151
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Bellott DW, Page DC. Dosage-sensitive functions in embryonic development drove the survival of genes on sex-specific chromosomes in snakes, birds, and mammals. Genome Res 2021; 31:198-210. [PMID: 33479023 PMCID: PMC7849413 DOI: 10.1101/gr.268516.120] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/04/2020] [Indexed: 12/18/2022]
Abstract
Different ancestral autosomes independently evolved into sex chromosomes in snakes, birds, and mammals. In snakes and birds, females are ZW and males are ZZ; in mammals, females are XX and males are XY. Although X and Z Chromosomes retain nearly all ancestral genes, sex-specific W and Y Chromosomes suffered extensive genetic decay. In both birds and mammals, the genes that survived on sex-specific chromosomes are enriched for broadly expressed, dosage-sensitive regulators of gene expression, subject to strong purifying selection. To gain deeper insight into the processes that govern survival on sex-specific chromosomes, we carried out a meta-analysis of survival across 41 species-three snakes, 24 birds, and 14 mammals-doubling the number of ancestral genes under investigation and increasing our power to detect enrichments among survivors relative to nonsurvivors. Of 2564 ancestral genes, representing an eighth of the ancestral amniote genome, only 324 survive on present-day sex-specific chromosomes. Survivors are enriched for dosage-sensitive developmental processes, particularly development of neural crest-derived structures, such as the face. However, there was no enrichment for expression in sex-specific tissues, involvement in sex determination or gonadogenesis pathways, or conserved sex-biased expression. Broad expression and dosage sensitivity contributed independently to gene survival, suggesting that pleiotropy imposes additional constraints on the evolution of dosage compensation. We propose that maintaining the viability of the heterogametic sex drove gene survival on amniote sex-specific chromosomes, and that subtle modulation of the expression of survivor genes and their autosomal orthologs has disproportionately large effects on development and disease.
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Affiliation(s)
| | - David C Page
- Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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152
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Shi P, Xia Y, Li Q, Kong X. Usefulness of copy number variant detection following monogenic disease exclusion in prenatal diagnosis. J Obstet Gynaecol Res 2021; 47:1002-1008. [PMID: 33474820 PMCID: PMC7986431 DOI: 10.1111/jog.14627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/13/2020] [Accepted: 12/12/2020] [Indexed: 12/01/2022]
Abstract
Aim Families with an adverse history of monogenic disease focus on single‐gene diagnosis instead of low‐depth whole‐genome sequence, during subsequent pregnancies. The aim of this study was to assess the potential usefulness of low‐depth whole‐genome sequencing (copy number variant sequencing [CNV‐seq]) detection following monogenic disease exclusion in prenatal diagnosis. Methods A total of 285 families with a history of monogenic disease (of 41 different types; eliminated during the current pregnancy) were recruited and retrospectively analyzed. Low‐depth whole‐genome sequencing (CNV‐Seq, Next‐Seq CN500 platform) was performed for all fetuses. Results The CNV detection results of the 285 samples were as follows: one case of 18‐trisomy chimera (0.35%), one case of pathogenic 3q29 microdeletion syndrome CNV (0.35%), four cases of variant of uncertain significance (VUS) CNVs (1.40%), and four cases of Duchenne muscular dystrophy (DMD) carriers (1.40%); and the remaining samples were normal (96.15%). Of note, 2/285 (0.70%) samples still exhibited pathogenic abnormalities. All positive samples were followed up where the two cases of pathogenic abnormalities elected the pregnancy termination, while the four VUS cases and four DMD‐carrier cases were born healthy. Conclusion In cases where prenatal fetal monogenic disease has been ruled out, CNV detection is still beneficial and should be performed to prevent missed pathogenic CNVs. However, the costs need to be balanced against benefits, and the research will need to assess other types of testing.
