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Acacio M, Mestres E, Clérico G, Domènech L, Formiguera G, Calderón G, Costa-Borges N. In vitro production of ICSI derived horse blastocysts. J Equine Vet Sci 2022. [DOI: 10.1016/j.jevs.2022.103974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Abstract
Tourette syndrome (TS) is a severe neuropsychiatric disorder characterized by recurrent, involuntary physical and verbal tics. With a prevalence as high as 1% in children, a deeper understanding of the etiology of the disorder and contributions to risk is critical. Here, we cover the current body of knowledge in scientific literature regarding the genetics of TS. We first review the history and diagnostic criteria for TS cases. We then cover the prevalence, and begin to address the etiology of the disorder. We highlight long-standing evidence for a genetic contribution to TS risk from epidemiology studies focused on twins, families, and population-scale data. Finally, we summarize current large-scale genetic studies of TS along specific classes of genetic variation, including common variation, rare copy number variation, and de novo variation that impact protein-coding sequence. Although these variants do not account for the entirety of TS genetic risk, current evidence is clear that each class of variation is a factor in the overall risk architecture across TS cases.
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Affiliation(s)
- Laura Domènech
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Carolina Cappi
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Matt Halvorsen
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Susak H, Serra-Saurina L, Demidov G, Rabionet R, Domènech L, Bosio M, Muyas F, Estivill X, Escaramís G, Ossowski S. Efficient and flexible Integration of variant characteristics in rare variant association studies using integrated nested Laplace approximation. PLoS Comput Biol 2021; 17:e1007784. [PMID: 33606672 PMCID: PMC7928502 DOI: 10.1371/journal.pcbi.1007784] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 03/03/2021] [Accepted: 01/04/2021] [Indexed: 12/02/2022] Open
Abstract
Rare variants are thought to play an important role in the etiology of complex diseases and may explain a significant fraction of the missing heritability in genetic disease studies. Next-generation sequencing facilitates the association of rare variants in coding or regulatory regions with complex diseases in large cohorts at genome-wide scale. However, rare variant association studies (RVAS) still lack power when cohorts are small to medium-sized and if genetic variation explains a small fraction of phenotypic variance. Here we present a novel Bayesian rare variant Association Test using Integrated Nested Laplace Approximation (BATI). Unlike existing RVAS tests, BATI allows integration of individual or variant-specific features as covariates, while efficiently performing inference based on full model estimation. We demonstrate that BATI outperforms established RVAS methods on realistic, semi-synthetic whole-exome sequencing cohorts, especially when using meaningful biological context, such as functional annotation. We show that BATI achieves power above 70% in scenarios in which competing tests fail to identify risk genes, e.g. when risk variants in sum explain less than 0.5% of phenotypic variance. We have integrated BATI, together with five existing RVAS tests in the 'Rare Variant Genome Wide Association Study' (rvGWAS) framework for data analyzed by whole-exome or whole genome sequencing. rvGWAS supports rare variant association for genes or any other biological unit such as promoters, while allowing the analysis of essential functionalities like quality control or filtering. Applying rvGWAS to a Chronic Lymphocytic Leukemia study we identified eight candidate predisposition genes, including EHMT2 and COPS7A.
