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Bandara D, Riccardi K. Graph Node Classification to Predict Autism Risk in Genes. Genes (Basel) 2024; 15:447. [PMID: 38674382 PMCID: PMC11049455 DOI: 10.3390/genes15040447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/28/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
This study explores the genetic risk associations with autism spectrum disorder (ASD) using graph neural networks (GNNs), leveraging the Sfari dataset and protein interaction network (PIN) data. We built a gene network with genes as nodes, chromosome band location as node features, and gene interactions as edges. Graph models were employed to classify the autism risk associated with newly introduced genes (test set). Three classification tasks were undertaken to test the ability of our models: binary risk association, multi-class risk association, and syndromic gene association. We tested graph convolutional networks, Graph Sage, graph transformer, and Multi-Layer Perceptron (Baseline) architectures on this problem. The Graph Sage model consistently outperformed the other models, showcasing its utility in classifying ASD-related genes. Our ablation studies show that the chromosome band location and protein interactions contain useful information for this problem. The models achieved 85.80% accuracy on the binary risk classification, 81.68% accuracy on the multi-class risk classification, and 90.22% on the syndromic classification.
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Affiliation(s)
- Danushka Bandara
- Department of Computer Science and Engineering, Fairfield University, Fairfield, CT 06824, USA;
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2
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Kim IB, Lee T, Lee J, Kim J, Lee S, Koh IG, Kim JH, An JY, Lee H, Kim WK, Ju YS, Cho Y, Yu SJ, Kim SA, Oh M, Han DW, Kim E, Choi JK, Yoo HJ, Lee JH. Non-coding de novo mutations in chromatin interactions are implicated in autism spectrum disorder. Mol Psychiatry 2022; 27:4680-4694. [PMID: 35840799 DOI: 10.1038/s41380-022-01697-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 06/27/2022] [Accepted: 07/01/2022] [Indexed: 12/14/2022]
Abstract
Three-dimensional chromatin interactions regulate gene expressions. The significance of de novo mutations (DNMs) in chromatin interactions remains poorly understood for autism spectrum disorder (ASD). We generated 813 whole-genome sequences from 242 Korean simplex families to detect DNMs, and identified target genes which were putatively affected by non-coding DNMs in chromatin interactions. Non-coding DNMs in chromatin interactions were significantly involved in transcriptional dysregulations related to ASD risk. Correspondingly, target genes showed spatiotemporal expressions relevant to ASD in developing brains and enrichment in biological pathways implicated in ASD, such as histone modification. Regarding clinical features of ASD, non-coding DNMs in chromatin interactions particularly contributed to low intelligence quotient levels in ASD probands. We further validated our findings using two replication cohorts, Simons Simplex Collection (SSC) and MSSNG, and showed the consistent enrichment of non-coding DNM-disrupted chromatin interactions in ASD probands. Generating human induced pluripotent stem cells in two ASD families, we were able to demonstrate that non-coding DNMs in chromatin interactions alter the expression of target genes at the stage of early neural development. Taken together, our findings indicate that non-coding DNMs in ASD probands lead to early neurodevelopmental disruption implicated in ASD risk via chromatin interactions.
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Affiliation(s)
- Il Bin Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.,Department of Psychiatry, Hanyang University Guri Hospital, Guri, 11923, Republic of Korea
| | - Taeyeop Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.,Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.,Department of Psychiatry, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Republic of Korea
| | - Junehawk Lee
- Center for Supercomputing Applications, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon, 34141, Republic of Korea
| | - Jonghun Kim
- Department of Genetics, Yale Stem Cell Center, Yale Child Study Center, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Suho Lee
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science, Daejeon, 34141, Republic of Korea
| | - In Gyeong Koh
- Industry-University Cooperation Foundation, Hanyang University, Seoul, 04763, Republic of Korea
| | - Jae Hyun Kim
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea.,BK21FOUR R&E Center for Learning Health Systems, Korea University, Seoul, 02841, Republic of Korea.,School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, 02841, Republic of Korea
| | - Joon-Yong An
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea.,BK21FOUR R&E Center for Learning Health Systems, Korea University, Seoul, 02841, Republic of Korea.,School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, 02841, Republic of Korea
| | - Hyunseong Lee
- Department of Stem Cell Biology, School of Medicine, Konkuk University, Seoul, 05030, Republic of Korea
| | - Woo Kyeong Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Young Seok Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Yongseong Cho
- Center for Supercomputing Applications, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon, 34141, Republic of Korea
| | - Seok Jong Yu
- Center for Supercomputing Applications, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon, 34141, Republic of Korea
| | - Soon Ae Kim
- Department of Pharmacology, Eulji University, Daejeon, 13135, Republic of Korea
| | - Miae Oh
- Department of Psychiatry, Kyung Hee University Hospital, Seoul, 02447, Republic of Korea
| | - Dong Wook Han
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, China.,Organoid sciences, Ltd., Bundang-gu, Seongnam, 13488, Republic of Korea
| | - Eunjoon Kim
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science, Daejeon, 34141, Republic of Korea. .,Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
| | - Jung Kyoon Choi
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
| | - Hee Jeong Yoo
- Department of Psychiatry, Seoul National University Bundang Hospital, Seongnam, 13620, Republic of Korea. .,Department of Psychiatry, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
| | - Jeong Ho Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea. .,Sovargen Co. Ltd., Daejeon, 34051, Republic of Korea.
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3
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Chen CA, Lattier J, Zhu W, Rosenfeld J, Wang L, Scott TM, Du H, Patel V, Dang A, Magoulas P, Streff H, Sebastian J, Svihovec S, Curry K, Delgado MR, Hanchard N, Lalani S, Marom R, Madan-Khetarpal S, Saenz M, Dai H, Meng L, Xia F, Bi W, Liu P, Posey JE, Scott DA, Lupski JR, Eng CM, Xiao R, Yuan B. Retrospective analysis of a clinical exome sequencing cohort reveals the mutational spectrum and identifies candidate disease-associated loci for BAFopathies. Genet Med 2022; 24:364-373. [PMID: 34906496 PMCID: PMC8957292 DOI: 10.1016/j.gim.2021.09.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/19/2021] [Accepted: 06/19/2021] [Indexed: 02/03/2023] Open
Abstract
PURPOSE BRG1/BRM-associated factor (BAF) complex is a chromatin remodeling complex that plays a critical role in gene regulation. Defects in the genes encoding BAF subunits lead to BAFopathies, a group of neurodevelopmental disorders with extensive locus and phenotypic heterogeneity. METHODS We retrospectively analyzed data from 16,243 patients referred for clinical exome sequencing (ES) with a focus on the BAF complex. We applied a genotype-first approach, combining predicted genic constraints to propose candidate BAFopathy genes. RESULTS We identified 127 patients carrying pathogenic variants, likely pathogenic variants, or de novo variants of unknown clinical significance in 11 known BAFopathy genes. Those include 34 patients molecularly diagnosed using ES reanalysis with new gene-disease evidence (n = 21) or variant reclassifications in known BAFopathy genes (n = 13). We also identified de novo or predicted loss-of-function variants in 4 candidate BAFopathy genes, including ACTL6A, BICRA (implicated in Coffin-Siris syndrome during this study), PBRM1, and SMARCC1. CONCLUSION We report the mutational spectrum of BAFopathies in an ES cohort. A genotype-driven and pathway-based reanalysis of ES data identified new evidence for candidate genes involved in BAFopathies. Further mechanistic and phenotypic characterization of additional patients are warranted to confirm their roles in human disease and to delineate their associated phenotypic spectrums.
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Affiliation(s)
- Chun-An Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | | | | | - Jill Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Lei Wang
- Baylor Genetics Laboratory, Houston, TX
| | - Tiana M. Scott
- Texas Children’s Hospital, Houston, TX, Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | | | - Anh Dang
- Baylor Genetics Laboratory, Houston, TX
| | - Pilar Magoulas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Texas Children’s Hospital, Houston, TX
| | - Haley Streff
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Texas Children’s Hospital, Houston, TX
| | | | - Shayna Svihovec
- University of Colorado Anschutz Medical Campus; Children’s Hospital Colorado, Aurora, CO
| | - Kathryn Curry
- Genetics and Metabolic Department, St. Luke’s Health System
| | - Mauricio R. Delgado
- Texas Scottish Rite Hospital for Children, Dallas, TX, USA, Neurology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Neil Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Texas Children’s Hospital, Houston, TX
| | - Seema Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Texas Children’s Hospital, Houston, TX
| | - Ronit Marom
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Texas Children’s Hospital, Houston, TX
| | | | - Margarita Saenz
- University of Colorado Anschutz Medical Campus; Children’s Hospital Colorado, Aurora, CO
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Baylor Genetics Laboratory, Houston, TX
| | - Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Baylor Genetics Laboratory, Houston, TX
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Baylor Genetics Laboratory, Houston, TX
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Baylor Genetics Laboratory, Houston, TX
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Baylor Genetics Laboratory, Houston, TX
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Daryl A. Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Texas Children’s Hospital, Houston, TX, Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Texas Children’s Hospital, Houston, TX, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - Christine M. Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Baylor Genetics Laboratory, Houston, TX
| | - Rui Xiao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Baylor Genetics Laboratory, Houston, TX
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Baylor Genetics Laboratory, Houston, TX, Current address: Department of Laboratories, Seattle Children’s Hospital, Seattle, WA
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Bucher M, Niebling S, Han Y, Molodenskiy D, Hassani Nia F, Kreienkamp HJ, Svergun D, Kim E, Kostyukova AS, Kreutz MR, Mikhaylova M. Autism-associated SHANK3 missense point mutations impact conformational fluctuations and protein turnover at synapses. eLife 2021; 10:66165. [PMID: 33945465 PMCID: PMC8169116 DOI: 10.7554/elife.66165] [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: 12/30/2020] [Accepted: 05/01/2021] [Indexed: 12/18/2022] Open
Abstract
Members of the SH3- and ankyrin repeat (SHANK) protein family are considered as master scaffolds of the postsynaptic density of glutamatergic synapses. Several missense mutations within the canonical SHANK3 isoform have been proposed as causative for the development of autism spectrum disorders (ASDs). However, there is a surprising paucity of data linking missense mutation-induced changes in protein structure and dynamics to the occurrence of ASD-related synaptic phenotypes. In this proof-of-principle study, we focus on two ASD-associated point mutations, both located within the same domain of SHANK3 and demonstrate that both mutant proteins indeed show distinct changes in secondary and tertiary structure as well as higher conformational fluctuations. Local and distal structural disturbances result in altered synaptic targeting and changes of protein turnover at synaptic sites in rat primary hippocampal neurons.
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Affiliation(s)
- Michael Bucher
- AG Optobiology, Institute of Biology, Humboldt-University, Berlin, Germany.,DFG Emmy Noether Guest Group 'Neuronal Protein Transport', Institute for Molecular Neurogenetics, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany.,RG Neuroplasticity, Leibniz-Institute for Neurobiology (LIN), Magdeburg, Germany
| | - Stephan Niebling
- Molecular Biophysics and High-Throughput Crystallization, European Molecular Biology Laboratory (EMBL), Hamburg, Germany
| | - Yuhao Han
- DFG Emmy Noether Guest Group 'Neuronal Protein Transport', Institute for Molecular Neurogenetics, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany.,Structural Cell Biology of Viruses, Centre for Structural Systems Biology (CSSB) and Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Dmitry Molodenskiy
- European Molecular Biology Laboratory (EMBL) Hamburg Unit, DESY, Hamburg, Germany
| | - Fatemeh Hassani Nia
- Institute of Human Genetics, Center for Obstetrics and Pediatrics, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Hans-Jürgen Kreienkamp
- Institute of Human Genetics, Center for Obstetrics and Pediatrics, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Dmitri Svergun
- European Molecular Biology Laboratory (EMBL) Hamburg Unit, DESY, Hamburg, Germany
| | - Eunjoon Kim
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science (IBS) and Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Alla S Kostyukova
- DFG Emmy Noether Guest Group 'Neuronal Protein Transport', Institute for Molecular Neurogenetics, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany.,The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University (WSU), Pullman, United States
| | - Michael R Kreutz
- RG Neuroplasticity, Leibniz-Institute for Neurobiology (LIN), Magdeburg, Germany.,Leibniz Group 'Dendritic Organelles and Synaptic Function', Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany.,German Center for Neurodegenerative Diseases, Magdeburg, Germany.,Center for Behavioral Brain Sciences, Magdeburg, Germany
| | - Marina Mikhaylova
- AG Optobiology, Institute of Biology, Humboldt-University, Berlin, Germany.,DFG Emmy Noether Guest Group 'Neuronal Protein Transport', Institute for Molecular Neurogenetics, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
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5
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Striessnig J. Voltage-Gated Ca 2+-Channel α1-Subunit de novo Missense Mutations: Gain or Loss of Function - Implications for Potential Therapies. Front Synaptic Neurosci 2021; 13:634760. [PMID: 33746731 PMCID: PMC7966529 DOI: 10.3389/fnsyn.2021.634760] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 02/02/2021] [Indexed: 12/12/2022] Open
Abstract
This review summarizes our current knowledge of human disease-relevant genetic variants within the family of voltage gated Ca2+ channels. Ca2+ channelopathies cover a wide spectrum of diseases including epilepsies, autism spectrum disorders, intellectual disabilities, developmental delay, cerebellar ataxias and degeneration, severe cardiac arrhythmias, sudden cardiac death, eye disease and endocrine disorders such as congential hyperinsulinism and hyperaldosteronism. A special focus will be on the rapidly increasing number of de novo missense mutations identified in the pore-forming α1-subunits with next generation sequencing studies of well-defined patient cohorts. In contrast to likely gene disrupting mutations these can not only cause a channel loss-of-function but can also induce typical functional changes permitting enhanced channel activity and Ca2+ signaling. Such gain-of-function mutations could represent therapeutic targets for mutation-specific therapy of Ca2+-channelopathies with existing or novel Ca2+-channel inhibitors. Moreover, many pathogenic mutations affect positive charges in the voltage sensors with the potential to form gating-pore currents through voltage sensors. If confirmed in functional studies, specific blockers of gating-pore currents could also be of therapeutic interest.
