tinnitus. Moreover, there is a significant interaction between greenness and genetic predisposition to tinnitus (P < 0.05). This study suggested that residential greenness is negatively associated with tinnitus. Greenness and genetic predisposition to tinnitus are found to have a significant interaction.
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Affiliation(s)
- Lan‐Lai Yuan
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhan430022China
| | - Dan‐Kang Li
- Ministry of Education Key Laboratory of Environment and Healthand State Key Laboratory of Environmental Health (Incubating)School of Public HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
- Department of Maternal and Child Health, School of Public Health, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
| | - Yao‐Hua Tian
- Ministry of Education Key Laboratory of Environment and Healthand State Key Laboratory of Environmental Health (Incubating)School of Public HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
- Department of Maternal and Child Health, School of Public Health, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
| | - Yu Sun
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhan430022China
- Institute of Otorhinolaryngology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhan430022China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and RegenerationWuhan430022China
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Zhai S, Mehrotra DV, Shen J. Applying polygenic risk score methods to pharmacogenomics GWAS: challenges and opportunities. Brief Bioinform 2023; 25:bbad470. [PMID: 38152980 PMCID: PMC10782924 DOI: 10.1093/bib/bbad470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 11/20/2023] [Accepted: 11/28/2023] [Indexed: 12/29/2023] Open
Abstract
Polygenic risk scores (PRSs) have emerged as promising tools for the prediction of human diseases and complex traits in disease genome-wide association studies (GWAS). Applying PRSs to pharmacogenomics (PGx) studies has begun to show great potential for improving patient stratification and drug response prediction. However, there are unique challenges that arise when applying PRSs to PGx GWAS beyond those typically encountered in disease GWAS (e.g. Eurocentric or trans-ethnic bias). These challenges include: (i) the lack of knowledge about whether PGx or disease GWAS/variants should be used in the base cohort (BC); (ii) the small sample sizes in PGx GWAS with corresponding low power and (iii) the more complex PRS statistical modeling required for handling both prognostic and predictive effects simultaneously. To gain insights in this landscape about the general trends, challenges and possible solutions, we first conduct a systematic review of both PRS applications and PRS method development in PGx GWAS. To further address the challenges, we propose (i) a novel PRS application strategy by leveraging both PGx and disease GWAS summary statistics in the BC for PRS construction and (ii) a new Bayesian method (PRS-PGx-Bayesx) to reduce Eurocentric or cross-population PRS prediction bias. Extensive simulations are conducted to demonstrate their advantages over existing PRS methods applied in PGx GWAS. Our systematic review and methodology research work not only highlights current gaps and key considerations while applying PRS methods to PGx GWAS, but also provides possible solutions for better PGx PRS applications and future research.
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Affiliation(s)
- Song Zhai
- Biostatistics and Research Decision Sciences, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Devan V Mehrotra
- Biostatistics and Research Decision Sciences, Merck & Co., Inc., North Wales, PA 19454, USA
| | - Judong Shen
- Biostatistics and Research Decision Sciences, Merck & Co., Inc., Rahway, NJ 07065, USA
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A Theory-Informed Systematic Review of Barriers and Enablers to Implementing Multi-Drug Pharmacogenomic Testing. J Pers Med 2022; 12:jpm12111821. [PMID: 36579514 PMCID: PMC9696651 DOI: 10.3390/jpm12111821] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/20/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022] Open
Abstract
PGx testing requires a complex set of activities undertaken by practitioners and patients, resulting in varying implementation success. This systematic review aimed (PROSPERO: CRD42019150940) to identify barriers and enablers to practitioners and patients implementing pharmacogenomic testing. We followed PRISMA guidelines to conduct and report this review. Medline, EMBASE, CINAHL, PsycINFO, and PubMed Central were systematically searched from inception to June 2022. The theoretical domain framework (TDF) guided the organisation and reporting of barriers or enablers relating to pharmacogenomic testing activities. From the twenty-five eligible reports, eleven activities were described relating to four implementation stages: ordering, facilitating, interpreting, and applying pharmacogenomic testing. Four themes were identified across the implementation stages: IT infrastructure, effort, rewards, and unknown territory. Barriers were most consistently mapped to TDF domains: memory, attention and decision-making processes, environmental context and resources, and belief about consequences.
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Fusar-Poli L, Rutten BPF, van Os J, Aguglia E, Guloksuz S. Polygenic risk scores for predicting outcomes and treatment response in psychiatry: hope or hype? Int Rev Psychiatry 2022; 34:663-675. [PMID: 36786114 DOI: 10.1080/09540261.2022.2101352] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Over the last years, the decreased costs and enhanced accessibility to large genome-wide association studies datasets have laid the foundations for the development of polygenic risk scores (PRSs). A PRS is calculated on the weighted sum of single nucleotide polymorphisms and measures the individual genetic predisposition to develop a certain phenotype. An increasing number of studies have attempted to utilize the PRSs for risk stratification and prognostic evaluation. The present narrative review aims to discuss the potential clinical utility of PRSs in predicting outcomes and treatment response in psychiatry. After summarizing the evidence on major mental disorders, we have discussed the advantages and limitations of currently available PRSs. Although PRSs represent stable trait features with a normal distribution in the general population and can be relatively easily calculated in terms of time and costs, their real-world applicability is reduced by several limitations, such as low predictive power and lack of population diversity. Even with the rapid expansion of the psychiatric genetic knowledge base, pure genetic prediction in clinical psychiatry appears to be out of reach in the near future. Therefore, combining genomic and exposomic vulnerabilities for mental disorders with a detailed clinical characterization is needed to personalize care.
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Affiliation(s)
- Laura Fusar-Poli
- Department of Clinical and Experimental Medicine, Psychiatry Unit, University of Catania, Catania, Italy
| | - Bart P F Rutten
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Jim van Os
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University Medical Centre, Maastricht, the Netherlands.,UMC Utrecht Brain Centre, University Medical Centre Utrecht, Utrecht University, Utrecht, the Netherlands.,Department of Psychosis Studies, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Eugenio Aguglia
- Department of Clinical and Experimental Medicine, Psychiatry Unit, University of Catania, Catania, Italy
| | - Sinan Guloksuz
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University Medical Centre, Maastricht, the Netherlands.,Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
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Ricardo-Silgado ML, Singh S, Cifuentes L, Decker PA, Gonzalez-Izundegui D, Moyer AM, Hurtado MD, Camilleri M, Bielinski SJ, Acosta A. Association between CYP metabolizer phenotypes and selective serotonin reuptake inhibitors induced weight gain: a retrospective cohort study. BMC Med 2022; 20:261. [PMID: 35879764 PMCID: PMC9317126 DOI: 10.1186/s12916-022-02433-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 06/13/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Prescription medications such as selective serotonin reuptake inhibitors (SSRIs), commonly used to treat depression, are associated with weight gain. The role of pharmacogenomics in predicting SSRI-induced weight gain is unclear. METHODS In this retrospective cohort study from participants in the Mayo Clinic RIGHT study who were prescribed citalopram, paroxetine, sertraline, or fluoxetine, our aim was to evaluate the association of metabolizer phenotype and total body weight after 6 months of SSRIs initiation. We evaluated the metabolizer phenotypes (poor/intermediate, normal, and rapid/ultra-rapid) of the cytochromes P450 enzymes genes: CYP2C9, CYP2C19, and CYP2D6 known to influence the metabolism of SSRI medications: CYP2C19 for citalopram, CYP2D6 for paroxetine, CYP2D6 and CYP2C19 for sertraline, and CYP2D6 and CYP2C9 fluoxetine. In addition, we assessed the association of metabolizer phenotype and total body weight change at six months following SSRI prescription using parametric analysis of covariance adjusted for baseline body weight and multivariate regression models. RESULTS CYP2C19 poor/intermediate metabolizers prescribed citalopram gained significantly more weight than normal or rapid/ultra-rapid metabolizers at 6 months (TBWG %: 2.6 [95% CI 1.3-4.1] vs. 0.4 [95% CI -0.5 - 1.3] vs. -0.1 [-95% CI -1.5-1.1]; p = 0.001). No significant differences in weight outcomes at six months of treatment with paroxetine, sertraline, or fluoxetine were observed by metabolizer status. CONCLUSIONS Weight gain observed with citalopram may be mediated by CYP2C19 metabolizer status.