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Affiliation(s)
- Hana Susak
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Laura Serra-Saurina
- Biomedical Research Networking Centre consortium of Public Health and Epidemiology (CIBERESP), Madrid, Spain
- Center for research in occupational Health (CiSAL), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Research Group on Statistics, Econometrics and Health (GRECS), Universitat de Girona (UdG), Girona, Spain
| | - German Demidov
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Raquel Rabionet
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, IBUB, Universitat de Barcelona; CIBERER, IRSJD, Barcelona, Spain
| | - Laura Domènech
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Biomedical Research Networking Centre consortium of Public Health and Epidemiology (CIBERESP), Madrid, Spain
| | - Mattia Bosio
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Francesc Muyas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Xavier Estivill
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Women’s Health Dexeus, Barcelona, Spain
| | - Geòrgia Escaramís
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Biomedical Research Networking Centre consortium of Public Health and Epidemiology (CIBERESP), Madrid, Spain
- Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona, Spain
| | - Stephan Ossowski
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
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Miarons M, Larrosa-García M, García-García S, Los-Arcos I, Moreso F, Berastegui C, Castells L, Pérez-Hoyos S, Varela J, Pau-Parra A, Varón-Galcera C, Parramon-Teixidó CJ, Martínez-Casanova J, Domènech L, García-Ortega P, Sánchez-Sancho P, Alonso-Martínez C, Gómez-Ganda L, Roch-Santed M, Gracia-Moya A, Del-Rio-Gutiérrez JM, Guillén-Del-Castillo A, Sans-Pola C, Antón A, Montoro B, Gorgas-Torner MQ. COVID-19 in Solid Organ Transplantation: A Matched Retrospective Cohort Study and Evaluation of Immunosuppression Management. Transplantation 2021; 105:138-150. [PMID: 32941394 DOI: 10.1097/tp.0000000000003460] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND The epidemiological and clinical characteristics of solid organ transplant (SOT) patients during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic remains unclear. We conducted a matched retrospective cohort study to compare clinical outcomes among SOT recipients with the general population and to assess immunosuppression management. METHODS Adult SOT recipients with laboratory polymerase chain reaction-confirmed SARS-CoV-2 infection admitted to a tertiary-care hospital in Barcelona, Spain, from March 11 to April 25, 2020, were matched to controls (1:4) on the basis of sex, age, and age-adjusted Charlson's Index. Patients were followed for up to 28 days from admission or until censored. Primary endpoint was mortality at 28 days. Secondary endpoints included admission to the intensive care unit and secondary complications. Drug-drug interactions (DDI) between immunosuppressants and coronavirus disease 2019 (COVID-19) management medication were collected. RESULTS Forty-six transplant recipients and 166 control patients were included. Mean (SD) age of transplant recipients and controls was 62.7 (12.6) and 66.0 (12.7) years, 33 (71.7%) and 122 (73.5%) were male, and median (interquartile range) Charlson's Index was 5 (3-7) and 4 (2-7), respectively. Mortality was 37.0% in SOT recipients and 22.9% in controls (P = 0.51). Thirty-three (71.7%) patients underwent transitory discontinuation of immunosuppressants due to potential or confirmed DDI. CONCLUSIONS In conclusion, hospitalized SOT recipients with COVID-19 had a trend toward higher mortality compared with controls, although it was not statistically significant, and a notable propensity for DDI.
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Affiliation(s)
- Marta Miarons
- Pharmacy Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - María Larrosa-García
- Pharmacy Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Sonia García-García
- Pharmacy Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Ibai Los-Arcos
- Infectious Diseases Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Francesc Moreso
- Nephrology Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Cristina Berastegui
- Pneumology Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Lluís Castells
- Liver Unit, Internal Medicine Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Santiago Pérez-Hoyos
- Statistic Unit, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Javier Varela
- Pharmacy Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Alba Pau-Parra
- Pharmacy Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Carlota Varón-Galcera
- Pharmacy Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | | | - Javier Martínez-Casanova
- Pharmacy Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Laura Domènech
- Pharmacy Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Patricia García-Ortega
- Pharmacy Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Pablo Sánchez-Sancho
- Pharmacy Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Carla Alonso-Martínez
- Pharmacy Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Laura Gómez-Ganda
- Pharmacy Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Maria Roch-Santed
- Pharmacy Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Ariadna Gracia-Moya
- Pharmacy Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | | | - Alfredo Guillén-Del-Castillo
- Internal Medicine Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Carla Sans-Pola
- Pharmacology Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Andrés Antón
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Bruno Montoro
- Pharmacy Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Maria-Queralt Gorgas-Torner
- Pharmacy Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
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Alemany-Navarro M, Cruz R, Real E, Segalàs C, Bertolín S, Baenas I, Domènech L, Rabionet R, Carracedo Á, Menchón JM, Alonso P. Corrigendum to `Exploring Genetic Variants in Obsessive Compulsive Disorder Severity: A GWAS Approach.' Journal of Affective Disorders 267 (2020) 23-32. J Affect Disord 2020; 274:1222. [PMID: 32663960 DOI: 10.1016/j.jad.2020.05.157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- María Alemany-Navarro
- Institut d' Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain; OCD Clinical and Research Unit, Psychiatry Department, Hospital Universitari de Bellvitge, Barcelona, Spain..
