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Han J, Chear S, Talbot J, Swier V, Booth C, Reuben-Thomas C, Dalvi S, Weimer JM, Hewitt AW, Cook AL, Singh R. Genetic and cellular basis of impaired phagocytosis and photoreceptor degeneration in CLN3 disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.09.597388. [PMID: 38895469 PMCID: PMC11185776 DOI: 10.1101/2024.06.09.597388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Purpose CLN3 Batten disease (also known as Juvenile Neuronal Ceroid Lipofuscinosis; JNCL) is a lysosomal storage disorder that typically initiates with retinal degeneration but is followed by seizure onset, motor decline and premature death. Patient-derived CLN3 disease iPSC-RPE cells show defective phagocytosis of photoreceptor outer segments (POSs). Because modifier genes are implicated in CLN3 disease, our goal here was to investigate a direct link between CLN3 mutation and POS phagocytosis defect. Methods Isogenic control and CLN3 mutant stem cell lines were generated by CRISPR-Cas9-mediated biallelic deletion of exons 7 and 8. A transgenic CLN3 Δ 7-8/ Δ 7-8 ( CLN3 ) Yucatan miniswine was also used to study the impact of CLN3 Δ 7-8/ Δ 7-8 mutation on POS phagocytosis. POS phagocytosis by cultured RPE cells was analyzed by Western blotting and immunohistochemistry. Electroretinogram, optical coherence tomography and histological analysis of CLN3 Δ 7/8 and wild-type miniswine eyes were carried out at 6-, 36-, or 48-month age. Results CLN3 Δ 7-8/ Δ 7-8 RPE ( CLN3 RPE) displayed reduced POS binding and consequently decreased uptake of POS compared to isogenic control RPE cells. Furthermore, wild-type miniswine RPE cells phagocytosed CLN3 Δ 7-8/ Δ 7-8 POS less efficiently than wild-type POS. Consistent with decreased POS phagocytosis, lipofuscin/autofluorescence was decreased in CLN3 miniswine RPE at 36 months-of-age and was followed by almost complete loss of photoreceptors at 48 months of age. Conclusions CLN3 Δ 7-8/ Δ 7-8 mutation (that affects up to 85% patients) affects both RPE and POSs and leads to photoreceptor cell loss in CLN3 disease. Furthermore, both primary RPE dysfunction and mutant POS independently contribute to impaired POS phagocytosis in CLN3 disease.
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Sha Z, Sun KY, Jung B, Barzilay R, Moore TM, Almasy L, Forsyth JK, Prem S, Gandal MJ, Seidlitz J, Glessner JT, Alexander-Bloch AF. The copy number variant architecture of psychopathology and cognitive development in the ABCD ® study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.14.24307376. [PMID: 38798629 PMCID: PMC11118651 DOI: 10.1101/2024.05.14.24307376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Importance Childhood is a crucial developmental phase for mental health and cognitive function, both of which are commonly affected in patients with psychiatric disorders. This neurodevelopmental trajectory is shaped by a complex interplay of genetic and environmental factors. While common genetic variants account for a large proportion of inherited genetic risk, rare genetic variations, particularly copy number variants (CNVs), play a significant role in the genetic architecture of neurodevelopmental disorders. Despite their importance, the relevance of CNVs to child psychopathology and cognitive function in the general population remains underexplored. Objective Investigating CNV associations with dimensions of child psychopathology and cognitive functions. Design Setting and Participants ABCD® study focuses on a cohort of over 11,875 youth aged 9 to 10, recruited from 21 sites in the US, aiming to investigate the role of various factors, including brain, environment, and genetic factors, in the etiology of mental and physical health from middle childhood through early adulthood. Data analysis occurred from April 2023 to April 2024. Main Outcomes and Measures In this study, we utilized PennCNV and QuantiSNP algorithms to identify duplications and deletions larger than 50Kb across a cohort of 11,088 individuals from the Adolescent Brain Cognitive Development® study. CNVs meeting quality control standards were subjected to a genome-wide association scan to identify regions associated with quantitative measures of broad psychiatric symptom domains and cognitive outcomes. Additionally, a CNV risk score, reflecting the aggregated burden of genetic intolerance to inactivation and dosage sensitivity, was calculated to assess its impact on variability in overall and dimensional child psychiatric and cognitive phenotypes. Results In a final sample of 8,564 individuals (mean age=9.9 years, 4,532 males) passing quality control, we identified 4,111 individuals carrying 5,760 autosomal CNVs. Our results revealed significant associations between specific CNVs and our phenotypes of interest, psychopathology and cognitive function. For instance, a duplication at 10q26.3 was associated with overall psychopathology, and somatic complaints in particular. Additionally, deletions at 1q12.1, along with duplications at 14q11.2 and 10q26.3, were linked to overall cognitive function, with particular contributions from fluid intelligence (14q11.2), working memory (10q26.3), and reading ability (14q11.2). Moreover, individuals carrying CNVs previously associated with neurodevelopmental disorders exhibited greater impairment in social functioning and cognitive performance across multiple domains, in particular working memory. Notably, a higher deletion CNV risk score was significantly correlated with increased overall psychopathology (especially in dimensions of social functioning, thought disorder, and attention) as well as cognitive impairment across various domains. Conclusions and Relevance In summary, our findings shed light on the contributions of CNVs to interindividual variability in complex traits related to neurocognitive development and child psychopathology.
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Affiliation(s)
- Zhiqiang Sha
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Lifespan Brain Institute, The Children’s Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
| | - Kevin Y. Sun
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Lifespan Brain Institute, The Children’s Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
| | - Benjamin Jung
- Section on Neurobehavioral and Clinical Research, Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ran Barzilay
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Lifespan Brain Institute, The Children’s Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
| | - Tyler M. Moore
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - Laura Almasy
- Lifespan Brain Institute, The Children’s Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Smrithi Prem
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA
- Graduate Program in Neuroscience, Rutgers University, Piscataway, NJ, USA
| | - Michael J. Gandal
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Lifespan Brain Institute, The Children’s Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jakob Seidlitz
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Lifespan Brain Institute, The Children’s Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
| | - Joseph T. Glessner
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Aaron F. Alexander-Bloch
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Lifespan Brain Institute, The Children’s Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
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3
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Schmilovich Z, Bourque VR, Douard E, Huguet G, Poulain C, Ross JP, Alipour P, Castonguay CÉ, Younis N, Jean-Louis M, Saci Z, Pausova Z, Paus T, Schuman G, Porteous D, Davies G, Redmond P, Harris SE, Deary IJ, Whalley H, Hayward C, Dion PA, Jacquemont S, Rouleau GA. Copy-number variants and polygenic risk for intelligence confer risk for autism spectrum disorder irrespective of their effects on cognitive ability. Front Psychiatry 2024; 15:1369767. [PMID: 38751416 PMCID: PMC11094536 DOI: 10.3389/fpsyt.2024.1369767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/05/2024] [Indexed: 05/18/2024] Open
Abstract
Introduction Rare copy number variants (CNVs) and polygenic risk for intelligence (PRS-IQ) both confer susceptibility for autism spectrum disorder (ASD) but have opposing effects on cognitive ability. The field has struggled to disentangle the effects of these two classes of genomic variants on cognitive ability from their effects on ASD susceptibility, in part because previous studies did not include controls with cognitive measures. We aim to investigate the impact of these genomic variants on ASD risk while adjusting for their known effects on cognitive ability. Methods In a cohort of 8,426 subjects with ASD and 169,804 controls with cognitive assessments, we found that rare coding CNVs and PRS-IQ increased ASD risk, even after adjusting for their effects on cognitive ability. Results Bottom decile PRS-IQ and CNVs both decreased cognitive ability but had opposing effects on ASD risk. Models combining both classes of variants showed that the effects of rare CNVs and PRS-IQ on ASD risk and cognitive ability were largely additive, further suggesting that susceptibility for ASD is conferred independently from its effects on cognitive ability. Despite imparting mostly additive effects on ASD risk, rare CNVs and PRS-IQ showed opposing effects on core and associated features and developmental history among subjects with ASD. Discussion Our findings suggest that cognitive ability itself may not be the factor driving the underlying liability for ASD conferred by these two classes of genomic variants. In other words, ASD risk and cognitive ability may be two distinct manifestations of CNVs and PRS-IQ. This study also highlights the challenge of understanding how genetic risk for ASD maps onto its dimensional traits.
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Affiliation(s)
- Zoe Schmilovich
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
| | - Vincent-Raphaël Bourque
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
- Département de Pédiatrie, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Elise Douard
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
- Département de Pédiatrie, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Guillaume Huguet
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
| | - Cécile Poulain
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
- Département de Pédiatrie, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Jay P. Ross
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
| | - Paria Alipour
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
| | - Charles-Étienne Castonguay
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
| | - Nadine Younis
- Département de Pédiatrie, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Martineau Jean-Louis
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
| | - Zohra Saci
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
| | - Zdenka Pausova
- The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
- Departments of Physiology and Nutritional Sciences, University of Toronto, Toronto, ON, Canada
| | - Tomas Paus
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
- Departments of Psychiatry of Neuroscience, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
- Departments of Psychology and Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Gunter Schuman
- Institute of Psychiatry, Psychology, and Neuroscience, King’s College London, London, United Kingdom
| | - David Porteous
- Lothian Birth Cohorts Group, Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, Edinburgh, United Kingdom
- Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, The University of Edinburgh, Edinburgh, United Kingdom
| | - Gail Davies
- Lothian Birth Cohorts Group, Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Paul Redmond
- Lothian Birth Cohorts Group, Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Sarah E. Harris
- Lothian Birth Cohorts Group, Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Ian J. Deary
- Lothian Birth Cohorts Group, Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Heather Whalley
- Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, The University of Edinburgh, Edinburgh, United Kingdom
| | - Caroline Hayward
- Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, The University of Edinburgh, Edinburgh, United Kingdom
| | - Patrick A. Dion
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
| | - Sébastien Jacquemont
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
- Département de Pédiatrie, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Guy A. Rouleau
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
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4
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Kopal J, Kumar K, Shafighi K, Saltoun K, Modenato C, Moreau CA, Huguet G, Jean-Louis M, Martin CO, Saci Z, Younis N, Douard E, Jizi K, Beauchamp-Chatel A, Kushan L, Silva AI, van den Bree MBM, Linden DEJ, Owen MJ, Hall J, Lippé S, Draganski B, Sønderby IE, Andreassen OA, Glahn DC, Thompson PM, Bearden CE, Zatorre R, Jacquemont S, Bzdok D. Using rare genetic mutations to revisit structural brain asymmetry. Nat Commun 2024; 15:2639. [PMID: 38531844 PMCID: PMC10966068 DOI: 10.1038/s41467-024-46784-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
Asymmetry between the left and right hemisphere is a key feature of brain organization. Hemispheric functional specialization underlies some of the most advanced human-defining cognitive operations, such as articulated language, perspective taking, or rapid detection of facial cues. Yet, genetic investigations into brain asymmetry have mostly relied on common variants, which typically exert small effects on brain-related phenotypes. Here, we leverage rare genomic deletions and duplications to study how genetic alterations reverberate in human brain and behavior. We designed a pattern-learning approach to dissect the impact of eight high-effect-size copy number variations (CNVs) on brain asymmetry in a multi-site cohort of 552 CNV carriers and 290 non-carriers. Isolated multivariate brain asymmetry patterns spotlighted regions typically thought to subserve lateralized functions, including language, hearing, as well as visual, face and word recognition. Planum temporale asymmetry emerged as especially susceptible to deletions and duplications of specific gene sets. Targeted analysis of common variants through genome-wide association study (GWAS) consolidated partly diverging genetic influences on the right versus left planum temporale structure. In conclusion, our gene-brain-behavior data fusion highlights the consequences of genetically controlled brain lateralization on uniquely human cognitive capacities.
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Affiliation(s)
- Jakub Kopal
- Mila - Québec Artificial Intelligence Institute, Montréal, QC, Canada
- Department of Biomedical Engineering, Faculty of Medicine, McGill University, Montreal, Canada
| | - Kuldeep Kumar
- Centre de recherche CHU Sainte-Justine, Montréal, Quebec, Canada
| | - Kimia Shafighi
- Mila - Québec Artificial Intelligence Institute, Montréal, QC, Canada
- Department of Biomedical Engineering, Faculty of Medicine, McGill University, Montreal, Canada
| | - Karin Saltoun
- Mila - Québec Artificial Intelligence Institute, Montréal, QC, Canada
- Department of Biomedical Engineering, Faculty of Medicine, McGill University, Montreal, Canada
| | - Claudia Modenato
- LREN - Department of Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
| | - Clara A Moreau
- Imaging Genetics Center, Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, Marina del Rey, CA, USA
| | - Guillaume Huguet
- Centre de recherche CHU Sainte-Justine, Montréal, Quebec, Canada
| | | | | | - Zohra Saci
- Centre de recherche CHU Sainte-Justine, Montréal, Quebec, Canada
| | - Nadine Younis
- Centre de recherche CHU Sainte-Justine, Montréal, Quebec, Canada
| | - Elise Douard
- Centre de recherche CHU Sainte-Justine, Montréal, Quebec, Canada
| | - Khadije Jizi
- Centre de recherche CHU Sainte-Justine, Montréal, Quebec, Canada
| | - Alexis Beauchamp-Chatel
- Institut universitaire en santé mentale de Montréal, University of Montréal, Montréal, Canada
- Department of Psychiatry, University of Montreal, Montréal, Canada
| | - Leila Kushan
- Semel Institute for Neuroscience and Human Behavior, Departments of Psychiatry and Biobehavioral Sciences and Psychology, UCLA, Los Angeles, USA
| | - Ana I Silva
- School for Mental Health and Neuroscience, Maastricht University, Maastricht, Netherlands
- Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Marianne B M van den Bree
- Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
- Neuroscience and Mental Health Innovation Institute, Cardiff University, Cardiff, UK
| | - David E J Linden
- School for Mental Health and Neuroscience, Maastricht University, Maastricht, Netherlands
- Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
- Neuroscience and Mental Health Innovation Institute, Cardiff University, Cardiff, UK
| | - Michael J Owen
- Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Jeremy Hall
- Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Sarah Lippé
- Centre de recherche CHU Sainte-Justine, Montréal, Quebec, Canada
| | - Bogdan Draganski
- LREN - Department of Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
- Neurology Department, Max-Planck-Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Ida E Sønderby
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital and University of Oslo, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway
| | - Ole A Andreassen
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital and University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway
| | - David C Glahn
- Department of Psychiatry, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Paul M Thompson
- Imaging Genetics Center, Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, Marina del Rey, CA, USA
| | - Carrie E Bearden
- Semel Institute for Neuroscience and Human Behavior, Departments of Psychiatry and Biobehavioral Sciences and Psychology, UCLA, Los Angeles, USA
| | - Robert Zatorre
- International Laboratory for Brain, Music and Sound Research, Montreal, QC, Canada
- TheNeuro - Montreal Neurological Institute (MNI), McConnell Brain Imaging Centre, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Sébastien Jacquemont
- Centre de recherche CHU Sainte-Justine, Montréal, Quebec, Canada
- Department of Pediatrics, University of Montréal, Montréal, Quebec, Canada
| | - Danilo Bzdok
- Mila - Québec Artificial Intelligence Institute, Montréal, QC, Canada.
- Department of Biomedical Engineering, Faculty of Medicine, McGill University, Montreal, Canada.
- TheNeuro - Montreal Neurological Institute (MNI), McConnell Brain Imaging Centre, Faculty of Medicine, McGill University, Montreal, QC, Canada.
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5
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Viggiano M, Ceroni F, Visconti P, Posar A, Scaduto MC, Sandoni L, Baravelli I, Cameli C, Rochat MJ, Maresca A, Vaisfeld A, Gentilini D, Calzari L, Carelli V, Zody MC, Maestrini E, Bacchelli E. Genomic analysis of 116 autism families strengthens known risk genes and highlights promising candidates. NPJ Genom Med 2024; 9:21. [PMID: 38519481 PMCID: PMC10959942 DOI: 10.1038/s41525-024-00411-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 02/27/2024] [Indexed: 03/25/2024] Open
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with a strong genetic component in which rare variants contribute significantly to risk. We performed whole genome and/or exome sequencing (WGS and WES) and SNP-array analysis to identify both rare sequence and copy number variants (SNVs and CNVs) in 435 individuals from 116 ASD families. We identified 37 rare potentially damaging de novo SNVs (pdSNVs) in the cases (n = 144). Interestingly, two of them (one stop-gain and one missense variant) occurred in the same gene, BRSK2. Moreover, the identification of 8 severe de novo pdSNVs in genes not previously implicated in ASD (AGPAT3, IRX5, MGAT5B, RAB8B, RAP1A, RASAL2, SLC9A1, YME1L1) highlighted promising candidates. Potentially damaging CNVs (pdCNVs) provided support to the involvement of inherited variants in PHF3, NEGR1, TIAM1 and HOMER1 in neurodevelopmental disorders (NDD), although mostly acting as susceptibility factors with incomplete penetrance. Interpretation of identified pdSNVs/pdCNVs according to the ACMG guidelines led to a molecular diagnosis in 19/144 cases, although this figure represents a lower limit and is expected to increase thanks to further clarification of the role of likely pathogenic variants in ASD/NDD candidate genes not yet established. In conclusion, our study highlights promising ASD candidate genes and contributes to characterize the allelic diversity, mode of inheritance and phenotypic impact of de novo and inherited risk variants in ASD/NDD genes.
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Affiliation(s)
- Marta Viggiano
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Fabiola Ceroni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Paola Visconti
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Disturbi dello Spettro Autistico, Bologna, Italy
| | - Annio Posar
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Disturbi dello Spettro Autistico, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Maria Cristina Scaduto
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Disturbi dello Spettro Autistico, Bologna, Italy
| | - Laura Sandoni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Irene Baravelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Cinzia Cameli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Magali J Rochat
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Functional and Molecular Neuroimaging Unit, Bologna, Italy
| | - Alessandra Maresca
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Alessandro Vaisfeld
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Davide Gentilini
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- Bioinformatics and Statistical Genomic Unit, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Luciano Calzari
- Bioinformatics and Statistical Genomic Unit, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Valerio Carelli
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | | | - Elena Maestrini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
| | - Elena Bacchelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
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6
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Al-Sarraj Y, Taha RZ, Al-Dous E, Ahram D, Abbasi S, Abuazab E, Shaath H, Habbab W, Errafii K, Bejaoui Y, AlMotawa M, Khattab N, Aqel YA, Shalaby KE, Al-Ansari A, Kambouris M, Abouzohri A, Ghazal I, Tolfat M, Alshaban F, El-Shanti H, Albagha OME. The genetic landscape of autism spectrum disorder in the Middle Eastern population. Front Genet 2024; 15:1363849. [PMID: 38572415 PMCID: PMC10987745 DOI: 10.3389/fgene.2024.1363849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 03/04/2024] [Indexed: 04/05/2024] Open
Abstract
Introduction: Autism spectrum disorder (ASD) is characterized by aberrations in social interaction and communication associated with repetitive behaviors and interests, with strong clinical heterogeneity. Genetic factors play an important role in ASD, but about 75% of ASD cases have an undetermined genetic risk. Methods: We extensively investigated an ASD cohort made of 102 families from the Middle Eastern population of Qatar. First, we investigated the copy number variations (CNV) contribution using genome-wide SNP arrays. Next, we employed Next Generation Sequencing (NGS) to identify de novo or inherited variants contributing to the ASD etiology and its associated comorbid conditions in families with complete trios (affected child and the parents). Results: Our analysis revealed 16 CNV regions located in genomic regions implicated in ASD. The analysis of the 88 ASD cases identified 41 genes in 39 ASD subjects with de novo (n = 24) or inherited variants (n = 22). We identified three novel de novo variants in new candidate genes for ASD (DTX4, ARMC6, and B3GNT3). Also, we have identified 15 de novo variants in genes that were previously implicated in ASD or related neurodevelopmental disorders (PHF21A, WASF1, TCF20, DEAF1, MED13, CREBBP, KDM6B, SMURF1, ADNP, CACNA1G, MYT1L, KIF13B, GRIA2, CHM, and KCNK9). Additionally, we defined eight novel recessive variants (RYR2, DNAH3, TSPYL2, UPF3B KDM5C, LYST, and WNK3), four of which were X-linked. Conclusion: Despite the ASD multifactorial etiology that hinders ASD genetic risk discovery, the number of identified novel or known putative ASD genetic variants was appreciable. Nevertheless, this study represents the first comprehensive characterization of ASD genetic risk in Qatar's Middle Eastern population.