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Affiliation(s)
- Jörg Striessnig
- Department of Pharmacology and Toxicology, Institute of Pharmacy, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
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6
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Harich B, van der Voet M, Klein M, Čížek P, Fenckova M, Schenck A, Franke B. From Rare Copy Number Variants to Biological Processes in ADHD. Am J Psychiatry 2020; 177:855-866. [PMID: 32600152 DOI: 10.1176/appi.ajp.2020.19090923] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
OBJECTIVE Attention deficit hyperactivity disorder (ADHD) is a highly heritable psychiatric disorder. The objective of this study was to define ADHD-associated candidate genes and their associated molecular modules and biological themes, based on the analysis of rare genetic variants. METHODS The authors combined data from 11 published copy number variation studies in 6,176 individuals with ADHD and 25,026 control subjects and prioritized genes by applying an integrative strategy based on criteria including recurrence in individuals with ADHD, absence in control subjects, complete coverage in copy number gains, and presence in the minimal region common to overlapping copy number variants (CNVs), as well as on protein-protein interactions and information from cross-species genotype-phenotype annotation. RESULTS The authors localized 2,241 eligible genes in the 1,532 reported CNVs, of which they classified 432 as high-priority ADHD candidate genes. The high-priority ADHD candidate genes were significantly coexpressed in the brain. A network of 66 genes was supported by ADHD-relevant phenotypes in the cross-species database. Four significantly interconnected protein modules were found among the high-priority ADHD genes. A total of 26 genes were observed across all applied bioinformatic methods. Lookup in the latest genome-wide association study for ADHD showed that among those 26 genes, POLR3C and RBFOX1 were also supported by common genetic variants. CONCLUSIONS Integration of a stringent filtering procedure in CNV studies with suitable bioinformatics approaches can identify ADHD candidate genes at increased levels of credibility. The authors' analytic pipeline provides additional insight into the molecular mechanisms underlying ADHD and allows prioritization of genes for functional validation in validated model organisms.
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Affiliation(s)
- Benjamin Harich
- Department of Human Genetics (Harich, van der Voet, Klein, Fenckova, Schenck, Franke) and Department of Psychiatry (Franke), Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands; and Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands (Čížek)
| | - Monique van der Voet
- Department of Human Genetics (Harich, van der Voet, Klein, Fenckova, Schenck, Franke) and Department of Psychiatry (Franke), Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands; and Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands (Čížek)
| | - Marieke Klein
- Department of Human Genetics (Harich, van der Voet, Klein, Fenckova, Schenck, Franke) and Department of Psychiatry (Franke), Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands; and Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands (Čížek)
| | - Pavel Čížek
- Department of Human Genetics (Harich, van der Voet, Klein, Fenckova, Schenck, Franke) and Department of Psychiatry (Franke), Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands; and Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands (Čížek)
| | - Michaela Fenckova
- Department of Human Genetics (Harich, van der Voet, Klein, Fenckova, Schenck, Franke) and Department of Psychiatry (Franke), Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands; and Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands (Čížek)
| | - Annette Schenck
- Department of Human Genetics (Harich, van der Voet, Klein, Fenckova, Schenck, Franke) and Department of Psychiatry (Franke), Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands; and Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands (Čížek)
| | - Barbara Franke
- Department of Human Genetics (Harich, van der Voet, Klein, Fenckova, Schenck, Franke) and Department of Psychiatry (Franke), Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands; and Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands (Čížek)
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7
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Kepler LD, McDiarmid TA, Rankin CH. Habituation in high-throughput genetic model organisms as a tool to investigate the mechanisms of neurodevelopmental disorders. Neurobiol Learn Mem 2020; 171:107208. [DOI: 10.1016/j.nlm.2020.107208] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/14/2020] [Accepted: 03/02/2020] [Indexed: 10/24/2022]
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8
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Johnstone M, Hillary RF, St Clair D. Stem Cells to Inform the Neurobiology of Mental Illness. Curr Top Behav Neurosci 2019; 40:13-43. [PMID: 30030769 DOI: 10.1007/7854_2018_57] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The inception of human-induced pluripotent stem cell (hiPSCs) technology has provided an exciting platform upon which the modelling and treatment of human neurodevelopmental and neuropsychiatric disorders may be expedited. Although the genetic architecture of these disorders is far more complex than previously imagined, many key loci have at last been identified. This has allowed in vivo and in vitro technologies to be refined to model specific high-penetrant genetic loci involved in both disorders. Animal models of neurodevelopmental disorders, such as schizophrenia and autism spectrum disorders, show limitations in recapitulating the full complexity and heterogeneity of human neurodevelopmental disease states. Indeed, patient-derived hiPSCs offer distinct advantages over classical animal models in the study of human neuropathologies. Here we have discussed the current, relative translational merit of hiPSCs in investigating human neurodevelopmental and neuropsychiatric disorders with a specific emphasis on the utility of such systems to aid in the identification of biomarkers. We have highlighted the promises and pitfalls of reprogramming cell fate for the study of these disorders and provide recommendations for future directions in this field in order to overcome current limitations. Ultimately, this will aid in the development of effective clinical strategies for diverse patient populations affected by these disorders with the aim of also leading to biomarker identification.
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Affiliation(s)
- Mandy Johnstone
- Division of Psychiatry, Royal Edinburgh Hospital, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, Scotland, UK.
| | - Robert F Hillary
- Division of Psychiatry, Royal Edinburgh Hospital, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, Scotland, UK
| | - David St Clair
- Division of Psychiatry, Royal Edinburgh Hospital, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, Scotland, UK
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9
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Wang W, Corominas R, Lin GN. De novo Mutations From Whole Exome Sequencing in Neurodevelopmental and Psychiatric Disorders: From Discovery to Application. Front Genet 2019; 10:258. [PMID: 31001316 PMCID: PMC6456656 DOI: 10.3389/fgene.2019.00258] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 03/08/2019] [Indexed: 12/13/2022] Open
Abstract
Neurodevelopmental and psychiatric disorders are a highly disabling and heterogeneous group of developmental and mental disorders, resulting from complex interactions of genetic and environmental risk factors. The nature of multifactorial traits and the presence of comorbidity and polygenicity in these disorders present challenges in both disease risk identification and clinical diagnoses. The genetic component has been firmly established, but the identification of all the causative variants remains elusive. The development of next-generation sequencing, especially whole exome sequencing (WES), has greatly enriched our knowledge of the precise genetic alterations of human diseases, including brain-related disorders. In particular, the extensive usage of WES in research studies has uncovered the important contribution of de novo mutations (DNMs) to these disorders. Trio and quad familial WES are a particularly useful approach to discover DNMs. Here, we review the major WES studies in neurodevelopmental and psychiatric disorders and summarize how genes hit by discovered DNMs are shared among different disorders. Next, we discuss different integrative approaches utilized to interrogate DNMs and to identify biological pathways that may disrupt brain development and shed light on our understanding of the genetic architecture underlying these disorders. Lastly, we discuss the current state of the transition from WES research to its routine clinical application. This review will assist researchers and clinicians in the interpretation of variants obtained from WES studies, and highlights the need to develop consensus analytical protocols and validated lists of genes appropriate for clinical laboratory analysis, in order to reach the growing demands.
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Affiliation(s)
- Weidi Wang
- Shanghai Mental Health Center, School of Biomedical Engineering, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai, China
- Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Roser Corominas
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Valencia, Spain
- Institut de Biomedicina de la Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Guan Ning Lin
- Shanghai Mental Health Center, School of Biomedical Engineering, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai, China
- Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
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10
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Lu C, Shi X, Allen A, Baez-Nieto D, Nikish A, Sanjana NE, Pan JQ. Overexpression of NEUROG2 and NEUROG1 in human embryonic stem cells produces a network of excitatory and inhibitory neurons. FASEB J 2019; 33:5287-5299. [PMID: 30698461 PMCID: PMC6436650 DOI: 10.1096/fj.201801110rr] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 01/02/2019] [Indexed: 01/19/2023]
Abstract
Overexpression of mouse neurogenin ( Neurog) 2 alone or in combination with mouse Neurog2/1 in human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs) can rapidly produce high-yield excitatory neurons. Here, we report a detailed characterization of human neuronal networks induced by the expression of human NEUROG2 together with human NEUROG2/1 in hESCs using molecular, cellular, and electrophysiological measurements over 60 d after induction. Both excitatory synaptic transmission and network firing activity increased over time. Strikingly, inhibitory synaptic transmission and GABAergic cells were identified from NEUROG2/1 induced neurons (iNs). To illustrate the application of such iNs, we demonstrated that the heterozygous knock out of SCN2A, whose loss-of-function mutation is strongly implicated in autism risk, led to a dramatic reduction in network activity in the NEUROG2/1 iNs. Our findings not only extend our understanding of the NEUROG2/1-induced human neuronal network but also substantiate NEUROG2/1 iNs as an in vitro system for modeling neuronal and functional deficits on a human genetic background.-Lu, C., Shi, X., Allen, A., Baez-Nieto, D., Nikish, A., Sanjana, N. E., Pan, J. Q. Overexpression of NEUROG2 and NEUROG1 in human embryonic stem cells produces a network of excitatory and inhibitory neurons.
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Affiliation(s)
- Congyi Lu
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts, USA
- New York Genome Center, New York, New York, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA
- Department of Biology, New York University, New York, New York, USA
| | - Xi Shi
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA
| | - Andrew Allen
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts, USA
| | - David Baez-Nieto
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts, USA
| | - Alexandria Nikish
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA
| | - Neville E. Sanjana
- New York Genome Center, New York, New York, USA
- Department of Biology, New York University, New York, New York, USA
| | - Jen Q. Pan
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts, USA
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11
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St Clair D, Johnstone M. Using mouse transgenic and human stem cell technologies to model genetic mutations associated with schizophrenia and autism. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0037. [PMID: 29352035 PMCID: PMC5790834 DOI: 10.1098/rstb.2017.0037] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2017] [Indexed: 12/22/2022] Open
Abstract
Solid progress has occurred over the last decade in our understanding of the molecular genetic basis of neurodevelopmental disorders, and of schizophrenia and autism in particular. Although the genetic architecture of both disorders is far more complex than previously imagined, many key loci have at last been identified. This has allowed in vivo and in vitro technologies to be refined to model specific high-penetrant genetic loci involved in both disorders. Using the DISC1/NDE1 and CYFIP1/EIF4E loci as exemplars, we explore the opportunities and challenges of using animal models and human-induced pluripotent stem cell technologies to further understand/treat and potentially reverse the worst consequences of these debilitating disorders. This article is part of a discussion meeting issue ‘Of mice and mental health: facilitating dialogue between basic and clinical neuroscientists’.