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Affiliation(s)
- Panlai Shi
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yanjie Xia
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qianqian Li
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiangdong Kong
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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153
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Leonardi E, Bettella E, Pelizza MF, Aspromonte MC, Polli R, Boniver C, Sartori S, Milani D, Murgia A. Identification of SETBP1 Mutations by Gene Panel Sequencing in Individuals With Intellectual Disability or With "Developmental and Epileptic Encephalopathy". Front Neurol 2021; 11:593446. [PMID: 33391157 PMCID: PMC7772201 DOI: 10.3389/fneur.2020.593446] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/16/2020] [Indexed: 11/17/2022] Open
Abstract
SETBP1 mutations are associated with the Schinzel-Giedion syndrome (SGS), characterized by profound neurodevelopmental delay, typical facial features, and multiple congenital malformations (OMIM 269150). Refractory epilepsy is a common feature of SGS. Loss of function mutations have been typically associated with a distinct and milder phenotype characterized by intellectual disability and expressive speech impairment. Here we report three variants of SETBP1, two novel de novo truncating mutations, identified by NGS analysis of an Intellectual Disability gene panel in 600 subjects with non-specific neurodevelopmental disorders, and one missense identified by a developmental epilepsy gene panel tested in 56 pediatric epileptic cases. The three individuals carrying the identified SETBP1 variants presented mild to severe developmental delay and lacked the cardinal features of classical SGS. One of these subjects, carrying the c.1765C>T (p.Arg589*) mutation, had mild Intellectual Disability with speech delay; the second one carrying the c.2199_2203del (p.Glu734Alafs19*) mutation had generalized epilepsy, responsive to treatment, and moderate Intellectual Disability; the third patient showed a severe cognitive defects and had a history of drug resistant epilepsy with West syndrome evolved into a Lennox-Gastaut syndrome. This latter subject carries the missense c.2572G>A (p.Glu858Lys) variant, which is absent from the control population, reported as de novo in a subject with ASD, and located close to the SETBP1 hot spot for SGS-associated mutations. Our findings contribute to further characterizing the associated phenotypes and suggest inclusion of SETBP1 in the list of prioritized genes for the genetic diagnosis of overlapping phenotypes ranging from non-specific neurodevelopmental disorders to “developmental and epileptic encephalopathy” (DEE).
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Affiliation(s)
- Emanuela Leonardi
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, Padua, Italy.,Fondazione Istituto di Ricerca Pediatrica (IRP), Città Della Speranza, Padua, Italy
| | - Elisa Bettella
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, Padua, Italy.,Fondazione Istituto di Ricerca Pediatrica (IRP), Città Della Speranza, Padua, Italy
| | - Maria Federica Pelizza
- Paediatric Neurology and Neurophysiology Unit, Department of Woman and Child Health, University Hospital of Padova, Padua, Italy
| | - Maria Cristina Aspromonte
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, Padua, Italy.,Fondazione Istituto di Ricerca Pediatrica (IRP), Città Della Speranza, Padua, Italy
| | - Roberta Polli
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, Padua, Italy.,Fondazione Istituto di Ricerca Pediatrica (IRP), Città Della Speranza, Padua, Italy
| | - Clementina Boniver
- Paediatric Neurology and Neurophysiology Unit, Department of Woman and Child Health, University Hospital of Padova, Padua, Italy
| | - Stefano Sartori
- Paediatric Neurology and Neurophysiology Unit, Department of Woman and Child Health, University Hospital of Padova, Padua, Italy
| | - Donatella Milani
- Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Alessandra Murgia
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, Padua, Italy.,Fondazione Istituto di Ricerca Pediatrica (IRP), Città Della Speranza, Padua, Italy
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154
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Pan YQ, Fu JH. Case Report: Clinical Description of a Patient Carrying a 12.48 Mb Microdeletion Involving the 10p13-15.3 Region. Front Pediatr 2021; 9:603666. [PMID: 33732667 PMCID: PMC7959834 DOI: 10.3389/fped.2021.603666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 01/13/2021] [Indexed: 11/13/2022] Open
Abstract
Partial deletion of 10p chromosome is a rare chromosomal aberration. Submicroscopic deletion of 10p15.3 is mainly related to cognitive deficits, speech disorders, motor delay, and hypotonia with the deleted region ranging from 0.15 to 4 Mb. The clinical phenotype is mainly determined by the ZMYND11 and DIP2C genes. Here, we report a rare case of feeding difficulties, hypocalcemia, and psychomotor retardation. Our patient has a 12.48 Mb deletion in 10p15.3-10p13, which is the second case of large 10p deletion among reported cases thus far.