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Affiliation(s)
- Yasser Al-Sarraj
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Rowaida Z. Taha
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Eman Al-Dous
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Dina Ahram
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
- Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, United States
| | - Somayyeh Abbasi
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Eman Abuazab
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Hibah Shaath
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Wesal Habbab
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Khaoula Errafii
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Yosra Bejaoui
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Maryam AlMotawa
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Namat Khattab
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Yasmin Abu Aqel
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Karim E. Shalaby
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Amina Al-Ansari
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Marios Kambouris
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
- Pathology & Laboratory Medicine Department, Genetics Division, Sidra Medicine, Doha, Qatar
| | - Adel Abouzohri
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Iman Ghazal
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Mohammed Tolfat
- The Shafallah Center for Children with Special Needs, Doha, Qatar
| | - Fouad Alshaban
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Hatem El-Shanti
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Omar M. E. Albagha
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
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7
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Goh CJ, Kwon HJ, Kim Y, Jung S, Park J, Lee IK, Park BR, Kim MJ, Kim MJ, Lee MS. Improving CNV Detection Performance in Microarray Data Using a Machine Learning-Based Approach. Diagnostics (Basel) 2023; 14:84. [PMID: 38201393 PMCID: PMC10871075 DOI: 10.3390/diagnostics14010084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/26/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
Copy number variation (CNV) is a primary source of structural variation in the human genome, leading to several disorders. Therefore, analyzing neonatal CNVs is crucial for managing CNV-related chromosomal disabilities. However, genomic waves can hinder accurate CNV analysis. To mitigate the influences of the waves, we adopted a machine learning approach and developed a new method that uses a modified log R ratio instead of the commonly used log R ratio. Validation results using samples with known CNVs demonstrated the superior performance of our method. We analyzed a total of 16,046 Korean newborn samples using the new method and identified CNVs related to 39 genetic disorders were identified in 342 cases. The most frequently detected CNV-related disorder was Joubert syndrome 4. The accuracy of our method was further confirmed by analyzing a subset of the detected results using NGS and comparing them with our results. The utilization of a genome-wide single nucleotide polymorphism array with wave offset was shown to be a powerful method for identifying CNVs in neonatal cases. The accurate screening and the ability to identify various disease susceptibilities offered by our new method could facilitate the identification of CNV-associated chromosomal disease etiologies.
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Affiliation(s)
- Chul Jun Goh
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (C.J.G.); (H.-J.K.); (Y.K.); (S.J.); (J.P.); (I.K.L.); (B.-R.P.); (M.-J.K.)
| | - Hyuk-Jung Kwon
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (C.J.G.); (H.-J.K.); (Y.K.); (S.J.); (J.P.); (I.K.L.); (B.-R.P.); (M.-J.K.)
- Department of Computer Science and Engineering, Incheon National University (INU), Incheon 22012, Republic of Korea
| | - Yoonhee Kim
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (C.J.G.); (H.-J.K.); (Y.K.); (S.J.); (J.P.); (I.K.L.); (B.-R.P.); (M.-J.K.)
| | - Seunghee Jung
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (C.J.G.); (H.-J.K.); (Y.K.); (S.J.); (J.P.); (I.K.L.); (B.-R.P.); (M.-J.K.)
| | - Jiwoo Park
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (C.J.G.); (H.-J.K.); (Y.K.); (S.J.); (J.P.); (I.K.L.); (B.-R.P.); (M.-J.K.)
| | - Isaac Kise Lee
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (C.J.G.); (H.-J.K.); (Y.K.); (S.J.); (J.P.); (I.K.L.); (B.-R.P.); (M.-J.K.)
- Department of Computer Science and Engineering, Incheon National University (INU), Incheon 22012, Republic of Korea
- NGENI Foundation, San Diego, CA 92127, USA
| | - Bo-Ram Park
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (C.J.G.); (H.-J.K.); (Y.K.); (S.J.); (J.P.); (I.K.L.); (B.-R.P.); (M.-J.K.)
| | - Myeong-Ji Kim
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (C.J.G.); (H.-J.K.); (Y.K.); (S.J.); (J.P.); (I.K.L.); (B.-R.P.); (M.-J.K.)
| | - Min-Jeong Kim
- Diagnomics, Inc., 5795 Kearny Villa Rd., San Diego, CA 92123, USA;
| | - Min-Seob Lee
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (C.J.G.); (H.-J.K.); (Y.K.); (S.J.); (J.P.); (I.K.L.); (B.-R.P.); (M.-J.K.)
- Diagnomics, Inc., 5795 Kearny Villa Rd., San Diego, CA 92123, USA;
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8
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Cheron J, Beccari L, Hagué P, Icick R, Despontin C, Carusone T, Defrance M, Bhogaraju S, Martin-Garcia E, Capellan R, Maldonado R, Vorspan F, Bonnefont J, de Kerchove d'Exaerde A. USP7/Maged1-mediated H2A monoubiquitination in the paraventricular thalamus: an epigenetic mechanism involved in cocaine use disorder. Nat Commun 2023; 14:8481. [PMID: 38123574 PMCID: PMC10733359 DOI: 10.1038/s41467-023-44120-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 11/30/2023] [Indexed: 12/23/2023] Open
Abstract
The risk of developing drug addiction is strongly influenced by the epigenetic landscape and chromatin remodeling. While histone modifications such as methylation and acetylation have been studied in the ventral tegmental area and nucleus accumbens (NAc), the role of H2A monoubiquitination remains unknown. Our investigations, initially focused on the scaffold protein melanoma-associated antigen D1 (Maged1), reveal that H2A monoubiquitination in the paraventricular thalamus (PVT) significantly contributes to cocaine-adaptive behaviors and transcriptional repression induced by cocaine. Chronic cocaine use increases H2A monoubiquitination, regulated by Maged1 and its partner USP7. Accordingly, Maged1 specific inactivation in thalamic Vglut2 neurons, or USP7 inhibition, blocks cocaine-evoked H2A monoubiquitination and cocaine locomotor sensitization. Additionally, genetic variations in MAGED1 and USP7 are linked to altered susceptibility to cocaine addiction and cocaine-associated symptoms in humans. These findings unveil an epigenetic modification in a non-canonical reward pathway of the brain and a potent marker of epigenetic risk factors for drug addiction in humans.
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Affiliation(s)
- Julian Cheron
- Université Libre de Bruxelles (ULB), ULB Neuroscience Institute, Neurophysiology Laboratory, Brussels, Belgium
| | - Leonardo Beccari
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain
- Université Claude Bernard Lyon 1, Pathophysiology and Genetics of Neuron and Muscle, CNRS UMR 5261, INSERM U1315, Lyon, France
| | - Perrine Hagué
- Université Libre de Bruxelles (ULB), ULB Neuroscience Institute, Neurophysiology Laboratory, Brussels, Belgium
| | - Romain Icick
- INSERM UMRS_1144, Université Paris Cité, Paris, France
| | - Chloé Despontin
- Université Libre de Bruxelles (ULB), ULB Neuroscience Institute, Neurophysiology Laboratory, Brussels, Belgium
| | | | - Matthieu Defrance
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | | | - Elena Martin-Garcia
- Laboratory of Neuropharmacology-Neurophar, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
- Departament de Psicobiologia i Metodologia de les Ciències de la Salut, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193, Barcelona, Spain
| | - Roberto Capellan
- Laboratory of Neuropharmacology-Neurophar, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Rafael Maldonado
- Laboratory of Neuropharmacology-Neurophar, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | | | - Jérôme Bonnefont
- Université Libre de Bruxelles (ULB), ULB Neuroscience Institute, Institut de Recherches en Biologie Humaine et Moléculaire (IRIBHM), Brussels, Belgium
| | - Alban de Kerchove d'Exaerde
- Université Libre de Bruxelles (ULB), ULB Neuroscience Institute, Neurophysiology Laboratory, Brussels, Belgium.
- WELBIO, Wavre, Belgium.
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9
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Schmilovich Z, Bourque VR, Douard E, Huguet G, Poulain C, Ross JP, Alipour P, Castonguay CÉ, Younis N, Jean-Louis M, Saci Z, Pausova Z, Paus T, Schuman G, Porteous D, Davies G, Redmond P, Harris SE, Deary IJ, Whalley H, Hayward C, Dion PA, Jacquemont S, Rouleau GA. Copy-number variants and polygenic risk for intelligence confer risk for autism spectrum disorder irrespective of their effects on cognitive ability. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.29.23299190. [PMID: 38076919 PMCID: PMC10705642 DOI: 10.1101/2023.11.29.23299190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Rare copy number variants (CNVs) and polygenic risk for intelligence (PRS-IQ) both confer risk for autism spectrum disorder (ASD) but have opposing effects on cognitive ability. The field has struggled to disentangle the effects of these two classes of genomic variants on cognitive ability from their effects on ASD risk, in part because previous studies did not include controls with cognitive measures. We aim to investigate the impact of these genomic variants on ASD risk while adjusting for their known effects on cognitive ability. In a cohort of 8,426 subjects with ASD and 169,804 controls with cognitive assessments, we found that rare coding CNVs and PRS-IQ increased ASD risk, even after adjusting for their effects on cognitive ability. Bottom decile PRS-IQ and CNVs both decreased cognitive ability but had opposing effects on ASD risk. Models combining both classes of variants showed that the effects of rare CNVs and PRS-IQ on ASD risk and cognitive ability were largely additive, further suggesting that risk for ASD is conferred independently from its effects on cognitive ability. Despite imparting mostly additive effects on ASD risk, rare CNVs and PRS-IQ showed opposing effects on core and associated features and developmental history among subjects with ASD. Our findings suggest that cognitive ability itself may not be the factor driving the underlying risk for ASD conferred by these two classes of genomic variants. In other words, ASD risk and cognitive ability may be two distinct manifestations of CNVs and PRS-IQ. This study also highlights the challenge of understanding how genetic risk for ASD maps onto its dimensional traits.
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Affiliation(s)
- Zoe Schmilovich
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
| | - Vincent-Raphaël Bourque
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
- Département de Pédiatrie, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Elise Douard
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
- Département de Pédiatrie, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Guillaume Huguet
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
| | - Cécile Poulain
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
- Département de Pédiatrie, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Jay P. Ross
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
| | - Paria Alipour
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
| | - Charles-Étienne Castonguay
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
| | - Nadine Younis
- Département de Pédiatrie, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Martineau Jean-Louis
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
| | - Zohra Saci
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
| | - Zdenka Pausova
- The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
- Departments of Physiology and Nutritional Sciences, University of Toronto, Toronto, ON, Canada
| | - Tomas Paus
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
- Departments of Psychiatry of Neuroscience, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
- Departments of Psychology and Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Gunter Schuman
- Institute of Psychiatry, Psychology, and Neuroscience, King’s College London, London, England
| | - David Porteous
- Lothian Birth Cohorts group, Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, Edinburgh, UK
- Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, UK
| | - Gail Davies
- Lothian Birth Cohorts group, Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, Edinburgh, UK
| | - Paul Redmond
- Lothian Birth Cohorts group, Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, Edinburgh, UK
| | - Sarah E. Harris
- Lothian Birth Cohorts group, Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, Edinburgh, UK
| | - Ian J. Deary
- Lothian Birth Cohorts group, Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, Edinburgh, UK
| | - Heather Whalley
- Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, UK
| | - Caroline Hayward
- Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, UK
| | - Patrick A. Dion
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, Canada
| | - Sébastien Jacquemont
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
- Département de Pédiatrie, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Guy A. Rouleau
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, Canada
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10
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Getmantseva L, Kolosova M, Fede K, Korobeinikova A, Kolosov A, Romanets E, Bakoev F, Romanets T, Yudin V, Keskinov A, Bakoev S. Finding Predictors of Leg Defects in Pigs Using CNV-GWAS. Genes (Basel) 2023; 14:2054. [PMID: 38002997 PMCID: PMC10671522 DOI: 10.3390/genes14112054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/04/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
One of the most important areas of modern genome research is the search for meaningful relationships between genetic variants and phenotypes. In the livestock field, there has been research demonstrating the influence of copy number variants (CNVs) on phenotypic variation. Despite the wide range in the number and size of detected CNVs, a significant proportion differ between breeds and their functional effects are underestimated in the pig industry. In this work, we focused on the problem of leg defects in pigs (lumps/growths in the area of the hock joint on the hind legs) and focused on searching for molecular genetic predictors associated with this trait for the selection of breeding stock. The study was conducted on Large White pigs using three CNV calling tools (PennCNV, QuantiSNP and R-GADA) and the CNVRanger association analysis tool (CNV-GWAS). As a result, the analysis identified three candidate CNVRs associated with the formation of limb defects. Subsequent functional analysis suggested that all identified CNVs may act as potential predictors of the hock joint phenotype of pigs. It should be noted that the results obtained indicate that all significant regions are localized in genes (CTH, SRSF11, MAN1A1 and LPIN1) responsible for the metabolism of amino acids, fatty acids, glycerolipids and glycerophospholipids, thereby related to the immune response, liver functions, content intramuscular fat and animal fatness. These results are consistent with previously published studies, according to which a predisposition to the formation of leg defects can be realized through genetic variants associated with the functions of the liver, kidneys and hematological characteristics.
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Affiliation(s)
- Lyubov Getmantseva
- Federal State Budgetary Educational Institution of Higher Education, Don State Agrarian University, 346493 Persianovsky, Russia; (L.G.); (A.K.)
- Federal State Budgetary Institution, “Center for Strategic Planning and Management of Medical and Biological Health Risks” of the Federal Medical and Biological Agency, 10/1 Pogodinskaya St., 119121 Moscow, Russia; (K.F.); (A.K.)
| | - Maria Kolosova
- Federal State Budgetary Educational Institution of Higher Education, Don State Agrarian University, 346493 Persianovsky, Russia; (L.G.); (A.K.)
| | - Kseniia Fede
- Federal State Budgetary Institution, “Center for Strategic Planning and Management of Medical and Biological Health Risks” of the Federal Medical and Biological Agency, 10/1 Pogodinskaya St., 119121 Moscow, Russia; (K.F.); (A.K.)
| | - Anna Korobeinikova
- Federal State Budgetary Institution, “Center for Strategic Planning and Management of Medical and Biological Health Risks” of the Federal Medical and Biological Agency, 10/1 Pogodinskaya St., 119121 Moscow, Russia; (K.F.); (A.K.)
| | - Anatoly Kolosov
- Federal State Budgetary Educational Institution of Higher Education, Don State Agrarian University, 346493 Persianovsky, Russia; (L.G.); (A.K.)
| | - Elena Romanets
- Federal State Budgetary Educational Institution of Higher Education, Don State Agrarian University, 346493 Persianovsky, Russia; (L.G.); (A.K.)
| | - Faridun Bakoev
- Federal State Budgetary Educational Institution of Higher Education, Don State Agrarian University, 346493 Persianovsky, Russia; (L.G.); (A.K.)
| | - Timofey Romanets
- Federal State Budgetary Educational Institution of Higher Education, Don State Agrarian University, 346493 Persianovsky, Russia; (L.G.); (A.K.)
| | - Vladimir Yudin
- Federal State Budgetary Institution, “Center for Strategic Planning and Management of Medical and Biological Health Risks” of the Federal Medical and Biological Agency, 10/1 Pogodinskaya St., 119121 Moscow, Russia; (K.F.); (A.K.)
| | - Anton Keskinov
- Federal State Budgetary Institution, “Center for Strategic Planning and Management of Medical and Biological Health Risks” of the Federal Medical and Biological Agency, 10/1 Pogodinskaya St., 119121 Moscow, Russia; (K.F.); (A.K.)
| | - Siroj Bakoev
- Federal State Budgetary Institution, “Center for Strategic Planning and Management of Medical and Biological Health Risks” of the Federal Medical and Biological Agency, 10/1 Pogodinskaya St., 119121 Moscow, Russia; (K.F.); (A.K.)
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11
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Bacchelli E, Viggiano M, Ceroni F, Visconti P, Posar A, Scaduto M, Sandoni L, Baravelli I, Cameli C, Rochat M, Maresca A, Vaisfeld A, Gentilini D, Calzari L, Carelli V, Zody M, Maestrini E. Whole genome analysis of rare deleterious variants adds further evidence to BRSK2 and other risk genes in Autism Spectrum Disorder. RESEARCH SQUARE 2023:rs.3.rs-3468592. [PMID: 37961520 PMCID: PMC10635364 DOI: 10.21203/rs.3.rs-3468592/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with a strong genetic component in which rare variants contribute significantly to risk. We have performed whole genome and/or exome sequencing (WGS and WES) and SNP-array analysis to identify both rare sequence and copy number variants (SNVs and CNVs) in 435 individuals from 116 ASD families. We identified 37 rare potentially damaging de novo SNVs (pdSNVs) in cases (n = 144). Interestingly, two of them (one stop-gain and one missense variant) occurred in the same gene, BRSK2. Moreover, the identification of 9 severe de novo pdSNVs in genes not previously implicated in ASD (RASAL2, RAP1A, IRX5, SLC9A1, AGPAT3, MGAT3, RAB8B, MGAT5B, YME1L1), highlighted novel candidates. Potentially damaging CNVs (pdCNVs) provided support to the involvement of inherited variants in PHF3, NEGR1, TIAM1 and HOMER1 in neurodevelopmental disorders (NDD), although mostly acting as susceptibility factors with incomplete penetrance. Interpretation of identified pdSNVs/pdCNVs according to the ACMG guidelines led to a molecular diagnosis in 19/144 cases, but this figure represents a lower limit and is expected to increase thanks to further clarification of the role of likely pathogenic variants in new ASD/NDD candidates. In conclusion, our study strengthens the role of BRSK2 and other neurodevelopmental genes in ASD risk, highlights novel candidates and contributes to characterize the allelic diversity, mode of inheritance and phenotypic impact of de novo and inherited risk variants in ASD/NDD genes.
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Affiliation(s)
| | | | | | | | - Annio Posar
- IRCCS Istituto delle Scienze Neurologiche di Bologna
| | - Maria Scaduto
- IRCCS Istituto delle Scienze Neurologiche di Bologna
| | | | | | | | - Magali Rochat
- IRCCS Istituto delle Scienze Neurologiche di Bologna
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12
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Carlisle SG, Albasha H, Michelena H, Sabate-Rotes A, Bianco L, De Backer J, Mosquera LM, Yetman AT, Bissell MM, Andreassi MG, Foffa I, Hui DS, Caffarelli A, Kim YY, Guo DC, Citro R, De Marco M, Tretter JT, McBride KL, Milewicz DM, Body SC, Prakash SK. Rare Genomic Copy Number Variants Implicate New Candidate Genes for Bicuspid Aortic Valve. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.23.23297397. [PMID: 37961530 PMCID: PMC10635161 DOI: 10.1101/2023.10.23.23297397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Bicuspid aortic valve (BAV), the most common congenital heart defect, is a major cause of aortic valve disease requiring valve interventions and thoracic aortic aneurysms predisposing to acute aortic dissections. The spectrum of BAV ranges from early onset valve and aortic complications (EBAV) to sporadic late onset disease. Rare genomic copy number variants (CNVs) have previously been implicated in the development of BAV and thoracic aortic aneurysms. We determined the frequency and gene content of rare CNVs in EBAV probands (n = 272) using genome-wide SNP microarray analysis and three complementary CNV detection algorithms (cnvPartition, PennCNV, and QuantiSNP). Unselected control genotypes from the Database of Genotypes and Phenotypes were analyzed using identical methods. We filtered the data to select large genic CNVs that were detected by multiple algorithms. Findings were replicated in cohorts with late onset sporadic disease (n = 5040). We identified 34 large and rare (< 1:1000 in controls) CNVs in EBAV probands. The burden of CNVs intersecting with genes known to cause BAV when mutated was increased in case-control analysis. CNVs intersecting with GATA4 and DSCAM were enriched in cases, recurrent in other datasets, and segregated with disease in families. In total, we identified potentially pathogenic CNVs in 8% of EBAV cases, implicating alterations of candidate genes at these loci in the pathogenesis of BAV.