| | - Raquel Cruz
- Grupo de Medicina Xenómica, CIBERER, Centre for Research in Molecular Medicine and Chronic Diseases, CIMUS-, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Eva Real
- Institut d' Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain; OCD Clinical and Research Unit, Psychiatry Department, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Cinto Segalàs
- Institut d' Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain; OCD Clinical and Research Unit, Psychiatry Department, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Sara Bertolín
- OCD Clinical and Research Unit, Psychiatry Department, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Isabel Baenas
- OCD Clinical and Research Unit, Psychiatry Department, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Laura Domènech
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Raquel Rabionet
- Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), CIBERER, and Dept. Genetics, Microbiology & statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Ángel Carracedo
- Grupo de Medicina Xenómica, CIBERER, Centre for Research in Molecular Medicine and Chronic Diseases, CIMUS-, Universidade de Santiago de Compostela, Santiago de Compostela, Spain; Fundación Pública Galega de Medicina Xenómica, SERGAS, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Jose M Menchón
- Institut d' Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain; OCD Clinical and Research Unit, Psychiatry Department, Hospital Universitari de Bellvitge, Barcelona, Spain; Department of Clinical Sciences, Bellvitge Campus, University of Barcelona, Barcelona, Spain; CIBERSAM (Centro de Investigación en Red de Salud Mental), Instituto de Salud Carlos III, Spain
| | - Pino Alonso
- OCD Clinical and Research Unit, Psychiatry Department, Hospital Universitari de Bellvitge, Barcelona, Spain; Department of Clinical Sciences, Bellvitge Campus, University of Barcelona, Barcelona, Spain; CIBERSAM (Centro de Investigación en Red de Salud Mental), Instituto de Salud Carlos III, Spain
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Alemany-Navarro M, Cruz R, Real E, Segalàs C, Bertolín S, Baenas I, Domènech L, Rabionet R, Carracedo Á, Menchón JM, Alonso P. Exploring genetic variants in obsessive compulsive disorder severity: A GWAS approach. J Affect Disord 2020; 267:23-32. [PMID: 32063569 DOI: 10.1016/j.jad.2020.01.161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 11/22/2019] [Accepted: 01/28/2020] [Indexed: 01/11/2023]
Abstract
BACKGROUND The severity of Obsessive-Compulsive Disorder (OCD) varies significantly among probands. No study has specifically investigated the genetic base of OCD severity. A previous study from our group found an OCD polygenic risk score to predict pre- and post-treatment severity. This study explores the genomic bases of OCD severity. METHODS We administered the Yale-Brown Obsessive Compulsive Scale (Y-BOCS) to 401 patients at their first visit to our clinic to measure their OCD severity. Genotyping data was collected by using the Infinium PsychArray-24 BeadChip kit (Illumina). We analyzed genetic association with OCD severity in a linear regression analysis at single-nucleotide polymorphism (SNP)- and gene-levels, this last also considering rare variants. Enrichment analyses were performed from gene-based analyses' results. RESULTS No SNP reached significant association (p < 10-8) with the YBOCS. Six markers showed suggestive association (p < 10-5). The top SNP was an intergenic variant in chromosome 2: rs7578149 (p < 1.89 × 10-6), located in a region suggestively associated with MDD. Linkage disequilibrium was found for two clusters of SNPs located between SLC16A14 and SP110 in chromosome 2, all of them forming one peak of association. Enrichment analyses revealed OCD genes to be associated with porin activity (FDR = 0.01) and transmembrane structure (FDR = 0.04). LIMITATIONS The size of the sample and the transversal nature of the severity measure are limitations of this study. CONCLUSION This study contributes to better characterize OCD at an individual level, helping to know more about the prognosis of the disorder and develop more individualized treatments.