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Affiliation(s)
- Maria L Ricardo-Silgado
- Precision Medicine for Obesity Program and Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Sneha Singh
- Precision Medicine for Obesity Program and Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Lizeth Cifuentes
- Precision Medicine for Obesity Program and Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Paul A Decker
- Division of Epidemiology, Department of Quantitative Health Research, Mayo Clinic, Rochester, MN, USA
| | - Daniel Gonzalez-Izundegui
- Precision Medicine for Obesity Program and Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ann M Moyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, MN, USA
| | - Maria D Hurtado
- Precision Medicine for Obesity Program and Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA.,Division of Endocrinology, Diabetes, Metabolism, and Nutrition, Department of Medicine, Mayo Clinic Health System, La Crosse, WI, USA
| | - Michael Camilleri
- Precision Medicine for Obesity Program and Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Suzette J Bielinski
- Division of Epidemiology, Department of Quantitative Health Research, Mayo Clinic, Rochester, MN, USA
| | - Andres Acosta
- Precision Medicine for Obesity Program and Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA.
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García-Marín LM, Rabinowitz JA, Ceja Z, Alcauter S, Medina-Rivera A, Rentería ME. The pharmacogenomics of selective serotonin reuptake inhibitors. Pharmacogenomics 2022; 23:597-607. [PMID: 35673953 DOI: 10.2217/pgs-2022-0037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Antidepressant medications are frequently used as the first line of treatment for depression. However, their effectiveness is highly variable and influenced by genetic factors. Recently, pharmacogenetic studies, including candidate-gene, genome-wide association studies or polygenic risk scores, have attempted to uncover the genetic architecture of antidepressant response. Genetic variants in at least 27 genes are linked to antidepressant treatment response in both coding and non-coding genomic regions, but evidence is largely inconclusive due to the high polygenicity of the trait and limited cohort sizes in published studies. Future studies should increase the number and diversity of participants to yield sufficient statistical power to characterize the genetic underpinnings and biological mechanisms of treatment response, improve results generalizability and reduce racial health-related inequities.
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Affiliation(s)
- Luis M García-Marín
- Department of Genetics & Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.,Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
| | - Jill A Rabinowitz
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Zuriel Ceja
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
| | - Sarael Alcauter
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
| | - Alejandra Medina-Rivera
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
| | - Miguel E Rentería
- Department of Genetics & Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
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The Potential of Polygenic Risk Scores to Predict Antidepressant Treatment Response in Major Depression: A Systematic Review. J Affect Disord 2022; 304:1-11. [PMID: 35151671 DOI: 10.1016/j.jad.2022.02.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 12/29/2021] [Accepted: 02/09/2022] [Indexed: 12/28/2022]
Abstract
BACKGROUND Understanding the genetic underpinnings of antidepressant treatment response in unipolar major depressive disorder (MDD) can be useful in identifying patients at risk for poor treatment response or treatment resistant depression. A polygenic risk score (PRS) is a useful tool to explore genetic liability of a complex trait such as antidepressant treatment response. Here, we review studies that use PRSs to examine genetic overlap between any trait and antidepressant treatment response in unipolar MDD. METHODS A systematic search of literature was conducted in PubMed, Embase, and PsycINFO. Our search included studies examining associations between PRSs of psychiatric as well as non-psychiatric traits and antidepressant treatment response in patients with unipolar MDD. A quality assessment of the included studies was performed. RESULTS In total, eleven articles were included which contained PRSs for 30 traits. Studies varied in sample size and endpoints used for antidepressant treatment response. Overall, PRSs for attention-deficit hyperactivity disorder, the personality trait openness, coronary artery disease, obesity, and stroke have been associated with antidepressant treatment response in patients with unipolar MDD. LIMITATIONS The endpoints used by included studies differed significantly, therefore it was not possible to perform a meta-analysis. CONCLUSIONS Associations between a PRS and antidepressant treatment response have been reported for a number of traits in patients with unipolar MDD. PRSs could be informative to predict antidepressant treatment response in this population, given advances in the field. Most importantly, there is a need for larger study cohorts and the use of standardized outcome measures.
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Johnson D, Wilke MA, Lyle SM, Kowalec K, Jorgensen A, Wright GE, Drögemöller BI. A systematic review and analysis of the use of polygenic scores in pharmacogenomics. Clin Pharmacol Ther 2021; 111:919-930. [PMID: 34953075 DOI: 10.1002/cpt.2520] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 12/18/2021] [Indexed: 11/09/2022]
Abstract
Polygenic scores (PGS) have emerged as promising tools for complex trait risk prediction. The application of these scores to pharmacogenomics provides new opportunities to improve the prediction of treatment outcomes. To gain insight into this area of research, we conducted a systematic review and accompanying analysis. This review uncovered 51 papers examining the use of PGS for drug-related outcomes, with the majority of these papers focusing on the treatment of psychiatric disorders (n=30). Due to difficulties in collecting large cohorts of uniformly treated patients, the majority of pharmacogenomic PGS were derived from large-scale genome-wide association studies of disease phenotypes that were related to the pharmacogenomic phenotypes under investigation (e.g. schizophrenia-derived PGS for antipsychotic response prediction). Examination of the research participants included in these studies revealed that the majority of cohort participants were of European descent (78.4%). These biases were also reflected in research affiliations, which were heavily weighted towards institutions located in Europe and North America, with no first or last authors originating from institutions in Africa or South Asia. There was also substantial variability in the methods used to develop PGS, with between 3 and 6.6 million variants included in the PGS. Finally, we observed significant inconsistencies in the reporting of PGS analyses and results, particularly in terms of risk model development and application, coupled with a lack of data transparency and availability, with only three pharmacogenomics PGS deposited on the PGS Catalog. These findings highlight current gaps and key areas for future pharmacogenomic PGS research.
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Affiliation(s)
- Danielle Johnson
- Department of Health Data Science, University of Liverpool, Liverpool, UK
| | - MacKenzie Ap Wilke
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Sarah M Lyle
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Kaarina Kowalec
- College of Pharmacy, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada.,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Andrea Jorgensen
- Department of Health Data Science, University of Liverpool, Liverpool, UK
| | - Galen Eb Wright
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada.,Department of Pharmacology and Therapeutics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada.,Neuroscience Research Program, Kleysen Institute for Advanced Medicine, Health Sciences Centre and Max Rady College of Medicine, University of Manitoba, Winnipeg, MB, Canada
| | - Britt I Drögemöller
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada.,CancerCare Manitoba Research Institute, Winnipeg, MB, Canada.,Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
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Stressful life events and openness to experience: Relevance to depression. J Affect Disord 2021; 295:711-716. [PMID: 34517244 PMCID: PMC8551051 DOI: 10.1016/j.jad.2021.08.112] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/30/2021] [Accepted: 08/28/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Stressful life events are known as risk factors for depression, though there is considerable heterogeneity in how people respond to stress. Previous studies have found an association between experience of stressful life events and the personality trait of openness to experience, which itself has been associated with intelligence, creativity, risk-taking, and other clinically relevant behaviors. In this study we explore the association between stressful life events and openness to experience as a potential developmental pathway to depression in the Amish and Mennonites, rural populations with high degree of social and environmental homogeneity. METHODS Participants in the Amish Connectome Project (n=531) were assessed with the NEO personality inventory, Beck Depression Inventory, Maryland Trait and State Depression scales, a Life Stressors Inventory, and cognitive tests. RESULTS We found that stressful life events were significantly associated with openness to experience; that participants with a history of depression exhibited higher levels of openness; and that openness to experience was related to overall intelligence but not processing speed or working memory. We found evidence that openness to experience partially mediates the relationship between stressful life events and depression. LIMITATIONS This was a cross-sectional study, limiting interpretation of causal pathways. High levels of inter-relatedness among participants may have led to exaggerated effects compared to the general population. CONCLUSIONS Together these findings indicate a complex developmental influence of major stressful life events, which paradoxically by enhancing openness may be associated with both greater intellectual engagement as well as psychopathology.
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Variability in the antioxidant MSRA gene affects the psychopathology of patients with anorexia nervosa. Acta Neuropsychiatr 2021; 33:307-316. [PMID: 34396949 DOI: 10.1017/neu.2021.24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The objective is to determine whether variability in the MSRA gene, related to obesity and several psychiatric conditions, may be relevant for psychopathological symptoms common in Anorexia Nervosa (AN) and/or for the susceptibility to the disorder. A total of 629 women (233 AN patients and 396 controls) were genotyped for 14 tag-SNPs. Psychometric evaluation was performed with the EDI-2 and SCL-90R questionnaires. Genetic associations were carried out by logistic regression controlling for age and adjusting for multiple comparisons (FDR method). Two tag-SNPs, rs11249969 and rs81442 (with a pairwise r2 value of 0.41), were associated with the global EDI-2 score, which measures EDI-related psychopathology (adjusted FDR-q = 0.02 and 0.04, respectively). Moreover, rs81442 significantly modulated all the scales of the SCL-90R test that evaluates general psychopathology (FDR-q values ranged from 4.1E-04 to 0.011). A sliding-window analysis using adjacent 3-SNP haplotypes revealed a proximal region of the MSRA gene spanning 187.8 Kbp whose variability deeply affected psychopathological symptoms of the AN patients. Depression was the symptom that showed the strongest association with any of the constructed haplotypes (FDR-q = 3.60E-06). No variants were found to be linked to AN risk or anthropometric parameters in patients or controls. Variability in the MSRA gene locus modulates psychopathology often presented by AN patients.