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Affiliation(s)
- Steven G Carlisle
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, Texas
| | - Hasan Albasha
- UCD School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Hector Michelena
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota
| | - Anna Sabate-Rotes
- Department of Pediatric Cardiology, Hospital Vall d'Hebron, Facultad de Medicina, Universidad Autònoma Barcelona, Barcelona, Spain
| | - Lisa Bianco
- Department of Pediatric Cardiology, Hospital Vall d'Hebron, Facultad de Medicina, Universidad Autònoma Barcelona, Barcelona, Spain
| | - Julie De Backer
- Centre for Medical Genetics, Ghent University Hospital, Ghent, Belgium; VASCERN HTAD European Reference Centre, Belgium; Department of Pediatrics, Division of Pediatric Cardiology, Ghent University Hospital, Ghent, Belgium; Department of Cardiology, Ghent University Hospital, Ghent, Belgium
| | | | - Anji T Yetman
- Children's Hospital and Medical Center, University of Nebraska, Omaha, Nebraska
| | - Malenka M Bissell
- Deparmentt of Biomedical Imaging Science, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, United Kingdom
| | | | - Ilenia Foffa
- Consiglio Nazionale delle Richerche (CNR), Instituto di Fisiologia Clinica, Pisa, Italy
| | - Dawn S Hui
- Department of Cardiothoracic Surgery, University of Texas Health Science Center San Antonio, Texas
| | - Anthony Caffarelli
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, California
| | - Yuli Y Kim
- Division of Cardiovascular Medicine, The Hospital of the University of Pennsylvania, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania; Philadelphia Adult Congenital Heart Center, The Children's Hospital of Philadelphia, Perelman Center for Advanced Medicine, Penn Medicine, Philadelphia, Pennsylvania
| | - Dong-Chuan Guo
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, Texas
| | - Rodolfo Citro
- Cardio-Thoracic and Vascular Department, University Hospital "San Giovanni di Dio e Ruggi d'Aragona," Salerno, Italy
| | - Margot De Marco
- Department of Medicine, Surgery and Dentistry Schola Medica Salernitana, University of Salerno, Baronissi, Italy
| | - Justin T Tretter
- Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Kim L McBride
- Division of Human Genetics, Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Dianna M Milewicz
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, Texas
| | - Simon C Body
- Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital/Harvard Medical School, Boston, Massachusetts
| | - Siddharth K Prakash
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, Texas
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13
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Weber SE, Chawla HS, Ehrig L, Hickey LT, Frisch M, Snowdon RJ. Accurate prediction of quantitative traits with failed SNP calls in canola and maize. FRONTIERS IN PLANT SCIENCE 2023; 14:1221750. [PMID: 37936929 PMCID: PMC10627008 DOI: 10.3389/fpls.2023.1221750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 10/05/2023] [Indexed: 11/09/2023]
Abstract
In modern plant breeding, genomic selection is becoming the gold standard to select superior genotypes in large breeding populations that are only partially phenotyped. Many breeding programs commonly rely on single-nucleotide polymorphism (SNP) markers to capture genome-wide data for selection candidates. For this purpose, SNP arrays with moderate to high marker density represent a robust and cost-effective tool to generate reproducible, easy-to-handle, high-throughput genotype data from large-scale breeding populations. However, SNP arrays are prone to technical errors that lead to failed allele calls. To overcome this problem, failed calls are often imputed, based on the assumption that failed SNP calls are purely technical. However, this ignores the biological causes for failed calls-for example: deletions-and there is increasing evidence that gene presence-absence and other kinds of genome structural variants can play a role in phenotypic expression. Because deletions are frequently not in linkage disequilibrium with their flanking SNPs, permutation of missing SNP calls can potentially obscure valuable marker-trait associations. In this study, we analyze published datasets for canola and maize using four parametric and two machine learning models and demonstrate that failed allele calls in genomic prediction are highly predictive for important agronomic traits. We present two statistical pipelines, based on population structure and linkage disequilibrium, that enable the filtering of failed SNP calls that are likely caused by biological reasons. For the population and trait examined, prediction accuracy based on these filtered failed allele calls was competitive to standard SNP-based prediction, underlying the potential value of missing data in genomic prediction approaches. The combination of SNPs with all failed allele calls or the filtered allele calls did not outperform predictions with only SNP-based prediction due to redundancy in genomic relationship estimates.
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Affiliation(s)
- Sven E. Weber
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
| | | | - Lennard Ehrig
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
| | - Lee T. Hickey
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Matthias Frisch
- Department of Biometry and Population Genetics, Justus Liebig University, Giessen, Germany
| | - Rod J. Snowdon
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
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14
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Mollon J, Schultz LM, Huguet G, Knowles EEM, Mathias SR, Rodrigue A, Alexander-Bloch A, Saci Z, Jean-Louis M, Kumar K, Douard E, Almasy L, Jacquemont S, Glahn DC. Impact of Copy Number Variants and Polygenic Risk Scores on Psychopathology in the UK Biobank. Biol Psychiatry 2023; 94:591-600. [PMID: 36764568 PMCID: PMC10409883 DOI: 10.1016/j.biopsych.2023.01.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 01/31/2023] [Accepted: 01/31/2023] [Indexed: 02/11/2023]
Abstract
BACKGROUND Our understanding of the impact of copy number variants (CNVs) on psychopathology and their joint influence with polygenic risk scores (PRSs) remains limited. METHODS The UK Biobank recruited 502,534 individuals ages 37 to 73 years living in the United Kingdom between 2006 and 2010. After quality control, genotype data from 459,855 individuals were available for CNV calling. A total of 61 commonly studied recurrent neuropsychiatric CNVs were selected for analyses and examined individually and in aggregate (any CNV, deletion, or duplication). CNV risk scores were used to quantify intolerance of CNVs to haploinsufficiency. Major depressive disorder and generalized anxiety disorder PRSs were generated for White British individuals (N = 408,870). Mood/anxiety factor scores were generated using item-level questionnaire data (N = 501,289). RESULTS CNV carriers showed higher mood/anxiety scores than noncarriers, with the largest effects seen for intolerant deletions. A total of 11 individual deletions and 8 duplications were associated with higher mood/anxiety. Carriers of the 9p24.3 (DMRT1) duplication showed lower mood/anxiety. Associations remained significant for most CNVs when excluding individuals with psychiatric diagnoses. Nominally significant CNV × PRS interactions provided preliminary evidence that associations between select individual CNVs, but not CNVs in aggregate, and mood/anxiety may be modulated by PRSs. CONCLUSIONS CNVs associated with risk for psychiatric disorders showed small to large effects on dimensional mood/anxiety scores in a general population cohort, even when excluding individuals with psychiatric diagnoses. CNV × PRS interactions showed that associations between select CNVs and mood/anxiety may be modulated by PRSs.
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Affiliation(s)
- Josephine Mollon
- Department of Psychiatry, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts.
| | - Laura M Schultz
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Guillaume Huguet
- Department of Pediatrics, Université de Montréal, Montreal, Quebec, Canada; Department of Pediatrics, Center Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Emma E M Knowles
- Department of Psychiatry, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Samuel R Mathias
- Department of Psychiatry, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Amanda Rodrigue
- Department of Psychiatry, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Aaron Alexander-Bloch
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Lifespan Brain Institute, The Children's Hospital of Philadelphia and Penn Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Neurodevelopment and Psychosis Section, Department of Psychiatry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Zohra Saci
- Department of Pediatrics, Center Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Martineau Jean-Louis
- Department of Pediatrics, Center Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Kuldeep Kumar
- Department of Pediatrics, Center Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Elise Douard
- Department of Pediatrics, Université de Montréal, Montreal, Quebec, Canada; Department of Pediatrics, Center Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Laura Almasy
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Department of Genetics, Perelman School of Medicine, Penn-CHOP Lifespan Brain Institute, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Sebastien Jacquemont
- Department of Pediatrics, Université de Montréal, Montreal, Quebec, Canada; Department of Pediatrics, Center Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - David C Glahn
- Department of Psychiatry, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts; Olin Neuropsychiatry Research Center, Institute of Living, Hartford, Connecticut
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15
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Lowther C, Valkanas E, Giordano JL, Wang HZ, Currall BB, O'Keefe K, Pierce-Hoffman E, Kurtas NE, Whelan CW, Hao SP, Weisburd B, Jalili V, Fu J, Wong I, Collins RL, Zhao X, Austin-Tse CA, Evangelista E, Lemire G, Aggarwal VS, Lucente D, Gauthier LD, Tolonen C, Sahakian N, Stevens C, An JY, Dong S, Norton ME, MacKenzie TC, Devlin B, Gilmore K, Powell BC, Brandt A, Vetrini F, DiVito M, Sanders SJ, MacArthur DG, Hodge JC, O'Donnell-Luria A, Rehm HL, Vora NL, Levy B, Brand H, Wapner RJ, Talkowski ME. Systematic evaluation of genome sequencing for the diagnostic assessment of autism spectrum disorder and fetal structural anomalies. Am J Hum Genet 2023; 110:1454-1469. [PMID: 37595579 PMCID: PMC10502737 DOI: 10.1016/j.ajhg.2023.07.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/25/2023] [Accepted: 07/25/2023] [Indexed: 08/20/2023] Open
Abstract
Short-read genome sequencing (GS) holds the promise of becoming the primary diagnostic approach for the assessment of autism spectrum disorder (ASD) and fetal structural anomalies (FSAs). However, few studies have comprehensively evaluated its performance against current standard-of-care diagnostic tests: karyotype, chromosomal microarray (CMA), and exome sequencing (ES). To assess the clinical utility of GS, we compared its diagnostic yield against these three tests in 1,612 quartet families including an individual with ASD and in 295 prenatal families. Our GS analytic framework identified a diagnostic variant in 7.8% of ASD probands, almost 2-fold more than CMA (4.3%) and 3-fold more than ES (2.7%). However, when we systematically captured copy-number variants (CNVs) from the exome data, the diagnostic yield of ES (7.4%) was brought much closer to, but did not surpass, GS. Similarly, we estimated that GS could achieve an overall diagnostic yield of 46.1% in unselected FSAs, representing a 17.2% increased yield over karyotype, 14.1% over CMA, and 4.1% over ES with CNV calling or 36.1% increase without CNV discovery. Overall, GS provided an added diagnostic yield of 0.4% and 0.8% beyond the combination of all three standard-of-care tests in ASD and FSAs, respectively. This corresponded to nine GS unique diagnostic variants, including sequence variants in exons not captured by ES, structural variants (SVs) inaccessible to existing standard-of-care tests, and SVs where the resolution of GS changed variant classification. Overall, this large-scale evaluation demonstrated that GS significantly outperforms each individual standard-of-care test while also outperforming the combination of all three tests, thus warranting consideration as the first-tier diagnostic approach for the assessment of ASD and FSAs.
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Affiliation(s)
- Chelsea Lowther
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Elise Valkanas
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Biological and Biomedical Sciences, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Jessica L Giordano
- Department of Obstetrics & Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Harold Z Wang
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Benjamin B Currall
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Kathryn O'Keefe
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Emma Pierce-Hoffman
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nehir E Kurtas
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Christopher W Whelan
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephanie P Hao
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ben Weisburd
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vahid Jalili
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jack Fu
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Isaac Wong
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ryan L Collins
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Bioinformatics and Integrative Genomics, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Xuefang Zhao
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Christina A Austin-Tse
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Emily Evangelista
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gabrielle Lemire
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vimla S Aggarwal
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Diane Lucente
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Laura D Gauthier
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Charlotte Tolonen
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nareh Sahakian
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christine Stevens
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joon-Yong An
- School of Biosystem and Biomedical Science, Korea University, Seoul, South Korea
| | - Shan Dong
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Mary E Norton
- Center for Maternal-Fetal Precision Medicine, University of California, San Francisco, San Francisco, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Tippi C MacKenzie
- Center for Maternal-Fetal Precision Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kelly Gilmore
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bradford C Powell
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alicia Brandt
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Francesco Vetrini
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Michelle DiVito
- Department of Obstetrics & Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Stephan J Sanders
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Daniel G MacArthur
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Centre for Population Genomics, Garvan Institute of Medical Research, and University of New South Wales Sydney, Sydney, NSW, Australia; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Jennelle C Hodge
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Anne O'Donnell-Luria
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Heidi L Rehm
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Neeta L Vora
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Ronald J Wapner
- Department of Obstetrics & Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA; Program in Biological and Biomedical Sciences, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA; Program in Bioinformatics and Integrative Genomics, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA.
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16
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Alibutud R, Hansali S, Cao X, Zhou A, Mahaganapathy V, Azaro M, Gwin C, Wilson S, Buyske S, Bartlett CW, Flax JF, Brzustowicz LM, Xing J. Structural Variations Contribute to the Genetic Etiology of Autism Spectrum Disorder and Language Impairments. Int J Mol Sci 2023; 24:13248. [PMID: 37686052 PMCID: PMC10487745 DOI: 10.3390/ijms241713248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by restrictive interests and/or repetitive behaviors and deficits in social interaction and communication. ASD is a multifactorial disease with a complex polygenic genetic architecture. Its genetic contributing factors are not yet fully understood, especially large structural variations (SVs). In this study, we aimed to assess the contribution of SVs, including copy number variants (CNVs), insertions, deletions, duplications, and mobile element insertions, to ASD and related language impairments in the New Jersey Language and Autism Genetics Study (NJLAGS) cohort. Within the cohort, ~77% of the families contain SVs that followed expected segregation or de novo patterns and passed our filtering criteria. These SVs affected 344 brain-expressed genes and can potentially contribute to the genetic etiology of the disorders. Gene Ontology and protein-protein interaction network analysis suggested several clusters of genes in different functional categories, such as neuronal development and histone modification machinery. Genes and biological processes identified in this study contribute to the understanding of ASD and related neurodevelopment disorders.
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Affiliation(s)
- Rohan Alibutud
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Sammy Hansali
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Xiaolong Cao
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Anbo Zhou
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Vaidhyanathan Mahaganapathy
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Marco Azaro
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Christine Gwin
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Sherri Wilson
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Steven Buyske
- Department of Statistics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA;
| | - Christopher W. Bartlett
- The Steve Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA;
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH 43205, USA
| | - Judy F. Flax
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Linda M. Brzustowicz
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
- The Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jinchuan Xing
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
- The Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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17
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Abstract
Strabismus, or misalignment of the eyes, is the most common ocular disorder in the pediatric population, affecting approximately 2%-4% of children. Strabismus leads to the disruption of binocular vision, amblyopia, social and occupational discrimination, and decreased quality of life. Although it has been recognized since ancient times that strabismus runs in families, its inheritance patterns are complex, and its precise genetic mechanisms have not yet been defined. Family, population, and twin studies all support a role of genetics in the development of strabismus. There are multiple forms of strabismus, and it is not known if they have shared genetic mechanisms or are distinct genetic disorders, which complicates studies of strabismus. Studies assuming that strabismus is a Mendelian disorder have found areas of linkage and candidate genes in particular families, but no definitive causal genes. Genome-wide association studies searching for common variation that contributes to strabismus risk have identified two risk loci and three copy number variants in white populations. Causative genes have been identified in congenital cranial dysinnervation disorders, syndromes in which eye movement is limited or paralyzed. The causative genes lead to either improper differentiation of cranial motor neurons or abnormal axon guidance. This article reviews the evidence for a genetic contribution to strabismus and the recent advances that have been made in the genetics of comitant strabismus, the most common form of strabismus.
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Affiliation(s)
- Mayra Martinez Sanchez
- Department of Ophthalmology, Boston Children’s Hospital, Boston, MA, United States
- Department of Ophthalmology, Harvard Medical School, Boston, MA, United States
| | - Mary C. Whitman
- Department of Ophthalmology, Boston Children’s Hospital, Boston, MA, United States
- Department of Ophthalmology, Harvard Medical School, Boston, MA, United States
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA, United States
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18
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Arias KD, Gutiérrez JP, Fernández I, Álvarez I, Goyache F. Copy Number Variation Regions Differing in Segregation Patterns Span Different Sets of Genes. Animals (Basel) 2023; 13:2351. [PMID: 37508128 PMCID: PMC10376189 DOI: 10.3390/ani13142351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Copy number variations regions (CNVRs) can be classified either as segregating, when found in both parents, and offspring, or non-segregating. A total of 65 segregating and 31 non-segregating CNVRs identified in at least 10 individuals within a dense pedigree of the Gochu Asturcelta pig breed was subjected to enrichment and functional annotation analyses to ascertain their functional independence and importance. Enrichment analyses allowed us to annotate 1018 and 351 candidate genes within the bounds of the segregating and non-segregating CNVRs, respectively. The information retrieved suggested that the candidate genes spanned by segregating and non-segregating CNVRs were functionally independent. Functional annotation analyses allowed us to identify nine different significantly enriched functional annotation clusters (ACs) in segregating CNVR candidate genes mainly involved in immunity and regulation of the cell cycle. Up to five significantly enriched ACs, mainly involved in reproduction and meat quality, were identified in non-segregating CNVRs. The current analysis fits with previous reports suggesting that segregating CNVRs would explain performance at the population level, whereas non-segregating CNVRs could explain between-individuals differences in performance.
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Affiliation(s)
- Katherine D Arias
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, 33394 Gijón, Spain
| | - Juan Pablo Gutiérrez
- Departamento de Producción Animal, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Iván Fernández
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, 33394 Gijón, Spain
| | - Isabel Álvarez
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, 33394 Gijón, Spain
| | - Félix Goyache
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, 33394 Gijón, Spain
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19
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Farrell M, Dietterich TE, Harner MK, Bruno LM, Filmyer DM, Shaughnessy RA, Lichtenstein ML, Britt AM, Biondi TF, Crowley JJ, Lázaro-Muñoz G, Forsingdal AE, Nielsen J, Didriksen M, Berg JS, Wen J, Szatkiewicz J, Mary Xavier R, Sullivan PF, Josiassen RC. Increased Prevalence of Rare Copy Number Variants in Treatment-Resistant Psychosis. Schizophr Bull 2023; 49:881-892. [PMID: 36454006 PMCID: PMC10318882 DOI: 10.1093/schbul/sbac175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
BACKGROUND It remains unknown why ~30% of patients with psychotic disorders fail to respond to treatment. Previous genomic investigations of treatment-resistant psychosis have been inconclusive, but some evidence suggests a possible link between rare disease-associated copy number variants (CNVs) and worse clinical outcomes in schizophrenia. Here, we identified schizophrenia-associated CNVs in patients with treatment-resistant psychotic symptoms and then compared the prevalence of these CNVs to previously published schizophrenia cases not selected for treatment resistance. METHODS CNVs were identified using chromosomal microarray (CMA) and whole exome sequencing (WES) in 509 patients with treatment-resistant psychosis (a lack of clinical response to ≥3 adequate antipsychotic medication trials over at least 5 years of psychiatric hospitalization). Prevalence of schizophrenia-associated CNVs in this sample was compared to that in a previously published large schizophrenia cohort study. RESULTS Integrating CMA and WES data, we identified 47 cases (9.2%) with at least one CNV of known or possible neuropsychiatric risk. 4.7% (n = 24) carried a known neurodevelopmental risk CNV. The prevalence of well-replicated schizophrenia-associated CNVs was 4.1%, with duplications of the 16p11.2 and 15q11.2-q13.1 regions, and deletions of the 22q11.2 chromosomal region as the most frequent CNVs. Pairwise loci-based analysis identified duplications of 15q11.2-q13.1 to be independently associated with treatment resistance. CONCLUSIONS These findings suggest that CNVs may uniquely impact clinical phenotypes beyond increasing risk for schizophrenia and may potentially serve as biological entry points for studying treatment resistance. Further investigation will be necessary to elucidate the spectrum of phenotypic characteristics observed in adult psychiatric patients with disease-associated CNVs.