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Affiliation(s)
- David St Clair
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, UK
| | - Mandy Johnstone
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK.,Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.,Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
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12
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Chapman NH, Bernier RA, Webb SJ, Munson J, Blue EM, Chen DH, Heigham E, Raskind WH, Wijsman EM. Replication of a rare risk haplotype on 1p36.33 for autism spectrum disorder. Hum Genet 2018; 137:807-815. [PMID: 30276537 PMCID: PMC6309233 DOI: 10.1007/s00439-018-1939-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 09/22/2018] [Indexed: 01/15/2023]
Abstract
Hundreds of genes have been implicated in autism spectrum disorders (ASDs). In genetically heterogeneous conditions, large families with multiple affected individuals provide strong evidence implicating a rare variant, and replication of the same variant in multiple families is unusual. We previously published linkage analyses and follow-up exome sequencing in seven large families with ASDs, implicating 14 rare exome variants. These included rs200195897, which was transmitted to four affected individuals in one family. We attempted replication of those variants in the MSSNG database. MSSNG is a unique resource for replication of ASD risk loci, containing whole genome sequence (WGS) on thousands of individuals diagnosed with ASDs and family members. For each exome variant, we obtained all carriers and their relatives in MSSNG, using a TDT test to quantify evidence for transmission and association. We replicated the transmission of rs200195897 to four affected individuals in three additional families. rs200195897 was also present in three singleton affected individuals, and no unaffected individuals other than transmitting parents. We identified two additional rare variants (rs566472488 and rs185038034) transmitted with rs200195897 on 1p36.33. Sanger sequencing confirmed the presence of these variants in the original family segregating rs200195897. To our knowledge, this is the first example of a rare haplotype being transmitted with ASD in multiple families. The candidate risk variants include a missense mutation in SAMD11, an intronic variant in NOC2L, and a regulatory region variant close to both genes. NOC2L is a transcription repressor, and several genes involved in transcription regulation have been previously associated with ASDs.
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Affiliation(s)
- N H Chapman
- Division of Medical Genetics, Department of Medicine, University of Washington, Box 359460, Seattle, WA, 98195, USA
| | - R A Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, 98195, USA
- Center on Human Development and Disability, University of Washington, Seattle, WA, 98195, USA
| | - S J Webb
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, 98195, USA
- Center on Human Development and Disability, University of Washington, Seattle, WA, 98195, USA
| | - J Munson
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, 98195, USA
- Center on Human Development and Disability, University of Washington, Seattle, WA, 98195, USA
| | - E M Blue
- Division of Medical Genetics, Department of Medicine, University of Washington, Box 359460, Seattle, WA, 98195, USA
| | - D-H Chen
- Department of Neurology, University of Washington, Seattle, WA, 98195, USA
| | - E Heigham
- Department of Neurology, University of Washington, Seattle, WA, 98195, USA
| | - W H Raskind
- Division of Medical Genetics, Department of Medicine, University of Washington, Box 359460, Seattle, WA, 98195, USA
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, 98195, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Ellen M Wijsman
- Division of Medical Genetics, Department of Medicine, University of Washington, Box 359460, Seattle, WA, 98195, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA.
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA.
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13
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Molinard-Chenu A, Dayer A. The Candidate Schizophrenia Risk Gene DGCR2 Regulates Early Steps of Corticogenesis. Biol Psychiatry 2018; 83:692-706. [PMID: 29305086 DOI: 10.1016/j.biopsych.2017.11.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 11/06/2017] [Accepted: 11/06/2017] [Indexed: 02/08/2023]
Abstract
BACKGROUND Alterations in early steps of cortical circuit assembly are thought to play a critical role in vulnerability to schizophrenia (SZ), but the pathogenic impact of SZ-risk mutations on corticogenesis remains to be determined. DiGeorge syndrome critical region 2 (DGCR2) is located in the 22q11.2 locus, whose deletion is a major risk factor for SZ. Moreover, exome sequencing of individuals with idiopathic SZ identified a rare missense mutation in DGCR2, further suggesting that DGCR2 is involved in SZ. METHODS Here we investigated the function of Dgcr2 and the pathogenic impact of the SZ-risk DGCR2 mutation in mouse corticogenesis using in utero electroporation targeted to projection neurons. RESULTS Dgcr2 knockdown impaired radial locomotion and final translocation of projection neurons, leading to persistent laminar positioning alterations. The DGCR2 missense SZ-risk mutation had a pathogenic impact on projection neuron laminar allocation by reducing protein expression. Mechanistically, we identified Dgcr2 as a novel member of the Reelin complex, regulating the phosphorylation of Reelin-dependent substrates and the expression of Reelin-dependent transcriptional targets. CONCLUSIONS Overall, this study provides biological evidence that the SZ-risk gene DGCR2 regulates critical steps of early corticogenesis possibly through a Reelin-dependent mechanism. Additionally, we found that the SZ-risk mutation in DGCR2 has a pathogenic impact on cortical formation by reducing protein expression level, suggesting a functional role for DGCR2 haploinsufficiency in the 22q11.2 deletion syndrome.
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Affiliation(s)
- Aude Molinard-Chenu
- Department of Psychiatry, University of Geneva Medical School, Geneva, Switzerland; Department of Basic Neurosciences, University of Geneva Medical School, Geneva, Switzerland; Institute of Genetics and Genomics in Geneva, University of Geneva Medical Center, Geneva, Switzerland
| | - Alexandre Dayer
- Department of Psychiatry, University of Geneva Medical School, Geneva, Switzerland; Department of Basic Neurosciences, University of Geneva Medical School, Geneva, Switzerland; Institute of Genetics and Genomics in Geneva, University of Geneva Medical Center, Geneva, Switzerland.
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14
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Jin ZB, Li Z, Liu Z, Jiang Y, Cai XB, Wu J. Identification of de novo germline mutations and causal genes for sporadic diseases using trio-based whole-exome/genome sequencing. Biol Rev Camb Philos Soc 2017; 93:1014-1031. [PMID: 29154454 DOI: 10.1111/brv.12383] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 09/28/2017] [Accepted: 10/10/2017] [Indexed: 12/14/2022]
Abstract
Whole-genome or whole-exome sequencing (WGS/WES) of the affected proband together with normal parents (trio) is commonly adopted to identify de novo germline mutations (DNMs) underlying sporadic cases of various genetic disorders. However, our current knowledge of the occurrence and functional effects of DNMs remains limited and accurately identifying the disease-causing DNM from a group of irrelevant DNMs is complicated. Herein, we provide a general-purpose discussion of important issues related to pathogenic gene identification based on trio-based WGS/WES data. Specifically, the relevance of DNMs to human sporadic diseases, current knowledge of DNM biogenesis mechanisms, and common strategies or software tools used for DNM detection are reviewed, followed by a discussion of pathogenic gene prioritization. In addition, several key factors that may affect DNM identification accuracy and causal gene prioritization are reviewed. Based on recent major advances, this review both sheds light on how trio-based WGS/WES technologies can play a significant role in the identification of DNMs and causal genes for sporadic diseases, and also discusses existing challenges.
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Affiliation(s)
- Zi-Bing Jin
- Division of Ophthalmic Genetics, The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China.,State Key Laboratory of Ophthalmology Optometry and Vision Science, Wenzhou Medical University, Wenzhou, 325027, China
| | - Zhongshan Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325000, China
| | - Zhenwei Liu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325000, China
| | - Yi Jiang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325000, China
| | - Xue-Bi Cai
- Division of Ophthalmic Genetics, The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China.,State Key Laboratory of Ophthalmology Optometry and Vision Science, Wenzhou Medical University, Wenzhou, 325027, China
| | - Jinyu Wu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325000, China
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15
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Bustamante ML, Herrera L, Gaspar PA, Nieto R, Maturana A, Villar MJ, Salinas V, Silva H. Shifting the focus toward rare variants in schizophrenia to close the gap from genotype to phenotype. Am J Med Genet B Neuropsychiatr Genet 2017; 174:663-670. [PMID: 28901686 DOI: 10.1002/ajmg.b.32550] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 04/25/2017] [Indexed: 01/16/2023]
Abstract
Schizophrenia (SZ) is a disorder with a high heritability and a complex architecture. Several dozen genetic variants have been identified as risk factors through genome-wide association studies including large population-based samples. However, the bulk of the risk cannot be accounted for by the genes associated to date. Rare mutations have been historically seen as relevant only for some infrequent, Mendelian forms of psychosis. Recent findings, however, show that the subset of patients that present a mutation with major effect is larger than expected. We discuss some of the molecular findings of these studies. SZ is clinically and genetically heterogeneous. To identify the genetic variation underlying the disorder, research should be focused on features that are more likely a product of genetic heterogeneity. Based on the phenotypical correlations with rare variants, cognition emerges as a relevant domain to study. Cognitive disturbances could be useful in selecting cases that have a higher probability of carrying deleterious mutations, as well as on the correct ascertainment of sporadic cases for the identification of de novo variants.
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Affiliation(s)
- M Leonor Bustamante
- Faculty of Medicine, Program of Human Genetics, Biomedical Sciences Institute, Universidad de Chile, Santiago de Chile, Chile.,Clínica Psiquiátrica Universitaria, Universidad de Chile, Santiago de Chile, Chile
| | - Luisa Herrera
- Faculty of Medicine, Program of Human Genetics, Biomedical Sciences Institute, Universidad de Chile, Santiago de Chile, Chile
| | - Pablo A Gaspar
- Clínica Psiquiátrica Universitaria, Universidad de Chile, Santiago de Chile, Chile.,Faculty of Medicine, Department of Neurosciences, Universidad de Chile, Santiago de Chile, Chile.,Biomedical Neurosciences Institute, Universidad de Chile, Santiago de Chile, Chile
| | - Rodrigo Nieto
- Clínica Psiquiátrica Universitaria, Universidad de Chile, Santiago de Chile, Chile.,Faculty of Medicine, Department of Neurosciences, Universidad de Chile, Santiago de Chile, Chile
| | - Alejandro Maturana
- Clínica Psiquiátrica Universitaria, Universidad de Chile, Santiago de Chile, Chile
| | - María José Villar
- Clínica Psiquiátrica Universitaria, Universidad de Chile, Santiago de Chile, Chile
| | - Valeria Salinas
- Faculty of Medicine, Program of Human Genetics, Biomedical Sciences Institute, Universidad de Chile, Santiago de Chile, Chile
| | - Hernán Silva
- Clínica Psiquiátrica Universitaria, Universidad de Chile, Santiago de Chile, Chile.,Faculty of Medicine, Department of Neurosciences, Universidad de Chile, Santiago de Chile, Chile.,Biomedical Neurosciences Institute, Universidad de Chile, Santiago de Chile, Chile
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16
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Zhang C, Shen Y. A Cell Type-Specific Expression Signature Predicts Haploinsufficient Autism-Susceptibility Genes. Hum Mutat 2017; 38:204-215. [PMID: 27860035 PMCID: PMC5865588 DOI: 10.1002/humu.23147] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 11/12/2016] [Accepted: 11/13/2016] [Indexed: 12/22/2022]
Abstract
Recent studies have identified many genes with rare de novo mutations in autism, but a limited number of these have been conclusively established as disease-susceptibility genes due to the lack of recurrence and confounding background mutations. Such extreme genetic heterogeneity severely limits recurrence-based statistical power even in studies with a large sample size. Here, we use cell-type specific expression profiles to differentiate mutations in autism patients from those in unaffected siblings. We report a gene expression signature in different neuronal cell types shared by genes with likely gene-disrupting (LGD) mutations in autism cases. This signature reflects haploinsufficiency of risk genes enriched in transcriptional and post-transcriptional regulators, with the strongest positive associations with specific types of neurons in different brain regions, including cortical neurons, cerebellar granule cells, and striatal medium spiny neurons. When used to prioritize genes with a single LGD mutation in cases, a D-score derived from the signature achieved a precision of 40% as compared with the 15% baseline with a minimal loss in sensitivity. An ensemble model combining D-score with mutation intolerance metrics from Exome Aggregation Consortium further improved the precision to 60%, resulting in 117 high-priority candidates. These prioritized lists can facilitate identification of additional autism-susceptibility genes.
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Affiliation(s)
- Chaolin Zhang
- Department of Systems Biology, Columbia University, New York NY
10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia
University, New York NY 10032, USA
- Center for Motor Neuron Biology and Disease, Columbia University,
New York NY 10032, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University, New York NY
10032, USA
- Department of Biomedical Informatics, Columbia University, New York
NY 10032, USA
- JP Sulzberger Genome Center, Columbia University, New York NY 10032,
USA
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17
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Forero DA, Prada CF, Perry G. Functional and Genomic Features of Human Genes Mutated in Neuropsychiatric Disorders. Open Neurol J 2016; 10:143-148. [PMID: 27990183 PMCID: PMC5120378 DOI: 10.2174/1874205x01610010143] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 09/08/2016] [Accepted: 09/16/2016] [Indexed: 11/22/2022] Open
Abstract
Background: In recent years, a large number of studies around the world have led to the identification of causal genes for hereditary types of common and rare neurological and psychiatric disorders. Objective: To explore the functional and genomic features of known human genes mutated in neuropsychiatric disorders. Methods: A systematic search was used to develop a comprehensive catalog of genes mutated in neuropsychiatric disorders (NPD). Functional enrichment and protein-protein interaction analyses were carried out. A false discovery rate approach was used for correction for multiple testing. Results: We found several functional categories that are enriched among NPD genes, such as gene ontologies, protein domains, tissue expression, signaling pathways and regulation by brain-expressed miRNAs and transcription factors. Sixty six of those NPD genes are known to be druggable. Several topographic parameters of protein-protein interaction networks and the degree of conservation between orthologous genes were identified as significant among NPD genes. Conclusion: These results represent one of the first analyses of enrichment of functional categories of genes known to harbor mutations for NPD. These findings could be useful for a future creation of computational tools for prioritization of novel candidate genes for NPD.