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Park H, Forthman KL, Kuplicki R, Victor TA, Yeh HW, Thompson WK, Paulus MP. Polygenic risk for neuroticism moderates response to gains and losses in amygdala and caudate: Evidence from a clinical cohort. J Affect Disord 2021; 293:124-132. [PMID: 34186230 PMCID: PMC8411869 DOI: 10.1016/j.jad.2021.06.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 05/06/2021] [Accepted: 06/13/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Neuroticism is a heritable trait that contributes to the vulnerability to depression. We used polygenic risk scores (PRS) to examine genetic vulnerability to neuroticism and its associations with reward/punishment processing in a clinical sample with mood, anxiety, and substance use disorders. It was hypothesized that higher PRS for neuroticism is associated with attenuated neural responses to reward/punishment. METHOD Four hundred sixty-nine participants were genotyped and their PRSs for neuroticism were computed. Associations between PRS for neuroticism and anticipatory processing of monetary incentives were examined using functional magnetic resonance imaging. RESULTS Individuals with higher PRS for neuroticism showed less anticipatory activation in the left amygdala and caudate region to incentives regardless of incentive valence. Further, these individuals exhibited altered sensitivity to gain/loss processing in the right anterior insula. Higher PRSs for neuroticism were also associated with reduced processing of gains in the precuneus. LIMITATIONS The study population consisted of a transdiagnostic sample with dysfunctions in positive and negative valence processing. PRS for neuroticism may be correlated with current clinical symptoms due to the vulnerability to psychiatric disorders. CONCLUSIONS Greater genetic loading for neuroticism was associated with attenuated anticipatory responsiveness in reward/punishment processing with altered sensitivity to valences. Thus, a higher genetic risk for neuroticism may limit the degree to which positive and/or negative outcomes influence the current mood state, which may contribute to the development of positive and negative affective dysfunctions in individuals with mood, anxiety, and addictive disorders.
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Affiliation(s)
| | | | | | | | | | - Hung-Wen Yeh
- Laureate Institute for Brain Research, Tulsa, OK, USA,Children’s Mercy Hospital, Kansas City, MO
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Bahrami S, Hindley G, Winsvold BS, O'Connell KS, Frei O, Shadrin A, Cheng W, Bettella F, Rødevand L, Odegaard KJ, Fan CC, Pirinen MJ, Hautakangas HM, Headache HAI, Dale AM, Djurovic S, Smeland OB, Andreassen OA. Dissecting the shared genetic basis of migraine and mental disorders using novel statistical tools. Brain 2021; 145:142-153. [PMID: 34273149 PMCID: PMC8967089 DOI: 10.1093/brain/awab267] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/18/2021] [Accepted: 06/21/2021] [Indexed: 11/24/2022] Open
Abstract
Migraine is three times more prevalent in people with bipolar disorder or depression. The relationship between schizophrenia and migraine is less certain although glutamatergic and serotonergic neurotransmission are implicated in both. A shared genetic basis to migraine and mental disorders has been suggested but previous studies have reported weak or non-significant genetic correlations and five shared risk loci. Using the largest samples to date and novel statistical tools, we aimed to determine the extent to which migraine’s polygenic architecture overlaps with bipolar disorder, depression and schizophrenia beyond genetic correlation, and to identify shared genetic loci. Summary statistics from genome-wide association studies were acquired from large-scale consortia for migraine (n cases = 59 674; n controls = 316 078), bipolar disorder (n cases = 20 352; n controls = 31 358), depression (n cases = 170 756; n controls = 328 443) and schizophrenia (n cases = 40 675, n controls = 64 643). We applied the bivariate causal mixture model to estimate the number of disorder-influencing variants shared between migraine and each mental disorder, and the conditional/conjunctional false discovery rate method to identify shared loci. Loci were functionally characterized to provide biological insights. Univariate MiXeR analysis revealed that migraine was substantially less polygenic (2.8 K disorder-influencing variants) compared to mental disorders (8100–12 300 disorder-influencing variants). Bivariate analysis estimated that 800 (SD = 300), 2100 (SD = 100) and 2300 (SD = 300) variants were shared between bipolar disorder, depression and schizophrenia, respectively. There was also extensive overlap with intelligence (1800, SD = 300) and educational attainment (2100, SD = 300) but not height (1000, SD = 100). We next identified 14 loci jointly associated with migraine and depression and 36 loci jointly associated with migraine and schizophrenia, with evidence of consistent genetic effects in independent samples. No loci were associated with migraine and bipolar disorder. Functional annotation mapped 37 and 298 genes to migraine and each of depression and schizophrenia, respectively, including several novel putative migraine genes such as L3MBTL2, CACNB2 and SLC9B1. Gene-set analysis identified several putative gene sets enriched with mapped genes including transmembrane transport in migraine and schizophrenia. Most migraine-influencing variants were predicted to influence depression and schizophrenia, although a minority of mental disorder-influencing variants were shared with migraine due to the difference in polygenicity. Similar overlap with other brain-related phenotypes suggests this represents a pool of ‘pleiotropic’ variants that influence vulnerability to diverse brain-related disorders and traits. We also identified specific loci shared between migraine and each of depression and schizophrenia, implicating shared molecular mechanisms and highlighting candidate migraine genes for experimental validation.
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Affiliation(s)
- Shahram Bahrami
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, 0407 Oslo, Norway
| | - Guy Hindley
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, 0407 Oslo, Norway.,Institute of Psychiatry, Psychology and Neuroscience, King's College London, 16 De Crespigny Park, London, SE5 8AB, UK
| | - Bendik Slagsvold Winsvold
- Department of Research, Innovation and Education, Division of Clinical Neuroscience, Oslo University Hospital, Oslo, Norway.,Department of Neurology, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Kevin S O'Connell
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, 0407 Oslo, Norway
| | - Oleksandr Frei
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, 0407 Oslo, Norway.,Center for Bioinformatics, Department of Informatics, University of Oslo, PO box 1080, Blindern, 0316 Oslo, Norway
| | - Alexey Shadrin
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, 0407 Oslo, Norway
| | - Weiqiu Cheng
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, 0407 Oslo, Norway
| | - Francesco Bettella
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, 0407 Oslo, Norway
| | - Linn Rødevand
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, 0407 Oslo, Norway
| | - Ketil J Odegaard
- NORMENT, Division of Psychiatry, Haukeland University Hospital and Department of Clinical Medicine, University of Bergen, 5020 Bergen, Norway
| | - Chun C Fan
- Multimodal Imaging Laboratory, University of California San Diego, La Jolla, CA 92093, USA.,Department of Cognitive Science, University of California, San Diego, La Jolla, CA, USA
| | - Matti J Pirinen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, 00014 Helsinki, Finland.,Department of Public Health, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland.,Department of Mathematics and Statistics, University of Helsinki, 00014 Helsinki, Finland
| | - Heidi M Hautakangas
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, 00014 Helsinki, Finland
| | - Hunt All-In Headache
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Anders M Dale
- Multimodal Imaging Laboratory, University of California San Diego, La Jolla, CA 92093, USA.,Department of Radiology, University of California, San Diego, La Jolla, CA 92093, USA.,Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA.,Department of Neurosciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Srdjan Djurovic
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, 0407 Oslo, Norway.,Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.,NORMENT Centre, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Olav B Smeland
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, 0407 Oslo, Norway
| | - Ole A Andreassen
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, 0407 Oslo, Norway
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13
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Fanelli G, Benedetti F, Kasper S, Zohar J, Souery D, Montgomery S, Albani D, Forloni G, Ferentinos P, Rujescu D, Mendlewicz J, Serretti A, Fabbri C. Higher polygenic risk scores for schizophrenia may be suggestive of treatment non-response in major depressive disorder. Prog Neuropsychopharmacol Biol Psychiatry 2021; 108:110170. [PMID: 33181205 DOI: 10.1016/j.pnpbp.2020.110170] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 10/22/2020] [Accepted: 11/04/2020] [Indexed: 02/06/2023]
Abstract
Up to 60% of patients with major depressive disorder (MDD) do not respond to the first treatment with antidepressants. Response to antidepressants is a polygenic trait, although its underpinning genetics has not been fully clarified. This study aimed to investigate if polygenic risk scores (PRSs) for major psychiatric disorders and trait neuroticism (NEU) were associated with non-response or resistance to antidepressants in MDD. PRSs for bipolar disorder, MDD, NEU, and schizophrenia (SCZ) were computed in 1,148 patients with MDD. Summary statistics from the largest meta-analyses of genome-wide association studies were used as base data. Patients were classified as responders, non-responders to one treatment, non-responders to two or more treatments (treatment-resistant depression or TRD). Regression analyses were adjusted for population stratification and recruitment sites. PRSs did not predict either non-response vs response or TRD vs response after Bonferroni correction. However, SCZ-PRS was nominally associated with non-response (p = 0.003). Patients in the highest SCZ-PRS quintile were more likely to be non-responders than those in the lowest quintile (OR = 2.23, 95% CI = 1.21-4.10, p = 0.02). Patients in the lowest SCZ-PRS quintile showed higher response rates when they did not receive augmentation with second-generation antipsychotics (SGAs), while those in the highest SCZ-PRS quintile had a poor response independently from the treatment strategy (p = 0.009). A higher genetic liability to SCZ may reduce treatment response in MDD, and patients with low SCZ-PRSs may show higher response rates without SGA augmentation. Multivariate approaches and methodological refinements will be necessary before clinical implementations of PRSs.