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Affiliation(s)
- Martilias Farrell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | | | - Lisa M Bruno
- Translational Neuroscience, LLC, Conshohocken, PA, USA
| | | | | | | | - Allison M Britt
- School of Nursing, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Tamara F Biondi
- Office of the Vice Chancellor for Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - James J Crowley
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Gabriel Lázaro-Muñoz
- Center for Bioethics, Harvard Medical School, Boston, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | | | - Jacob Nielsen
- Division of Neuroscience, H. Lundbeck A/S, Valby, Denmark
| | | | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jia Wen
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jin Szatkiewicz
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rose Mary Xavier
- School of Nursing, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Patrick F Sullivan
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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20
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Tenney AP, Di Gioia SA, Webb BD, Chan WM, de Boer E, Garnai SJ, Barry BJ, Ray T, Kosicki M, Robson CD, Zhang Z, Collins TE, Gelber A, Pratt BM, Fujiwara Y, Varshney A, Lek M, Warburton PE, Van Ryzin C, Lehky TJ, Zalewski C, King KA, Brewer CC, Thurm A, Snow J, Facio FM, Narisu N, Bonnycastle LL, Swift A, Chines PS, Bell JL, Mohan S, Whitman MC, Staffieri SE, Elder JE, Demer JL, Torres A, Rachid E, Al-Haddad C, Boustany RM, Mackey DA, Brady AF, Fenollar-Cortés M, Fradin M, Kleefstra T, Padberg GW, Raskin S, Sato MT, Orkin SH, Parker SCJ, Hadlock TA, Vissers LELM, van Bokhoven H, Jabs EW, Collins FS, Pennacchio LA, Manoli I, Engle EC. Noncoding variants alter GATA2 expression in rhombomere 4 motor neurons and cause dominant hereditary congenital facial paresis. Nat Genet 2023; 55:1149-1163. [PMID: 37386251 PMCID: PMC10335940 DOI: 10.1038/s41588-023-01424-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/10/2023] [Indexed: 07/01/2023]
Abstract
Hereditary congenital facial paresis type 1 (HCFP1) is an autosomal dominant disorder of absent or limited facial movement that maps to chromosome 3q21-q22 and is hypothesized to result from facial branchial motor neuron (FBMN) maldevelopment. In the present study, we report that HCFP1 results from heterozygous duplications within a neuron-specific GATA2 regulatory region that includes two enhancers and one silencer, and from noncoding single-nucleotide variants (SNVs) within the silencer. Some SNVs impair binding of NR2F1 to the silencer in vitro and in vivo and attenuate in vivo enhancer reporter expression in FBMNs. Gata2 and its effector Gata3 are essential for inner-ear efferent neuron (IEE) but not FBMN development. A humanized HCFP1 mouse model extends Gata2 expression, favors the formation of IEEs over FBMNs and is rescued by conditional loss of Gata3. These findings highlight the importance of temporal gene regulation in development and of noncoding variation in rare mendelian disease.
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Affiliation(s)
- Alan P Tenney
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
| | - Silvio Alessandro Di Gioia
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Bryn D Webb
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Wai-Man Chan
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Elke de Boer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Sarah J Garnai
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Harvard-MIT Health Sciences and Technology, Harvard Medical School, Boston, MA, USA
| | - Brenda J Barry
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Tammy Ray
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael Kosicki
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Caroline D Robson
- Department of Radiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Zhongyang Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas E Collins
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Alon Gelber
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Brandon M Pratt
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yuko Fujiwara
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Arushi Varshney
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Monkol Lek
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Peter E Warburton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carol Van Ryzin
- Metabolic Medicine Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Tanya J Lehky
- EMG Section, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Christopher Zalewski
- Audiology Unit, Otolaryngology Branch, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD, USA
| | - Kelly A King
- Audiology Unit, Otolaryngology Branch, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD, USA
| | - Carmen C Brewer
- Audiology Unit, Otolaryngology Branch, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD, USA
| | - Audrey Thurm
- Neurodevelopmental and Behavioral Phenotyping Service, National Institute of Mental Health, NIH, Bethesda, MD, USA
| | - Joseph Snow
- Office of the Clinical Director, National Institute of Mental Health, NIH, Bethesda, MD, USA
| | - Flavia M Facio
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, MD, USA
- Invitae Corporation, San Francisco, CA, USA
| | - Narisu Narisu
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Lori L Bonnycastle
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Amy Swift
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Peter S Chines
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Jessica L Bell
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Suresh Mohan
- Department of Otolaryngology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Mary C Whitman
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sandra E Staffieri
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, and University of Melbourne, Melbourne, Victoria, Australia
- Department of Ophthalmology, Royal Children's Hospital, Parkville, Victoria, Australia
| | - James E Elder
- Department of Ophthalmology, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Joseph L Demer
- Stein Eye Institute and Departments of Ophthalmology, Neurology, and Bioengineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Alcy Torres
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatrics, Boston Medical Center, Boston University Aram V. Chobanian & Edward Avedisian School of Medicine, Boston, MA, USA
| | - Elza Rachid
- Department of Ophthalmology, American University of Beirut Medical Center, Beirut, Lebanon
| | - Christiane Al-Haddad
- Department of Ophthalmology, American University of Beirut Medical Center, Beirut, Lebanon
| | - Rose-Mary Boustany
- Pediatrics & Adolescent Medicine/Biochemistry & Molecular Genetics, American University of Beirut Medical Center, Beirut, Lebanon
| | - David A Mackey
- Lions Eye Institute, University of Western Australia, Perth, Australia
| | - Angela F Brady
- North West Thames Regional Genetics Service, Northwick Park Hospital, Harrow, UK
| | - María Fenollar-Cortés
- Unidad de Genética Clínica, Instituto de Medicina del Laboratorio. IdISSC, Hospital Clínico San Carlos, Madrid, Spain
| | - Melanie Fradin
- Service de Génétique Clinique, CHU Rennes, Centre Labellisé Anomalies du Développement, Rennes, France
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
- Center of Excellence for Neuropsychiatry, Vincent van Gogh Institute for Psychiatry, Venray, the Netherlands
| | - George W Padberg
- Department of Neurology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Salmo Raskin
- Centro de Aconselhamento e Laboratório Genetika, Curitiba, Paraná, Brazil
| | - Mario Teruo Sato
- Department of Ophthalmology & Otorhinolaryngology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Stuart H Orkin
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Stephen C J Parker
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Tessa A Hadlock
- Department of Otolaryngology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Hans van Bokhoven
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ethylin Wang Jabs
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Francis S Collins
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Len A Pennacchio
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Irini Manoli
- Metabolic Medicine Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Elizabeth C Engle
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
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21
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Siavrienė E, Petraitytė G, Mikštienė V, Maldžienė Ž, Sasnauskienė A, Žitkutė V, Ambrozaitytė L, Rančelis T, Utkus A, Kučinskas V, Preikšaitienė E. Molecular and Functional Characterisation of a Novel Intragenic 12q24.21 Deletion Resulting in MED13L Haploinsufficiency Syndrome. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:1225. [PMID: 37512036 PMCID: PMC10385642 DOI: 10.3390/medicina59071225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/17/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023]
Abstract
Background and Objectives: Heterozygous pathogenic variants in the MED13L gene cause impaired intellectual development and distinctive facial features with or without cardiac defects (MIM #616789). This complex neurodevelopmental disorder is characterised by various phenotypic features, including plagiocephaly, strabismus, clubfoot, poor speech, and developmental delay. The aim of this study was to evaluate the clinical significance and consequences of a novel heterozygous intragenic MED13L deletion in a proband with clinical features of a MED13L-related disorder through extensive clinical, molecular, and functional characterisation. Materials and Methods: Combined comparative genomic hybridisation and single-nucleotide polymorphism array (SNP-CGH) was used to identify the changes in the proband's gDNA sequence (DECIPHER #430183). Intragenic MED13L deletion was specified via quantitative polymerase chain reaction (qPCR) and Sanger sequencing of the proband's cDNA sample. Western blot and bioinformatics analyses were used to investigate the consequences of this copy number variant (CNV) at the protein level. CRISPR-Cas9 technology was used for a MED13L-gene-silencing experiment in a culture of the control individual's skin fibroblasts. After the MED13L-gene-editing experiment, subsequent functional fibroblast culture analyses were performed. Results: The analysis of the proband's cDNA sample allowed for specifying the regions of the breakpoints and identifying the heterozygous deletion that spanned exons 3 to 10 of MED13L, which has not been reported previously. In silico, the deletion was predicted to result in a truncated protein NP_056150.1:p.(Val104Glyfs*5), partly altering the Med13_N domain and losing the MedPIWI and Med13_C domains. After MED13L gene editing was performed, reduced cell viability; an accelerated aging process; and inhibition of the RB1, E2F1, and CCNC gene expression were found to exist. Conclusions: Based on these findings, heterozygous intragenic 12q24.21 deletion in the affected individual resulted in MED13L haploinsufficiency due to the premature termination of protein translation, therefore leading to MED13L haploinsufficiency syndrome.
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Affiliation(s)
- Evelina Siavrienė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, 08410 Vilnius, Lithuania
| | - Gunda Petraitytė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, 08410 Vilnius, Lithuania
| | - Violeta Mikštienė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, 08410 Vilnius, Lithuania
| | - Živilė Maldžienė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, 08410 Vilnius, Lithuania
| | - Aušra Sasnauskienė
- Department of Biochemistry and Molecular Biology, Institute of Biosciences, Life Sciences Centre, Vilnius University, 10257 Vilnius, Lithuania
| | - Vilmantė Žitkutė
- Department of Biochemistry and Molecular Biology, Institute of Biosciences, Life Sciences Centre, Vilnius University, 10257 Vilnius, Lithuania
| | - Laima Ambrozaitytė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, 08410 Vilnius, Lithuania
| | - Tautvydas Rančelis
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, 08410 Vilnius, Lithuania
| | - Algirdas Utkus
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, 08410 Vilnius, Lithuania
| | - Vaidutis Kučinskas
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, 08410 Vilnius, Lithuania
| | - Eglė Preikšaitienė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, 08410 Vilnius, Lithuania
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22
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Moreau CA, Kumar K, Harvey A, Huguet G, Urchs SGW, Schultz LM, Sharmarke H, Jizi K, Martin CO, Younis N, Tamer P, Martineau JL, Orban P, Silva AI, Hall J, van den Bree MBM, Owen MJ, Linden DEJ, Lippé S, Bearden CE, Almasy L, Glahn DC, Thompson PM, Bourgeron T, Bellec P, Jacquemont S. Brain functional connectivity mirrors genetic pleiotropy in psychiatric conditions. Brain 2023; 146:1686-1696. [PMID: 36059063 PMCID: PMC10319760 DOI: 10.1093/brain/awac315] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/13/2022] [Accepted: 08/11/2022] [Indexed: 02/03/2023] Open
Abstract
Pleiotropy occurs when a genetic variant influences more than one trait. This is a key property of the genomic architecture of psychiatric disorders and has been observed for rare and common genomic variants. It is reasonable to hypothesize that the microscale genetic overlap (pleiotropy) across psychiatric conditions and cognitive traits may lead to similar overlaps at the macroscale brain level such as large-scale brain functional networks. We took advantage of brain connectivity, measured by resting-state functional MRI to measure the effects of pleiotropy on large-scale brain networks, a putative step from genes to behaviour. We processed nine resting-state functional MRI datasets including 32 726 individuals and computed connectome-wide profiles of seven neuropsychiatric copy-number-variants, five polygenic scores, neuroticism and fluid intelligence as well as four idiopathic psychiatric conditions. Nine out of 19 pairs of conditions and traits showed significant functional connectivity correlations (rFunctional connectivity), which could be explained by previously published levels of genomic (rGenetic) and transcriptomic (rTranscriptomic) correlations with moderate to high concordance: rGenetic-rFunctional connectivity = 0.71 [0.40-0.87] and rTranscriptomic-rFunctional connectivity = 0.83 [0.52; 0.94]. Extending this analysis to functional connectivity profiles associated with rare and common genetic risk showed that 30 out of 136 pairs of connectivity profiles were correlated above chance. These similarities between genetic risks and psychiatric disorders at the connectivity level were mainly driven by the overconnectivity of the thalamus and the somatomotor networks. Our findings suggest a substantial genetic component for shared connectivity profiles across conditions and traits, opening avenues to delineate general mechanisms-amenable to intervention-across psychiatric conditions and genetic risks.
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Affiliation(s)
- Clara A Moreau
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, Université Paris Cité, Paris, France
- Sainte Justine Research Center, University of Montréal, Montréal, QC H3T 1C5, Canada
- Centre de Recherche de l’Institut Universitaire de Gériatrie de Montréal, UdeM, Montreal, QC H3W 1W5, Canada
| | - Kuldeep Kumar
- Sainte Justine Research Center, University of Montréal, Montréal, QC H3T 1C5, Canada
| | - Annabelle Harvey
- Sainte Justine Research Center, University of Montréal, Montréal, QC H3T 1C5, Canada
- Centre de Recherche de l’Institut Universitaire de Gériatrie de Montréal, UdeM, Montreal, QC H3W 1W5, Canada
| | - Guillaume Huguet
- Sainte Justine Research Center, University of Montréal, Montréal, QC H3T 1C5, Canada
| | - Sebastian G W Urchs
- Centre de Recherche de l’Institut Universitaire de Gériatrie de Montréal, UdeM, Montreal, QC H3W 1W5, Canada
- Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Laura M Schultz
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hanad Sharmarke
- Centre de Recherche de l’Institut Universitaire de Gériatrie de Montréal, UdeM, Montreal, QC H3W 1W5, Canada
| | - Khadije Jizi
- Sainte Justine Research Center, University of Montréal, Montréal, QC H3T 1C5, Canada
| | | | - Nadine Younis
- Sainte Justine Research Center, University of Montréal, Montréal, QC H3T 1C5, Canada
| | - Petra Tamer
- Sainte Justine Research Center, University of Montréal, Montréal, QC H3T 1C5, Canada
| | - Jean-Louis Martineau
- Sainte Justine Research Center, University of Montréal, Montréal, QC H3T 1C5, Canada
| | - Pierre Orban
- Centre de Recherche de l’Institut Universitaire en Santé Mentale de Montréal, UdeM, Montréal, QC H1N 3V2, Canada
- Département de Psychiatrie et d’Addictologie, Université de Montréal, Pavillon Roger-Gaudry, C.P. 6128, Succursale Centre-ville, Montréal, QC H3C 3J7, Canada
| | - Ana Isabel Silva
- Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, UK
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
- School for Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Jeremy Hall
- Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, UK
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Marianne B M van den Bree
- Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, UK
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Michael J Owen
- Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, UK
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - David E J Linden
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
- School for Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Sarah Lippé
- Sainte Justine Research Center, University of Montréal, Montréal, QC H3T 1C5, Canada
| | - Carrie E Bearden
- Integrative Center for Neurogenetics, Semel Institute for Neuroscience and Human Behavior, Los Angeles, CA 90095, USA
- Department of Psychiatry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Biobehavioral Sciences and Psychology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Laura Almasy
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Lifespan Brain Institute, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - David C Glahn
- Department of Psychiatry, Harvard Medical School, Cambridge, MA 02115, USA
- Boston Children’s Hospital, Tommy Fuss Center for Neuropsychiatric Disease Research, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Paul M Thompson
- Imaging Genetics Center, Stevens Institute for Neuroimaging and Informatics, Keck USC School of Medicine, Marina del Rey, CA, USA
| | - Thomas Bourgeron
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, Université Paris Cité, Paris, France
| | - Pierre Bellec
- Centre de Recherche de l’Institut Universitaire de Gériatrie de Montréal, UdeM, Montreal, QC H3W 1W5, Canada
| | - Sebastien Jacquemont
- Sainte Justine Research Center, University of Montréal, Montréal, QC H3T 1C5, Canada
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23
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Fevga C, Tesson C, Carreras Mascaro A, Courtin T, van Coller R, Sakka S, Ferraro F, Farhat N, Bardien S, Damak M, Carr J, Ferrien M, Boumeester V, Hundscheid J, Grillenzoni N, Kessissoglou IA, Kuipers DJS, Quadri M, Corvol JC, Mhiri C, Hassan BA, Breedveld GJ, Lesage S, Mandemakers W, Brice A, Bonifati V. PTPA variants and impaired PP2A activity in early-onset parkinsonism with intellectual disability. Brain 2023; 146:1496-1510. [PMID: 36073231 PMCID: PMC10115167 DOI: 10.1093/brain/awac326] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 06/24/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
The protein phosphatase 2A complex (PP2A), the major Ser/Thr phosphatase in the brain, is involved in a number of signalling pathways and functions, including the regulation of crucial proteins for neurodegeneration, such as alpha-synuclein, tau and LRRK2. Here, we report the identification of variants in the PTPA/PPP2R4 gene, encoding a major PP2A activator, in two families with early-onset parkinsonism and intellectual disability. We carried out clinical studies and genetic analyses, including genome-wide linkage analysis, whole-exome sequencing, and Sanger sequencing of candidate variants. We next performed functional studies on the disease-associated variants in cultured cells and knock-down of ptpa in Drosophila melanogaster. We first identified a homozygous PTPA variant, c.893T>G (p.Met298Arg), in patients from a South African family with early-onset parkinsonism and intellectual disability. Screening of a large series of additional families yielded a second homozygous variant, c.512C>A (p.Ala171Asp), in a Libyan family with a similar phenotype. Both variants co-segregate with disease in the respective families. The affected subjects display juvenile-onset parkinsonism and intellectual disability. The motor symptoms were responsive to treatment with levodopa and deep brain stimulation of the subthalamic nucleus. In overexpression studies, both the PTPA p.Ala171Asp and p.Met298Arg variants were associated with decreased PTPA RNA stability and decreased PTPA protein levels; the p.Ala171Asp variant additionally displayed decreased PTPA protein stability. Crucially, expression of both variants was associated with decreased PP2A complex levels and impaired PP2A phosphatase activation. PTPA orthologue knock-down in Drosophila neurons induced a significant impairment of locomotion in the climbing test. This defect was age-dependent and fully reversed by L-DOPA treatment. We conclude that bi-allelic missense PTPA variants associated with impaired activation of the PP2A phosphatase cause autosomal recessive early-onset parkinsonism with intellectual disability. Our findings might also provide new insights for understanding the role of the PP2A complex in the pathogenesis of more common forms of neurodegeneration.