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Affiliation(s)
- Yu-Qing Pan
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Jian-Hua Fu
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
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155
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Saarentaus EC, Havulinna AS, Mars N, Ahola-Olli A, Kiiskinen TTJ, Partanen J, Ruotsalainen S, Kurki M, Urpa LM, Chen L, Perola M, Salomaa V, Veijola J, Männikkö M, Hall IM, Pietiläinen O, Kaprio J, Ripatti S, Daly M, Palotie A. Polygenic burden has broader impact on health, cognition, and socioeconomic outcomes than most rare and high-risk copy number variants. Mol Psychiatry 2021; 26:4884-4895. [PMID: 33526825 PMCID: PMC8589645 DOI: 10.1038/s41380-021-01026-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 12/18/2020] [Accepted: 01/11/2021] [Indexed: 12/29/2022]
Abstract
Copy number variants (CNVs) are associated with syndromic and severe neurological and psychiatric disorders (SNPDs), such as intellectual disability, epilepsy, schizophrenia, and bipolar disorder. Although considered high-impact, CNVs are also observed in the general population. This presents a diagnostic challenge in evaluating their clinical significance. To estimate the phenotypic differences between CNV carriers and non-carriers regarding general health and well-being, we compared the impact of SNPD-associated CNVs on health, cognition, and socioeconomic phenotypes to the impact of three genome-wide polygenic risk score (PRS) in two Finnish cohorts (FINRISK, n = 23,053 and NFBC1966, n = 4895). The focus was on CNV carriers and PRS extremes who do not have an SNPD diagnosis. We identified high-risk CNVs (DECIPHER CNVs, risk gene deletions, or large [>1 Mb] CNVs) in 744 study participants (2.66%), 36 (4.8%) of whom had a diagnosed SNPD. In the remaining 708 unaffected carriers, we observed lower educational attainment (EA; OR = 0.77 [95% CI 0.66-0.89]) and lower household income (OR = 0.77 [0.66-0.89]). Income-associated CNVs also lowered household income (OR = 0.50 [0.38-0.66]), and CNVs with medical consequences lowered subjective health (OR = 0.48 [0.32-0.72]). The impact of PRSs was broader. At the lowest extreme of PRS for EA, we observed lower EA (OR = 0.31 [0.26-0.37]), lower-income (OR = 0.66 [0.57-0.77]), lower subjective health (OR = 0.72 [0.61-0.83]), and increased mortality (Cox's HR = 1.55 [1.21-1.98]). PRS for intelligence had a similar impact, whereas PRS for schizophrenia did not affect these traits. We conclude that the majority of working-age individuals carrying high-risk CNVs without SNPD diagnosis have a modest impact on morbidity and mortality, as well as the limited impact on income and educational attainment, compared to individuals at the extreme end of common genetic variation. Our findings highlight that the contribution of traditional high-risk variants such as CNVs should be analyzed in a broader genetic context, rather than evaluated in isolation.