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Affiliation(s)
- Giuseppe Fanelli
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Francesco Benedetti
- Vita-Salute San Raffaele University, Milan, Italy; Psychiatry and Clinical Psychobiology Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Siegfried Kasper
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Vienna, Austria
| | - Joseph Zohar
- Department of Psychiatry, Sheba Medical Center, Tel Hashomer, and Sackler School of Medicine, Tel Aviv University, Tel Hashomer, Israel
| | - Daniel Souery
- Laboratoire de Psychologie Médicale, Université Libre de Bruxelles and Psy Pluriel, Centre Européen de Psychologie Médicale, Brussels, Belgium
| | | | - Diego Albani
- Laboratory of Biology of Neurodegenerative Disorders, Department of Neuroscience, IRCCS Mario Negri Institute for Pharmacological Research, Milan, Italy
| | - Gianluigi Forloni
- Laboratory of Biology of Neurodegenerative Disorders, Department of Neuroscience, IRCCS Mario Negri Institute for Pharmacological Research, Milan, Italy
| | | | - Dan Rujescu
- University Clinic for Psychiatry, Psychotherapy and Psychosomatic, Martin-Luther-University, Halle-Wittenberg, Germany
| | | | - Alessandro Serretti
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy.
| | - Chiara Fabbri
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy; Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
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14
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Chekroud AM, Bondar J, Delgadillo J, Doherty G, Wasil A, Fokkema M, Cohen Z, Belgrave D, DeRubeis R, Iniesta R, Dwyer D, Choi K. The promise of machine learning in predicting treatment outcomes in psychiatry. World Psychiatry 2021; 20:154-170. [PMID: 34002503 PMCID: PMC8129866 DOI: 10.1002/wps.20882] [Citation(s) in RCA: 142] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
For many years, psychiatrists have tried to understand factors involved in response to medications or psychotherapies, in order to personalize their treatment choices. There is now a broad and growing interest in the idea that we can develop models to personalize treatment decisions using new statistical approaches from the field of machine learning and applying them to larger volumes of data. In this pursuit, there has been a paradigm shift away from experimental studies to confirm or refute specific hypotheses towards a focus on the overall explanatory power of a predictive model when tested on new, unseen datasets. In this paper, we review key studies using machine learning to predict treatment outcomes in psychiatry, ranging from medications and psychotherapies to digital interventions and neurobiological treatments. Next, we focus on some new sources of data that are being used for the development of predictive models based on machine learning, such as electronic health records, smartphone and social media data, and on the potential utility of data from genetics, electrophysiology, neuroimaging and cognitive testing. Finally, we discuss how far the field has come towards implementing prediction tools in real-world clinical practice. Relatively few retrospective studies to-date include appropriate external validation procedures, and there are even fewer prospective studies testing the clinical feasibility and effectiveness of predictive models. Applications of machine learning in psychiatry face some of the same ethical challenges posed by these techniques in other areas of medicine or computer science, which we discuss here. In short, machine learning is a nascent but important approach to improve the effectiveness of mental health care, and several prospective clinical studies suggest that it may be working already.
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Affiliation(s)
- Adam M Chekroud
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- Spring Health, New York City, NY, USA
| | | | - Jaime Delgadillo
- Clinical Psychology Unit, Department of Psychology, University of Sheffield, Sheffield, UK
| | - Gavin Doherty
- School of Computer Science and Statistics, Trinity College Dublin, Dublin, Ireland
| | - Akash Wasil
- Department of Psychology, University of Pennsylvania, Philadelphia, PA, USA
| | - Marjolein Fokkema
- Department of Methods and Statistics, Institute of Psychology, Leiden University, Leiden, The Netherlands
| | - Zachary Cohen
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Robert DeRubeis
- Department of Psychology, University of Pennsylvania, Philadelphia, PA, USA
| | - Raquel Iniesta
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neurosciences, King's College London, London, UK
| | - Dominic Dwyer
- Department of Psychiatry and Psychotherapy, Section for Neurodiagnostic Applications, Ludwig-Maximilian University, Munich, Germany
| | - Karmel Choi
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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15
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Voorhies K, Sordillo JE, McGeachie M, Ampleford E, Wang AL, Lasky-Su J, Tantisira K, Dahlin A, Kelly RS, Ortega VE, Lutz SM, Wu AC. Age by Single Nucleotide Polymorphism Interactions on Bronchodilator Response in Asthmatics. J Pers Med 2021; 11:jpm11010059. [PMID: 33477890 PMCID: PMC7833432 DOI: 10.3390/jpm11010059] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/10/2021] [Accepted: 01/12/2021] [Indexed: 12/15/2022] Open
Abstract
An unaddressed and important issue is the role age plays in modulating response to short acting β2-agonists in individuals with asthma. The objective of this study was to identify whether age modifies genetic associations of single nucleotide polymorphisms (SNPs) with bronchodilator response (BDR) to β2-agonists. Using three cohorts with a total of 892 subjects, we ran a genome wide interaction study (GWIS) for each cohort to examine SNP by age interactions with BDR. A fixed effect meta-analysis was used to combine the results. In order to determine if previously identified BDR SNPs had an age interaction, we also examined 16 polymorphisms in candidate genes from two published genome wide association studies (GWAS) of BDR. There were no significant SNP by age interactions on BDR using the genome wide significance level of 5 × 10−8. Using a suggestive significance level of 5 × 10−6, three interactions, including one for a SNP within PRAG1 (rs4840337), were significant and replicated at the significance level of 0.05. Considering candidate genes from two previous GWAS of BDR, three SNPs (rs10476900 (near ADRB2) [p-value = 0.009], rs10827492 (CREM) [p-value = 0.02], and rs72646209 (NCOA3) [p-value = 0.02]) had a marginally significant interaction with age on BDR (p < 0.05). Our results suggest age may be an important modifier of genetic associations for BDR in asthma.
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Affiliation(s)
- Kirsten Voorhies
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA 02215, USA; (K.V.); (J.E.S.); (S.M.L.)
| | - Joanne E. Sordillo
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA 02215, USA; (K.V.); (J.E.S.); (S.M.L.)
| | - Michael McGeachie
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA; (M.M.); (A.L.W.); (J.L.-S.); (K.T.); (A.D.); (R.S.K.)
| | - Elizabeth Ampleford
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA; (E.A.); (V.E.O.)
| | - Alberta L. Wang
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA; (M.M.); (A.L.W.); (J.L.-S.); (K.T.); (A.D.); (R.S.K.)
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA; (M.M.); (A.L.W.); (J.L.-S.); (K.T.); (A.D.); (R.S.K.)
| | - Kelan Tantisira
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA; (M.M.); (A.L.W.); (J.L.-S.); (K.T.); (A.D.); (R.S.K.)
- Division of Pediatric Respiratory Medicine, Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | - Amber Dahlin
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA; (M.M.); (A.L.W.); (J.L.-S.); (K.T.); (A.D.); (R.S.K.)
| | - Rachel S. Kelly
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA; (M.M.); (A.L.W.); (J.L.-S.); (K.T.); (A.D.); (R.S.K.)
| | - Victor E. Ortega
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA; (E.A.); (V.E.O.)
| | - Sharon M. Lutz
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA 02215, USA; (K.V.); (J.E.S.); (S.M.L.)
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Ann C. Wu
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA 02215, USA; (K.V.); (J.E.S.); (S.M.L.)