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Affiliation(s)
- Christina Fevga
- Department of Clinical Genetics, Erasmus University Medical Center Rotterdam, Erasmus MC, 3015 GD Rotterdam, The Netherlands
| | - Christelle Tesson
- Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Sorbonne Université, Paris, France
| | - Ana Carreras Mascaro
- Department of Clinical Genetics, Erasmus University Medical Center Rotterdam, Erasmus MC, 3015 GD Rotterdam, The Netherlands
| | - Thomas Courtin
- Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Sorbonne Université, Paris, France
- Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Département de Génétique, DMU BioGeM, Paris, France
| | - Riaan van Coller
- Department of Neurology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Salma Sakka
- Research Unit in Neurogenetics, Clinical Investigation Center (CIC) at the CHU Habib Bourguiba, Sfax, Tunisia
| | - Federico Ferraro
- Department of Clinical Genetics, Erasmus University Medical Center Rotterdam, Erasmus MC, 3015 GD Rotterdam, The Netherlands
| | - Nouha Farhat
- Research Unit in Neurogenetics, Clinical Investigation Center (CIC) at the CHU Habib Bourguiba, Sfax, Tunisia
| | - Soraya Bardien
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Research Unit, Stellenbosch University, Cape Town, South Africa
| | - Mariem Damak
- Research Unit in Neurogenetics, Clinical Investigation Center (CIC) at the CHU Habib Bourguiba, Sfax, Tunisia
| | - Jonathan Carr
- Division of Neurology, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Mélanie Ferrien
- Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Sorbonne Université, Paris, France
| | - Valerie Boumeester
- Department of Clinical Genetics, Erasmus University Medical Center Rotterdam, Erasmus MC, 3015 GD Rotterdam, The Netherlands
| | - Jasmijn Hundscheid
- Department of Clinical Genetics, Erasmus University Medical Center Rotterdam, Erasmus MC, 3015 GD Rotterdam, The Netherlands
| | - Nicola Grillenzoni
- Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Sorbonne Université, Paris, France
| | - Irini A Kessissoglou
- Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Sorbonne Université, Paris, France
| | - Demy J S Kuipers
- Department of Clinical Genetics, Erasmus University Medical Center Rotterdam, Erasmus MC, 3015 GD Rotterdam, The Netherlands
| | - Marialuisa Quadri
- Department of Clinical Genetics, Erasmus University Medical Center Rotterdam, Erasmus MC, 3015 GD Rotterdam, The Netherlands
| | - Jean-Christophe Corvol
- Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Sorbonne Université, Paris, France
- Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Département de Neurologie, Centre d'Investigation Clinique Neurosciences, DMU Neuroscience, Paris, France
| | - Chokri Mhiri
- Research Unit in Neurogenetics, Clinical Investigation Center (CIC) at the CHU Habib Bourguiba, Sfax, Tunisia
| | - Bassem A Hassan
- Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Sorbonne Université, Paris, France
| | - Guido J Breedveld
- Department of Clinical Genetics, Erasmus University Medical Center Rotterdam, Erasmus MC, 3015 GD Rotterdam, The Netherlands
| | - Suzanne Lesage
- Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Sorbonne Université, Paris, France
| | - Wim Mandemakers
- Department of Clinical Genetics, Erasmus University Medical Center Rotterdam, Erasmus MC, 3015 GD Rotterdam, The Netherlands
| | - Alexis Brice
- Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Sorbonne Université, Paris, France
- Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Département de Génétique, DMU BioGeM, Paris, France
| | - Vincenzo Bonifati
- Department of Clinical Genetics, Erasmus University Medical Center Rotterdam, Erasmus MC, 3015 GD Rotterdam, The Netherlands
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Jung B, Ahn K, Justice C, Norman L, Price J, Sudre G, Shaw P. Rare copy number variants in males and females with childhood attention-deficit/hyperactivity disorder. Mol Psychiatry 2023; 28:1240-1247. [PMID: 36517639 PMCID: PMC10010944 DOI: 10.1038/s41380-022-01906-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/18/2022] [Accepted: 11/29/2022] [Indexed: 12/15/2022]
Abstract
While childhood attention-deficit/hyperactivity disorder (ADHD) is more prevalent in males than females, genetic contributors to this effect have not been established. Here, we explore sex differences in the contribution of common and/or rare genetic variants to ADHD. Participants were from the Adolescent Brain and Cognitive Development study (N = 1253 youth meeting DSM-5 criteria for ADHD [mean age = 11.46 years [SD = 0.87]; 31% female] and 5577 unaffected individuals [mean age = 11.42 years [SD = 0.89]; 50% female], overall 66% White, non-Hispanic (WNH), 19% Black/African American, and 15% other races. Logistic regression tested for interactions between sex (defined genotypically) and both rare copy number variants (CNV) and polygenic (common variant) risk in association with ADHD. There was a significant interaction between sex and the presence of a CNV deletion larger than 200 kb, both in the entire cohort (β = -0.74, CI = [-1.27 to -0.20], FDR-corrected p = 0.048) and, at nominal significance levels in the WNH ancestry subcohort (β = -0.86, CI = [-1.51 to -0.20], p = 0.010). Additionally, the number of deleted genes interacted with sex in association with ADHD (whole cohort. β = -0.13, CI = [-0.23 to -0.029], FDR-corrected p = 0.048; WNH. β = -0.17, CI = [-0.29 to -0.050], FDR-corrected p = 0.044) as did the total length of CNV deletions (whole cohort. β = -0.12, CI = [-0.19 to -0.044], FDR-corrected p = 0.028; WNH. β = -0.17, CI = [-0.28 to -0.061], FDR-corrected p = 0.034). This sex effect was driven by increased odds of childhood ADHD for females but not males in the presence of CNV deletions. No similar sex effect was found for CNV duplications or polygenic risk scores. The association between CNV deletions and ADHD was partially mediated by measures of cognitive flexibility. In summary, CNV deletions were associated with increased odds for childhood ADHD in females, but not males.
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Affiliation(s)
- Benjamin Jung
- Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kwangmi Ahn
- Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Cristina Justice
- Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Luke Norman
- Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Intramural Research Program, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jolie Price
- Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Gustavo Sudre
- Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Philip Shaw
- Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
- Intramural Research Program, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, 20892, USA.
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Zhang H, Alarcon C, Cavallari LH, Nutescu E, Carvill GL, Perera MA, Hernandez W. Genomewide Association Study Identifies Copy Number Variants Associated With Warfarin Dose Response and Risk of Venous Thromboembolism in African Americans. Clin Pharmacol Ther 2023; 113:624-633. [PMID: 36507737 DOI: 10.1002/cpt.2820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
The anticoagulant warfarin is commonly used to control and prevent thrombotic disorders, such as venous thromboembolism (VTE), which disproportionately afflicts African Americans. Despite the importance of copy number variants (CNVs), few studies have focused on characterizing and understanding their role in drug response and disease risk among African Americans. In this study, we conduct the first genome-wide analysis of CNVs to more comprehensively account for the contribution of genetic variation in warfarin dose requirement and VTE risk among African Americans. We used hidden Markov models to detect CNVs from high-throughput single-nucleotide polymorphism arrays for 340 African American participants in the International Warfarin Pharmacogenetics Consortium. We identified 11,570 CNVs resulting in 2,038 copy number variable regions (CNVRs) and found 3 CNVRs associated with warfarin dose requirement and 3 CNVRs associated with VTE risk in African Americans. CNVRs 1q31.2del and 6q14.1del were associated with increased warfarin dose requirement (β = 11.18 and 4.94, respectively; Pemp = < 0.002); CNVR 19p13.31del was associated with decreased warfarin dose requirement (β = -1.41, Pemp = 0.0004); CNVRs (2p22.1del and 5q35.1-q35.2del) were found to be associated with increased risk of VTE (odds ratios (ORs) = 1.88 and 14.9, respectively; Pemp ≤0.02); and CNVR 10q26.12del was associated with a decreased risk of VTE (OR = 0.6; Pemp = 0.05). Modeling of the 10q26.12del in HepG2 cells revealed that this deletion results in decreased fibrinogen gene expression, decreased fibrinogen and WDR11 protein levels, and decreased secretion of fibrinogen into the extracellular matrix. We found robust evidence that CNVRs could contribute to warfarin dose requirement and risk of VTE in African Americans and for 10q26.3del describe a possible pathogenic mechanism.
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Affiliation(s)
- Honghong Zhang
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Cristina Alarcon
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Larisa H Cavallari
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Edith Nutescu
- Department of Pharmacy Practice, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois, USA
| | - Gemma L Carvill
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.,Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Minoli A Perera
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Wenndy Hernandez
- Section of Cardiology, University of Chicago, Chicago, Illinois, USA
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26
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Lim TY, Verbitsky M, Sanna-Cherchi S. ParseCNV2: a versatile and integrated tool for copy number variation association studies. Eur J Hum Genet 2023; 31:275-277. [PMID: 36631543 PMCID: PMC9995335 DOI: 10.1038/s41431-022-01280-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 12/19/2022] [Indexed: 01/13/2023] Open
Affiliation(s)
- Tze Y Lim
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Miguel Verbitsky
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Simone Sanna-Cherchi
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA.
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27
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Arias KD, Pablo Gutiérrez J, Fernandez I, Menéndez-Arias NA, Álvarez I, Goyache F. Segregation patterns and inheritance rate of copy number variations regions assessed in a Gochu Asturcelta pig pedigree. Gene X 2023; 854:147111. [PMID: 36509293 DOI: 10.1016/j.gene.2022.147111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/30/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
Copy Number Variation Regions (CNVR) were subjected to pedigree analysis to contribute to the understanding of their segregation patterns. Up to 492 Gochu Asturcelta pig individuals forming 478 different parents-offspring trios (61 different families) were genotyped using the Axiom_PigHDv1 Array (658,692 SNPs). CNVR calling, performed using two different platforms (PennCNV and QuantiSNP), allowed to identify a total of 344 candidate CNVR on the 18 porcine autosomes covering about 106.8 Mb of the pig genome. Sixty-nine CNVR were identified, to some extent, in both the parents and the offspring and were classified as segregating CNVR. The other candidate CNVR were called in one or more progeny but in neither parent and classified either as singleton or recurrent de novo CNVR. Segregating CNVR were, on average, larger and more frequent than the recurrent de novo CNVR (444.8 kb vs 287.9 kb long and 34 vs 5 individuals, respectively). In any case, segregating CNVR did not conform to strict Mendelian inheritance patterns: estimates of average paternal and maternal transmission rates ranged from 11.0 % to 13.4 % and mean inheritance rate was below 21 %. This issue should be carefully considered when interpreting the results of CNV studies. Segregating CNVR, present across generations, are unlikely to be artifacts or false positives and can be hypothesized to be important at the population level.
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Affiliation(s)
| | - Juan Pablo Gutiérrez
- Departamento de Producción Animal, Universidad Complutense de Madrid, Avda. Puerta de Hierro s/n, 28040 Madrid, Spain
| | | | | | | | - Félix Goyache
- SERIDA-Deva, Camino de Rioseco 1225, 33394-Gijón, Spain.
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28
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Wang H, Wang LS, Schellenberg G, Lee WP. The role of structural variations in Alzheimer's disease and other neurodegenerative diseases. Front Aging Neurosci 2023; 14:1073905. [PMID: 36846102 PMCID: PMC9944073 DOI: 10.3389/fnagi.2022.1073905] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 12/31/2022] [Indexed: 02/10/2023] Open
Abstract
Dozens of single nucleotide polymorphisms (SNPs) related to Alzheimer's disease (AD) have been discovered by large scale genome-wide association studies (GWASs). However, only a small portion of the genetic component of AD can be explained by SNPs observed from GWAS. Structural variation (SV) can be a major contributor to the missing heritability of AD; while SV in AD remains largely unexplored as the accurate detection of SVs from the widely used array-based and short-read technology are still far from perfect. Here, we briefly summarized the strengths and weaknesses of available SV detection methods. We reviewed the current landscape of SV analysis in AD and SVs that have been found associated with AD. Particularly, the importance of currently less explored SVs, including insertions, inversions, short tandem repeats, and transposable elements in neurodegenerative diseases were highlighted.
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Affiliation(s)
- Hui Wang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Li-San Wang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Gerard Schellenberg
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Wan-Ping Lee
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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29
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Microdeletions and microduplications linked to severe congenital disorders in infertile men. Sci Rep 2023; 13:574. [PMID: 36631630 PMCID: PMC9834233 DOI: 10.1038/s41598-023-27750-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/06/2023] [Indexed: 01/13/2023] Open
Abstract
Data on the clinical validity of DNA copy number variants (CNVs) in spermatogenic failure (SPGF) is limited. This study analyzed the genome-wide CNV profile in 215 men with idiopathic SPGF and 62 normozoospermic fertile men, recruited at the Andrology Clinic, Tartu University Hospital, Estonia. A two-fold higher representation of > 1 Mb CNVs was observed in men with SPGF (13%, n = 28) compared to controls (6.5%, n = 4). Seven patients with SPGF were identified as carriers of microdeletions (1q21.1; 2.4 Mb) or microduplications (3p26.3, 1.1 Mb; 7p22.3-p22.2, 1.56 Mb; 10q11.22, 1.42 Mb, three cases; Xp22.33; 2.3 Mb) linked to severe congenital conditions. Large autosomal CNV carriers had oligozoospermia, reduced or low-normal bitesticular volume (22-28 ml). The 7p22.3-p22.2 microduplication carrier presented mild intellectual disability, neuropsychiatric problems, and short stature. The Xp22.33 duplication at the PAR1/non-PAR boundary, previously linked to uterine agenesis, was detected in a patient with non-obstructive azoospermia. A novel recurrent intragenic deletion in testis-specific LRRC69 was significantly overrepresented in patients with SPGF compared to the general population (3.3% vs. 0.85%; χ2 test, OR = 3.9 [95% CI 1.8-8.4], P = 0.0001). Assessment of clinically valid CNVs in patients with SPGF will improve their management and counselling for general and reproductive health, including risk of miscarriage and congenital disorders in future offspring.
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30
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Moreau CA, Harvey A, Kumar K, Huguet G, Urchs SGW, Douard EA, Schultz LM, Sharmarke H, Jizi K, Martin CO, Younis N, Tamer P, Rolland T, Martineau JL, Orban P, Silva AI, Hall J, van den Bree MBM, Owen MJ, Linden DEJ, Labbe A, Lippé S, Bearden CE, Almasy L, Glahn DC, Thompson PM, Bourgeron T, Bellec P, Jacquemont S. Genetic Heterogeneity Shapes Brain Connectivity in Psychiatry. Biol Psychiatry 2023; 93:45-58. [PMID: 36372570 PMCID: PMC10936195 DOI: 10.1016/j.biopsych.2022.08.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 02/03/2023]
Abstract
BACKGROUND Polygenicity and genetic heterogeneity pose great challenges for studying psychiatric conditions. Genetically informed approaches have been implemented in neuroimaging studies to address this issue. However, the effects on functional connectivity of rare and common genetic risks for psychiatric disorders are largely unknown. Our objectives were to estimate and compare the effect sizes on brain connectivity of psychiatric genomic risk factors with various levels of complexity: oligogenic copy number variants (CNVs), multigenic CNVs, and polygenic risk scores (PRSs) as well as idiopathic psychiatric conditions and traits. METHODS Resting-state functional magnetic resonance imaging data were processed using the same pipeline across 9 datasets. Twenty-nine connectome-wide association studies were performed to characterize the effects of 15 CNVs (1003 carriers), 7 PRSs, 4 idiopathic psychiatric conditions (1022 individuals with autism, schizophrenia, bipolar conditions, or attention-deficit/hyperactivity disorder), and 2 traits (31,424 unaffected control subjects). RESULTS Effect sizes on connectivity were largest for psychiatric CNVs (estimates: 0.2-0.65 z score), followed by psychiatric conditions (0.15-0.42), neuroticism and fluid intelligence (0.02-0.03), and PRSs (0.01-0.02). Effect sizes of CNVs on connectivity were correlated to their effects on cognition and risk for disease (r = 0.9, p = 5.93 × 10-6). However, effect sizes of CNVs adjusted for the number of genes significantly decreased from small oligogenic to large multigenic CNVs (r = -0.88, p = 8.78 × 10-6). PRSs had disproportionately low effect sizes on connectivity compared with CNVs conferring similar risk for disease. CONCLUSIONS Heterogeneity and polygenicity affect our ability to detect brain connectivity alterations underlying psychiatric manifestations.
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Affiliation(s)
- Clara A Moreau
- Human Genetics and Cognitive Functions, Institut Pasteur, Université Paris Cité, Paris, France; Sainte-Justine Research Center, University of Montréal, Montréal, Canada; Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal, Montreal, Canada.
| | - Annabelle Harvey
- Sainte-Justine Research Center, University of Montréal, Montréal, Canada; Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal, Montreal, Canada
| | - Kuldeep Kumar
- Sainte-Justine Research Center, University of Montréal, Montréal, Canada
| | - Guillaume Huguet
- Sainte-Justine Research Center, University of Montréal, Montréal, Canada
| | - Sebastian G W Urchs
- Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal, Montreal, Canada; Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Elise A Douard
- Sainte-Justine Research Center, University of Montréal, Montréal, Canada
| | - Laura M Schultz
- Lifespan Brain Institute, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Hanad Sharmarke
- Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal, Montreal, Canada
| | - Khadije Jizi
- Sainte-Justine Research Center, University of Montréal, Montréal, Canada
| | | | - Nadine Younis
- Sainte-Justine Research Center, University of Montréal, Montréal, Canada
| | - Petra Tamer
- Sainte-Justine Research Center, University of Montréal, Montréal, Canada
| | - Thomas Rolland
- Human Genetics and Cognitive Functions, Institut Pasteur, Université Paris Cité, Paris, France
| | | | - Pierre Orban
- Centre de Recherche de l'Institut Universitaire en Santé Mentale de Montréal, Montréal, Canada; Département de Psychiatrie et d'Addictologie, Université de Montréal, Montréal, Canada
| | - Ana Isabel Silva
- Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, United Kingdom; MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, United Kingdom; School for Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, The Netherlands
| | - Jeremy Hall
- Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, United Kingdom; MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, United Kingdom
| | - Marianne B M van den Bree
- Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, United Kingdom; MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, United Kingdom
| | - Michael J Owen
- Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, United Kingdom; MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, United Kingdom
| | - David E J Linden
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, United Kingdom; School for Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, The Netherlands
| | - Aurelie Labbe
- Département des Sciences de la Décision, HEC, Québec, Montréal, Canada
| | - Sarah Lippé
- Sainte-Justine Research Center, University of Montréal, Montréal, Canada
| | - Carrie E Bearden
- Integrative Center for Neurogenetics, Semel Institute for Neuroscience and Human Behavior, Departments of Psychiatry and Biobehavioral Sciences and Psychology, University of California, Los Angeles, Los Angeles, California
| | - Laura Almasy
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Pennsylvania; Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania; Lifespan Brain Institute, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
| | - David C Glahn
- Harvard Medical School, Department of Psychiatry, Boston, Massachusetts; Boston Children's Hospital, Tommy Fuss Center for Neuropsychiatric Disease Research, Boston, Massachusetts
| | - Paul M Thompson
- Imaging Genetics Center, Stevens Institute for Neuroimaging and Informatics, Keck USC School of Medicine, Marina del Rey, California
| | - Thomas Bourgeron
- Human Genetics and Cognitive Functions, Institut Pasteur, Université Paris Cité, Paris, France
| | - Pierre Bellec
- Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal, Montreal, Canada
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Montalbano S, Sánchez XC, Vaez M, Helenius D, Werge T, Ingason A. Accurate and Effective Detection of Recurrent Copy Number Variants in Large SNP Genotype Datasets. Curr Protoc 2022; 2:e621. [PMID: 36469582 PMCID: PMC9729012 DOI: 10.1002/cpz1.621] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Structural variations, including recurrent Copy Number Variants (CNVs) at specific genomic loci, have been found to be associated with increased risk of several diseases and syndromes. CNV carrier status can be determined in large collections of samples using SNP arrays and, more recently, sequencing data. Although there is some consensus among researchers about the essential steps required in such analysis (i.e., CNV calling, filtering of putative carriers, and visual validation using intensity data plots of the genomic region), standard methodologies and processes to control the quality and consistency of the results are lacking. Here, we present a comprehensive and user-friendly protocol that we have refined from our extensive research experience in the field. We cover every aspect of the analysis, from input data curation to final results. For each step, we highlight which parameters affect the analysis the most and how different settings may lead to different results. We provide a pipeline to run the complete analysis with effective (but customizable) pre-sets. We present software that we developed to better handle and filter putative CNV carriers and perform visual inspection to validate selected candidates. Finally, we describe methods to evaluate the critical sections and actions to counterbalance potential problems. The current implementation is focused on Illumina SNP array data. All the presented software is freely available and provided in a ready-to-use docker container. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: From raw intensity data files to CNV calls Basic Protocol 2: From CNV calls to validated CNV carriers. Basic Protocol 3: Quality control and quality assessment Basic Protocol 4: Install the necessary software.