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Affiliation(s)
- Elmo Christian Saarentaus
- grid.7737.40000 0004 0410 2071Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Aki Samuli Havulinna
- grid.7737.40000 0004 0410 2071Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland ,grid.14758.3f0000 0001 1013 0499Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Nina Mars
- grid.7737.40000 0004 0410 2071Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Ari Ahola-Olli
- grid.7737.40000 0004 0410 2071Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland ,grid.66859.34Stanley Center for Psychiatric Research, The Broad Institute of Harvard and MIT, Cambridge, MA USA ,grid.32224.350000 0004 0386 9924Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, USA
| | | | - Juulia Partanen
- grid.7737.40000 0004 0410 2071Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Sanni Ruotsalainen
- grid.7737.40000 0004 0410 2071Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Mitja Kurki
- grid.7737.40000 0004 0410 2071Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland ,grid.66859.34Stanley Center for Psychiatric Research, The Broad Institute of Harvard and MIT, Cambridge, MA USA ,grid.32224.350000 0004 0386 9924Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, USA
| | - Lea Martta Urpa
- grid.7737.40000 0004 0410 2071Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Lei Chen
- grid.47100.320000000419368710Department of Genetics, Yale School of Medicine, New Haven, CT USA ,grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO USA
| | - Markus Perola
- grid.14758.3f0000 0001 1013 0499Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Veikko Salomaa
- grid.14758.3f0000 0001 1013 0499Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Juha Veijola
- grid.10858.340000 0001 0941 4873Research Unit of Clinical Neuroscience, University of Oulu & Oulu University Hospital, Oulu, Finland
| | - Minna Männikkö
- grid.10858.340000 0001 0941 4873Northern Finland Birth Cohorts, Infrastructure for Population Studies, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Ira M. Hall
- grid.47100.320000000419368710Department of Genetics, Yale School of Medicine, New Haven, CT USA ,grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO USA
| | - Olli Pietiläinen
- grid.66859.34Stanley Center for Psychiatric Research, The Broad Institute of Harvard and MIT, Cambridge, MA USA ,grid.38142.3c000000041936754XStem Cell and Regenerative Biology, Harvard University, Cambridge, USA ,grid.7737.40000 0004 0410 2071Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Jaakko Kaprio
- grid.7737.40000 0004 0410 2071Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland ,grid.7737.40000 0004 0410 2071Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Samuli Ripatti
- grid.7737.40000 0004 0410 2071Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland ,grid.66859.34Stanley Center for Psychiatric Research, The Broad Institute of Harvard and MIT, Cambridge, MA USA ,grid.32224.350000 0004 0386 9924Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, USA ,grid.7737.40000 0004 0410 2071Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Mark Daly
- grid.7737.40000 0004 0410 2071Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland ,grid.66859.34Stanley Center for Psychiatric Research, The Broad Institute of Harvard and MIT, Cambridge, MA USA ,grid.32224.350000 0004 0386 9924Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, USA
| | - Aarno Palotie
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland. .,Stanley Center for Psychiatric Research, The Broad Institute of Harvard and MIT, Cambridge, MA, USA. .,Analytic and Translational Genetics Unit, Department of Medicine, Department of Neurology and Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA.
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156
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Godoy VCSMD, Bellucco FT, Colovati M, Oliveira-Junior HRD, Moysés-Oliveira M, Melaragno MI. Copy number variation (CNV) identification, interpretation, and database from Brazilian patients. Genet Mol Biol 2020; 43:e20190218. [PMID: 33306777 PMCID: PMC7783508 DOI: 10.1590/1678-4685-gmb-2019-0218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 09/25/2020] [Indexed: 11/22/2022] Open
Abstract
Copy number variations (CNVs) constitute an important class of variation in the
human genome and the interpretation of their pathogenicity considering different
frequencies across populations is still a challenge for geneticists. Since the
CNV databases are predominantly composed of European and non-admixed
individuals, and Brazilian genetic constitution is admixed and ethnically
diverse, diagnostic screenings on Brazilian variants are greatly difficulted by
the lack of populational references. We analyzed a clinical sample of 268
Brazilian individuals, including patients with neurodevelopment disorders and/or
congenital malformations. The pathogenicity of CNVs was classified according to
their gene content and overlap with known benign and pathogenic variants. A
total of 1,504 autosomal CNVs (1,207 gains and 297 losses) were classified as
benign (92.9%), likely benign (1.6%), VUS (2.6%), likely pathogenic (0.2%) and
pathogenic (2.7%). Some of the CNVs were recurrent and with frequency increased
in our sample, when compared to populational open resources of structural
variants: 14q32.33, 22q11.22, 1q21.1, and 1p36.32 gains. Thus, these highly
recurrent CNVs classified as likely benign or VUS were considered non-pathogenic
in our Brazilian sample. This study shows the relevance of introducing CNV data
from diverse cohorts to improve on the interpretation of clinical impact of
genomic variations.