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Affiliation(s)
- Diego A Forero
- Laboratory of NeuroPsychiatric Genetics, Biomedical Sciences Research Group, School of Medicine, Universidad Antonio Nariño, Bogotá, Colombia
| | - Carlos F Prada
- Grupo de Citogenética, Filogenia y Evolución de Poblaciones, Universidad del Tolima. Ibagué, Colombia
| | - George Perry
- College of Sciences, University of Texas at San Antonio, San Antonio, Texas, USA
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18
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Pulit SL, de With SAJ, de Bakker PIW. Resetting the bar: Statistical significance in whole-genome sequencing-based association studies of global populations. Genet Epidemiol 2016; 41:145-151. [PMID: 27990689 DOI: 10.1002/gepi.22032] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 10/31/2016] [Accepted: 10/31/2016] [Indexed: 12/29/2022]
Abstract
Genome-wide association studies (GWAS) of common disease have been hugely successful in implicating loci that modify disease risk. The bulk of these associations have proven robust and reproducible, in part due to community adoption of statistical criteria for claiming significant genotype-phenotype associations. As the cost of sequencing continues to drop, assembling large samples in global populations is becoming increasingly feasible. Sequencing studies interrogate not only common variants, as was true for genotyping-based GWAS, but variation across the full allele frequency spectrum, yielding many more (independent) statistical tests. We sought to empirically determine genome-wide significance thresholds for various analysis scenarios. Using whole-genome sequence data, we simulated sequencing-based disease studies of varying sample size and ancestry. We determined that future sequencing efforts in >2,000 samples of European, Asian, or admixed ancestry should set genome-wide significance at approximately P = 5 × 10-9 , and studies of African samples should apply a more stringent genome-wide significance threshold of P = 1 × 10-9 . Adoption of a revised multiple test correction will be crucial in avoiding irreproducible claims of association.
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Affiliation(s)
- Sara L Pulit
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sera A J de With
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Paul I W de Bakker
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
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19
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Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism. Nature 2016; 540:423-427. [PMID: 27919067 DOI: 10.1038/nature20612] [Citation(s) in RCA: 427] [Impact Index Per Article: 53.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 11/07/2016] [Indexed: 12/11/2022]
Abstract
Autism spectrum disorder (ASD) involves substantial genetic contributions. These contributions are profoundly heterogeneous but may converge on common pathways that are not yet well understood. Here, through post-mortem genome-wide transcriptome analysis of the largest cohort of samples analysed so far, to our knowledge, we interrogate the noncoding transcriptome, alternative splicing, and upstream molecular regulators to broaden our understanding of molecular convergence in ASD. Our analysis reveals ASD-associated dysregulation of primate-specific long noncoding RNAs (lncRNAs), downregulation of the alternative splicing of activity-dependent neuron-specific exons, and attenuation of normal differences in gene expression between the frontal and temporal lobes. Our data suggest that SOX5, a transcription factor involved in neuron fate specification, contributes to this reduction in regional differences. We further demonstrate that a genetically defined subtype of ASD, chromosome 15q11.2-13.1 duplication syndrome (dup15q), shares the core transcriptomic signature observed in idiopathic ASD. Co-expression network analysis reveals that individuals with ASD show age-related changes in the trajectory of microglial and synaptic function over the first two decades, and suggests that genetic risk for ASD may influence changes in regional cortical gene expression. Our findings illustrate how diverse genetic perturbations can lead to phenotypic convergence at multiple biological levels in a complex neuropsychiatric disorder.
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20
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Advancing the understanding of autism disease mechanisms through genetics. Nat Med 2016; 22:345-61. [PMID: 27050589 DOI: 10.1038/nm.4071] [Citation(s) in RCA: 513] [Impact Index Per Article: 64.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 02/26/2016] [Indexed: 12/11/2022]
Abstract
Progress in understanding the genetic etiology of autism spectrum disorders (ASD) has fueled remarkable advances in our understanding of its potential neurobiological mechanisms. Yet, at the same time, these findings highlight extraordinary causal diversity and complexity at many levels ranging from molecules to circuits and emphasize the gaps in our current knowledge. Here we review current understanding of the genetic architecture of ASD and integrate genetic evidence, neuropathology and studies in model systems with how they inform mechanistic models of ASD pathophysiology. Despite the challenges, these advances provide a solid foundation for the development of rational, targeted molecular therapies.
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21
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Gratten J, Wray NR, Peyrot WJ, McGrath JJ, Visscher PM, Goddard ME. Risk of psychiatric illness from advanced paternal age is not predominantly from de novo mutations. Nat Genet 2016; 48:718-24. [PMID: 27213288 DOI: 10.1038/ng.3577] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 04/29/2016] [Indexed: 12/17/2022]
Abstract
The offspring of older fathers have higher risk of psychiatric disorders such as schizophrenia and autism. Paternal-age-related de novo mutations are widely assumed to be the underlying causal mechanism, and, although such mutations must logically make some contribution, there are alternative explanations (for example, elevated liability to psychiatric illness may delay fatherhood). We used population genetic models based on empirical observations of key parameters (for example, mutation rate, prevalence, and heritability) to assess the genetic relationship between paternal age and risk of psychiatric illness. These models suggest that age-related mutations are unlikely to explain much of the increased risk of psychiatric disorders in children of older fathers. Conversely, a model incorporating a weak correlation between age at first child and liability to psychiatric illness matched epidemiological observations. Our results suggest that genetic risk factors shared by older fathers and their offspring are a credible alternative explanation to de novo mutations for risk to children of older fathers.
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Affiliation(s)
- Jacob Gratten
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Naomi R Wray
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Wouter J Peyrot
- Department of Psychiatry, VU University Medical Center, Amsterdam, the Netherlands
| | - John J McGrath
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia.,Queensland Centre for Mental Health Research, Park Centre for Mental Health, Wacol, Queensland, Australia
| | - Peter M Visscher
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia.,University of Queensland Diamantina Institute, University of Queensland, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Michael E Goddard
- Department of Primary Industries, Biosciences Research Division, Melbourne, Victoria, Australia.,Department of Agriculture and Food Systems, University of Melbourne, Melbourne, Victoria, Australia
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22
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Herbert J, Lucassen PJ. Depression as a risk factor for Alzheimer's disease: Genes, steroids, cytokines and neurogenesis - What do we need to know? Front Neuroendocrinol 2016; 41:153-71. [PMID: 26746105 DOI: 10.1016/j.yfrne.2015.12.001] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 12/23/2015] [Accepted: 12/27/2015] [Indexed: 01/18/2023]
Abstract
Depression (MDD) is prodromal to, and a component of, Alzheimer's disease (AD): it may also be a trigger for incipient AD. MDD is not a unitary disorder, so there may be particular subtypes of early life MDD that pose independent high risks for later AD, though the identification of these subtypes is problematical. There may either be a common pathological event underlying both MDD and AD, or MDD may sensitize the brain to a second event ('hit') that precipitates AD. MDD may also accelerate brain ageing, including altered DNA methylation, increased cortisol but decreasing DHEA and thus the risk for AD. So far, genes predicting AD (e.g. APOEε4) are not risk factors for MDD, and those implicated in MDD (e.g. SLC6A4) are not risks for AD, so a common genetic predisposition looks unlikely. There is as yet no strong indication that an epigenetic event occurs during some forms of MDD that predisposes to later AD, though the evidence is limited. Glucocorticoids (GCs) are disturbed in some cases of MDD and in AD. GCs have marked degenerative actions on the hippocampus, a site of early β-amyloid deposition, and rare genetic variants of GC-regulating enzymes (e.g. 11β-HSD) predispose to AD. GCs also inhibit hippocampal neurogenesis and plasticity, and thus episodic memory, a core symptom of AD. Disordered GCs in MDD may inhibit neurogenesis, but the contribution of diminished neurogenesis to the onset or progression of AD is still debated. GCs and cytokines also reduce BDNF, implicated in both MDD and AD and hippocampal neurogenesis, reinforcing the notion that those cases of MDD with disordered GCs may be a risk for AD. Cytokines, including IL1β, IL6 and TNFα, are increased in the blood in some cases of MDD. They also reduce hippocampal neurogenesis, and increased cytokines are a known risk for later AD. Inflammatory changes occur in both MDD and AD (e.g. raised CRP, TNFα). Both cytokines and GCs can have pro-inflammatory actions in the brain. Inflammation (e.g. microglial activation) may be a common link, but this has not been systematically investigated. We lack substantial, rigorous and comprehensive follow-up studies to better identify possible subtypes of MDD that may represent a major predictor for later AD. This would enable specific interventions during critical episodes of these subtypes of MDD that should reduce this substantial risk.
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Affiliation(s)
- Joe Herbert
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, UK.
| | - Paul J Lucassen
- Swammerdam Institute for Life Sciences, Center for Neuroscience, University of Amsterdam, The Netherlands
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23
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Lammert DB, Howell BW. RELN Mutations in Autism Spectrum Disorder. Front Cell Neurosci 2016; 10:84. [PMID: 27064498 PMCID: PMC4814460 DOI: 10.3389/fncel.2016.00084] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 03/18/2016] [Indexed: 11/13/2022] Open
Abstract
RELN encodes a large, secreted glycoprotein integral to proper neuronal positioning during development and regulation of synaptic function postnatally. Rare, homozygous, null mutations lead to lissencephaly with cerebellar hypoplasia (LCH), accompanied by developmental delay and epilepsy. Until recently, little was known about the frequency or consequences of heterozygous mutations. Several lines of evidence from multiple studies now implicate heterozygous mutations in RELN in autism spectrum disorders (ASD). RELN maps to the AUTS1 locus on 7q22, and at this time over 40 distinct mutations have been identified that would alter the protein sequence, four of which are de novo. The RELN mutations that are most clearly consequential are those that are predicted to inactivate the signaling function of the encoded protein and those that fall in a highly conserved RXR motif found at the core of the 16 Reelin subrepeats. Despite the growing evidence of RELN dysfunction in ASD, it appears that these mutations in isolation are insufficient and that secondary genetic or environmental factors are likely required for a diagnosis.
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Affiliation(s)
- Dawn B Lammert
- Department of Neuroscience and Physiology, SUNY Upstate Medical School Syracuse, NY, USA
| | - Brian W Howell
- Department of Neuroscience and Physiology, SUNY Upstate Medical School Syracuse, NY, USA
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24
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Peyrot WJ, Boomsma DI, Penninx BWJH, Wray NR. Disease and Polygenic Architecture: Avoid Trio Design and Appropriately Account for Unscreened Control Subjects for Common Disease. Am J Hum Genet 2016; 98:382-91. [PMID: 26849113 DOI: 10.1016/j.ajhg.2015.12.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 12/17/2015] [Indexed: 01/17/2023] Open
Abstract
Genome-wide association studies (GWASs) are an optimal design for discovery of disease risk loci for diseases whose underlying genetic architecture includes many common causal loci of small effect (a polygenic architecture). We consider two designs that deserve careful consideration if the true underlying genetic architecture of the trait is polygenic: parent-offspring trios and unscreened control subjects. We assess these designs in terms of quantification of the total contribution of genome-wide genetic markers to disease risk (SNP heritability) and power to detect an associated risk allele. First, we show that trio designs should be avoided when: (1) the disease has a lifetime risk > 1%; (2) trio probands are ascertained from families with more than one affected sibling under which scenario the SNP heritability can drop by more than 50% and power can drop as much as from 0.9 to 0.15 for a sample of 20,000 subjects; or (3) assortative mating occurs (spouse correlation of the underlying liability to the disorder), which decreases the SNP heritability but not the power to detect a single locus in the trio design. Some studies use unscreened rather than screened control subjects because these can be easier to collect; we show that the estimated SNP heritability should then be scaled by dividing by (1 - K × u)(2) for disorders with population prevalence K and proportion of unscreened control subjects u. When omitting to scale appropriately, the SNP heritability of, for example, major depressive disorder (K = 0.15) would be underestimated by 28% when none of the control subjects are screened.