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Affiliation(s)
- Simone Montalbano
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
- These authors contributed equally to this work
| | - Xabier Calle Sánchez
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
- These authors contributed equally to this work
| | - Morteza Vaez
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
| | - Dorte Helenius
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
| | - Thomas Werge
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
- Lundbeck Foundation Center for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Andrés Ingason
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
- Lundbeck Foundation Center for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
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Maihofer AX, Engchuan W, Huguet G, Klein M, MacDonald JR, Shanta O, Thiruvahindrapuram B, Jean-Louis M, Saci Z, Jacquemont S, Scherer SW, Ketema E, Aiello AE, Amstadter AB, Avdibegović E, Babic D, Baker DG, Bisson JI, Boks MP, Bolger EA, Bryant RA, Bustamante AC, Caldas-de-Almeida JM, Cardoso G, Deckert J, Delahanty DL, Domschke K, Dunlop BW, Dzubur-Kulenovic A, Evans A, Feeny NC, Franz CE, Gautam A, Geuze E, Goci A, Hammamieh R, Jakovljevic M, Jett M, Jones I, Kaufman ML, Kessler RC, King AP, Kremen WS, Lawford BR, Lebois LAM, Lewis C, Liberzon I, Linnstaedt SD, Lugonja B, Luykx JJ, Lyons MJ, Mavissakalian MR, McLaughlin KA, McLean SA, Mehta D, Mellor R, Morris CP, Muhie S, Orcutt HK, Peverill M, Ratanatharathorn A, Risbrough VB, Rizzo A, Roberts AL, Rothbaum AO, Rothbaum BO, Roy-Byrne P, Ruggiero KJ, Rutten BPF, Schijven D, Seng JS, Sheerin CM, Sorenson MA, Teicher MH, Uddin M, Ursano RJ, Vinkers CH, Voisey J, Weber H, Winternitz S, Xavier M, Yang R, McD Young R, Zoellner LA, Salem RM, Shaffer RA, Wu T, Ressler KJ, Stein MB, Koenen KC, Sebat J, Nievergelt CM. Rare copy number variation in posttraumatic stress disorder. Mol Psychiatry 2022; 27:5062-5069. [PMID: 36131047 PMCID: PMC9763110 DOI: 10.1038/s41380-022-01776-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 08/24/2022] [Accepted: 09/02/2022] [Indexed: 01/27/2023]
Abstract
Posttraumatic stress disorder (PTSD) is a heritable (h2 = 24-71%) psychiatric illness. Copy number variation (CNV) is a form of rare genetic variation that has been implicated in the etiology of psychiatric disorders, but no large-scale investigation of CNV in PTSD has been performed. We present an association study of CNV burden and PTSD symptoms in a sample of 114,383 participants (13,036 cases and 101,347 controls) of European ancestry. CNVs were called using two calling algorithms and intersected to a consensus set. Quality control was performed to remove strong outlier samples. CNVs were examined for association with PTSD within each cohort using linear or logistic regression analysis adjusted for population structure and CNV quality metrics, then inverse variance weighted meta-analyzed across cohorts. We examined the genome-wide total span of CNVs, enrichment of CNVs within specified gene-sets, and CNVs overlapping individual genes and implicated neurodevelopmental regions. The total distance covered by deletions crossing over known neurodevelopmental CNV regions was significant (beta = 0.029, SE = 0.005, P = 6.3 × 10-8). The genome-wide neurodevelopmental CNV burden identified explains 0.034% of the variation in PTSD symptoms. The 15q11.2 BP1-BP2 microdeletion region was significantly associated with PTSD (beta = 0.0206, SE = 0.0056, P = 0.0002). No individual significant genes interrupted by CNV were identified. 22 gene pathways related to the function of the nervous system and brain were significant in pathway analysis (FDR q < 0.05), but these associations were not significant once NDD regions were removed. A larger sample size, better detection methods, and annotated resources of CNV are needed to explore this relationship further.
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Affiliation(s)
- Adam X Maihofer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA.
- Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA.
- Veterans Affairs San Diego Healthcare System, Center of Excellence for Stress and Mental Health, San Diego, CA, USA.
| | - Worrawat Engchuan
- The Hospital for Sick Children, Genetics and Genome Biology, Toronto, Ontario, Canada
- The Hospital for Sick Children, The Centre for Applied Genomics, Toronto, Ontario, Canada
| | - Guillaume Huguet
- Centre Hospitalier Universitaire Sainte-Justine Centre de Recherche, Montreal, Quebec, Canada
| | - Marieke Klein
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Jeffrey R MacDonald
- The Hospital for Sick Children, Genetics and Genome Biology, Toronto, Ontario, Canada
| | - Omar Shanta
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | | | - Martineau Jean-Louis
- Department of Pediatrics, Centre Hospitalier Universitaire Sainte-Justine Centre de Recherche, Montreal, Quebec, Canada
| | - Zohra Saci
- Centre Hospitalier Universitaire Sainte-Justine Centre de Recherche, Montreal, Quebec, Canada
| | - Sebastien Jacquemont
- Centre Hospitalier Universitaire Sainte-Justine Centre de Recherche, Montreal, Quebec, Canada
- Department of Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Vaud, Switzerland
- Department of Pediatrics, University of Montreal, Montreal, Quebec, Canada
| | - Stephen W Scherer
- The Hospital for Sick Children, Genetics and Genome Biology, Toronto, Ontario, Canada
- University of Toronto, McLaughlin Centre, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Elizabeth Ketema
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, Center of Excellence for Stress and Mental Health, San Diego, CA, USA
- Research Service, Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
| | - Allison E Aiello
- Department of Epidemiology, Robert N Butler Columbia Aging Center, Columbia University, New York, NY, USA
| | - Ananda B Amstadter
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Richmond, VA, USA
| | - Esmina Avdibegović
- Department of Psychiatry, University Clinical Center of Tuzla, Tuzla, Bosnia and Herzegovina
| | - Dragan Babic
- Department of Psychiatry, University Clinical Center of Mostar, Mostar, Bosnia and Herzegovina
| | - Dewleen G Baker
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, Center of Excellence for Stress and Mental Health, San Diego, CA, USA
- Psychiatry Service, Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
| | - Jonathan I Bisson
- MRC Centre for Psychiatric Genetics and Genomics, Cardiff University, National Centre for Mental Health, Cardiff, South Glamorgan, UK
| | - Marco P Boks
- Department of Psychiatry, UMC Utrecht Brain Center, Utrecht, the Netherlands
| | - Elizabeth A Bolger
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- McLean Hospital, Belmont, MA, USA
| | - Richard A Bryant
- Department of Psychology, University of New South Wales, Sydney, NSW, Australia
| | - Angela C Bustamante
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Graça Cardoso
- Lisbon Institute of Global Mental Health and Comprehensive Health Research Centre, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Jurgen Deckert
- University Hospital of Wuerzburg, Center of Mental Health, Psychiatry, Psychosomatics and Psychotherapy, Wuerzburg, Germany
| | - Douglas L Delahanty
- Department of Psychological Sciences, Kent State University, Kent, OH, USA
- Research and Sponsored Programs, Kent State University, Kent, OH, USA
| | - Katharina Domschke
- Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, Freiburg, Germany
- Faculty of Medicine, Centre for Basics in Neuromodulation, University of Freiburg, Freiburg, Germany
| | - Boadie W Dunlop
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Alma Dzubur-Kulenovic
- Department of Psychiatry, University Clinical Center of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Alexandra Evans
- MRC Centre for Psychiatric Genetics and Genomics, Cardiff University, National Centre for Mental Health, Cardiff, South Glamorgan, UK
| | - Norah C Feeny
- Department of Psychological Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Carol E Franz
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Aarti Gautam
- Walter Reed Army Institute of Research, Medical Readiness Systems Biology, Center for Military Psychiatry and Neuroscience, Silver Spring, MD, USA
| | - Elbert Geuze
- Netherlands Ministry of Defence, Brain Research and Innovation Centre, Utrecht, the Netherlands
- Department of Psychiatry, UMC Utrecht Brain Center Rudolf Magnus, Utrecht, the Netherlands
| | - Aferdita Goci
- Department of Psychiatry, University Clinical Centre of Kosovo, Prishtina, Kosovo
| | - Rasha Hammamieh
- Walter Reed Army Institute of Research, Medical Readiness Systems Biology, Center for Military Psychiatry and Neuroscience, Silver Spring, MD, USA
| | - Miro Jakovljevic
- Department of Psychiatry, University Hospital Center of Zagreb, Zagreb, Croatia
| | - Marti Jett
- US Medical Research & Development Comm, Fort Detrick, MD, USA
- Walter Reed Army Institute of Research, Headquarter, Silver Spring, MD, USA
| | - Ian Jones
- MRC Centre for Psychiatric Genetics and Genomics, Cardiff University, National Centre for Mental Health, Cardiff, South Glamorgan, UK
| | - Milissa L Kaufman
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- McLean Hospital, Belmont, MA, USA
| | - Ronald C Kessler
- Department of Health Care Policy, Harvard Medical School, Boston, MA, USA
| | - Anthony P King
- Ohio State University, College of Medicine, Institute for Behavioral Medicine Research, Columbus, OH, USA
| | - William S Kremen
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Bruce R Lawford
- School of Biomedical Sciences, Queensland University of Technology, Kelvin Grove, QLD, Australia
| | - Lauren A M Lebois
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- McLean Hospital, Belmont, MA, USA
| | - Catrin Lewis
- MRC Centre for Psychiatric Genetics and Genomics, Cardiff University, National Centre for Mental Health, Cardiff, South Glamorgan, UK
| | - Israel Liberzon
- Department of Psychiatry and Behavioral Sciences, Texas A&M University College of Medicine, Bryan, TX, USA
| | - Sarah D Linnstaedt
- Institute for Trauma Recovery, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bozo Lugonja
- MRC Centre for Psychiatric Genetics and Genomics, Cardiff University, National Centre for Mental Health, Cardiff, South Glamorgan, UK
| | - Jurjen J Luykx
- Department of Psychiatry, UMC Utrecht Brain Center Rudolf Magnus, Utrecht, the Netherlands
- Department of Translational Neuroscience, UMC Utrecht Brain Center Rudolf Magnus, Utrecht, the Netherlands
| | - Michael J Lyons
- Department of Psychological & Brain Sciences, Boston University, Boston, MA, USA
| | | | | | - Samuel A McLean
- Institute for Trauma Recovery, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Emergency Medicine, UNC Institute for Trauma Recovery, Chapel Hill, NC, USA
| | - Divya Mehta
- School of Biomedical Sciences, Queensland University of Technology, Kelvin Grove, QLD, Australia
- Queensland University of Technology, Centre for Genomics and Personalised Health, Kelvin Grove, QLD, Australia
| | - Rebecca Mellor
- Gallipoli Medical Research Foundation, Greenslopes Private Hospital, Greenslopes, QLD, Australia
| | - Charles Phillip Morris
- School of Biomedical Sciences, Queensland University of Technology, Kelvin Grove, QLD, Australia
| | - Seid Muhie
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Holly K Orcutt
- Department of Psychology, Northern Illinois University, DeKalb, IL, USA
| | - Matthew Peverill
- Department of Psychology, University of Washington, Seattle, WA, USA
| | - Andrew Ratanatharathorn
- Department of Epidemiology, Columbia University Mailmain School of Public Health, New York, NY, USA
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Victoria B Risbrough
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, Center of Excellence for Stress and Mental Health, San Diego, CA, USA
- Research Service, Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
| | - Albert Rizzo
- University of Southern California, Institute for Creative Technologies, Los Angeles, CA, USA
| | - Andrea L Roberts
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Alex O Rothbaum
- Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Barbara O Rothbaum
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Peter Roy-Byrne
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Kenneth J Ruggiero
- Department of Nursing and Department of Psychiatry, Medical University of South Carolina, Charleston, SC, USA
| | - Bart P F Rutten
- Department of Psychiatry and Neuropsychology, Maastricht Universitair Medisch Centrum, School for Mental Health and Neuroscience, Maastricht, Limburg, the Netherlands
| | - Dick Schijven
- Department of Psychiatry, UMC Utrecht Brain Center Rudolf Magnus, Utrecht, the Netherlands
- Department of Translational Neuroscience, UMC Utrecht Brain Center Rudolf Magnus, Utrecht, the Netherlands
| | - Julia S Seng
- University of Michigan, School of Nursing, Ann Arbor, MI, USA
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA
- Department of Women's and Gender Studies, University of Michigan, Ann Arbor, MI, USA
- University of Michigan, Institute for Research on Women and Gender, Ann Arbor, MI, USA
| | - Christina M Sheerin
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Richmond, VA, USA
| | - Michael A Sorenson
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Martin H Teicher
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- Developmental Biopsychiatry Research Program, McLean Hospital, Belmont, MA, USA
| | - Monica Uddin
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Robert J Ursano
- Department of Psychiatry, Uniformed Services University, Bethesda, MD, USA
| | - Christiaan H Vinkers
- Amsterdam Neuroscience, Mood, Anxiety, Psychosis, Sleep & Stress Program, Amsterdam, the Netherlands
- Department of Psychiatry, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Department of Anatomy and Neurosciences, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Joanne Voisey
- School of Biomedical Sciences, Queensland University of Technology, Kelvin Grove, QLD, Australia
- Queensland University of Technology, Centre for Genomics and Personalised Health, Kelvin Grove, QLD, Australia
| | - Heike Weber
- University Hospital of Wuerzburg, Center of Mental Health, Psychiatry, Psychosomatics and Psychotherapy, Wuerzburg, Germany
| | - Sherry Winternitz
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- McLean Hospital, Belmont, MA, USA
| | - Miguel Xavier
- Universidade Nova de Lisboa, Nova Medical School, Lisboa, Portugal
| | - Ruoting Yang
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Ross McD Young
- Queensland University of Technology, School of Clinical Sciences, Kelvin Grove, QLD, Australia
- University of the Sunshine Coast, The Chancellory, Sippy Downs, QLD, Australia
| | - Lori A Zoellner
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Rany M Salem
- University of California San Diego, Herbert Wertheim School of Public Health and Human Longevity Science, La Jolla, CA, USA
| | - Richard A Shaffer
- Department of Epidemiology and Health Sciences, Naval Health Research Center, San Diego, CA, USA
| | - Tianying Wu
- Division of Epidemiology and Biostatistics, San Diego State University, School of Public Health, San Diego, CA, USA
- University of California, San Diego, Moores Cancer Center, San Diego, CA, USA
| | - Kerry J Ressler
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- McLean Hospital, Belmont, MA, USA
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Murray B Stein
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Psychiatry Service, Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
- University of California San Diego, School of Public Health, La Jolla, CA, USA
| | - Karestan C Koenen
- Broad Institute of MIT and Harvard, Stanley Center for Psychiatric Research, Cambridge, MA, USA
- Department of Epidemiology, Harvard T. H. School of Public Health, Boston, MA, USA
- Psychiatric and Neurodevelopmental Genetics Unit (PNGU), Massachusetts General Hospital, Boston, MA, USA
| | - Jonathan Sebat
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Caroline M Nievergelt
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, Center of Excellence for Stress and Mental Health, San Diego, CA, USA
- Research Service, Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
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Chear S, Perry S, Wilson R, Bindoff A, Talbot J, Ware TL, Grubman A, Vickers JC, Pébay A, Ruddle JB, King AE, Hewitt AW, Cook AL. Lysosomal alterations and decreased electrophysiological activity in CLN3 disease patient-derived cortical neurons. Dis Model Mech 2022; 15:dmm049651. [PMID: 36453132 PMCID: PMC10655821 DOI: 10.1242/dmm.049651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 11/17/2022] [Indexed: 12/02/2022] Open
Abstract
CLN3 disease is a lysosomal storage disorder associated with fatal neurodegeneration that is caused by mutations in CLN3, with most affected individuals carrying at least one allele with a 966 bp deletion. Using CRISPR/Cas9, we corrected the 966 bp deletion mutation in human induced pluripotent stem cells (iPSCs) of a compound heterozygous patient (CLN3 Δ 966 bp and E295K). We differentiated these isogenic iPSCs, and iPSCs from an unrelated healthy control donor, to neurons and identified disease-related changes relating to protein synthesis, trafficking and degradation, and in neuronal activity, which were not apparent in CLN3-corrected or healthy control neurons. CLN3 neurons showed numerous membrane-bound vacuoles containing diverse storage material and hyperglycosylation of the lysosomal LAMP1 protein. Proteomic analysis showed increase in lysosomal-related proteins and many ribosomal subunit proteins in CLN3 neurons, accompanied by downregulation of proteins related to axon guidance and endocytosis. CLN3 neurons also had lower electrophysical activity as recorded using microelectrode arrays. These data implicate inter-related pathways in protein homeostasis and neurite arborization as contributing to CLN3 disease, and which could be potential targets for therapy.
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Affiliation(s)
- Sueanne Chear
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS 7001, Australia
| | - Sharn Perry
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS 7001, Australia
| | - Richard Wilson
- Central Science Laboratory, University of Tasmania, Hobart, TAS 7001, Australia
| | - Aidan Bindoff
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS 7001, Australia
| | - Jana Talbot
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS 7001, Australia
| | - Tyson L. Ware
- Department of Paediatrics, Royal Hobart Hospital, Hobart, TAS 7000, Australia
| | - Alexandra Grubman
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia
| | - James C. Vickers
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS 7001, Australia
| | - Alice Pébay
- Department of Anatomy and Physiology, University of Melbourne, Parkville, VIC 3010, Australia
- Department of Surgery, Royal Melbourne Hospital, University of Melbourne, Parkville, VIC 3010, Australia
| | - Jonathan B. Ruddle
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
| | - Anna E. King
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS 7001, Australia
| | - Alex W. Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7001, Australia
| | - Anthony L. Cook
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS 7001, Australia
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Hujoel MLA, Sherman MA, Barton AR, Mukamel RE, Sankaran VG, Terao C, Loh PR. Influences of rare copy-number variation on human complex traits. Cell 2022; 185:4233-4248.e27. [PMID: 36306736 PMCID: PMC9800003 DOI: 10.1016/j.cell.2022.09.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 07/22/2022] [Accepted: 09/19/2022] [Indexed: 11/06/2022]
Abstract
The human genome contains hundreds of thousands of regions harboring copy-number variants (CNV). However, the phenotypic effects of most such polymorphisms are unknown because only larger CNVs have been ascertainable from SNP-array data generated by large biobanks. We developed a computational approach leveraging haplotype sharing in biobank cohorts to more sensitively detect CNVs. Applied to UK Biobank, this approach accounted for approximately half of all rare gene inactivation events produced by genomic structural variation. This CNV call set enabled a detailed analysis of associations between CNVs and 56 quantitative traits, identifying 269 independent associations (p < 5 × 10-8) likely to be causally driven by CNVs. Putative target genes were identifiable for nearly half of the loci, enabling insights into dosage sensitivity of these genes and uncovering several gene-trait relationships. These results demonstrate the ability of haplotype-informed analysis to provide insights into the genetic basis of human complex traits.
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Affiliation(s)
- Margaux L A Hujoel
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Maxwell A Sherman
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alison R Barton
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Bioinformatics and Integrative Genomics Program, Harvard Medical School, Boston, MA, USA
| | - Ronen E Mukamel
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vijay G Sankaran
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan; Department of Applied Genetics, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Po-Ru Loh
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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35
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Lepamets M, Auwerx C, Nõukas M, Claringbould A, Porcu E, Kals M, Jürgenson T, Morris AP, Võsa U, Bochud M, Stringhini S, Wijmenga C, Franke L, Peterson H, Vilo J, Lepik K, Mägi R, Kutalik Z. Omics-informed CNV calls reduce false-positive rates and improve power for CNV-trait associations. HGG ADVANCES 2022; 3:100133. [PMID: 36035246 PMCID: PMC9399386 DOI: 10.1016/j.xhgg.2022.100133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 07/26/2022] [Indexed: 11/29/2022] Open
Abstract
Copy-number variations (CNV) are believed to play an important role in a wide range of complex traits, but discovering such associations remains challenging. While whole-genome sequencing (WGS) is the gold-standard approach for CNV detection, there are several orders of magnitude more samples with available genotyping microarray data. Such array data can be exploited for CNV detection using dedicated software (e.g., PennCNV); however, these calls suffer from elevated false-positive and -negative rates. In this study, we developed a CNV quality score that weights PennCNV calls (pCNVs) based on their likelihood of being true positive. First, we established a measure of pCNV reliability by leveraging evidence from multiple omics data (WGS, transcriptomics, and methylomics) obtained from the same samples. Next, we built a predictor of omics-confirmed pCNVs, termed omics-informed quality score (OQS), using only PennCNV software output parameters. Promisingly, OQS assigned to pCNVs detected in close family members was up to 35% higher than the OQS of pCNVs not carried by other relatives (p < 3.0 × 10−90), outperforming other scores. Finally, in an association study of four anthropometric traits in 89,516 Estonian Biobank samples, the use of OQS led to a relative increase in the trait variance explained by CNVs of up to 56% compared with published quality filtering methods or scores. Overall, we put forward a flexible framework to improve any CNV detection method leveraging multi-omics evidence, applied it to improve PennCNV calls, and demonstrated its utility by improving the statistical power for downstream association analyses.