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Affiliation(s)
| | - Fernanda Teixeira Bellucco
- Universidade Federal de São Paulo, Departamento de Morfologia e Genética, Disciplina de Genética, São Paulo, SP, Brazil
| | - Mileny Colovati
- Universidade Federal de São Paulo, Departamento de Morfologia e Genética, Disciplina de Genética, São Paulo, SP, Brazil
| | | | - Mariana Moysés-Oliveira
- Universidade Federal de São Paulo, Departamento de Morfologia e Genética, Disciplina de Genética, São Paulo, SP, Brazil
| | - Maria Isabel Melaragno
- Universidade Federal de São Paulo, Departamento de Morfologia e Genética, Disciplina de Genética, São Paulo, SP, Brazil
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157
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El Bitar F, Al Sudairy N, Qadi N, Al Rajeh S, Alghamdi F, Al Amari H, Al Dawsari G, Alsubaie S, Al Sudairi M, Abdulaziz S, Al Tassan N. A Comprehensive Analysis of Unique and Recurrent Copy Number Variations in Alzheimer's Disease and its Related Disorders. Curr Alzheimer Res 2020; 17:926-938. [PMID: 33256577 DOI: 10.2174/1567205017666201130111424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 08/20/2020] [Accepted: 10/29/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Copy number variations (CNVs) play an important role in the genetic etiology of various neurological disorders, including Alzheimer's disease (AD). Type 2 diabetes mellitus (T2DM) and major depressive disorder (MDD) were shown to have share mechanisms and signaling pathways with AD. OBJECTIVE We aimed to assess CNVs regions that may harbor genes contributing to AD, T2DM, and MDD in 67 Saudi familial and sporadic AD patients, with no alterations in the known genes of AD and genotyped previously for APOE. METHODS DNA was analyzed using the CytoScan-HD array. Two layers of filtering criteria were applied. All the identified CNVs were checked in the Database of Genomic Variants (DGV). RESULTS A total of 1086 CNVs (565 gains and 521 losses) were identified in our study. We found 73 CNVs harboring genes that may be associated with AD, T2DM or MDD. Nineteen CNVs were novel. Most importantly, 42 CNVs were unique in our studied cohort existing only in one patient. Two large gains on chromosomes 1 and 13 harbored genes implicated in the studied disorders. We identified CNVs in genes that encode proteins involved in the metabolism of amyloid-β peptide (AGRN, APBA2, CR1, CR2, IGF2R, KIAA0125, MBP, RER1, RTN4R, VDR and WISPI) or Tau proteins (CACNAIC, CELF2, DUSP22, HTRA1 and SLC2A14). CONCLUSION The present work provided information on the presence of CNVs related to AD, T2DM, and MDD in Saudi Alzheimer's patients.
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Affiliation(s)
- Fadia El Bitar
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nourah Al Sudairy
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Najeeb Qadi
- Department of Neurosciences, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | | | - Fatimah Alghamdi
- Institute of Biology and Environmental Research, National Center for Biotechnology, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Hala Al Amari
- Institute of Biology and Environmental Research, National Center for Biotechnology, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Ghadeer Al Dawsari
- Institute of Biology and Environmental Research, National Center for Genomics Technology, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Sahar Alsubaie
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mishael Al Sudairi
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sara Abdulaziz
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nada Al Tassan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
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158
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Kendall KM, John A, Lee SC, Rees E, Pardiñas AF, Banos MDP, Owen MJ, O'Donovan MC, Kirov G, Lloyd K, Jones I, Legge SE, Walters JTR. Impact of schizophrenia genetic liability on the association between schizophrenia and physical illness: data-linkage study. BJPsych Open 2020; 6:e139. [PMID: 33168126 PMCID: PMC7745237 DOI: 10.1192/bjo.2020.42] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 04/02/2020] [Accepted: 04/28/2020] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Individuals with schizophrenia are at higher risk of physical illnesses, which are a major contributor to their 20-year reduced life expectancy. It is currently unknown what causes the increased risk of physical illness in schizophrenia. AIMS To link genetic data from a clinically ascertained sample of individuals with schizophrenia to anonymised National Health Service (NHS) records. To assess (a) rates of physical illness in those with schizophrenia, and (b) whether physical illness in schizophrenia is associated with genetic liability. METHOD We linked genetic data from a clinically ascertained sample of individuals with schizophrenia (Cardiff Cognition in Schizophrenia participants, n = 896) to anonymised NHS records held in the Secure Anonymised Information Linkage (SAIL) databank. Physical illnesses were defined from the General Practice Database and Patient Episode Database for Wales. Genetic liability for schizophrenia was indexed by (a) rare copy number variants (CNVs), and (b) polygenic risk scores. RESULTS Individuals with schizophrenia in SAIL had increased rates of epilepsy (standardised rate ratio (SRR) = 5.34), intellectual disability (SRR = 3.11), type 2 diabetes (SRR = 2.45), congenital disorders (SRR = 1.77), ischaemic heart disease (SRR = 1.57) and smoking (SRR = 1.44) in comparison with the general SAIL population. In those with schizophrenia, carrier status for schizophrenia-associated CNVs and neurodevelopmental disorder-associated CNVs was associated with height (P = 0.015-0.017), with carriers being 7.5-7.7 cm shorter than non-carriers. We did not find evidence that the increased rates of poor physical health outcomes in schizophrenia were associated with genetic liability for the disorder. CONCLUSIONS This study demonstrates the value of and potential for linking genetic data from clinically ascertained research studies to anonymised health records. The increased risk for physical illness in schizophrenia is not caused by genetic liability for the disorder.