- Division of General Pediatrics, Department of Pediatrics, Children’s Hospital, Boston, MA 02215, USA
- Correspondence: ; Tel.: +1-(617)-867-4823; Fax: +1-(617)-867-4276
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16
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Ren Z, Liu C, Meng J, Liu Q, Shi L, Wu X, Song L, Qiu J. Effects of the Openness to Experience Polygenic Score on Cortical Thickness and Functional Connectivity. Front Neurosci 2021; 14:607912. [PMID: 33505240 PMCID: PMC7829912 DOI: 10.3389/fnins.2020.607912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/09/2020] [Indexed: 11/16/2022] Open
Abstract
Openness to experience (OTE) has relatively stable and heritable characteristics. Previous studies have used candidate gene approaches to explore the genetic mechanisms of OTE, but genome-wide polygenic scores have a greater genetic effect than other genetic analysis methods, and previous studies have never examined the potential effect of OTE on this cumulative effect at the level of the brain mechanism. In the present study, we aim to explore the associations between polygenic scores (PGSs) of OTE and brain structure and functions. First, the results of PGSs of OTE at seven different thresholds were calculated in a large Chinese sample (N = 586). Then, we determined the associations between PGSs of OTE and cortical thickness and functional connectivity. The results showed that PGSs of OTE was negatively correlated with the thickness of the fusiform gyrus, and PGSs of OTE were negatively associated with the functional connectivity between the left intraparietal sulcus (IPS) and the right posterior occipital lobe. These findings may suggest that the brain structure of fusiform gyrus and brain functions of IPS and posterior occipital lobe are partly regulated by OTE-related genetic factors.
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Affiliation(s)
- Zhiting Ren
- Key Laboratory of Cognition and Personality (SWU), Ministry of Education, Chongqing, China
- Faculty of Psychology, Southwest University (SWU), Chongqing, China
| | - Cheng Liu
- Key Laboratory of Cognition and Personality (SWU), Ministry of Education, Chongqing, China
- Faculty of Psychology, Southwest University (SWU), Chongqing, China
| | - Jie Meng
- Key Laboratory of Cognition and Personality (SWU), Ministry of Education, Chongqing, China
- Faculty of Psychology, Southwest University (SWU), Chongqing, China
| | - Qiang Liu
- Key Laboratory of Cognition and Personality (SWU), Ministry of Education, Chongqing, China
- Faculty of Psychology, Southwest University (SWU), Chongqing, China
| | - Liang Shi
- Key Laboratory of Cognition and Personality (SWU), Ministry of Education, Chongqing, China
- Faculty of Psychology, Southwest University (SWU), Chongqing, China
| | - Xinran Wu
- Key Laboratory of Cognition and Personality (SWU), Ministry of Education, Chongqing, China
- Faculty of Psychology, Southwest University (SWU), Chongqing, China
| | - Li Song
- Key Laboratory of Cognition and Personality (SWU), Ministry of Education, Chongqing, China
- Faculty of Psychology, Southwest University (SWU), Chongqing, China
| | - Jiang Qiu
- Key Laboratory of Cognition and Personality (SWU), Ministry of Education, Chongqing, China
- Faculty of Psychology, Southwest University (SWU), Chongqing, China
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17
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Kautzky A, Möller H, Dold M, Bartova L, Seemüller F, Laux G, Riedel M, Gaebel W, Kasper S. Combining machine learning algorithms for prediction of antidepressant treatment response. Acta Psychiatr Scand 2021; 143:36-49. [PMID: 33141944 PMCID: PMC7839691 DOI: 10.1111/acps.13250] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 06/29/2020] [Accepted: 10/12/2020] [Indexed: 12/13/2022]
Abstract
OBJECTIVES Predictors for unfavorable treatment outcome in major depressive disorder (MDD) applicable for treatment selection are still lacking. The database of a longitudinal multicenter study on 1079 acutely depressed patients, performed by the German research network on depression (GRND), allows supervised and unsupervised learning to further elucidate the interplay of clinical and psycho-sociodemographic variables and their predictive impact on treatment outcome phenotypes. EXPERIMENTAL PROCEDURES Treatment response was defined by a change of HAM-D 17-item baseline score ≥50% and remission by the established threshold of ≤7, respectively, after up to eight weeks of inpatient treatment. After hierarchical symptom clustering and stratification by treatment subtypes (serotonin reuptake inhibitors, tricyclic antidepressants, antipsychotic, and lithium augmentation), prediction models for different outcome phenotypes were computed with random forest in a cross-center validation design. In total, 88 predictors were implemented. RESULTS Clustering revealed four distinct HAM-D subscores related to emotional, anxious, sleep, and appetite symptoms, respectively. After feature selection, classification models reached moderate to high accuracies up to 0.85. Highest accuracies were observed for the SSRI and TCA subgroups and for sleep and appetite symptoms, while anxious symptoms showed poor predictability. CONCLUSION Our results support a decisive role for machine learning in the management of antidepressant treatment. Treatment- and symptom-specific algorithms may increase accuracies by reducing heterogeneity. Especially, predictors related to duration of illness, baseline depression severity, anxiety and somatic symptoms, and personality traits moderate treatment success. However, prospectives application of machine learning models will be necessary to prove their value for the clinic.
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Affiliation(s)
- Alexander Kautzky
- Department of Psychiatry and PsychotherapyMedical University of ViennaViennaAustria
| | - Hans‐Juergen Möller
- Department of Psychiatry and PsychotherapyLudwig‐Maximilians‐Q3 University MunichMunichGermany
| | - Markus Dold
- Department of Psychiatry and PsychotherapyMedical University of ViennaViennaAustria
| | - Lucie Bartova
- Department of Psychiatry and PsychotherapyMedical University of ViennaViennaAustria
| | - Florian Seemüller
- Department of Psychiatry and PsychotherapyLudwig‐Maximilians‐Q3 University MunichMunichGermany,Department of Psychiatry and Psychotherapykbo‐Lech‐Mangfall‐KlinikGarmisch‐PartenkirchenGermany
| | - Gerd Laux
- Department of Psychiatry and Psychotherapykbo‐Inn‐Salzach‐KlinikumWasserburgGermany
| | - Michael Riedel
- Department of Psychiatry and PsychotherapyLudwig‐Maximilians‐Q3 University MunichMunichGermany,Department of PsychiatrySächsisches KrankenhausRodewischGermany
| | - Wolfgang Gaebel
- Department of Psychiatry and PsychotherapyMedical FacultyHeinrich‐Heine‐UniversityDüsseldorfGermany
| | - Siegfried Kasper
- Department of Psychiatry and PsychotherapyMedical University of ViennaViennaAustria
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18
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Tamargo-Gómez I, Fernández ÁF, Mariño G. Pathogenic Single Nucleotide Polymorphisms on Autophagy-Related Genes. Int J Mol Sci 2020; 21:ijms21218196. [PMID: 33147747 PMCID: PMC7672651 DOI: 10.3390/ijms21218196] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/28/2020] [Accepted: 10/30/2020] [Indexed: 02/06/2023] Open
Abstract
In recent years, the study of single nucleotide polymorphisms (SNPs) has gained increasing importance in biomedical research, as they can either be at the molecular origin of a determined disorder or directly affect the efficiency of a given treatment. In this regard, sequence variations in genes involved in pro-survival cellular pathways are commonly associated with pathologies, as the alteration of these routes compromises cellular homeostasis. This is the case of autophagy, an evolutionarily conserved pathway that counteracts extracellular and intracellular stressors by mediating the turnover of cytosolic components through lysosomal degradation. Accordingly, autophagy dysregulation has been extensively described in a wide range of human pathologies, including cancer, neurodegeneration, or inflammatory alterations. Thus, it is not surprising that pathogenic gene variants in genes encoding crucial effectors of the autophagosome/lysosome axis are increasingly being identified. In this review, we present a comprehensive list of clinically relevant SNPs in autophagy-related genes, highlighting the scope and relevance of autophagy alterations in human disease.
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Affiliation(s)
- Isaac Tamargo-Gómez
- Instituto de Investigación Sanitaria del Principado de Asturias, 33011 Oviedo, Spain;
- Departamento de Biología Funcional, Universidad de Oviedo, 33011 Oviedo, Spain
| | - Álvaro F. Fernández
- Instituto de Investigación Sanitaria del Principado de Asturias, 33011 Oviedo, Spain;
- Departamento de Biología Funcional, Universidad de Oviedo, 33011 Oviedo, Spain
- Correspondence: (Á.F.F.); (G.M.); Tel.: +34-985652416 (G.M.)
| | - Guillermo Mariño
- Instituto de Investigación Sanitaria del Principado de Asturias, 33011 Oviedo, Spain;
- Departamento de Biología Funcional, Universidad de Oviedo, 33011 Oviedo, Spain
- Correspondence: (Á.F.F.); (G.M.); Tel.: +34-985652416 (G.M.)