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Affiliation(s)
- Maarja Lepamets
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
- Corresponding author
| | - Chiara Auwerx
- Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
- Center for Primary Care and Public Health (Unisanté), Department of Epidemiology and Health Systems, University of Lausanne, Lausanne 1010, Switzerland
| | - Margit Nõukas
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | | | - Eleonora Porcu
- Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
- Center for Primary Care and Public Health (Unisanté), Department of Epidemiology and Health Systems, University of Lausanne, Lausanne 1010, Switzerland
| | - Mart Kals
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki 00014, Finland
| | - Tuuli Jürgenson
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
- Institute of Mathematics and Statistics, University of Tartu, Tartu 51009, Estonia
| | | | - Andrew Paul Morris
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, The University of Manchester, Manchester M13 9PL, UK
| | - Urmo Võsa
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Murielle Bochud
- Center for Primary Care and Public Health (Unisanté), Department of Epidemiology and Health Systems, University of Lausanne, Lausanne 1010, Switzerland
| | - Silvia Stringhini
- Unit of Population Epidemiology, Division of Primary Care, Geneva 1205, Switzerland
| | - Cisca Wijmenga
- University of Groningen, University Medical Center Groningen, Department of Genetics, 9713 AV Groningen, the Netherlands
| | - Lude Franke
- University of Groningen, University Medical Center Groningen, Department of Genetics, 9713 AV Groningen, the Netherlands
- Oncode Institute, 3521 AL Utrecht, the Netherlands
| | - Hedi Peterson
- Institute of Computer Science, University of Tartu, Tartu 51009, Estonia
| | - Jaak Vilo
- Institute of Computer Science, University of Tartu, Tartu 51009, Estonia
| | - Kaido Lepik
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
- Center for Primary Care and Public Health (Unisanté), Department of Epidemiology and Health Systems, University of Lausanne, Lausanne 1010, Switzerland
- Institute of Computer Science, University of Tartu, Tartu 51009, Estonia
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Zoltán Kutalik
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
- Center for Primary Care and Public Health (Unisanté), Department of Epidemiology and Health Systems, University of Lausanne, Lausanne 1010, Switzerland
- Corresponding author
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Radzevičius M, Dirsė V, Klimienė I, Matuzevičienė R, Kučinskienė ZA, Pečeliūnas V. Multiple Myeloma Immunophenotype Related to Chromosomal Abnormalities Used in Risk Assessment. Diagnostics (Basel) 2022; 12:diagnostics12092049. [PMID: 36140450 PMCID: PMC9498268 DOI: 10.3390/diagnostics12092049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/02/2022] [Accepted: 08/22/2022] [Indexed: 11/25/2022] Open
Abstract
(1) Background: At diagnosis, multiplemyeloma risk estimation includes disease burden, end-organ damage, and biomarkers, with increasing emphasis on genetic abnormalities. Multicolor flow cytometry (MFC) is not always considered in risk estimation. We demonstrate associations found between genetic abnormalities and antigen expression of plasma cells measured by MFC. (2) Methods: Single nucleotide polymorphism microarray (SNP-A) karyotyping as well as MFC using standardized next-generation flow (NGF) panels and instrument settings were performed from bone marrow aspirates at the time of diagnosis. (3) Results: We uncovered specific immunophenotype features related to different genetic risk factors. Specifically, we found higher malignant/normal plasma cell ratio and lower expression of CD27, CD38, CD45, CD56, CD117 and CD138 in higher-risk genetic groups or risk categories.
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Affiliation(s)
- Mantas Radzevičius
- Department of Physiology, Biochemistry, Microbiology and Laboratory Medicine, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, 03101 Vilnius, Lithuania
- Correspondence: ; Tel.: +370-656-87976
| | - Vaidas Dirsė
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, 08661 Vilnius, Lithuania
| | - Indrė Klimienė
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, 08661 Vilnius, Lithuania
| | - Rėda Matuzevičienė
- Department of Physiology, Biochemistry, Microbiology and Laboratory Medicine, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, 03101 Vilnius, Lithuania
- Center of Laboratory Medicine, Vilnius University Hospital Santaros Klinikos, 08661 Vilnius, Lithuania
| | - Zita Aušrelė Kučinskienė
- Department of Physiology, Biochemistry, Microbiology and Laboratory Medicine, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, 03101 Vilnius, Lithuania
| | - Valdas Pečeliūnas
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, 08661 Vilnius, Lithuania
- Clinic of Internal Diseases, Family Medicine and Oncology, Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, 03101 Vilnius, Lithuania
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37
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Identification and Characterization of Copy Number Variations Regions in West African Taurine Cattle. Animals (Basel) 2022; 12:ani12162130. [PMID: 36009719 PMCID: PMC9405125 DOI: 10.3390/ani12162130] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/29/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
A total of 106 West African taurine cattle belonging to the Lagunaire breed of Benin (33), the N’Dama population of Burkina Faso (48), and N’Dama cattle sampled in Congo (25) were analyzed for Copy Number Variations (CNVs) using the BovineHDBeadChip of Illumina and two different CNV calling programs: PennCNV and QuantiSNP. Furthermore, 89 West African zebu samples (Bororo cattle of Mali and Zebu Peul sampled in Benin and Burkina Faso) were used as an outgroup to ensure that analyses reflect the taurine cattle genomic background. Analyses identified 307 taurine-specific CNV regions (CNVRs), covering about 56 Mb on all bovine autosomes. Gene annotation enrichment analysis identified a total of 840 candidate genes on 168 taurine-specific CNVRs. Three different statistically significant functional term annotation clusters (from ACt1 to ACt3) involved in the immune function were identified: ACt1 includes genes encoding lipocalins, proteins involved in the modulation of immune response and allergy; ACt2 includes genes encoding coding B-box-type zinc finger proteins and butyrophilins, involved in innate immune processes; and Act3 includes genes encoding lectin receptors, involved in the inflammatory responses to pathogens and B- and T-cell differentiation. The overlap between taurine-specific CNVRs and QTL regions associated with trypanotolerant response and tick-resistance was relatively low, suggesting that the mechanisms underlying such traits may not be determined by CNV alterations. However, four taurine-specific CNVRs overlapped with QTL regions associated with both traits on BTA23, therefore suggesting that CNV alterations in major histocompatibility complex (MHC) genes can partially explain the existence of genetic mechanisms shared between trypanotolerance and tick resistance in cattle. This research contributes to the understanding of the genomic features of West African taurine cattle.
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38
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Balagué-Dobón L, Cáceres A, González JR. Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure. Brief Bioinform 2022; 23:6535682. [PMID: 35211719 PMCID: PMC8921734 DOI: 10.1093/bib/bbac043] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/25/2022] [Accepted: 01/28/2022] [Indexed: 12/12/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) are the most abundant type of genomic variation and the most accessible to genotype in large cohorts. However, they individually explain a small proportion of phenotypic differences between individuals. Ancestry, collective SNP effects, structural variants, somatic mutations or even differences in historic recombination can potentially explain a high percentage of genomic divergence. These genetic differences can be infrequent or laborious to characterize; however, many of them leave distinctive marks on the SNPs across the genome allowing their study in large population samples. Consequently, several methods have been developed over the last decade to detect and analyze different genomic structures using SNP arrays, to complement genome-wide association studies and determine the contribution of these structures to explain the phenotypic differences between individuals. We present an up-to-date collection of available bioinformatics tools that can be used to extract relevant genomic information from SNP array data including population structure and ancestry; polygenic risk scores; identity-by-descent fragments; linkage disequilibrium; heritability and structural variants such as inversions, copy number variants, genetic mosaicisms and recombination histories. From a systematic review of recently published applications of the methods, we describe the main characteristics of R packages, command-line tools and desktop applications, both free and commercial, to help make the most of a large amount of publicly available SNP data.
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39
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Gordeeva V, Sharova E, Arapidi G. Progress in Methods for Copy Number Variation Profiling. Int J Mol Sci 2022; 23:ijms23042143. [PMID: 35216262 PMCID: PMC8879278 DOI: 10.3390/ijms23042143] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/09/2022] [Accepted: 02/11/2022] [Indexed: 02/04/2023] Open
Abstract
Copy number variations (CNVs) are the predominant class of structural genomic variations involved in the processes of evolutionary adaptation, genomic disorders, and disease progression. Compared with single-nucleotide variants, there have been challenges associated with the detection of CNVs owing to their diverse sizes. However, the field has seen significant progress in the past 20–30 years. This has been made possible due to the rapid development of molecular diagnostic methods which ensure a more detailed view of the genome structure, further complemented by recent advances in computational methods. Here, we review the major approaches that have been used to routinely detect CNVs, ranging from cytogenetics to the latest sequencing technologies, and then cover their specific features.
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Affiliation(s)
- Veronika Gordeeva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (E.S.); (G.A.)
- Moscow Institute of Physics and Technology, National Research University, Moscow Oblast, 141701 Moscow, Russia
- Correspondence:
| | - Elena Sharova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (E.S.); (G.A.)
| | - Georgij Arapidi
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (E.S.); (G.A.)
- Moscow Institute of Physics and Technology, National Research University, Moscow Oblast, 141701 Moscow, Russia
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
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40
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Analysis of the Curative Effect of Continuous Nursing Based on Data Mining on Patients with Liver Tumors. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:5115089. [PMID: 35198037 PMCID: PMC8860545 DOI: 10.1155/2022/5115089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 01/30/2023]
Abstract
Studies have shown that the physical, psychological, and social problems of liver cancer patients are more serious than those of other cancer patients and their quality of life is significantly reduced. This may be related to the poor treatment effect of patients with advanced liver cancer. Patients often have adverse symptoms such as cancer pain, pleural effusion, and ascites, etc., which have a great impact on patients' psychology and recovery from illness. With the change of the medical model, it has become history to rely solely on drugs to care for patients with advanced liver cancer and comprehensive nursing intervention has become very important. Continuous nursing intervention focuses on individualized and full-hearted care, effectively alleviating patients' anxiety and fear and improving patients' environmental adaptability and psychological defense mechanisms. However, in the field of liver cancer, there is no detailed comparison between the efficacy of continuous nursing and traditional conventional nursing. This article applies the hidden Markov model, starts with medical data mining, and describes the process achieved by the application of this article and the analysis of the results obtained by the two nursing methods, which reflect the difference in curative effect evaluation, and it proves that continuous nursing has more advantages in the curative effect of patients with liver tumors.
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41
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Igoshin AV, Deniskova TE, Yurchenko AA, Yudin NS, Dotsev AV, Selionova MI, Zinovieva NA, Larkin DM. Copy number variants in genomes of local sheep breeds from Russia. Anim Genet 2021; 53:119-132. [PMID: 34904242 DOI: 10.1111/age.13163] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2021] [Indexed: 01/21/2023]
Abstract
Copy number variants (CNVs) are genomic structural variations that contribute to many adaptive and economically important traits in livestock. In this study, we detected CNVs in 354 animals from 16 Russian indigenous sheep breeds and analysed their possible functional roles. Our analysis of the entire sample set resulted in 4527 CNVs forming 1450 CNV regions (CNVRs). When constructing CNVRs for individual breeds, a total of 2715 regions ranging from 88 in Groznensk to 337 in Osetin breeds were identified. To make interbreed CNVR frequency comparison possible, we also identified core CNVRs using CNVs with overlapping chromosomal locations found in different breeds. This resulted in 137 interbreed CNVRs with frequency >15% in at least one breed. Functional enrichment analysis of genes affected by CNVRs in individual breeds revealed 12 breeds with significant enrichments in olfactory perception, PRAME family proteins, and immune response. Function of genes affected by interbreed and breed-specific CNVRs revealed candidates related to domestication, adaptation to high altitudes and cold climates, reproduction, parasite resistance, milk and meat qualities, wool traits, fat storage, and fat metabolism. Our work is the first attempt to uncover and characterise the CNV makeup of Russian indigenous sheep breeds. Further experimental and functional validation of CNVRs would help in developing new and improving existing sheep breeds.
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Affiliation(s)
- A V Igoshin
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia
| | - T E Deniskova
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, 142132, Russia
| | - A A Yurchenko
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia
| | - N S Yudin
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - A V Dotsev
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, 142132, Russia
| | - M I Selionova
- Russian State Agrarian University, Moscow Timiryazev Agricultural Academy, Moscow, 127550, Russia
| | - N A Zinovieva
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, 142132, Russia
| | - D M Larkin
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia.,Royal Veterinary College, University of London, London, NW1 0TU, UK
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42
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Rafter P, Gormley IC, Parnell AC, Naderi S, Berry DP. The Contribution of Copy Number Variants and Single Nucleotide Polymorphisms to the Additive Genetic Variance of Carcass Traits in Cattle. Front Genet 2021; 12:761503. [PMID: 34795696 PMCID: PMC8593468 DOI: 10.3389/fgene.2021.761503] [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: 08/19/2021] [Accepted: 10/04/2021] [Indexed: 11/13/2022] Open
Abstract
The relative contributions of both copy number variants (CNVs) and single nucleotide polymorphisms (SNPs) to the additive genetic variance of carcass traits in cattle is not well understood. A detailed understanding of the relative importance of CNVs in cattle may have implications for study design of both genomic predictions and genome-wide association studies. The first objective of the present study was to quantify the relative contributions of CNV data and SNP genotype data to the additive genetic variance of carcass weight, fat, and conformation for 945 Charolais, 923 Holstein-Friesian, and 974 Limousin sires. The second objective was to jointly consider SNP and CNV data in a least absolute selection and shrinkage operator (LASSO) regression model to identify genomic regions associated with carcass weight, fat, and conformation within each of the three breeds separately. A genomic relationship matrix (GRM) based on just CNV data did not capture any variance in the three carcass traits when jointly evaluated with a SNP-derived GRM. In the LASSO regression analysis, a total of 987 SNPs and 18 CNVs were associated with at least one of the three carcass traits in at least one of the three breeds. The quantitative trait loci (QTLs) corresponding to the associated SNPs and CNVs overlapped with several candidate genes including previously reported candidate genes such as MSTN and RSAD2, and several potential novel candidate genes such as ACTN2 and THOC1. The results of the LASSO regression analysis demonstrated that CNVs can be used to detect associations with carcass traits which were not detected using the set of SNPs available in the present study. Therefore, the CNVs and SNPs available in the present study were not redundant forms of genomic data.
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Affiliation(s)
- Pierce Rafter
- Animal & Grassland Research and Innovation Centre, Fermoy, Ireland.,School of Mathematics and Statistics, University College Dublin, Dublin, Ireland
| | | | | | - Saeid Naderi
- Irish Cattle Breeding Federation, Bandon, Ireland
| | - Donagh P Berry
- Animal & Grassland Research and Innovation Centre, Fermoy, Ireland
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43
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Wang Z, Guo Y, Liu S, Meng Q. Genome-Wide Assessment Characteristics of Genes Overlapping Copy Number Variation Regions in Duroc Purebred Population. Front Genet 2021; 12:753748. [PMID: 34721540 PMCID: PMC8552909 DOI: 10.3389/fgene.2021.753748] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 09/23/2021] [Indexed: 11/13/2022] Open
Abstract
Copy number variations (CNVs) are important structural variations that can cause significant phenotypic diversity. Reliable CNVs mapping can be achieved by identification of CNVs from different genetic backgrounds. Investigations on the characteristics of overlapping between CNV regions (CNVRs) and protein-coding genes (CNV genes) or miRNAs (CNV-miRNAs) can reveal the potential mechanisms of their regulation. In this study, we used 50 K SNP arrays to detect CNVs in Duroc purebred pig. A total number of 211 CNVRs were detected with a total length of 118.48 Mb, accounting for 5.23% of the autosomal genome sequence. Of these CNVRs, 32 were gains, 175 losses, and four contained both types (loss and gain within the same region). The CNVRs we detected were non-randomly distributed in the swine genome and were significantly enriched in the segmental duplication and gene density region. Additionally, these CNVRs were overlapping with 1,096 protein-coding genes (CNV-genes), and 39 miRNAs (CNV-miRNAs), respectively. The CNV-genes were enriched in terms of dosage-sensitive gene list. The expression of the CNV genes was significantly higher than that of the non-CNV genes in the adult Duroc prostate. Of all detected CNV genes, 22.99% genes were tissue-specific (TSI > 0.9). Strong negative selection had been underway in the CNV-genes as the ones that were located entirely within the loss CNVRs appeared to be evolving rapidly as determined by the median dN plus dS values. Non-CNV genes tended to be miRNA target than CNV-genes. Furthermore, CNV-miRNAs tended to target more genes compared to non-CNV-miRNAs, and a combination of two CNV-miRNAs preferentially synergistically regulated the same target genes. We also focused our efforts on examining CNV genes and CNV-miRNAs functions, which were also involved in the lipid metabolism, including DGAT1, DGAT2, MOGAT2, miR143, miR335, and miRLET7. Further molecular experiments and independent large studies are needed to confirm our findings.
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Affiliation(s)
- Zhipeng Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Bioinformatics Center, Northeast Agricultural University, Harbin, China
| | - Yuanyuan Guo
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Bioinformatics Center, Northeast Agricultural University, Harbin, China
| | - Shengwei Liu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Bioinformatics Center, Northeast Agricultural University, Harbin, China
| | - Qingli Meng
- Beijing Breeding Swine Center, Beijing, China
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44
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Rafter P, Gormley IC, Purfield D, Parnell AC, Naderi S, Berry DP. Genome-wide association analyses of carcass traits using copy number variants and raw intensity values of single nucleotide polymorphisms in cattle. BMC Genomics 2021; 22:757. [PMID: 34688258 PMCID: PMC8542340 DOI: 10.1186/s12864-021-08075-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 10/07/2021] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The carcass value of cattle is a function of carcass weight and quality. Given the economic importance of carcass merit to producers, it is routinely included in beef breeding objectives. A detailed understanding of the genetic variants that contribute to carcass merit is useful to maximize the efficiency of breeding for improved carcass merit. The objectives of the present study were two-fold: firstly, to perform genome-wide association analyses of carcass weight, carcass conformation, and carcass fat using copy number variant (CNV) data in a population of 923 Holstein-Friesian, 945 Charolais, and 974 Limousin bulls; and secondly to perform separate association analyses of carcass traits on the same population of cattle using the Log R ratio (LRR) values of 712,555 single nucleotide polymorphisms (SNPs). The LRR value of a SNP is a measure of the signal intensity of the SNP generated during the genotyping process. RESULTS A total of 13,969, 3,954, and 2,805 detected CNVs were tested for association with the three carcass traits for the Holstein-Friesian, Charolais, and Limousin, respectively. The copy number of 16 CNVs and the LRR of 34 SNPs were associated with at least one of the three carcass traits in at least one of the three cattle breeds. With the exception of three SNPs, none of the quantitative trait loci detected in the CNV association analyses or the SNP LRR association analyses were also detected using traditional association analyses based on SNP allele counts. Many of the CNVs and SNPs associated with the carcass traits were located near genes related to the structure and function of the spliceosome and the ribosome; in particular, U6 which encodes a spliceosomal subunit and 5S rRNA which encodes a ribosomal subunit. CONCLUSIONS The present study demonstrates that CNV data and SNP LRR data can be used to detect genomic regions associated with carcass traits in cattle providing information on quantitative trait loci over and above those detected using just SNP allele counts, as is the approach typically employed in genome-wide association analyses.
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Affiliation(s)
- Pierce Rafter
- Animal & Grassland Research and Innovation Centre, Teagasc, Moorepark, Cork, Fermoy, Ireland
- School of Mathematics and Statistics, University College Dublin, Belfield, Dublin 4, Ireland
| | - Isobel Claire Gormley
- School of Mathematics and Statistics, University College Dublin, Belfield, Dublin 4, Ireland
| | - Deirdre Purfield
- Department of Biological Sciences, Munster Technological University Institute, Cork, Bishopstown, Ireland
| | - Andrew C Parnell
- Hamilton Institute, Insight Centre for Data Analytics, Maynooth University, Kildare, Ireland
| | - Saeid Naderi
- Irish Cattle Breeding Federation, Cork, Bandon, Ireland
| | - Donagh P Berry
- Animal & Grassland Research and Innovation Centre, Teagasc, Moorepark, Cork, Fermoy, Ireland.