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Affiliation(s)
- María Alemany-Navarro
- Institut d' Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain; OCD Clinical and Research Unit, Psychiatry Department, Hospital Universitari de Bellvitge, Barcelona, Spain.
| | - Raquel Cruz
- Grupo de Medicina Xenómica, CIBERER, Centre for Research in Molecular Medicine and Chronic Diseases, CIMUS-, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Eva Real
- Institut d' Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain; OCD Clinical and Research Unit, Psychiatry Department, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Cinto Segalàs
- Institut d' Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain; OCD Clinical and Research Unit, Psychiatry Department, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Sara Bertolín
- OCD Clinical and Research Unit, Psychiatry Department, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Isabel Baenas
- OCD Clinical and Research Unit, Psychiatry Department, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Laura Domènech
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Raquel Rabionet
- Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), CIBERER, and Dept. Genetics, Microbiology & statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Ángel Carracedo
- Grupo de Medicina Xenómica, CIBERER, Centre for Research in Molecular Medicine and Chronic Diseases, CIMUS-, Universidade de Santiago de Compostela, Santiago de Compostela, Spain; Fundación Pública Galega de Medicina Xenómica, SERGAS, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Jose M Menchón
- Institut d' Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain; OCD Clinical and Research Unit, Psychiatry Department, Hospital Universitari de Bellvitge, Barcelona, Spain; Department of Clinical Sciences, Bellvitge Campus, University of Barcelona, Barcelona, Spain; CIBERSAM (Centro de Investigación en Red de Salud Mental), Instituto de Salud Carlos III, Spain
| | - Pino Alonso
- OCD Clinical and Research Unit, Psychiatry Department, Hospital Universitari de Bellvitge, Barcelona, Spain; Department of Clinical Sciences, Bellvitge Campus, University of Barcelona, Barcelona, Spain; CIBERSAM (Centro de Investigación en Red de Salud Mental), Instituto de Salud Carlos III, Spain
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Alemany-Navarro M, Costas J, Real E, Segalàs C, Bertolín S, Domènech L, Rabionet R, Carracedo Á, Menchón JM, Alonso P. Do polygenic risk and stressful life events predict pharmacological treatment response in obsessive compulsive disorder? A gene-environment interaction approach. Transl Psychiatry 2019; 9:70. [PMID: 30718812 PMCID: PMC6362161 DOI: 10.1038/s41398-019-0410-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 08/18/2018] [Accepted: 11/08/2018] [Indexed: 12/13/2022] Open
Abstract
The rate of response to pharmacological treatment in Obsessive-compulsive disorder (OCD) oscillates between 40 and 70%. Genetic and environmental factors have been associated with treatment response in OCD. This study analyzes the predictive ability of a polygenic risk score (PRS) built from OCD-risk variants, for treatment response in OCD, and the modulation role of stressful life events (SLEs) at the onset of the disorder. PRSs were calculated for a sample of 103 patients. Yale-Brown Obsessive Compulsive Scale (YBOCS) scores were obtained before and after a 12-week treatment. Regression analyses were performed to analyze the influence of the PRS and SLEs at onset on treatment response. PRS did not predict treatment response. The best predictive model for post-treatment YBOCS (post YBOCS) included basal YBOCS and age. PRS appeared as a predictor for basal and post YBOCS. SLEs at onset were not a predictor for treatment response when included in the regression model. No evidence for PRS predictive ability for treatment response was found. The best predictor for treatment response was age, agreeing with previous literature specific for SRI treatment. Suggestions are made on the possible role of neuroplasticity as a mediator on this association. PRS significantly predicted OCD severity independent on pharmacological treatment. SLE at onset modulation role was not evidenced. Further research is needed to elucidate the genetic and environmental bases of treatment response in OCD.
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Affiliation(s)
- María Alemany-Navarro
- Institut d' Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat (Barcelona), Spain. .,OCD Clinical and Research Unit, Psychiatry Department, Hospital Universitari de Bellvitge, L'Hospitalet de Llobregat (Barcelona), Spain.