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19
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Clifford RE, Maihofer AX, Stein MB, Ryan AF, Nievergelt CM. Novel Risk Loci in Tinnitus and Causal Inference With Neuropsychiatric Disorders Among Adults of European Ancestry. JAMA Otolaryngol Head Neck Surg 2020; 146:1015-1025. [PMID: 32970095 PMCID: PMC7516809 DOI: 10.1001/jamaoto.2020.2920] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 07/27/2020] [Indexed: 02/06/2023]
Abstract
Importance Tinnitus affects at least 16 million US adults, but its pathophysiology is complicated, and treatment options remain limited. A heritable component has been identified in family and twin studies; however, no large-scale genome-wide association studies (GWAS) have been accomplished. Objective To identify genetic risk loci associated with tinnitus, determine genetic correlations, and infer possible relationships of tinnitus with hearing loss and neuropsychiatric disorders and traits. Design, Setting, and Participants A GWAS of self-reported tinnitus was performed in the UK Biobank (UKB) cohort using a linear mixed-model method implemented in BOLT-LMM (linear mixed model). Replication of significant findings was sought in the nonoverlapping US Million Veteran Program (MVP) cohort. A total of 172 995 UKB (discovery) and 260 832 MVP (replication) participants of European ancestry with self-report regarding tinnitus and hearing loss underwent genomic analysis. Linkage-disequilibrium score regression and mendelian randomization were performed between tinnitus and hearing loss and neuropsychiatric disorders. Data from the UKB were acquired and analyzed from September 24, 2018, to December 13, 2019. Data acquisition for the MVP cohort was completed July 22, 2019. Data analysis for both cohorts was completed on February 11, 2020. Main Outcomes and Measures Estimates of single nucleotide variation (SNV)-based heritability for tinnitus, identification of genetic risk loci and genes, functional mapping, and replication were performed. Genetic association and inferred causality of tinnitus compared with hearing loss and neuropsychiatric disorders and traits were analyzed. Results Of 172 995 UKB participants (53.7% female; mean [SD], 58.0 [8.2] years), 155 395 unrelated participants underwent SNV-based heritability analyses across a range of tinnitus phenotype definitions that explained approximately 6% of the heritability. The GWAS based on the most heritable model in the full UKB cohort identified 6 genome-wide significant loci and 27 genes in gene-based analyses, with replication of 3 of 6 loci and 8 of 27 genes in 260 832 MVP cohort participants (92.8% men; mean [SD] age, 63.8 [13.2] years). Mendelian randomization indicated that major depressive disorder had a permissive effect (β = 0.133; P = .003) and years of education had a protective effect (β = -0.322, P = <.001) on tinnitus, whereas tinnitus and hearing loss inferred a bidirectional association (β = 0.072, P = .001 and β = 1.546, P = <.001, respectively). Conclusions and Relevance This large GWAS characterizes the genetic architecture of tinnitus, demonstrating modest but significant heritability and a polygenic profile with multiple significant risk loci and genes. Genetic correlation and inferred causation between tinnitus and major depressive disorder, educational level, and hearing impairment were identified, consistent with clinical and neuroimaging evidence. These findings may guide gene-based diagnostic and therapeutic approaches to this pervasive disorder.
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Affiliation(s)
- Royce E Clifford
- Division of Otolaryngology, Department of Surgery, University of California, San Diego, La Jolla
- Harvard School of Public Health, Boston, Massachusetts
- Research Service, Veterans Affairs San Diego Healthcare System, San Diego, California
| | - Adam X Maihofer
- Research Service, Veterans Affairs San Diego Healthcare System, San Diego, California
- Department of Psychiatry, University of California, San Diego, La Jolla
| | - Murray B Stein
- Department of Psychiatry, University of California, San Diego, La Jolla
- Psychiatry Service, Veterans Affairs San Diego Healthcare System, San Diego, California
| | - Allen F Ryan
- Division of Otolaryngology, Department of Surgery, University of California, San Diego, La Jolla
- Research Service, Veterans Affairs San Diego Healthcare System, San Diego, California
| | - Caroline M Nievergelt
- Research Service, Veterans Affairs San Diego Healthcare System, San Diego, California
- Department of Psychiatry, University of California, San Diego, La Jolla
- Center of Excellence for Stress and Mental Health, Veterans Affairs San Diego Healthcare System, San Diego, California
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20
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Wang J, Zhang P, Li W, Wen Q, Liu F, Xu J, Xu Q, Zhu D, Ye Z, Yu C. Right Posterior Insula and Putamen Volume Mediate the Effect of Oxytocin Receptor Polygenic Risk for Autism Spectrum Disorders on Reward Dependence in Healthy Adults. Cereb Cortex 2020; 31:746-756. [PMID: 32710107 DOI: 10.1093/cercor/bhaa198] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 06/29/2020] [Accepted: 06/29/2020] [Indexed: 12/24/2022] Open
Abstract
Much evidence indicates the influence of the oxytocin receptor (OXTR) gene on autism spectrum disorders (ASDs), a set of disorders characterized by a range of deficits in prosocial behaviors, which are closely related to the personality trait of reward dependence (RD). However, we do not know the effect of the OXTR polygenic risk score for ASDs (OXTR-PRSASDs) on RD and its underlying neuroanatomical substrate. Here, we aimed to investigate associations among the OXTR-PRSASDs, gray matter volume (GMV), and RD in two independent datasets of healthy young adults (n = 450 and 540). We found that the individuals with higher OXTR-PRSASDs had lower RD and significantly smaller GMV in the right posterior insula and putamen. The GMV of this region showed a positive correlation with RD and a mediation effect on the association between OXTR-PRSASDs and RD. Moreover, the correlation map between OXTR-PRSASDs and GMV showed spatial correlation with OXTR gene expression. All results were highly consistent between the two datasets. These findings highlight a possible neural pathway by which the common variants in the OXTR gene associated with ASDs may jointly impact the GMV of the right posterior insula and putamen and further affect the personality trait of RD.
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Affiliation(s)
- Junping Wang
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Peng Zhang
- Department of Radiology, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Wei Li
- Department of Radiology, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Qin Wen
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Feng Liu
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Jiayuan Xu
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Qiang Xu
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Dan Zhu
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Zhaoxiang Ye
- Department of Radiology, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Chunshui Yu
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China.,CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
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21
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Chu X, Liu L, Wen Y, Li P, Cheng B, Cheng S, Zhang L, Mei Ma, Qi X, Liang C, Ye J, Kafle OP, Wu C, Wang S, Wang X, Ning Y, Zhang F. A genome-wide multiphenotypic association analysis identified common candidate genes for subjective well-being, depressive symptoms and neuroticism. J Psychiatr Res 2020; 124:22-28. [PMID: 32109668 DOI: 10.1016/j.jpsychires.2020.02.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/10/2020] [Accepted: 02/11/2020] [Indexed: 01/19/2023]
Abstract
Subjective well-being (SWB), depressive symptoms, and neuroticism are common and vital traits of mental disorders. Genetic mechanisms of SWB, depressive symptoms and neuroticism remain elusive now. The large-scale GWAS summary datasets of SWB (n = 229,883), depressive symptoms (n = 180,866), and neuroticism (n = 170,911) were obtained from published studies. MASH tool was applied to the GWAS datasets for identifying candidate SNPs shared by SWB, depressive symptoms and neuroticism. SNPs detected by MASH, were then mapped to target genes considering regulatory SNP (rSNP), methylated quantitative trait locus (MeQTL) and the SNPs near to known genes. Gene set enrichment analysis (GSEA) was conducted by the FUMA platform. A total of 122 candidate SNPs were detected by MASH analysis, mapping to 29 target genes, such as CLDN23, MSRA and XKR6. GO enrichment analysis identified multiple immune related gene sets for SWB, depressive symptoms and neuroticism, such as GSE2770_UNTREATED_VS_IL4_TREATED_ACT_CD4_TCELL_48H_DN (P = 7.32 × 10-3), GSE6259_FLT3L_INDUCED_DEC205_POS_DC_VS_CD4_TCELL_DN (P = 2.52 × 10-2). We also found some mental disorders related gene sets were associated with three phenotypes, such as mood instability (P = 1.15 × 10-6) and neuroticism (P = 1.72 × 10-6). We identified multiple candidate genes and GO terms shared by SWB, depressive symptoms and neuroticism. Our results support the overlapping genetic mechanisms, and suggest a functional correlation between immunity and SWB, depressive symptoms and neuroticism.
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Affiliation(s)
- Xiaomeng Chu
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Li Liu
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Yan Wen
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Ping Li
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Bolun Cheng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Shiqiang Cheng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Lu Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Mei Ma
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Xin Qi
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Chujun Liang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Jing Ye
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Om Prakash Kafle
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Cuiyan Wu
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Sen Wang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Xi Wang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Yujie Ning
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China.