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Affiliation(s)
- Wouter J Peyrot
- Department of Psychiatry, VU University Medical Center & GGZ inGeest, Amsterdam 1081 HL, the Netherlands; Queensland Brain Institute, University of Queensland, Brisbane 4072, Australia.
| | - Dorret I Boomsma
- Department of Biological Psychology, VU University Amsterdam, Amsterdam 1081 BT, the Netherlands
| | - Brenda W J H Penninx
- Department of Psychiatry, VU University Medical Center & GGZ inGeest, Amsterdam 1081 HL, the Netherlands
| | - Naomi R Wray
- Queensland Brain Institute, University of Queensland, Brisbane 4072, Australia.
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25
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Li J, Cai T, Jiang Y, Chen H, He X, Chen C, Li X, Shao Q, Ran X, Li Z, Xia K, Liu C, Sun ZS, Wu J. Genes with de novo mutations are shared by four neuropsychiatric disorders discovered from NPdenovo database. Mol Psychiatry 2016; 21:290-7. [PMID: 25849321 PMCID: PMC4837654 DOI: 10.1038/mp.2015.40] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 02/26/2015] [Accepted: 03/02/2015] [Indexed: 12/16/2022]
Abstract
Currently, many studies on neuropsychiatric disorders have utilized massive trio-based whole-exome sequencing (WES) and whole-genome sequencing (WGS) to identify numerous de novo mutations (DNMs). Here, we retrieved 17,104 DNMs from 3555 trios across four neuropsychiatric disorders: autism spectrum disorder, epileptic encephalopathy, intellectual disability and schizophrenia, in addition to unaffected siblings (control), from 36 studies by WES/WGS. After eliminating non-exonic variants, we focused on 3334 exonic DNMs for evaluation of their association with these diseases. Our results revealed a higher prevalence of DNMs in the probands of all four disorders compared with the one in the controls (P<1.3 × 10(-7)). The elevated DNM frequency is dominated by loss-of-function/deleterious single-nucleotide variants and frameshift indels (that is, extreme mutations, P<4.5 × 10(-5)). With extensive annotation of these 'extreme' mutations, we prioritized 764 candidate genes in these four disorders. A combined analysis of Gene Ontology, microRNA targets and transcription factor targets revealed shared biological process and non-coding regulatory elements of candidate genes in the pathology of neuropsychiatric disorders. In addition, weighted gene co-expression network analysis of human laminar-specific neocortical expression data showed that candidate genes are convergent on eight shared modules with specific layer enrichment and biological process features. Furthermore, we identified that 53 candidate genes are associated with more than one disorder (P<0.000001), suggesting a possibly shared genetic etiology underlying these disorders. Particularly, DNMs of the SCN2A gene are frequently occurred across all four disorders. Finally, we constructed a freely available NPdenovo database, which provides a comprehensive catalog of the DNMs identified in neuropsychiatric disorders.
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Affiliation(s)
- Jinchen Li
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China,Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China,State Key Laboratory of Medical Genetics, Central South University, Changsha, China
| | - Tao Cai
- Experimental Medicine Section, NIDCR/NIH, Bethesda, Maryland, USA
| | - Yi Jiang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Huiqian Chen
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Xin He
- Department of Human Genetics, University of Chicago, Chicago, USA
| | - Chao Chen
- State Key Laboratory of Medical Genetics, Central South University, Changsha, China,Department of Psychiatry, University of Illinois at Chicago, Chicago, USA
| | - Xianfeng Li
- State Key Laboratory of Medical Genetics, Central South University, Changsha, China
| | - Qianzhi Shao
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Xia Ran
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Zhongshan Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Kun Xia
- State Key Laboratory of Medical Genetics, Central South University, Changsha, China
| | - Chunyu Liu
- State Key Laboratory of Medical Genetics, Central South University, Changsha, China,Department of Psychiatry, University of Illinois at Chicago, Chicago, USA,Correspondence should be addressed to: Jinyu Wu (), Zhong Sheng Sun (), or Chunyu Liu ()
| | - Zhong Sheng Sun
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China,Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China,Correspondence should be addressed to: Jinyu Wu (), Zhong Sheng Sun (), or Chunyu Liu ()
| | - Jinyu Wu
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China,Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China,Correspondence should be addressed to: Jinyu Wu (), Zhong Sheng Sun (), or Chunyu Liu ()
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26
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Abstract
Genetic factors play a major part in intellectual disability (ID), but genetic studies have been complicated for a long time by the extreme clinical and genetic heterogeneity. Recently, progress has been made using different next-generation sequencing approaches in combination with new functional readout systems. This approach has provided novel insights into the biological pathways underlying ID, improved the diagnostic process and offered new targets for therapy. In this Review, we highlight the insights obtained from recent studies on the role of genetics in ID and its impact on diagnosis, prognosis and therapy. We also discuss the future directions of genetics research for ID and related neurodevelopmental disorders.
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27
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Chapman NH, Nato AQ, Bernier R, Ankenman K, Sohi H, Munson J, Patowary A, Archer M, Blue EM, Webb SJ, Coon H, Raskind WH, Brkanac Z, Wijsman EM. Whole exome sequencing in extended families with autism spectrum disorder implicates four candidate genes. Hum Genet 2015; 134:1055-68. [PMID: 26204995 PMCID: PMC4578871 DOI: 10.1007/s00439-015-1585-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 07/11/2015] [Indexed: 12/26/2022]
Abstract
Autism spectrum disorders (ASDs) are a group of neurodevelopmental disorders, characterized by impairment in communication and social interactions, and by repetitive behaviors. ASDs are highly heritable, and estimates of the number of risk loci range from hundreds to >1000. We considered 7 extended families (size 12-47 individuals), each with ≥3 individuals affected by ASD. All individuals were genotyped with dense SNP panels. A small subset of each family was typed with whole exome sequence (WES). We used a 3-step approach for variant identification. First, we used family-specific parametric linkage analysis of the SNP data to identify regions of interest. Second, we filtered variants in these regions based on frequency and function, obtaining exactly 200 candidates. Third, we compared two approaches to narrowing this list further. We used information from the SNP data to impute exome variant dosages into those without WES. We regressed affected status on variant allele dosage, using pedigree-based kinship matrices to account for relationships. The p value for the test of the null hypothesis that variant allele dosage is unrelated to phenotype was used to indicate strength of evidence supporting the variant. A cutoff of p = 0.05 gave 28 variants. As an alternative third filter, we required Mendelian inheritance in those with WES, resulting in 70 variants. The imputation- and association-based approach was effective. We identified four strong candidate genes for ASD (SEZ6L, HISPPD1, FEZF1, SAMD11), all of which have been previously implicated in other studies, or have a strong biological argument for their relevance.
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Affiliation(s)
- Nicola H Chapman
- Division of Medical Genetics, School of Medicine, University of Washington, Seattle, WA, USA
| | - Alejandro Q Nato
- Division of Medical Genetics, School of Medicine, University of Washington, Seattle, WA, USA
| | - Raphael Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Katy Ankenman
- Department of Psychiatry, University of California, San Francisco, CA, USA
| | - Harkirat Sohi
- Division of Medical Genetics, School of Medicine, University of Washington, Seattle, WA, USA
| | - Jeff Munson
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
- Center on Child Development and Disability, University of Washington, Seattle, WA, USA
| | - Ashok Patowary
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Marilyn Archer
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Elizabeth M Blue
- Division of Medical Genetics, School of Medicine, University of Washington, Seattle, WA, USA
| | - Sara Jane Webb
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
- Center on Child Development and Disability, University of Washington, Seattle, WA, USA
| | - Hilary Coon
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
- Department of Psychiatry, School of Medicine, University of Utah, Salt Lake City, UT, USA
| | - Wendy H Raskind
- Division of Medical Genetics, School of Medicine, University of Washington, Seattle, WA, USA
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Zoran Brkanac
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Ellen M Wijsman
- Division of Medical Genetics, School of Medicine, University of Washington, Seattle, WA, USA.
- Department of Biostatistics, University of Washington, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- University of Washington, University of Washington Tower, T15, 4333 Brooklyn Ave, NE, BOX 359460, Seattle, WA, 98195-9460, USA.
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28
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Rovelet-Lecrux A, Charbonnier C, Wallon D, Nicolas G, Seaman MNJ, Pottier C, Breusegem SY, Mathur PP, Jenardhanan P, Le Guennec K, Mukadam AS, Quenez O, Coutant S, Rousseau S, Richard AC, Boland A, Deleuze JF, Frebourg T, Hannequin D, Campion D. De novo deleterious genetic variations target a biological network centered on Aβ peptide in early-onset Alzheimer disease. Mol Psychiatry 2015; 20:1046-56. [PMID: 26194182 DOI: 10.1038/mp.2015.100] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 05/27/2015] [Accepted: 06/16/2015] [Indexed: 12/21/2022]
Abstract
We hypothesized that de novo variants (DNV) might participate in the genetic determinism of sporadic early-onset Alzheimer disease (EOAD, onset before 65 years). We investigated 14 sporadic EOAD trios first by array-comparative genomic hybridization. Two patients carried a de novo copy number variation (CNV). We then performed whole-exome sequencing in the 12 remaining trios and identified 12 non-synonymous DNVs in six patients. The two de novo CNVs (an amyloid precursor protein (APP) duplication and a BACE2 intronic deletion) and 3/12 non-synonymous DNVs (in PSEN1, VPS35 and MARK4) targeted genes from a biological network centered on the Amyloid beta (Aβ) peptide. We showed that this a priori-defined genetic network was significantly enriched in amino acid-altering DNV, compared with the rest of the exome. The causality of the APP de novo duplication (which is the first reported one) was obvious. In addition, we provided evidence of the functional impact of the following three non-synonymous DNVs targeting this network: the novel PSEN1 variant resulted in exon 9 skipping in patient's RNA, leading to a pathogenic missense at exons 8-10 junction; the VPS35 missense variant led to partial loss of retromer function, which may impact neuronal APP trafficking and Aβ secretion; and the MARK4 multiple nucleotide variant resulted into increased Tau phosphorylation, which may trigger enhanced Aβ-induced toxicity. Despite the difficulty to recruit Alzheimer disease (AD) trios owing to age structures of the pedigrees and the genetic heterogeneity of the disease, this strategy allowed us to highlight the role of de novo pathogenic events, the putative involvement of new genes in AD genetics and the key role of Aβ network alteration in AD.