| | - Javier Costas
- 0000 0000 9403 4738grid.420359.9Grupo de Xenética Psiquiátrica, Instituto de Investigación Sanitaria de Santiago, Complexo Hospitalario Universitario de Santiago de Compostela, Servizo Galego de Saúde, Santiago de Compostela, Spain
| | - Eva Real
- Institut d’ Investigació Biomèdica de Bellvitge (IDIBELL), L’Hospitalet de Llobregat (Barcelona), Spain ,0000 0000 8836 0780grid.411129.eOCD Clinical and Research Unit, Psychiatry Department, Hospital Universitari de Bellvitge, L’Hospitalet de Llobregat (Barcelona), Spain
| | - Cinto Segalàs
- Institut d’ Investigació Biomèdica de Bellvitge (IDIBELL), L’Hospitalet de Llobregat (Barcelona), Spain ,0000 0000 8836 0780grid.411129.eOCD Clinical and Research Unit, Psychiatry Department, Hospital Universitari de Bellvitge, L’Hospitalet de Llobregat (Barcelona), Spain
| | - Sara Bertolín
- 0000 0000 8836 0780grid.411129.eOCD Clinical and Research Unit, Psychiatry Department, Hospital Universitari de Bellvitge, L’Hospitalet de Llobregat (Barcelona), Spain
| | - Laura Domènech
- grid.473715.3Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003 Spain ,0000 0001 2172 2676grid.5612.0Universitat Pompeu Fabra (UPF), Barcelona, Spain ,CIBER in Epidemiology and Public Health (CIBERESP), Barcelona, Spain
| | - Raquel Rabionet
- grid.473715.3Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003 Spain ,0000 0001 2172 2676grid.5612.0Universitat Pompeu Fabra (UPF), Barcelona, Spain ,CIBER in Epidemiology and Public Health (CIBERESP), Barcelona, Spain
| | - Ángel Carracedo
- 0000 0000 9403 4738grid.420359.9Grupo de Xenética Psiquiátrica, Instituto de Investigación Sanitaria de Santiago, Complexo Hospitalario Universitario de Santiago de Compostela, Servizo Galego de Saúde, Santiago de Compostela, Spain ,0000000109410645grid.11794.3aGrupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro Nacional de Genotipado - Instituto Carlos III, Santiago de Compostela, Spain ,0000 0004 1791 1185grid.452372.5Centro de Investigación Biomédica en Red de Enfermedades Raras, Santiago de Compostela, Spain
| | - Jose M. Menchón
- Institut d’ Investigació Biomèdica de Bellvitge (IDIBELL), L’Hospitalet de Llobregat (Barcelona), Spain ,0000 0000 8836 0780grid.411129.eOCD Clinical and Research Unit, Psychiatry Department, Hospital Universitari de Bellvitge, L’Hospitalet de Llobregat (Barcelona), Spain ,0000 0000 9314 1427grid.413448.eCIBERSAM (Centro de Investigación en Red de Salud Mental), Instituto de Salud Carlos III, Madrid, Spain ,0000 0004 1937 0247grid.5841.8Department of Clinical Sciences, Bellvitge Campus, University of Barcelona, Barcelona, Spain
| | - Pino Alonso
- Institut d’ Investigació Biomèdica de Bellvitge (IDIBELL), L’Hospitalet de Llobregat (Barcelona), Spain ,0000 0000 8836 0780grid.411129.eOCD Clinical and Research Unit, Psychiatry Department, Hospital Universitari de Bellvitge, L’Hospitalet de Llobregat (Barcelona), Spain ,0000 0000 9314 1427grid.413448.eCIBERSAM (Centro de Investigación en Red de Salud Mental), Instituto de Salud Carlos III, Madrid, Spain ,0000 0004 1937 0247grid.5841.8Department of Clinical Sciences, Bellvitge Campus, University of Barcelona, Barcelona, Spain
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Muyas F, Bosio M, Puig A, Susak H, Domènech L, Escaramis G, Zapata L, Demidov G, Estivill X, Rabionet R, Ossowski S. Allele balance bias identifies systematic genotyping errors and false disease associations. Hum Mutat 2018; 40:115-126. [PMID: 30353964 PMCID: PMC6587442 DOI: 10.1002/humu.23674] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 09/17/2018] [Accepted: 10/20/2018] [Indexed: 12/13/2022]
Abstract
In recent years, next‐generation sequencing (NGS) has become a cornerstone of clinical genetics and diagnostics. Many clinical applications require high precision, especially if rare events such as somatic mutations in cancer or genetic variants causing rare diseases need to be identified. Although random sequencing errors can be modeled statistically and deep sequencing minimizes their impact, systematic errors remain a problem even at high depth of coverage. Understanding their source is crucial to increase precision of clinical NGS applications. In this work, we studied the relation between recurrent biases in allele balance (AB), systematic errors, and false positive variant calls across a large cohort of human samples analyzed by whole exome sequencing (WES). We have modeled the AB distribution for biallelic genotypes in 987 WES samples in order to identify positions recurrently deviating significantly from the expectation, a phenomenon we termed allele balance bias (ABB). Furthermore, we have developed a genotype callability score based on ABB for all positions of the human exome, which detects false positive variant calls that passed state‐of‐the‐art filters. Finally, we demonstrate the use of ABB for detection of false associations proposed by rare variant association studies. Availability: https://github.com/Francesc-Muyas/ABB.