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Affiliation(s)
- Kimberley M. Kendall
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, UK
| | - Ann John
- Health Data Research UK, Swansea University Medical School, Swansea University, UK
| | - Sze Chim Lee
- Health Data Research UK, Swansea University Medical School, Swansea University, UK
| | - Elliott Rees
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, UK
| | - Antonio F. Pardiñas
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, UK
| | | | - Michael J. Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, UK
| | - Michael C. O'Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, UK
| | - George Kirov
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, UK
| | - Keith Lloyd
- Health Data Research UK, Swansea University Medical School, Swansea University, UK
| | - Ian Jones
- National Centre for Mental Health, MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, UK
| | - Sophie E. Legge
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, UK
| | - James T. R. Walters
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, UK
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159
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Functional in vivo and in vitro effects of 20q11.21 genetic aberrations on hPSC differentiation. Sci Rep 2020; 10:18582. [PMID: 33122739 PMCID: PMC7596514 DOI: 10.1038/s41598-020-75657-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 10/15/2020] [Indexed: 01/01/2023] Open
Abstract
Human pluripotent stem cells (hPSCs) have promising therapeutic applications due to their infinite capacity for self-renewal and pluripotency. Genomic stability is imperative for the clinical use of hPSCs; however, copy number variation (CNV), especially recurrent CNV at 20q11.21, may contribute genomic instability of hPSCs. Furthermore, the effects of CNVs in hPSCs at the whole-transcriptome scale are poorly understood. This study aimed to examine the functional in vivo and in vitro effects of frequently detected CNVs at 20q11.21 during early-stage differentiation of hPSCs. Comprehensive transcriptome profiling of abnormal hPSCs revealed that the differential gene expression patterns had a negative effect on differentiation potential. Transcriptional heterogeneity identified by single-cell RNA sequencing (scRNA-seq) of embryoid bodies from two different isogenic lines of hPSCs revealed alterations in differentiated cell distributions compared with that of normal cells. RNA-seq analysis of 22 teratomas identified several differentially expressed lineage-specific markers in hPSCs with CNVs, consistent with the histological results of the altered ecto/meso/endodermal ratio due to CNVs. Our results suggest that CNV amplification contributes to cell proliferation, apoptosis, and cell fate specification. This work shows the functional consequences of recurrent genetic abnormalities and thereby provides evidence to support the development of cell-based applications.