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Affiliation(s)
- A Rovelet-Lecrux
- Inserm U1079, Institute for Research and Innovation in Biomedicine, University of Rouen, Rouen, France
| | - C Charbonnier
- Inserm U1079, Institute for Research and Innovation in Biomedicine, University of Rouen, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France
| | - D Wallon
- Inserm U1079, Institute for Research and Innovation in Biomedicine, University of Rouen, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France.,Department of Neurology, Rouen University Hospital, Rouen, France
| | - G Nicolas
- Inserm U1079, Institute for Research and Innovation in Biomedicine, University of Rouen, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France.,Department of Genetics, Rouen University Hospital, Rouen, France
| | - M N J Seaman
- Cambridge Institute for Medical Research/Dept of Clinical Biochemistry, University of Cambridge, Addenbrookes Hospital, Cambridge, UK
| | - C Pottier
- Inserm U1079, Institute for Research and Innovation in Biomedicine, University of Rouen, Rouen, France
| | - S Y Breusegem
- Cambridge Institute for Medical Research/Dept of Clinical Biochemistry, University of Cambridge, Addenbrookes Hospital, Cambridge, UK
| | - P P Mathur
- Centre of Bioinformatics and Department of Biochemistry & Molecular Biology, School of Life Sciences, Pondicherry University, Pondicherry, India.,KIIT University, Bhubaneshwar, Odisha, India
| | - P Jenardhanan
- Centre of Bioinformatics and Department of Biochemistry & Molecular Biology, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - K Le Guennec
- Inserm U1079, Institute for Research and Innovation in Biomedicine, University of Rouen, Rouen, France
| | - A S Mukadam
- Cambridge Institute for Medical Research/Dept of Clinical Biochemistry, University of Cambridge, Addenbrookes Hospital, Cambridge, UK
| | - O Quenez
- Inserm U1079, Institute for Research and Innovation in Biomedicine, University of Rouen, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France
| | - S Coutant
- Inserm U1079, Institute for Research and Innovation in Biomedicine, University of Rouen, Rouen, France
| | - S Rousseau
- Inserm U1079, Institute for Research and Innovation in Biomedicine, University of Rouen, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France
| | - A-C Richard
- Inserm U1079, Institute for Research and Innovation in Biomedicine, University of Rouen, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France
| | - A Boland
- Centre National de Génotypage, Evry, France
| | | | - T Frebourg
- Inserm U1079, Institute for Research and Innovation in Biomedicine, University of Rouen, Rouen, France.,Department of Genetics, Rouen University Hospital, Rouen, France
| | - D Hannequin
- Inserm U1079, Institute for Research and Innovation in Biomedicine, University of Rouen, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France.,Department of Neurology, Rouen University Hospital, Rouen, France.,Department of Genetics, Rouen University Hospital, Rouen, France
| | - D Campion
- Inserm U1079, Institute for Research and Innovation in Biomedicine, University of Rouen, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France.,Department of Research, Centre Hospitalier du Rouvray, Sotteville-Les-Rouen, France
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29
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Francioli LC, Polak PP, Koren A, Menelaou A, Chun S, Renkens I, van Duijn CM, Swertz M, Wijmenga C, van Ommen G, Slagboom PE, Boomsma DI, Ye K, Guryev V, Arndt PF, Kloosterman WP, de Bakker PIW, Sunyaev SR. Genome-wide patterns and properties of de novo mutations in humans. Nat Genet 2015; 47:822-826. [PMID: 25985141 PMCID: PMC4485564 DOI: 10.1038/ng.3292] [Citation(s) in RCA: 247] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 04/07/2015] [Indexed: 12/12/2022]
Abstract
Mutations create variation in the population, fuel evolution, and cause genetic diseases. Current knowledge about de novo mutations is incomplete and mostly indirect 1–10. Here, we analyze 11,020 de novo mutations from whole-genomes of 250 families. We show that de novo mutations in offspring of older fathers are not only more numerous 11–13 but also occur more frequently in early-replicating, genic regions. Functional regions exhibit higher mutation rates due to CpG dinucleotides and reveal signatures of transcription-coupled repair, while mutation clusters with a unique signature point to a novel mutational mechanism. Mutation and recombination rates independently associate with nucleotide diversity, and regional variation in human-chimpanzee divergence is only partly explained by mutation rate heterogeneity. Finally, we provide a genome-wide mutation rate map for medical and population genetics applications. Our results reveal novel insights and refine long-standing hypotheses about human mutagenesis.
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Affiliation(s)
- Laurent C Francioli
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Paz P Polak
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Amnon Koren
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Androniki Menelaou
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sung Chun
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ivo Renkens
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | - Morris Swertz
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, The Netherlands
| | - Cisca Wijmenga
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, The Netherlands
| | - Gertjan van Ommen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - P Eline Slagboom
- Section of Molecular Epidemiology, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
| | - Kai Ye
- Section of Molecular Epidemiology, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands.,The Genome Institute, Washington University, St. Louis, MO, USA
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Peter F Arndt
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Wigard P Kloosterman
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Paul I W de Bakker
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Shamil R Sunyaev
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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30
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Marangi G, Traynor BJ. Genetic causes of amyotrophic lateral sclerosis: new genetic analysis methodologies entailing new opportunities and challenges. Brain Res 2015; 1607:75-93. [PMID: 25316630 PMCID: PMC5916786 DOI: 10.1016/j.brainres.2014.10.009] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 10/03/2014] [Accepted: 10/05/2014] [Indexed: 12/11/2022]
Abstract
The genetic architecture of amyotrophic lateral sclerosis (ALS) is being increasingly understood. In this far-reaching review, we examine what is currently known about ALS genetics and how these genes were initially identified. We also discuss the various types of mutations that might underlie this fatal neurodegenerative condition and outline some of the strategies that might be useful in untangling them. These include expansions of short repeat sequences, common and low-frequency genetic variations, de novo mutations, epigenetic changes, somatic mutations, epistasis, oligogenic and polygenic hypotheses. This article is part of a Special Issue entitled ALS complex pathogenesis.
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Affiliation(s)
- Giuseppe Marangi
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA; Institute of Medical Genetics, Catholic University, Roma, Italy.
| | - Bryan J Traynor
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA; Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
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31
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Park L, Kim JH. A novel approach for identifying causal models of complex diseases from family data. Genetics 2015; 199:1007-16. [PMID: 25701286 PMCID: PMC4391573 DOI: 10.1534/genetics.114.174102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 02/16/2015] [Indexed: 02/01/2023] Open
Abstract
Causal models including genetic factors are important for understanding the presentation mechanisms of complex diseases. Familial aggregation and segregation analyses based on polygenic threshold models have been the primary approach to fitting genetic models to the family data of complex diseases. In the current study, an advanced approach to obtaining appropriate causal models for complex diseases based on the sufficient component cause (SCC) model involving combinations of traditional genetics principles was proposed. The probabilities for the entire population, i.e., normal-normal, normal-disease, and disease-disease, were considered for each model for the appropriate handling of common complex diseases. The causal model in the current study included the genetic effects from single genes involving epistasis, complementary gene interactions, gene-environment interactions, and environmental effects. Bayesian inference using a Markov chain Monte Carlo algorithm (MCMC) was used to assess of the proportions of each component for a given population lifetime incidence. This approach is flexible, allowing both common and rare variants within a gene and across multiple genes. An application to schizophrenia data confirmed the complexity of the causal factors. An analysis of diabetes data demonstrated that environmental factors and gene-environment interactions are the main causal factors for type II diabetes. The proposed method is effective and useful for identifying causal models, which can accelerate the development of efficient strategies for identifying causal factors of complex diseases.
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Affiliation(s)
- Leeyoung Park
- Natural Science Research Institute, Yonsei University, Seoul, Korea 120-749
| | - Ju H Kim
- Seoul National University Biomedical Informatics (SNUBI), Seoul National University College of Medicine, Seoul 110-799, Korea Systems Biomedical Informatics National Core Research Center (SBI-NCRC), Seoul National University College of Medicine, Seoul 110-799, Korea
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32
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Sullivan PF, Posthuma D. Biological pathways and networks implicated in psychiatric disorders. Curr Opin Behav Sci 2015. [DOI: 10.1016/j.cobeha.2014.09.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Drogemöller BI, Niehaus DJH, Chiliza B, van der Merwe L, Asmal L, Malhotra AK, Wright GEB, Emsley R, Warnich L. Patterns of variation influencing antipsychotic treatment outcomes in South African first-episode schizophrenia patients. Pharmacogenomics 2015; 15:189-99. [PMID: 24444409 DOI: 10.2217/pgs.13.218] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
AIM Many antipsychotic pharmacogenetics studies have been performed examining candidate genes or known variation; however, our understanding of the genetic factors involved in antipsychotic pharmacogenetic traits remains limited. MATERIALS & METHODS A well-characterized cohort of first-episode schizophrenia (FES) patients was used to identify a subset of nonresponders and responders to antipsychotic treatment for exome sequencing (n = 11). The variation observed in the responders and nonresponders was subsequently compared and a prioritization strategy was employed to identify variants for genotyping in the entire FES cohort (n = 103) as well as an additional Xhosa schizophrenia cohort (n = 222). RESULTS Examination of coding variation revealed a potential role for rare loss-of-function variants in treatment response outcomes. One variant, rs11368509, was found to be weakly associated with better treatment outcomes in the FES cohort (p = 0.057) and the Xhosa schizophrenia cohort (p = 0.016). In addition, the majority of the loss-of-function variation that was considered likely to be involved in antipsychotic treatment response was either novel or rare in Asian and European populations. CONCLUSION This pilot study has highlighted the importance of exome sequencing for antipsychotic pharmacogenomics studies, particularly in African individuals. Furthermore, the results emphasize once again the complexity of antipsychotic pharmacogenomics and the need for future research.
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Affiliation(s)
- Britt I Drogemöller
- Department of Genetics, Stellenbosch University, Private Bag XI, Matieland, 7602, Western Cape, South Africa
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Li J, Jiang Y, Wang T, Chen H, Xie Q, Shao Q, Ran X, Xia K, Sun ZS, Wu J. mirTrios: an integrated pipeline for detection of de novo and rare inherited mutations from trios-based next-generation sequencing. J Med Genet 2015; 52:275-81. [PMID: 25596308 DOI: 10.1136/jmedgenet-2014-102656] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVES Recently, several studies documented that de novo mutations (DNMs) play important roles in the aetiology of sporadic diseases. Next-generation sequencing (NGS) enables variant calling at single-base resolution on a genome-wide scale. However, accurate identification of DNMs from NGS data still remains a major challenge. We developed mirTrios, a web server, to accurately detect DNMs and rare inherited mutations from NGS data in sporadic diseases. METHODS The expectation-maximisation (EM) model was adopted to accurately identify DNMs from variant call files of a trio generated by GATK (Genome Analysis Toolkit). The GATK results, which contain certain basic properties (such as PL, PRT and PART), are iteratively integrated into the EM model to strike a threshold for DNMs detection. Training sets of true and false positive DNMs in the EM model were built from whole genome sequencing data of 64 trios. RESULTS With our in-house whole exome sequencing datasets from 20 trios, mirTrios totally identified 27 DNMs in the coding region, 25 of which (92.6%) are validated as true positives. In addition, to facilitate the interpretation of diverse mutations, mirTrios can also be employed in the identification of rare inherited mutations. Embedded with abundant annotation of DNMs and rare inherited mutations, mirTrios also supports known diagnostic variants and causative gene identification, as well as the prioritisation of novel and promising candidate genes. CONCLUSIONS mirTrios provides an intuitive interface for the general geneticist and clinician, and can be widely used for detection of DNMs and rare inherited mutations, and annotation in sporadic diseases. mirTrios is freely available at http://centre.bioinformatics.zj.cn/mirTrios/.
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Affiliation(s)
- Jinchen Li
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China State Key Laboratory of Medical Genetics, Central South University, Changsha, China
| | - Yi Jiang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Tao Wang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Huiqian Chen
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Qing Xie
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Qianzhi Shao
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Xia Ran
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Kun Xia
- State Key Laboratory of Medical Genetics, Central South University, Changsha, China
| | - Zhong Sheng Sun
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Jinyu Wu
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
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De novo FUS mutations in 2 Korean patients with sporadic amyotrophic lateral sclerosis. Neurobiol Aging 2014; 36:1604.e17-9. [PMID: 25457557 DOI: 10.1016/j.neurobiolaging.2014.10.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 10/05/2014] [Indexed: 12/14/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is an adult-onset neurodegenerative disorder. Approximately 5% of ALS patients are familial (fALS) cases, and the remaining 95% are apparently sporadic (sALS) cases. To date, a number of genes have been discovered as associated with ALS, but the genetic background of sALS is not yet fully understood. The occurrence of de novo mutations in ALS genes might be an explanation for sALS, but reduced penetrance could be an alternative theory. Previously, we screened mutations in 5 ALS genes including SOD1 and FUS in 9 fALS and 249 sALS patients and found a total of 15 patients with either SOD1 (7 fALS and 3 sALS) or FUS (1 fALS and 4 sALS) mutations. Interestingly, only 1 fALS patient had the FUS mutation, whereas 4 sALS patients had mutations in this gene. To determine if the FUS mutations in sALS were de novo, we performed genetic analysis on 2 sALS patients with living parents. Genetic analysis confirmed that 2 FUS mutations, including the c.1483C>T (p.Arg495*) and the c.1509_1510delAG (p.Gly504Trpfs*12) mutations, were found only in the patients and not in their parents, confirming the de novo occurrence of these mutations. These findings support the notion that de novo mutations are responsible for a certain proportion of sALS.