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Affiliation(s)
- Francesc Muyas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Mattia Bosio
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Anna Puig
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Hana Susak
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Laura Domènech
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER in Epidemiology and Public Health (CIBERESP), Barcelona, Spain
| | - Georgia Escaramis
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER in Epidemiology and Public Health (CIBERESP), Barcelona, Spain
| | - Luis Zapata
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - German Demidov
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Xavier Estivill
- Sidra Medicine, Doha, Qatar.,Women's Health Dexeus, Barcelona, Spain
| | - Raquel Rabionet
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER in Epidemiology and Public Health (CIBERESP), Barcelona, Spain.,Institut de Recerca Sant Joan de Déu; Institut de Biomedicina de la Universitat de Barcelona (IBUB), ; & Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - Stephan Ossowski
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
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9
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Costas J, Carrera N, Alonso P, Gurriarán X, Segalàs C, Real E, López-Solà C, Mas S, Gassó P, Domènech L, Morell M, Quintela I, Lázaro L, Menchón JM, Estivill X, Carracedo Á. Exon-focused genome-wide association study of obsessive-compulsive disorder and shared polygenic risk with schizophrenia. Transl Psychiatry 2016; 6:e768. [PMID: 27023174 PMCID: PMC4872458 DOI: 10.1038/tp.2016.34] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 12/11/2015] [Accepted: 02/10/2016] [Indexed: 12/17/2022] Open
Abstract
Common single-nucleotide polymorphisms (SNPs) account for a large proportion of the heritability of obsessive-compulsive disorder (OCD). Co-ocurrence of OCD and schizophrenia is commoner than expected based on their respective prevalences, complicating the clinical management of patients. This study addresses two main objectives: to identify particular genes associated with OCD by SNP-based and gene-based tests; and to test the existence of a polygenic risk shared with schizophrenia. The primary analysis was an exon-focused genome-wide association study of 370 OCD cases and 443 controls from Spain. A polygenic risk model based on the Psychiatric Genetics Consortium schizophrenia data set (PGC-SCZ2) was tested in our OCD data. A polygenic risk model based on our OCD data was tested on previous data of schizophrenia from our group. The most significant association at the gene-based test was found at DNM3 (P=7.9 × 10(-5)), a gene involved in synaptic vesicle endocytosis. The polygenic risk model from PGC-SCZ2 data was strongly associated with disease status in our OCD sample, reaching its most significant value after removal of the major histocompatibility complex region (lowest P=2.3 × 10(-6), explaining 3.7% of the variance). The shared polygenic risk was confirmed in our schizophrenia data. In conclusion, DNM3 may be involved in risk to OCD. The shared polygenic risk between schizophrenia and OCD may be partially responsible for the frequent comorbidity of both disorders, explaining epidemiological data on cross-disorder risk. This common etiology may have clinical implications.