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160
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Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution. Genome Res 2020; 30:1680-1693. [PMID: 33093070 PMCID: PMC7605249 DOI: 10.1101/gr.265322.120] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 09/02/2020] [Indexed: 12/14/2022]
Abstract
Rhesus macaque is an Old World monkey that shared a common ancestor with human ∼25 Myr ago and is an important animal model for human disease studies. A deep understanding of its genetics is therefore required for both biomedical and evolutionary studies. Among structural variants, inversions represent a driving force in speciation and play an important role in disease predisposition. Here we generated a genome-wide map of inversions between human and macaque, combining single-cell strand sequencing with cytogenetics. We identified 375 total inversions between 859 bp and 92 Mbp, increasing by eightfold the number of previously reported inversions. Among these, 19 inversions flanked by segmental duplications overlap with recurrent copy number variants associated with neurocognitive disorders. Evolutionary analyses show that in 17 out of 19 cases, the Hominidae orientation of these disease-associated regions is always derived. This suggests that duplicated sequences likely played a fundamental role in generating inversions in humans and great apes, creating architectures that nowadays predispose these regions to disease-associated genetic instability. Finally, we identified 861 genes mapping at 156 inversions breakpoints, with some showing evidence of differential expression in human and macaque cell lines, thus highlighting candidates that might have contributed to the evolution of species-specific features. This study depicts the most accurate fine-scale map of inversions between human and macaque using a two-pronged integrative approach, such as single-cell strand sequencing and cytogenetics, and represents a valuable resource toward understanding of the biology and evolution of primate species.
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161
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3q29 microduplication syndrome: Clinical and molecular description of eleven new cases. Eur J Med Genet 2020; 63:104083. [PMID: 33039685 DOI: 10.1016/j.ejmg.2020.104083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 09/18/2020] [Accepted: 10/04/2020] [Indexed: 01/14/2023]
Abstract
Interstitial duplications of 3q29 have recently been described in association with a new genetic syndrome characterized by a neurodevelopmental phenotype. A total of 16 individuals with the 3q29 duplication have been reported in the literature with clinical features that include intellectual disability, language delay, epilepsy, structural brain anomalies, micro/macrocephaly, generalized obesity, ocular abnormalities, distinctive facial features, cleft palate, and musculoskeletal anomalies. In this paper, we summarize the current literature and present eleven additional cases from nine families with the 3q29 microduplication identified by microarray analysis at the Cincinnati Children's Hospital Medical Center Laboratory of Genetics and Genomics. Three diagnoses were made prenatally, making this the first case series to describe 3q29 duplications incidentally identified during the prenatal period. We further delineate the minimal region of overlap previously described in the literature and explore the modifying effects of "second hit" genetic aberrations, which were frequent in our cohort.
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162
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Tinker RJ, Burghel GJ, Garg S, Steggall M, Cuvertino S, Banka S. Haploinsufficiency of ATP6V0C possibly underlies 16p13.3 deletions that cause microcephaly, seizures, and neurodevelopmental disorder. Am J Med Genet A 2020; 185:196-202. [PMID: 33090716 DOI: 10.1002/ajmg.a.61905] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/15/2020] [Accepted: 09/19/2020] [Indexed: 12/11/2022]
Abstract
We recently contributed to the description of eight individuals with a novel condition caused by 16p13.3 microdeletions encompassing TBC1D24, ATP6V0C, and PDPK1 and resulting in epilepsy, microcephaly and neurodevelopmental problems. The phenotypic spectrum, the minimum overlapping region and the underlying disease mechanism for this disorder remain to be clarified. Here we report a 3.5-year-old male, with microcephaly, autism spectrum disorder and a de novo 16p13.3 microdeletion. We performed detailed in silico analysis to show that the minimum overlapping region for the condition is ~80Kb encompassing five protein coding genes. Analysis of loss of function constraint metrics, transcript-aware evaluation of the population variants, GeVIR scores, analysis of reported pathogenic point variants, detailed review of the known functions of gene products and their animal models showed that the haploinsufficiency of ATP6V0C likely underlies the phenotype of this condition. Protein-protein interaction network, gene phenology and analysis of topologically associating domain showed that it was unlikely that the disorder has an epistatic or regulatory basis. 16p13.3 deletions encompassing ATP6V0C cause a neurodevelopmental disorder. Our results broaden the phenotypic spectrum of this disorder and clarify the likely underlying disease mechanism for the condition.