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22
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Tomasi J, Lisoway AJ, Zai CC, Harripaul R, Müller DJ, Zai GCM, McCabe RE, Richter MA, Kennedy JL, Tiwari AK. Towards precision medicine in generalized anxiety disorder: Review of genetics and pharmaco(epi)genetics. J Psychiatr Res 2019; 119:33-47. [PMID: 31563039 DOI: 10.1016/j.jpsychires.2019.09.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 08/15/2019] [Accepted: 09/05/2019] [Indexed: 02/06/2023]
Abstract
Generalized anxiety disorder (GAD) is a prevalent and chronic mental disorder that elicits widespread functional impairment. Given the high degree of non-response/partial response among patients with GAD to available pharmacological treatments, there is a strong need for novel approaches that can optimize outcomes, and lead to medications that are safer and more effective. Although investigations have identified interesting targets predicting treatment response through pharmacogenetics (PGx), pharmaco-epigenetics, and neuroimaging methods, these studies are often solitary, not replicated, and carry several limitations. This review provides an overview of the current status of GAD genetics and PGx and presents potential strategies to improve treatment response by combining better phenotyping with PGx and improved analytical methods. These strategies carry the dual benefit of delivering data on biomarkers of treatment response as well as pointing to disease mechanisms through the biology of the markers associated with response. Overall, these efforts can serve to identify clinical, genetic, and epigenetic factors that can be incorporated into a pharmaco(epi)genetic test that may ultimately improve treatment response and reduce the socioeconomic burden of GAD.
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Affiliation(s)
- Julia Tomasi
- Molecular Brain Science Department, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada; Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Amanda J Lisoway
- Molecular Brain Science Department, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada; Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Clement C Zai
- Molecular Brain Science Department, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada; Institute of Medical Science, University of Toronto, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Ricardo Harripaul
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada; Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Daniel J Müller
- Molecular Brain Science Department, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada; Institute of Medical Science, University of Toronto, Toronto, ON, Canada; Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Gwyneth C M Zai
- Molecular Brain Science Department, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada; Institute of Medical Science, University of Toronto, Toronto, ON, Canada; Department of Psychiatry, University of Toronto, Toronto, ON, Canada; General Adult Psychiatry and Health Systems Division, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Randi E McCabe
- Department of Psychiatry & Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada; Anxiety Treatment and Research Clinic, St. Joseph's Healthcare Hamilton, Hamilton, ON, Canada
| | - Margaret A Richter
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada; Department of Psychiatry, University of Toronto, Toronto, ON, Canada; Frederick W. Thompson Anxiety Disorders Centre, Department of Psychiatry, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - James L Kennedy
- Molecular Brain Science Department, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada; Institute of Medical Science, University of Toronto, Toronto, ON, Canada; Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Arun K Tiwari
- Molecular Brain Science Department, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada; Department of Psychiatry, University of Toronto, Toronto, ON, Canada.
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23
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Predicting rehospitalization within 2 years of initial patient admission for a major depressive episode: a multimodal machine learning approach. Transl Psychiatry 2019; 9:285. [PMID: 31712550 PMCID: PMC6848135 DOI: 10.1038/s41398-019-0615-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 10/08/2019] [Accepted: 10/20/2019] [Indexed: 01/12/2023] Open
Abstract
Machine learning methods show promise to translate univariate biomarker findings into clinically useful multivariate decision support systems. At current, works in major depressive disorder have predominantly focused on neuroimaging and clinical predictor modalities, with genetic, blood-biomarker, and cardiovascular modalities lacking. In addition, the prediction of rehospitalization after an initial inpatient major depressive episode is yet to be explored, despite its clinical importance. To address this gap in the literature, we have used baseline clinical, structural imaging, blood-biomarker, genetic (polygenic risk scores), bioelectrical impedance and electrocardiography predictors to predict rehospitalization within 2 years of an initial inpatient episode of major depression. Three hundred and eighty patients from the ongoing 12-year Bidirect study were included in the analysis (rehospitalized: yes = 102, no = 278). Inclusion criteria was age ≥35 and <66 years, a current or recent hospitalisation for a major depressive episode and complete structural imaging and genetic data. Optimal performance was achieved with a multimodal panel containing structural imaging, blood-biomarker, clinical, medication type, and sleep quality predictors, attaining a test AUC of 67.74 (p = 9.99-05). This multimodal solution outperformed models based on clinical variables alone, combined biomarkers, and individual data modality prognostication for rehospitalization prediction. This finding points to the potential of predictive models that combine multimodal clinical and biomarker data in the development of clinical decision support systems.
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24
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Xia L, Ou J, Li K, Guo H, Hu Z, Bai T, Zhao J, Xia K, Zhang F. Genome-wide association analysis of autism identified multiple loci that have been reported as strong signals for neuropsychiatric disorders. Autism Res 2019; 13:382-396. [PMID: 31647196 DOI: 10.1002/aur.2229] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 09/17/2019] [Accepted: 09/22/2019] [Indexed: 12/13/2022]
Abstract
Autism is a common neurodevelopmental disorder with a moderate to a high degree of heritability, but only a few common genetic variants that explain the heritability have been associated. We performed a genome-wide transmission disequilibrium test analysis of a newly genotyped autism case-parent triad samples (127 trios) in Han Chinese, identified top association signals at multiple single nucleotide polymorphisms (SNPs), including rs9839376 (OR = 2.59, P = 1.27 × 10-05 ) at KCNMB2, rs6044680 (OR = 0.319, P = 4.82 × 10-05 ) and rs7274133 (OR = 0.313, P = 3.22 × 10-05 ) at PCSK2, and rs310619 (OR = 2.40, P = 7.44 × 10-05 ) at EEF1A2. Furthermore, a genome-wide combined P-value of individual SNPs in two independent case-parent triad samples (total 402 triads, n = 1,206) identified SNPs at EGFLAM, ZDHHC2, AGBL1, and SNX29 as additional association signals for autism. While none of these signals achieved a genome-wide significance in the two samples of our study, they have been reported in a previous genome-wide association study of neuropsychiatric disorders, and the majority of these SNP have a significant cis-regulatory association with mRNA in human tissues (false discovery rate (FDR) < 0.05). Our study warrants further study or replication with additional sample for association with autism and other neuropsychiatric disorders. Autism Res 2020, 13: 382-396. © 2019 International Society for Autism Research, Wiley Periodicals, Inc. LAY SUMMARY: Autism is a common neurodevelopmental disorder, heritable, but only a few common genetic variants that explain the heritability have been associated. We conducted a genome-wide association study with two cohorts of autism case-parent triad samples in Han Chinese and identified multiple single nucleotide polymorphisms that were reported as strong association signals in a previous genome-wide association study of other neuropsychiatric disorders or related traits. Our study provides evidence for shared genetic variants among autism and other neuropsychiatric disorders.
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Affiliation(s)
- Lu Xia
- Center for Medical Genetics and Hunan Provincial Key Laboratory for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Jianjun Ou
- Mental Health Institute, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Kuokuo Li
- Center for Medical Genetics and Hunan Provincial Key Laboratory for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Hui Guo
- Center for Medical Genetics and Hunan Provincial Key Laboratory for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Zhengmao Hu
- Center for Medical Genetics and Hunan Provincial Key Laboratory for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Ting Bai
- Center for Medical Genetics and Hunan Provincial Key Laboratory for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Jingping Zhao
- Mental Health Institute, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Kun Xia
- Center for Medical Genetics and Hunan Provincial Key Laboratory for Medical Genetics, School of Life Sciences, Central South University, Changsha, China.,CAS Center for Excellence in Brain Science and Intelligences Technology (CEBSIT), Shanghai, China.,Key Laboratory of Medical Information Research, Central South University, Changsha, Hunan, China
| | - Fengyu Zhang
- Mental Health Institute, The Second Xiangya Hospital, Central South University, Changsha, China.,Global Clinical and Translational Research Institute, Bethesda, Maryland.,Peking University Huilongguan Clinical Medical School and Beijing Huilongguan Hospital, Beijing, China
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25
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Abstract
The promise of personalized genomic medicine is that knowledge of a person's gene sequences and activity will facilitate more appropriate medical interventions, particularly drug prescriptions, to reduce the burden of disease. Early successes in oncology and pediatrics have affirmed the power of positive diagnosis and are mostly based on detection of one or a few mutations that drive the specific pathology. However, genetically more complex diseases require the development of polygenic risk scores (PRSs) that have variable accuracy. The rarity of events often means that they have necessarily low precision: many called positives are actually not at risk, and only a fraction of cases are prevented by targeted therapy. In some situations, negative prediction may better define the population at low risk. Here, I review five conditions across a broad spectrum of chronic disease (opioid pain medication, hypertension, type 2 diabetes, major depression, and osteoporotic bone fracture), considering in each case how genetic prediction might be used to target drug prescription. This leads to a call for more research designed to evaluate genetic likelihood of response to therapy and a call for evaluation of PRS, not just in terms of sensitivity and specificity but also with respect to potential clinical efficacy.