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Affiliation(s)
- J Costas
- Grupo de Xenética Psiquiátrica, Instituto de Investigación Sanitaria de Santiago, Complexo Hospitalario Universitario de Santiago de Compostela, Servizo Galego de Saúde, Santiago de Compostela, Spain,Grupo de Xenética Psiquiátrica, Instituto de Investigación Sanitaria de Santiago, Complexo Hospitalario Universitario de Santiago de Compostela, Servizo Galego de Saúde, despacho 15, E-15706 Santiago de Compostela, Spain. E-mail:
| | - N Carrera
- Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK,Fundación Pública Galega de Medicina Xenómica, Servicio Galego de Saúde, Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain
| | - P Alonso
- OCD Clinical and Research Unit, Department of Psychiatry, Hospital de Bellvitge, Barcelona, Spain,Bellvitge Biomedical Research Institute-IDIBELL, Barcelona, Spain,Centro de Investigación Biomédica en Red de Salud Mental, Carlos III Health Institute, Madrid, Spain,Department of Clinical Sciences, Bellvitge Campus, University of Barcelona, Barcelona, Spain
| | - X Gurriarán
- Grupo de Xenética Psiquiátrica, Instituto de Investigación Sanitaria de Santiago, Complexo Hospitalario Universitario de Santiago de Compostela, Servizo Galego de Saúde, Santiago de Compostela, Spain,Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - C Segalàs
- OCD Clinical and Research Unit, Department of Psychiatry, Hospital de Bellvitge, Barcelona, Spain,Bellvitge Biomedical Research Institute-IDIBELL, Barcelona, Spain,Centro de Investigación Biomédica en Red de Salud Mental, Carlos III Health Institute, Madrid, Spain
| | - E Real
- OCD Clinical and Research Unit, Department of Psychiatry, Hospital de Bellvitge, Barcelona, Spain,Bellvitge Biomedical Research Institute-IDIBELL, Barcelona, Spain,Centro de Investigación Biomédica en Red de Salud Mental, Carlos III Health Institute, Madrid, Spain
| | - C López-Solà
- OCD Clinical and Research Unit, Department of Psychiatry, Hospital de Bellvitge, Barcelona, Spain,Bellvitge Biomedical Research Institute-IDIBELL, Barcelona, Spain,Centro de Investigación Biomédica en Red de Salud Mental, Carlos III Health Institute, Madrid, Spain
| | - S Mas
- Centro de Investigación Biomédica en Red de Salud Mental, Carlos III Health Institute, Madrid, Spain,Department of Anatomic Pathology, Pharmacology and Microbiology, University of Barcelona, Barcelona, Spain,Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - P Gassó
- Department of Anatomic Pathology, Pharmacology and Microbiology, University of Barcelona, Barcelona, Spain,Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain,Department of Psychiatry and Clinical Psychobiology, University of Barcelona, Barcelona, Spain
| | - L Domènech
- Genomics and Disease Group, Centre for Genomic Regulation, Barcelona, Spain,Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain,Centro de Investigación Biomédica en Red Epidemiología y Salud Pública, Centre for Genomic Regulation, Barcelona, Spain,Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - M Morell
- Genomics and Disease Group, Centre for Genomic Regulation, Barcelona, Spain,Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain,Centro de Investigación Biomédica en Red Epidemiología y Salud Pública, Centre for Genomic Regulation, Barcelona, Spain,Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - I Quintela
- Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro Nacional de Genotipado - Instituto Carlos III, Santiago de Compostela, Spain,Centro de Investigación Biomédica en Red de Enfermedades Raras, Santiago de Compostela, Spain
| | - L Lázaro
- Centro de Investigación Biomédica en Red de Salud Mental, Carlos III Health Institute, Madrid, Spain,Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain,Department of Psychiatry and Clinical Psychobiology, University of Barcelona, Barcelona, Spain,Department of Child and Adolescent Psychiatry and Psychology, Institute of Neurosciences, Hospital Clínic Universitari, Barcelona, Spain
| | - J M Menchón
- OCD Clinical and Research Unit, Department of Psychiatry, Hospital de Bellvitge, Barcelona, Spain,Bellvitge Biomedical Research Institute-IDIBELL, Barcelona, Spain,Centro de Investigación Biomédica en Red de Salud Mental, Carlos III Health Institute, Madrid, Spain,Department of Clinical Sciences, Bellvitge Campus, University of Barcelona, Barcelona, Spain
| | - X Estivill
- Genomics and Disease Group, Centre for Genomic Regulation, Barcelona, Spain,Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain,Centro de Investigación Biomédica en Red Epidemiología y Salud Pública, Centre for Genomic Regulation, Barcelona, Spain,Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Á Carracedo
- Fundación Pública Galega de Medicina Xenómica, Servicio Galego de Saúde, Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain,Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro Nacional de Genotipado - Instituto Carlos III, Santiago de Compostela, Spain,Centro de Investigación Biomédica en Red de Enfermedades Raras, Santiago de Compostela, Spain
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