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45
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Parikh FR, Athalye AS, Kulkarni DK, Sanap RR, Dhumal SB, Warang DJ, Naik DJ, Madon PF. Evolution and Utility of Preimplantation Genetic Testing for Monogenic Disorders in Assisted Reproduction - A Narrative Review. J Hum Reprod Sci 2021; 14:329-339. [PMID: 35197677 PMCID: PMC8812395 DOI: 10.4103/jhrs.jhrs_148_21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/20/2021] [Accepted: 11/20/2021] [Indexed: 11/04/2022] Open
Abstract
Preimplantation genetic testing (PGT) for monogenic disorders and assisted reproductive technology have evolved and progressed in tandem. PGT started with single-cell polymerase chain reaction (PCR) followed by fluorescent in situ hybridisation for a limited number of chromosomes, later called 'preimplantation genetic diagnosis (PGD) version 1'. This review highlights the various molecular genetic techniques that have evolved to detect specific inherited monogenic disorders in the preimplantation embryo. Literature review in English was performed in PubMed from 1990 to 2021, using the term 'preimplantation genetic diagnosis'. With whole-genome amplification, multiple copies of embryonic DNA were created. This helped in avoiding misdiagnosis caused by allele dropout. Multiplex fluorescent PCR analysed informative short tandem repeats (STR) and detected mutations simultaneously on automated capillary electrophoresis sequencers by mini-sequencing. Comparative genomic hybridisation (CGH) and array CGH were used for 24 chromosome aneuploidy screening. Subsequently, aneuploidies were detected by next-generation sequencing using single-nucleotide polymorphism arrays, while STR markers were used for haplotyping. 'PGD version 2' included accurate marker-based diagnosis of most monogenic disorders and detection of aneuploidy of all chromosomes. Human leukocyte antigen matching of embryos has important implications in diagnosis and cure of haemoglobinopathies and immunodeficiencies in children by means of matched related haematopoietic stem cell transplantation from an unaffected 'saviour sibling' obtained by PGT.
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Affiliation(s)
- Firuza R. Parikh
- Department of Assisted Reproduction and Genetics, Jaslok-FertilTree International Fertility Centre, Jaslok Hospital and Research Centre, Mumbai, Maharashtra, India
| | - Arundhati S. Athalye
- Department of Assisted Reproduction and Genetics, Jaslok-FertilTree International Fertility Centre, Jaslok Hospital and Research Centre, Mumbai, Maharashtra, India
| | - Dhananjaya K. Kulkarni
- Department of Assisted Reproduction and Genetics, Jaslok-FertilTree International Fertility Centre, Jaslok Hospital and Research Centre, Mumbai, Maharashtra, India
| | - Rupesh R. Sanap
- Department of Assisted Reproduction and Genetics, Jaslok-FertilTree International Fertility Centre, Jaslok Hospital and Research Centre, Mumbai, Maharashtra, India
| | - Suresh B. Dhumal
- Department of Assisted Reproduction and Genetics, Jaslok-FertilTree International Fertility Centre, Jaslok Hospital and Research Centre, Mumbai, Maharashtra, India
| | - Dhanashree J. Warang
- Department of Assisted Reproduction and Genetics, Jaslok-FertilTree International Fertility Centre, Jaslok Hospital and Research Centre, Mumbai, Maharashtra, India
| | - Dattatray J. Naik
- Department of Assisted Reproduction and Genetics, Jaslok-FertilTree International Fertility Centre, Jaslok Hospital and Research Centre, Mumbai, Maharashtra, India
| | - Prochi F. Madon
- Department of Assisted Reproduction and Genetics, Jaslok-FertilTree International Fertility Centre, Jaslok Hospital and Research Centre, Mumbai, Maharashtra, India
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Schierbaum LM, Schneider S, Herms S, Sivalingam S, Fabian J, Reutter H, Weber S, Merz WM, Tkaczyk M, Miklaszewska M, Sikora P, Szmigielska A, Krzemien G, Zachwieja K, Szczepanska M, Taranta-Janusz K, Kroll P, Polok M, Zaniew M, Hilger AC. Genome-Wide Survey for Microdeletions or -Duplications in 155 Patients with Lower Urinary Tract Obstructions (LUTO). Genes (Basel) 2021; 12:genes12091449. [PMID: 34573432 PMCID: PMC8468665 DOI: 10.3390/genes12091449] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/13/2021] [Accepted: 09/13/2021] [Indexed: 01/28/2023] Open
Abstract
Lower urinary tract obstruction (LUTO) is, in most cases, caused by anatomical blockage of the bladder outlet. The most common form are posterior urethral valves (PUVs), a male-limited phenotype. Here, we surveyed the genome of 155 LUTO patients to identify disease-causing CNVs. Raw intensity data were collected for CNVs detected in LUTO patients and 4.392 healthy controls using CNVPartition, QuantiSNP and PennCNV. Overlapping CNVs between patients and controls were discarded. Additional filtering implicated CNV frequency in the database of genomic variants, gene content and final visual inspection detecting 37 ultra-rare CNVs. After, prioritization qPCR analysis confirmed 3 microduplications, all detected in PUV patients. One microduplication (5q23.2) occurred de novo in the two remaining microduplications found on chromosome 1p36.21 and 10q23.31. Parental DNA was not available for segregation analysis. All three duplications comprised 11 coding genes: four human specific lncRNA and one microRNA. Three coding genes (FBLIM1, SLC16A12, SNCAIP) and the microRNA MIR107 have previously been shown to be expressed in the developing urinary tract of mouse embryos. We propose that duplications, rare or de novo, contribute to PUV formation, a male-limited phenotype.
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Affiliation(s)
- Luca M. Schierbaum
- Institute of Human Genetics, University Hospital of Bonn, 53127 Bonn, Germany; (L.M.S.); (S.S.); (S.H.); (J.F.); (H.R.)
| | - Sophia Schneider
- Institute of Human Genetics, University Hospital of Bonn, 53127 Bonn, Germany; (L.M.S.); (S.S.); (S.H.); (J.F.); (H.R.)
| | - Stefan Herms
- Institute of Human Genetics, University Hospital of Bonn, 53127 Bonn, Germany; (L.M.S.); (S.S.); (S.H.); (J.F.); (H.R.)
- Human Genomics Research Group, Department of Biomedicine, University of Basel, 4031 Basel, Switzerland
| | - Sugirthan Sivalingam
- Institute for Medical Biometry, Informatics and Epidemiology, Medical Faculty, University of Bonn, 53127 Bonn, Germany;
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, 53127 Bonn, Germany
- Core Unit for Bioinformatics Data Analysis, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Julia Fabian
- Institute of Human Genetics, University Hospital of Bonn, 53127 Bonn, Germany; (L.M.S.); (S.S.); (S.H.); (J.F.); (H.R.)
| | - Heiko Reutter
- Institute of Human Genetics, University Hospital of Bonn, 53127 Bonn, Germany; (L.M.S.); (S.S.); (S.H.); (J.F.); (H.R.)
- Department of Neonatology and Pediatric Intensive Care, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Stefanie Weber
- Department of Pediatrics, University Hospital Marburg, 35033 Marburg, Germany;
| | - Waltraut M. Merz
- Department of Obstetrics and Prenatal Medicine, University of Bonn, 53127 Bonn, Germany;
| | - Marcin Tkaczyk
- Department of Pediatrics, Immunology and Nephrology, Polish Mother’s Memorial Hospital Research Institute of Lodz, 93-428 Łódź, Poland;
- Department of Pediatrics, Cardiology and Immunology, Medical University of Łódź, 93-428 Łódź, Poland
| | - Monika Miklaszewska
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, 31-007 Krakow, Poland; (M.M.); (K.Z.)
| | - Przemyslaw Sikora
- Department of Pediatric Nephrology Medical University of Lublin, 20-059 Lublin, Poland;
| | - Agnieszka Szmigielska
- Department of Pediatrics and Nephrology, Medical University of Warsaw, 02-091 Warsaw, Poland; (A.S.); (G.K.)
| | - Grazyna Krzemien
- Department of Pediatrics and Nephrology, Medical University of Warsaw, 02-091 Warsaw, Poland; (A.S.); (G.K.)
| | - Katarzyna Zachwieja
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, 31-007 Krakow, Poland; (M.M.); (K.Z.)
| | - Maria Szczepanska
- Department of Pediatrics, School of Medicine with the Division of Dentistry in Zabrze, Medical University of Silesia in Katowice, 40-055 Katowice, Poland;
| | - Katarzyna Taranta-Janusz
- Department of Pediatrics and Nephrology, Medical University of Białystok, 15-089 Białystok, Poland;
| | - Pawel Kroll
- Neurourology Unit, Pediatric Surgery and Urology Clinic, 61-701 Poznań, Poland;
- Neurourology Unit, Poznan University of Medical Sciences, 61-701 Poznań, Poland
| | - Marcin Polok
- Department of Pediatric Surgery and Urology, University of Zielona Góra, 65-417 Zielona Góra, Poland;
| | - Marcin Zaniew
- Department of Pediatrics, University of Zielona Góra, 65-417 Zielona Góra, Poland;
| | - Alina C. Hilger
- Institute of Human Genetics, University Hospital of Bonn, 53127 Bonn, Germany; (L.M.S.); (S.S.); (S.H.); (J.F.); (H.R.)
- Department of Neonatology and Pediatric Intensive Care, University Hospital Erlangen, 91054 Erlangen, Germany
- Correspondence:
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Glessner JT, Hou X, Zhong C, Zhang J, Khan M, Brand F, Krawitz P, Sleiman PMA, Hakonarson H, Wei Z. DeepCNV: a deep learning approach for authenticating copy number variations. Brief Bioinform 2021; 22:bbaa381. [PMID: 33429424 PMCID: PMC8681111 DOI: 10.1093/bib/bbaa381] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/24/2020] [Accepted: 11/26/2020] [Indexed: 12/14/2022] Open
Abstract
Copy number variations (CNVs) are an important class of variations contributing to the pathogenesis of many disease phenotypes. Detecting CNVs from genomic data remains difficult, and the most currently applied methods suffer from an unacceptably high false positive rate. A common practice is to have human experts manually review original CNV calls for filtering false positives before further downstream analysis or experimental validation. Here, we propose DeepCNV, a deep learning-based tool, intended to replace human experts when validating CNV calls, focusing on the calls made by one of the most accurate CNV callers, PennCNV. The sophistication of the deep neural network algorithm is enriched with over 10 000 expert-scored samples that are split into training and testing sets. Variant confidence, especially for CNVs, is a main roadblock impeding the progress of linking CNVs with the disease. We show that DeepCNV adds to the confidence of the CNV calls with an optimal area under the receiver operating characteristic curve of 0.909, exceeding other machine learning methods. The superiority of DeepCNV was also benchmarked and confirmed using an experimental wet-lab validation dataset. We conclude that the improvement obtained by DeepCNV results in significantly fewer false positive results and failures to replicate the CNV association results.
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Affiliation(s)
- Joseph T Glessner
- Center for Applied Genomics, Department of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19102, USA
| | - Xiurui Hou
- Department of Computer Science, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | - Cheng Zhong
- Department of Computer Science, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | | | - Munir Khan
- Center for Applied Genomics, Department of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19102, USA
| | | | | | - Patrick M A Sleiman
- Perelman School of Medicine, Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19102, USA
| | - Hakon Hakonarson
- Perelman School of Medicine, Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19102, USA
| | - Zhi Wei
- Department of Computer Science, New Jersey Institute of Technology, Newark, NJ 07102, USA
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48
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Lo Faro V, Ten Brink JB, Snieder H, Jansonius NM, Bergen AA. Genome-wide CNV investigation suggests a role for cadherin, Wnt, and p53 pathways in primary open-angle glaucoma. BMC Genomics 2021; 22:590. [PMID: 34348663 PMCID: PMC8336345 DOI: 10.1186/s12864-021-07846-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/18/2021] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND To investigate whether copy number variations (CNVs) are implicated in molecular mechanisms underlying primary open-angle glaucoma (POAG), we used genotype data of POAG individuals and healthy controls from two case-control studies, AGS (n = 278) and GLGS-UGLI (n = 1292). PennCNV, QuantiSNP, and cnvPartition programs were used to detect CNV. Stringent quality controls at both sample and marker levels were applied. The identified CNVs were intersected in CNV region (CNVR). After, we performed burden analysis, CNV-genome-wide association analysis, gene set overrepresentation and pathway analysis. In addition, in human eye tissues we assessed the expression of the genes lying within significant CNVRs. RESULTS We reported a statistically significant greater burden of CNVs in POAG cases compared to controls (p-value = 0,007). In common between the two cohorts, CNV-association analysis identified statistically significant CNVRs associated with POAG that span 11 genes (APC, BRCA2, COL3A1, HLA-DRB1, HLA-DRB5, HLA-DRB6, MFSD8, NIPBL, SCN1A, SDHB, and ZDHHC11). Functional annotation and pathway analysis suggested the involvement of cadherin, Wnt signalling, and p53 pathways. CONCLUSIONS Our data suggest that CNVs may have a role in the susceptibility of POAG and they can reveal more information on the mechanism behind this disease. Additional genetic and functional studies are warranted to ascertain the contribution of CNVs in POAG.
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Affiliation(s)
- Valeria Lo Faro
- Department of Ophthalmology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Departments of Clinical Genetics and Ophthalmology, Amsterdam University Medical Center (AMC), Location AMC K2-217
- AMC-UvA, P.O.Box 22700, 1100 DE, Amsterdam, The Netherlands
| | - Jacoline B Ten Brink
- Departments of Clinical Genetics and Ophthalmology, Amsterdam University Medical Center (AMC), Location AMC K2-217
- AMC-UvA, P.O.Box 22700, 1100 DE, Amsterdam, The Netherlands
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Nomdo M Jansonius
- Department of Ophthalmology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Arthur A Bergen
- Departments of Clinical Genetics and Ophthalmology, Amsterdam University Medical Center (AMC), Location AMC K2-217
- AMC-UvA, P.O.Box 22700, 1100 DE, Amsterdam, The Netherlands. .,Department of Ophthalmology, Amsterdam UMC, Location AMC, Amsterdam, The Netherlands. .,Netherlands Institute for Neuroscience (NIN-KNAW), Amsterdam, The Netherlands.
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49
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Yu Y, Werdyani S, Carey M, Parfrey P, Yilmaz YE, Savas S. A comprehensive analysis of SNPs and CNVs identifies novel markers associated with disease outcomes in colorectal cancer. Mol Oncol 2021; 15:3329-3347. [PMID: 34309201 PMCID: PMC8637572 DOI: 10.1002/1878-0261.13067] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/29/2021] [Accepted: 07/24/2021] [Indexed: 12/15/2022] Open
Abstract
We aimed to examine the associations of a genome-wide set of single nucleotide polymorphisms (SNPs) and 254 copy number variations (CNVs) and/or insertion/deletions (INDELs) with clinical outcomes in colorectal cancer patients (n = 505). We also aimed to investigate whether their associations changed (e.g., appeared, diminished) over time. Multivariable Cox proportional hazards and piece-wise Cox regression models were used to examine the associations. The Cancer Genome Atlas (TCGA) datasets were used for replication purposes and to examine the gene expression differences between tumor and nontumor tissue samples. A common SNP (WBP11-rs7314075) was associated with disease-specific survival with P-value of 3.2 × 10-8 . Association of this region with disease-specific survival was also detected in the TCGA patient cohort. Two expression quantitative trait loci (eQTLs) were identified in this locus that were implicated in the regulation of ERP27 expression. Interestingly, expression levels of ERP27 and WBP11 were significantly different between colorectal tumors and nontumor tissues. Three SNPs predicted the risk of recurrent disease only after 5 years postdiagnosis. Overall, our study identified novel variants, one of which also showed an association in the TCGA dataset, but no CNVs/INDELs, that associated with outcomes in colorectal cancer. Three SNPs were candidate predictors of long-term recurrence/metastasis risk.
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Affiliation(s)
- Yajun Yu
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, NL, Canada
| | - Salem Werdyani
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, NL, Canada
| | - Megan Carey
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, NL, Canada
| | - Patrick Parfrey
- Discipline of Medicine, Faculty of Medicine, Memorial University, St. John's, NL, Canada
| | - Yildiz E Yilmaz
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, NL, Canada.,Discipline of Medicine, Faculty of Medicine, Memorial University, St. John's, NL, Canada.,Department of Mathematics and Statistics, Faculty of Science, Memorial University, St. John's, NL, Canada
| | - Sevtap Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, NL, Canada.,Discipline of Oncology, Faculty of Medicine, Memorial University, St. John's, NL, Canada
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50
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Cole JW, Adigun T, Akinyemi R, Akpa OM, Bell S, Chen B, Jimenez Conde J, Lazcano Dobao U, Fernandez I, Fornage M, Gallego-Fabrega C, Jern C, Krawczak M, Lindgren A, Markus HS, Melander O, Owolabi M, Schlicht K, Söderholm M, Srinivasasainagendra V, Soriano Tárraga C, Stenman M, Tiwari H, Corasaniti M, Fecteau N, Guizzardi B, Lopez H, Nguyen K, Gaynor B, O’Connor T, Stine OC, Kittner SJ, McArdle P, Mitchell BD, Xu H, Grond-Ginsbach C. The copy number variation and stroke (CaNVAS) risk and outcome study. PLoS One 2021; 16:e0248791. [PMID: 33872305 PMCID: PMC8055008 DOI: 10.1371/journal.pone.0248791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 03/04/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND AND PURPOSE The role of copy number variation (CNV) variation in stroke susceptibility and outcome has yet to be explored. The Copy Number Variation and Stroke (CaNVAS) Risk and Outcome study addresses this knowledge gap. METHODS Over 24,500 well-phenotyped IS cases, including IS subtypes, and over 43,500 controls have been identified, all with readily available genotyping on GWAS and exome arrays, with case measures of stroke outcome. To evaluate CNV-associated stroke risk and stroke outcome it is planned to: 1) perform Risk Discovery using several analytic approaches to identify CNVs that are associated with the risk of IS and its subtypes, across the age-, sex- and ethnicity-spectrums; 2) perform Risk Replication and Extension to determine whether the identified stroke-associated CNVs replicate in other ethnically diverse datasets and use biomarker data (e.g. methylation, proteomic, RNA, miRNA, etc.) to evaluate how the identified CNVs exert their effects on stroke risk, and lastly; 3) perform outcome-based Replication and Extension analyses of recent findings demonstrating an inverse relationship between CNV burden and stroke outcome at 3 months (mRS), and then determine the key CNV drivers responsible for these associations using existing biomarker data. RESULTS The results of an initial CNV evaluation of 50 samples from each participating dataset are presented demonstrating that the existing GWAS and exome chip data are excellent for the planned CNV analyses. Further, some samples will require additional considerations for analysis, however such samples can readily be identified, as demonstrated by a sample demonstrating clonal mosaicism. CONCLUSION The CaNVAS study will cost-effectively leverage the numerous advantages of using existing case-control data sets, exploring the relationships between CNV and IS and its subtypes, and outcome at 3 months, in both men and women, in those of African and European-Caucasian descent, this, across the entire adult-age spectrum.
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Affiliation(s)
- John W. Cole
- Veterans Affairs Maryland Health Care System, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | | | | | | | - Steven Bell
- Unversity of Cambridge, Cambridge, England, United Kingdom
| | - Bowang Chen
- National Center for Cardiovascular Diseases, Beijing, China
| | | | - Uxue Lazcano Dobao
- IMIM-Hospital del Mar; Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Israel Fernandez
- Institute of Research Hospital de la Santa Creu I Sant Pau, Barcelona, Spain
| | - Myriam Fornage
- University of Texas Health Science at Houston, Institute of Molecular Medicine & School of Public Health, Houston, TX, United States of America
| | | | | | - Michael Krawczak
- Institute of Medical Statistics and Informatics, University of Kiel, Kiel, Germany
| | | | - Hugh S. Markus
- Unversity of Cambridge, Cambridge, England, United Kingdom
| | | | | | - Kristina Schlicht
- Institute of Medical Statistics and Informatics, University of Kiel, Kiel, Germany
| | - Martin Söderholm
- Department of Clinical Sciences Malmö, Lund University, Lund, Sweden
- Department of Neurology, Skåne University Hospital Malmö and Lund, Lund, Sweden
| | | | | | | | - Hemant Tiwari
- School of Public Health, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Margaret Corasaniti
- University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Natalie Fecteau
- Veterans Affairs Maryland Health Care System, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Beth Guizzardi
- University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Haley Lopez
- Veterans Affairs Maryland Health Care System, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Kevin Nguyen
- University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Brady Gaynor
- University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Timothy O’Connor
- University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - O. Colin Stine
- University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Steven J. Kittner
- Veterans Affairs Maryland Health Care System, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Patrick McArdle
- University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Braxton D. Mitchell
- University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Huichun Xu
- University of Maryland School of Medicine, Baltimore, MD, United States of America
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