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Balan S, Iwayama Y, Maekawa M, Toyota T, Ohnishi T, Toyoshima M, Shimamoto C, Esaki K, Yamada K, Iwata Y, Suzuki K, Ide M, Ota M, Fukuchi S, Tsujii M, Mori N, Shinkai Y, Yoshikawa T. Exon resequencing of H3K9 methyltransferase complex genes, EHMT1, EHTM2 and WIZ, in Japanese autism subjects. Mol Autism 2014; 5:49. [PMID: 25400900 PMCID: PMC4233047 DOI: 10.1186/2040-2392-5-49] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 09/23/2014] [Indexed: 12/21/2022] Open
Abstract
Background Histone H3 methylation at lysine 9 (H3K9) is a conserved epigenetic signal, mediating heterochromatin formation by trimethylation, and transcriptional silencing by dimethylation. Defective GLP (Ehmt1) and G9a (Ehmt2) histone lysine methyltransferases, involved in mono and dimethylation of H3K9, confer autistic phenotypes and behavioral abnormalities in animal models. Moreover, EHMT1 loss of function results in Kleefstra syndrome, characterized by severe intellectual disability, developmental delays and psychiatric disorders. We examined the possible role of histone methyltransferases in the etiology of autism spectrum disorders (ASD) and suggest that rare functional variants in these genes that regulate H3K9 methylation may be associated with ASD. Methods Since G9a-GLP-Wiz forms a heteromeric methyltransferase complex, all the protein-coding regions and exon/intron boundaries of EHMT1, EHMT2 and WIZ were sequenced in Japanese ASD subjects. The detected variants were prioritized based on novelty and functionality. The expression levels of these genes were tested in blood cells and postmortem brain samples from ASD and control subjects. Expression of EHMT1 and EHMT2 isoforms were determined by digital PCR. Results We identified six nonsynonymous variants: three in EHMT1, two in EHMT2 and one in WIZ. Two variants, the EHMT1 ankyrin repeat domain (Lys968Arg) and EHMT2 SET domain (Thr961Ile) variants were present exclusively in cases, but showed no statistically significant association with ASD. The EHMT2 transcript expression was significantly elevated in the peripheral blood cells of ASD when compared with control samples; but not for EHMT1 and WIZ. Gene expression levels of EHMT1, EHMT2 and WIZ in Brodmann area (BA) 9, BA21, BA40 and the dorsal raphe nucleus (DoRN) regions from postmortem brain samples showed no significant changes between ASD and control subjects. Nor did expression levels of EHMT1 and EHMT2 isoforms in the prefrontal cortex differ significantly between ASD and control groups. Conclusions We identified two novel rare missense variants in the EHMT1 and EHMT2 genes of ASD patients. We surmise that these variants alone may not be sufficient to exert a significant effect on ASD pathogenesis. The elevated expression of EHMT2 in the peripheral blood cells may support the notion of a restrictive chromatin state in ASD, similar to schizophrenia. Electronic supplementary material The online version of this article (doi:10.1186/2040-2392-5-49) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shabeesh Balan
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198 Japan
| | - Yoshimi Iwayama
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198 Japan
| | - Motoko Maekawa
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198 Japan
| | - Tomoko Toyota
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198 Japan
| | - Tetsuo Ohnishi
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198 Japan
| | - Manabu Toyoshima
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198 Japan
| | - Chie Shimamoto
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198 Japan
| | - Kayoko Esaki
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198 Japan
| | - Kazuo Yamada
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198 Japan
| | - Yasuhide Iwata
- Department of Psychiatry and Neurology, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Katsuaki Suzuki
- Department of Psychiatry and Neurology, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Masayuki Ide
- Department of Psychiatry, Division of Clinical Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Motonori Ota
- Graduate School of Information Science, Nagoya University, Nagoya, Aichi, Japan
| | - Satoshi Fukuchi
- Faculty of Engineering, Maebashi Institute of Technology, Maebashi, Japan
| | - Masatsugu Tsujii
- Faculty of Sociology, Chukyo University, Chukyo, Aichi, Japan ; Research Center for Child Mental Development, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Norio Mori
- Department of Psychiatry and Neurology, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan ; Research Center for Child Mental Development, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Yoichi Shinkai
- Cellular Memory Laboratory, RIKEN, Wako, Saitama, Japan ; CREST (Core Research for Evolutionary Science and Technology), Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Takeo Yoshikawa
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198 Japan ; CREST (Core Research for Evolutionary Science and Technology), Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
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Wray NR, Lee SH, Mehta D, Vinkhuyzen AAE, Dudbridge F, Middeldorp CM. Research review: Polygenic methods and their application to psychiatric traits. J Child Psychol Psychiatry 2014; 55:1068-87. [PMID: 25132410 DOI: 10.1111/jcpp.12295] [Citation(s) in RCA: 454] [Impact Index Per Article: 45.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/13/2014] [Indexed: 12/18/2022]
Abstract
BACKGROUND Despite evidence from twin and family studies for an important contribution of genetic factors to both childhood and adult onset psychiatric disorders, identifying robustly associated specific DNA variants has proved challenging. In the pregenomics era the genetic architecture (number, frequency and effect size of risk variants) of complex genetic disorders was unknown. Empirical evidence for the genetic architecture of psychiatric disorders is emerging from the genetic studies of the last 5 years. METHODS AND SCOPE We review the methods investigating the polygenic nature of complex disorders. We provide mini-guides to genomic profile (or polygenic) risk scoring and to estimation of variance (or heritability) from common SNPs; a glossary of key terms is also provided. We review results of applications of the methods to psychiatric disorders and related traits and consider how these methods inform on missing heritability, hidden heritability and still-missing heritability. FINDINGS Genome-wide genotyping and sequencing studies are providing evidence that psychiatric disorders are truly polygenic, that is they have a genetic architecture of many genetic variants, including risk variants that are both common and rare in the population. Sample sizes published to date are mostly underpowered to detect effect sizes of the magnitude presented by nature, and these effect sizes may be constrained by the biological validity of the diagnostic constructs. CONCLUSIONS Increasing the sample size for genome wide association studies of psychiatric disorders will lead to the identification of more associated genetic variants, as already found for schizophrenia. These loci provide the starting point of functional analyses that might eventually lead to new prevention and treatment options and to improved biological validity of diagnostic constructs. Polygenic analyses will contribute further to our understanding of complex genetic traits as sample sizes increase and as sample resources become richer in phenotypic descriptors, both in terms of clinical symptoms and of nongenetic risk factors.
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Affiliation(s)
- Naomi R Wray
- Queensland Brain Institute, The University of Queensland, St Lucia, Qld, Australia
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Genetic Basis of Complex Genetic Disease: The Contribution of Disease Heterogeneity to Missing Heritability. CURR EPIDEMIOL REP 2014. [DOI: 10.1007/s40471-014-0023-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Abstract
INTRODUCTION Next-generation sequencing (NGS) is transforming the conduct of genetic research and diagnostic investigation. This creates new challenges as it generates additional information, including unsought and unwanted information. Nevertheless, this information must be deliberately managed-interpreted, disclosed and then either stored or destroyed. AREAS OF AGREEMENT Handling the process of consent to exome or genome sequencing should include discussion about the possible detection of variants of uncertain significance (VUSs) or incidental findings (IFs) that the patient may prefer not to hear about. A plan should be drawn up that specifies whether and how the patient would be recontacted in the future with new interpretations. AREAS OF CONTROVERSY There is an active debate about which IFs or VUSs should be disclosed to the patient when an exome or genome sequence has been performed, or whether all findings of any possible relevance should always be disclosed. How this is managed has important implications for the initial explanation of the test to the patient and the process of consent. The assumption is often made that all sequence information should be stored, but this may not be sustainable or useful. GROWING POINTS Efforts are being made to build a consensus on what 'incidental' information should be disclosed. These policy questions are being addressed in many centres and practices are evolving rapidly. AREAS TIMELY FOR DEVELOPING RESEARCH Those interested in genetics, public health, bioethics and medical ethics may wish to debate these issues and influence future practice in both genetic research and genetic diagnostic services.
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Affiliation(s)
- Angus J Clarke
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XW, UK
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Shen J, Lincoln S, Miller DT. Advances in Genetic Discovery and Implications for Counseling of Patients and Families with Autism Spectrum Disorders. CURRENT GENETIC MEDICINE REPORTS 2014; 2:124-134. [PMID: 30345165 PMCID: PMC6192539 DOI: 10.1007/s40142-014-0047-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The prevalence of autism spectrum disorders (ASD) continues to increase. Genetic factors play an important role in the etiology of ASD, although specific genetic causes are identified in only a minority of cases. Recent advances have accelerated the discovery of genes implicated in ASD through convergent genomic analysis of genome-wide association studies, chromosomal microarray, exome sequencing, genome sequencing, and gene networks. Hundreds of candidate genes for ASD have been reported, yet only a handful have proven causative. Symptoms are complex and highly variable, and most cases are likely due to cumulative genetic factors, the interactions among them, as well as environmental factors. Here we summarize recent findings in genomic research regarding discovery of candidate genes, describe the major molecular processes in neural development that may be disrupted in ASD, and discuss the implication of research findings in clinical genetic diagnostic testing and counseling. Continued advances in genetic research will eventually translate into innovative approaches to prevention and treatment of ASD.
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Affiliation(s)
- Jun Shen
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115
- Harvard Medical School, Boston, MA 02115
| | - Sharyn Lincoln
- Division of Genetics, Boston Children's Hospital, Boston, MA 02115
| | - David T Miller
- Harvard Medical School, Boston, MA 02115
- Division of Genetics, Boston Children's Hospital, Boston, MA 02115
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Sundquist J, Sundquist K, Ji J. Autism and attention-deficit/hyperactivity disorder among individuals with a family history of alcohol use disorders. eLife 2014; 3:e02917. [PMID: 25139954 PMCID: PMC4135348 DOI: 10.7554/elife.02917] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Recent studies suggest de novo mutations may involve the pathogenesis of autism and attention-deficit/hyperactivity disorder (ADHD). Based on the evidence that excessive alcohol consumption may be associated with an increased rate of de novo mutations in germ cells (sperms or eggs), we examine here whether the risks of autism and ADHD are increased among individuals with a family history of alcohol use disorders (AUDs). The standardized incidence ratios (SIRs) of autism and ADHD among individuals with a biological parental history of AUDs were 1.39 (95% CI 1.34–1.44) and 2.19 (95% CI 2.15–2.23), respectively, compared to individuals without an affected parent. Among offspring whose parents were diagnosed with AUDs before their birth, the corresponding risks were 1.46 (95% CI 1.36–1.58) and 2.70 (95% CI 2.59–2.81), respectively. Our study calls for extra surveillance for children with a family history of AUDs, and further studies examining the underlying mechanisms are needed. DOI:http://dx.doi.org/10.7554/eLife.02917.001 Children learn to talk, manage their emotions, and control their behavior in a period when the brain is developing rapidly. The first signs of several developmental disorders, such as autism and attention-deficit/hyperactivity disorder (ADHD), may also emerge during this period. Children with autism may have difficulties with social interactions and communication, while those with attention-deficit/hyperactivity disorder may struggle to pay attention to a task and may be more active than other children. Autism or ADHD are diagnosed based on the child's behavior because the underlying causes of the disorders are not well understood. Both genes and the environment have been linked to the conditions; and it was recently suggested that certain common genetic mutations are more common in children with ADHD or autism. However, as some of the mutations linked to autism are not found in the genes of the affected children's parents, it is likely that they occurred in either of the sperm or the egg cell from the parents. Exposure to harmful substances in the environment can cause mutations in egg or sperm cells, or alter the expression of genes without changing the gene sequence. Excessive alcohol consumption is one environmental factor that can mutate genes or alter gene expression. Here, Sundquist et al. have looked to see if there is a relationship between a child having a parent with an alcohol use problem and the child's risk of developing autism or ADHD. Examining national medical registries identified 24,157 people with autism and 49,348 with ADHD in Sweden between 1987 and 2010. Sundquist et al. discovered that autism and ADHD were more common in individuals who had a parent with a history of an alcohol use disorder than in those whose parents had no history of an alcohol use disorder. There was also an even greater risk of either condition if the parent had been diagnosed with an alcohol use problem before the birth of the child. Adopted children who had a biological parent with an alcohol use disorder were at a greater risk of autism and ADHD than those whose adoptive parent had an alcohol use disorder. However, as very few adopted parents were diagnosed with an alcohol use problem, it is important to be cautious about drawing firm conclusions from this observation. Sundquist et al. estimate that around 4% of autism cases and 11% of ADHD cases could be avoided if parents abstained from heavy alcohol consumption. Though these findings are consistent with parents with an alcohol use disorder being more likely to pass on mutations to their children, there are also other possible explanations. As such, further research examining the underlying cause is still needed. DOI:http://dx.doi.org/10.7554/eLife.02917.002
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Affiliation(s)
- Jan Sundquist
- Center for Primary Health Care Research, Lund University, Malmö, Sweden Stanford Prevention Research Center, Stanford University School of Medicine, Stanford, United States
| | - Kristina Sundquist
- Center for Primary Health Care Research, Lund University, Malmö, Sweden Stanford Prevention Research Center, Stanford University School of Medicine, Stanford, United States
| | - Jianguang Ji
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
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Bahlo M, Tankard R, Lukic V, Oliver KL, Smith KR. Using familial information for variant filtering in high-throughput sequencing studies. Hum Genet 2014; 133:1331-41. [PMID: 25129038 PMCID: PMC4185103 DOI: 10.1007/s00439-014-1479-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 08/07/2014] [Indexed: 12/30/2022]
Abstract
High-throughput sequencing studies (HTS) have been highly successful in identifying the genetic causes of human disease, particularly those following Mendelian inheritance. Many HTS studies to date have been performed without utilizing available family relationships between samples. Here, we discuss the many merits and occasional pitfalls of using identity by descent information in conjunction with HTS studies. These methods are not only applicable to family studies but are also useful in cohorts of apparently unrelated, ‘sporadic’ cases and small families underpowered for linkage and allow inference of relationships between individuals. Incorporating familial/pedigree information not only provides powerful filtering options for the extensive variant lists that are usually produced by HTS but also allows valuable quality control checks, insights into the genetic model and the genotypic status of individuals of interest. In particular, these methods are valuable for challenging discovery scenarios in HTS analysis, such as in the study of populations poorly represented in variant databases typically used for filtering, and in the case of poor-quality HTS data.