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Affiliation(s)
- Greg Gibson
- Center for Integrative Genomics and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- * E-mail:
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26
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Amare AT, Schubert KO, Tekola-Ayele F, Hsu YH, Sangkuhl K, Jenkins G, Whaley RM, Barman P, Batzler A, Altman RB, Arolt V, Brockmöller J, Chen CH, Domschke K, Hall-Flavin DK, Hong CJ, Illi A, Ji Y, Kampman O, Kinoshita T, Leinonen E, Liou YJ, Mushiroda T, Nonen S, Skime MK, Wang L, Kato M, Liu YL, Praphanphoj V, Stingl JC, Bobo WV, Tsai SJ, Kubo M, Klein TE, Weinshilboum RM, Biernacka JM, Baune BT. The association of obesity and coronary artery disease genes with response to SSRIs treatment in major depression. J Neural Transm (Vienna) 2019; 126:35-45. [PMID: 30610379 DOI: 10.1007/s00702-018-01966-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 12/18/2018] [Indexed: 01/22/2023]
Abstract
Selective serotonin reuptake inhibitors (SSRIs) are first-line antidepressants for the treatment of major depressive disorder (MDD). However, treatment response during an initial therapeutic trial is often poor and is difficult to predict. Heterogeneity of response to SSRIs in depressed patients is partly driven by co-occurring somatic disorders such as coronary artery disease (CAD) and obesity. CAD and obesity may also be associated with metabolic side effects of SSRIs. In this study, we assessed the association of CAD and obesity with treatment response to SSRIs in patients with MDD using a polygenic score (PGS) approach. Additionally, we performed cross-trait meta-analyses to pinpoint genetic variants underpinnings the relationship of CAD and obesity with SSRIs treatment response. First, PGSs were calculated at different p value thresholds (PT) for obesity and CAD. Next, binary logistic regression was applied to evaluate the association of the PGSs to SSRIs treatment response in a discovery sample (ISPC, N = 865), and in a replication cohort (STAR*D, N = 1,878). Finally, a cross-trait GWAS meta-analysis was performed by combining summary statistics. We show that the PGSs for CAD and obesity were inversely associated with SSRIs treatment response. At the most significant thresholds, the PGS for CAD and body mass index accounted 1.3%, and 0.8% of the observed variability in treatment response to SSRIs, respectively. In the cross-trait meta-analyses, we identified (1) 14 genetic loci (including NEGR1, CADM2, PMAIP1, PARK2) that are associated with both obesity and SSRIs treatment response; (2) five genetic loci (LINC01412, PHACTR1, CDKN2B, ATXN2, KCNE2) with effects on CAD and SSRIs treatment response. Our findings implicate that the genetic variants of CAD and obesity are linked to SSRIs treatment response in MDD. A better SSRIs treatment response might be achieved through a stratified allocation of treatment for MDD patients with a genetic risk for obesity or CAD.
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Affiliation(s)
- Azmeraw T Amare
- Discipline of Psychiatry, School of Medicine, University of Adelaide, North Terrace, Adelaide, SA, 5005, Australia
- South Australian Academic Health Science and Translation Centre, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia
| | - Klaus Oliver Schubert
- Discipline of Psychiatry, School of Medicine, University of Adelaide, North Terrace, Adelaide, SA, 5005, Australia
- Northern Adelaide Local Health Network, Mental Health Services, Adelaide, SA, Australia
| | - Fasil Tekola-Ayele
- Epidemiology Branch, Division of Intramural Population Health Research, National Institute of Child Health and Human Development, Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yi-Hsiang Hsu
- HSL Institute for Aging Research, Harvard Medical School, Boston, MA, USA
- Program for Quantitative Genomics, Harvard School of Public Health, Boston, MA, USA
| | - Katrin Sangkuhl
- Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Gregory Jenkins
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Ryan M Whaley
- Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Poulami Barman
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Anthony Batzler
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Russ B Altman
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Volker Arolt
- Department of Psychiatry and Psychotherapy, University of Muenster, Muenster, Germany
| | - Jürgen Brockmöller
- Department of Clinical Pharmacology, University Göttingen, Göttingen, Germany
| | - Chia-Hui Chen
- Department of Psychiatry, Taipei Medical University-Shuangho Hospital, New Taipei City, Taiwan
| | - Katharina Domschke
- Department of Psychiatry and Psychotherapy, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | | | - Chen-Jee Hong
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan
- Division of Psychiatry, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Ari Illi
- Department of Psychiatry, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Yuan Ji
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Olli Kampman
- Department of Psychiatry, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
- Department of Psychiatry, Seinäjoki Hospital District, Seinäjoki, Finland
| | | | - Esa Leinonen
- Department of Psychiatry, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
- Department of Psychiatry, Tampere University Hospital, Tampere, Finland
| | - Ying-Jay Liou
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan
- Division of Psychiatry, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Taisei Mushiroda
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Shinpei Nonen
- Department of Pharmacy, Hyogo University of Health Sciences, Kobe, Hyogo, Japan
| | - Michelle K Skime
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Masaki Kato
- Department of Neuropsychiatry, Kansai Medical University, Osaka, Japan
| | - Yu-Li Liu
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli, Taiwan
| | - Verayuth Praphanphoj
- Center for Medical Genetics Research, Department of Mental Health, Ministry of Public Health Bangkok, Rajanukul Institute, Bangkok, Thailand
| | - Julia C Stingl
- Research Division Federal Institute for Drugs and Medical Devices, Bonn, Germany
| | - William V Bobo
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Shih-Jen Tsai
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan
- Division of Psychiatry, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Teri E Klein
- Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Richard M Weinshilboum
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Joanna M Biernacka
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Bernhard T Baune
- Discipline of Psychiatry, School of Medicine, University of Adelaide, North Terrace, Adelaide, SA, 5005, Australia.
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27
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Clark SR, Schubert KO, Olagunju AT, Lyrtzis EA, Baune BT. Cognitive and Functional Assessment of Psychosis Stratification Study (CoFAPSS): Rationale, Design, and Characteristics. Front Psychiatry 2018; 9:662. [PMID: 30559688 PMCID: PMC6287598 DOI: 10.3389/fpsyt.2018.00662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/19/2018] [Indexed: 11/13/2022] Open
Abstract
Prediction of treatment response and illness trajectory in psychotic disorders including schizophrenia, bipolar affective disorder, schizoaffective disorder, and psychotic depression is difficult due to heterogeneity in presentation and outcome. Consequently, patients may receive prolonged ineffective treatments leading to functional decline, illness chronicity, and iatrogenic physical illness. One approach to addressing these problems is to stratify patients based on historical, clinical, and biological signatures. Such an approach has the potential to improve categorization resulting in better understanding of underlying mechanisms and earlier evidence-based treatment with reduced side effect burden. To investigate these multimodal signatures we developed the Cognitive and Functional Assessment of Psychosis Stratification Study (CoFAPSS) employing a prospective study design and a healthy control group comparison. The main aim of this study is to investigate cognitive, and biological "genomics" markers of psychotic illnesses that can be integrated with clinical data to improve prediction of risk and define functional trajectories. We also aim to identify biological "genomic" signatures underpinning variation in treatment response and adverse medical outcomes. The study commenced in June 2016, including patients with primary diagnosis of psychotic disorders including schizophrenia, bipolar affective disorder, schizoaffective disorder, and psychotic depression according to DSM-5 criteria. The assessment covers a wide range of participant history (life stressors, trauma, and family history), cognitive dimensions (social perception, memory and learning, attention, executive function, and general cognition), measures to assess psychosocial function and quality of life, psychotic symptom severity, clinical course of illness, and parameters for adverse medical outcome. Blood is collected for comprehensive genomic discovery analyses of biological (genomic, transcriptomic, proteomic, and cell-biologic) markers. The CoFAPSS is a novel approach that integrates clinical, cognitive and biological "genomic" markers to clarify clinico-pathological basis of risk, functional trajectories, disease stratification, treatment response, and adverse medical outcome. The CoFAPSS team welcomes collaborations with both national and international investigators.
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Affiliation(s)
- Scott R Clark
- Discipline of Psychiatry, School of Medicine, The University of Adelaide Adelaide, SA, Australia
| | - K Oliver Schubert
- Discipline of Psychiatry, School of Medicine, The University of Adelaide Adelaide, SA, Australia
| | - Andrew T Olagunju
- Discipline of Psychiatry, School of Medicine, The University of Adelaide Adelaide, SA, Australia.,Department of Psychiatry University of Lagos, Lagos, Nigeria
| | - Ellen Alexandra Lyrtzis
- Discipline of Psychiatry, School of Medicine, The University of Adelaide Adelaide, SA, Australia
| | - Bernhard T Baune
- Discipline of Psychiatry, School of Medicine, The University of Adelaide Adelaide, SA, Australia.,Department of Psychiatry, Melbourne Medical School, The University of Melbourne Melbourne, VIC, Australia
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