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Affiliation(s)
- Melanie Bahlo
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia,
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Common DNA methylation alterations in multiple brain regions in autism. Mol Psychiatry 2014; 19:862-71. [PMID: 23999529 PMCID: PMC4184909 DOI: 10.1038/mp.2013.114] [Citation(s) in RCA: 221] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2013] [Revised: 07/03/2013] [Accepted: 07/25/2013] [Indexed: 12/13/2022]
Abstract
Autism spectrum disorders (ASD) are increasingly common neurodevelopmental disorders defined clinically by a triad of features including impairment in social interaction, impairment in communication in social situations and restricted and repetitive patterns of behavior and interests, with considerable phenotypic heterogeneity among individuals. Although heritability estimates for ASD are high, conventional genetic-based efforts to identify genes involved in ASD have yielded only few reproducible candidate genes that account for only a small proportion of ASDs. There is mounting evidence to suggest environmental and epigenetic factors play a stronger role in the etiology of ASD than previously thought. To begin to understand the contribution of epigenetics to ASD, we have examined DNA methylation (DNAm) in a pilot study of postmortem brain tissue from 19 autism cases and 21 unrelated controls, among three brain regions including dorsolateral prefrontal cortex, temporal cortex and cerebellum. We measured over 485,000 CpG loci across a diverse set of functionally relevant genomic regions using the Infinium HumanMethylation450 BeadChip and identified four genome-wide significant differentially methylated regions (DMRs) using a bump hunting approach and a permutation-based multiple testing correction method. We replicated 3/4 DMRs identified in our genome-wide screen in a different set of samples and across different brain regions. The DMRs identified in this study represent suggestive evidence for commonly altered methylation sites in ASD and provide several promising new candidate genes.
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Whole-genome sequence variation, population structure and demographic history of the Dutch population. Nat Genet 2014; 46:818-25. [PMID: 24974849 DOI: 10.1038/ng.3021] [Citation(s) in RCA: 486] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 06/06/2014] [Indexed: 12/16/2022]
Abstract
Whole-genome sequencing enables complete characterization of genetic variation, but geographic clustering of rare alleles demands many diverse populations be studied. Here we describe the Genome of the Netherlands (GoNL) Project, in which we sequenced the whole genomes of 250 Dutch parent-offspring families and constructed a haplotype map of 20.4 million single-nucleotide variants and 1.2 million insertions and deletions. The intermediate coverage (∼13×) and trio design enabled extensive characterization of structural variation, including midsize events (30-500 bp) previously poorly catalogued and de novo mutations. We demonstrate that the quality of the haplotypes boosts imputation accuracy in independent samples, especially for lower frequency alleles. Population genetic analyses demonstrate fine-scale structure across the country and support multiple ancient migrations, consistent with historical changes in sea level and flooding. The GoNL Project illustrates how single-population whole-genome sequencing can provide detailed characterization of genetic variation and may guide the design of future population studies.
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Hansen FH, Skjørringe T, Yasmeen S, Arends NV, Sahai MA, Erreger K, Andreassen TF, Holy M, Hamilton PJ, Neergheen V, Karlsborg M, Newman AH, Pope S, Heales SJR, Friberg L, Law I, Pinborg LH, Sitte HH, Loland C, Shi L, Weinstein H, Galli A, Hjermind LE, Møller LB, Gether U. Missense dopamine transporter mutations associate with adult parkinsonism and ADHD. J Clin Invest 2014; 124:3107-20. [PMID: 24911152 DOI: 10.1172/jci73778] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 04/24/2014] [Indexed: 11/17/2022] Open
Abstract
Parkinsonism and attention deficit hyperactivity disorder (ADHD) are widespread brain disorders that involve disturbances of dopaminergic signaling. The sodium-coupled dopamine transporter (DAT) controls dopamine homeostasis, but its contribution to disease remains poorly understood. Here, we analyzed a cohort of patients with atypical movement disorder and identified 2 DAT coding variants, DAT-Ile312Phe and a presumed de novo mutant DAT-Asp421Asn, in an adult male with early-onset parkinsonism and ADHD. According to DAT single-photon emission computed tomography (DAT-SPECT) scans and a fluoro-deoxy-glucose-PET/MRI (FDG-PET/MRI) scan, the patient suffered from progressive dopaminergic neurodegeneration. In heterologous cells, both DAT variants exhibited markedly reduced dopamine uptake capacity but preserved membrane targeting, consistent with impaired catalytic activity. Computational simulations and uptake experiments suggested that the disrupted function of the DAT-Asp421Asn mutant is the result of compromised sodium binding, in agreement with Asp421 coordinating sodium at the second sodium site. For DAT-Asp421Asn, substrate efflux experiments revealed a constitutive, anomalous efflux of dopamine, and electrophysiological analyses identified a large cation leak that might further perturb dopaminergic neurotransmission. Our results link specific DAT missense mutations to neurodegenerative early-onset parkinsonism. Moreover, the neuropsychiatric comorbidity provides additional support for the idea that DAT missense mutations are an ADHD risk factor and suggests that complex DAT genotype and phenotype correlations contribute to different dopaminergic pathologies.
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Gratten J, Wray NR, Keller MC, Visscher PM. Large-scale genomics unveils the genetic architecture of psychiatric disorders. Nat Neurosci 2014; 17:782-90. [PMID: 24866044 DOI: 10.1038/nn.3708] [Citation(s) in RCA: 286] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 03/27/2014] [Indexed: 12/11/2022]
Abstract
Family study results are consistent with genetic effects making substantial contributions to risk of psychiatric disorders such as schizophrenia, yet robust identification of specific genetic variants that explain variation in population risk had been disappointing until the advent of technologies that assay the entire genome in large samples. We highlight recent progress that has led to a better understanding of the number of risk variants in the population and the interaction of allele frequency and effect size. The emerging genetic architecture implies a large number of contributing loci (that is, a high genome-wide mutational target) and suggests that genetic risk of psychiatric disorders involves the combined effects of many common variants of small effect, as well as rare and de novo variants of large effect. The capture of a substantial proportion of genetic risk facilitates new study designs to investigate the combined effects of genes and the environment.
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Affiliation(s)
- Jacob Gratten
- 1] Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia. [2] These authors contributed equally to this work
| | - Naomi R Wray
- 1] Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia. [2] These authors contributed equally to this work
| | - Matthew C Keller
- 1] Department of Psychology and Neuroscience, University of Colorado, Boulder, Colorado, USA. [2] These authors contributed equally to this work
| | - Peter M Visscher
- 1] Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia. [2] The Translational Research Institute, University of Queensland Diamantina Institute, Brisbane, Queensland, Australia. [3] These authors contributed equally to this work
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Brain-expressed exons under purifying selection are enriched for de novo mutations in autism spectrum disorder. Nat Genet 2014; 46:742-7. [PMID: 24859339 DOI: 10.1038/ng.2980] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 04/10/2014] [Indexed: 02/08/2023]
Abstract
A universal challenge in genetic studies of autism spectrum disorders (ASDs) is determining whether a given DNA sequence alteration will manifest as disease. Among different population controls, we observed, for specific exons, an inverse correlation between exon expression level in brain and burden of rare missense mutations. For genes that harbor de novo mutations predicted to be deleterious, we found that specific critical exons were significantly enriched in individuals with ASD relative to their siblings without ASD (P < 1.13 × 10(-38); odds ratio (OR) = 2.40). Furthermore, our analysis of genes with high exonic expression in brain and low burden of rare mutations demonstrated enrichment for known ASD-associated genes (P < 3.40 × 10(-11); OR = 6.08) and ASD-relevant fragile-X protein targets (P < 2.91 × 10(-157); OR = 9.52). Our results suggest that brain-expressed exons under purifying selection should be prioritized in genotype-phenotype studies for ASD and related neurodevelopmental conditions.
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Marioni RE, Penke L, Davies G, Huffman JE, Hayward C, Deary IJ. The total burden of rare, non-synonymous exome genetic variants is not associated with childhood or late-life cognitive ability. Proc Biol Sci 2014; 281:20140117. [PMID: 24573858 PMCID: PMC3953855 DOI: 10.1098/rspb.2014.0117] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 01/27/2014] [Indexed: 11/22/2022] Open
Abstract
Human cognitive ability shows consistent, positive associations with fitness components across the life-course. Underlying genetic variation should therefore be depleted by selection, which is not observed. Genetic variation in general cognitive ability (intelligence) could be maintained by a mutation-selection balance, with rare variants contributing to its genetic architecture. This study examines the association between the total number of rare stop-gain/loss, splice and missense exonic variants and cognitive ability in childhood and old age in the same individuals. Exome array data were obtained in the Lothian Birth Cohorts of 1921 and 1936 (combined N = 1596). General cognitive ability was assessed at age 11 years and in late life (79 and 70 years, respectively) and was modelled against the total number of stop-gain/loss, splice, and missense exonic variants, with minor allele frequency less than or equal to 0.01, using linear regression adjusted for age and sex. In both cohorts and in both the childhood and late-life models, there were no significant associations between rare variant burden in the exome and cognitive ability that survived correction for multiple testing. Contrary to our a priori hypothesis, we observed no evidence for an association between the total number of rare exonic variants and either childhood cognitive ability or late-life cognitive ability.
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Affiliation(s)
- Riccardo E. Marioni
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh EH8 9JZ, UK
| | - Lars Penke
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh EH8 9JZ, UK
- Institute of Psychology, Georg August University Göttingen, Goßlerstr. 14, Göttingen 37073, Germany
| | - Gail Davies
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh EH8 9JZ, UK
- Medical Genetics Section, Centre for Genomics and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Jennifer E. Huffman
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Ian J. Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh EH8 9JZ, UK
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Reading and language disorders: the importance of both quantity and quality. Genes (Basel) 2014; 5:285-309. [PMID: 24705331 PMCID: PMC4094934 DOI: 10.3390/genes5020285] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 03/11/2014] [Accepted: 03/12/2014] [Indexed: 01/25/2023] Open
Abstract
Reading and language disorders are common childhood conditions that often co-occur with each other and with other neurodevelopmental impairments. There is strong evidence that disorders, such as dyslexia and Specific Language Impairment (SLI), have a genetic basis, but we expect the contributing genetic factors to be complex in nature. To date, only a few genes have been implicated in these traits. Their functional characterization has provided novel insight into the biology of neurodevelopmental disorders. However, the lack of biological markers and clear diagnostic criteria have prevented the collection of the large sample sizes required for well-powered genome-wide screens. One of the main challenges of the field will be to combine careful clinical assessment with high throughput genetic technologies within multidisciplinary collaborations.
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50
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Robinson MR, Wray NR, Visscher PM. Explaining additional genetic variation in complex traits. Trends Genet 2014; 30:124-32. [PMID: 24629526 DOI: 10.1016/j.tig.2014.02.003] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 02/10/2014] [Accepted: 02/12/2014] [Indexed: 12/11/2022]
Abstract
Genome-wide association studies (GWAS) have provided valuable insights into the genetic basis of complex traits, discovering >6000 variants associated with >500 quantitative traits and common complex diseases in humans. The associations identified so far represent only a fraction of those that influence phenotype, because there are likely to be many variants across the entire frequency spectrum, each of which influences multiple traits, with only a small average contribution to the phenotypic variance. This presents a considerable challenge to further dissection of the remaining unexplained genetic variance within populations, which limits our ability to predict disease risk, identify new drug targets, improve and maintain food sources, and understand natural diversity. This challenge will be met within the current framework through larger sample size, better phenotyping, including recording of nongenetic risk factors, focused study designs, and an integration of multiple sources of phenotypic and genetic information. The current evidence supports the application of quantitative genetic approaches, and we argue that one should retain simpler theories until simplicity can be traded for greater explanatory power.
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Affiliation(s)
- Matthew R Robinson
- The Queensland Brain Institute, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Naomi R Wray
- The Queensland Brain Institute, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Peter M Visscher
- The Queensland Brain Institute, The University of Queensland, St Lucia, QLD 4072, Australia; The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia.
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