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Affiliation(s)
- Rory J Tinker
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University Foundation NHS Trust, Manchester, UK
| | - George J Burghel
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University Foundation NHS Trust, Manchester, UK
| | - Shruti Garg
- Division of Neuroscience & Experimental Psychology, School of Biological Sciences, University of Manchester, Manchester, UK
- Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Greater Manchester Mental Health NHS Trust, Manchester, UK
- Department of Child and Adolescent Psychiatry, Royal Manchester Children's Hospital, Manchester, UK
| | - Maggie Steggall
- Department of Paediatric Medicine, Royal Manchester Children's Hospital, Manchester, UK
| | - Sara Cuvertino
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University Foundation NHS Trust, Manchester, UK
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
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163
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Brain-Enriched Coding and Long Non-coding RNA Genes Are Overrepresented in Recurrent Neurodevelopmental Disorder CNVs. Cell Rep 2020; 33:108307. [PMID: 33113368 DOI: 10.1016/j.celrep.2020.108307] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 03/15/2020] [Accepted: 10/02/2020] [Indexed: 11/20/2022] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental condition with substantial phenotypic and etiological heterogeneity. Although 10%-20% of ASD cases are attributable to copy number variation (CNV), causative genomic loci and constituent genes remain unclarified. We have developed SNATCNV, a tool that outperforms existing tools, to identify 47 recurrent ASD CNV regions from 19,663 cases and 6,479 controls documented in the AutDB database. Analysis of ASD CNV gene content using FANTOM5 shows that constituent coding genes and long non-coding RNAs have brain-enriched patterns of expression. Notably, such enrichment is not observed for regions identified by using other tools. We also find evidence of sexual dimorphism, one locus uniquely comprising a single lncRNA gene, and correlation of CNVs to distinct clinical and behavioral traits. Finally, we analyze a large dataset for schizophrenia to further demonstrate that SNATCNV is an effective, publicly available tool to define genomic loci and causative genes for multiple CNV-associated conditions.
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164
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Kaplanis J, Samocha KE, Wiel L, Zhang Z, Arvai KJ, Eberhardt RY, Gallone G, Lelieveld SH, Martin HC, McRae JF, Short PJ, Torene RI, de Boer E, Danecek P, Gardner EJ, Huang N, Lord J, Martincorena I, Pfundt R, Reijnders MRF, Yeung A, Yntema HG, Vissers LELM, Juusola J, Wright CF, Brunner HG, Firth HV, FitzPatrick DR, Barrett JC, Hurles ME, Gilissen C, Retterer K. Evidence for 28 genetic disorders discovered by combining healthcare and research data. Nature 2020; 586:757-762. [PMID: 33057194 PMCID: PMC7116826 DOI: 10.1038/s41586-020-2832-5] [Citation(s) in RCA: 288] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 07/17/2020] [Indexed: 01/28/2023]
Abstract
De novo mutations in protein-coding genes are a well-established cause of developmental disorders1. However, genes known to be associated with developmental disorders account for only a minority of the observed excess of such de novo mutations1,2. Here, to identify previously undescribed genes associated with developmental disorders, we integrate healthcare and research exome-sequence data from 31,058 parent-offspring trios of individuals with developmental disorders, and develop a simulation-based statistical test to identify gene-specific enrichment of de novo mutations. We identified 285 genes that were significantly associated with developmental disorders, including 28 that had not previously been robustly associated with developmental disorders. Although we detected more genes associated with developmental disorders, much of the excess of de novo mutations in protein-coding genes remains unaccounted for. Modelling suggests that more than 1,000 genes associated with developmental disorders have not yet been described, many of which are likely to be less penetrant than the currently known genes. Research access to clinical diagnostic datasets will be critical for completing the map of genes associated with developmental disorders.
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Affiliation(s)
- Joanna Kaplanis
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Kaitlin E Samocha
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Laurens Wiel
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | | | - Ruth Y Eberhardt
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Giuseppe Gallone
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Stefan H Lelieveld
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hilary C Martin
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Jeremy F McRae
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Patrick J Short
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Elke de Boer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Petr Danecek
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Eugene J Gardner
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Ni Huang
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Jenny Lord
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Iñigo Martincorena
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Margot R F Reijnders
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Alison Yeung
- Victorian Clinical Genetics Services, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Helger G Yntema
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Caroline F Wright
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, UK
| | - Han G Brunner
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
- GROW School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, The Netherlands
- MHENS School for Mental Health and Neuroscience, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Helen V Firth
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - David R FitzPatrick
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Jeffrey C Barrett
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Matthew E Hurles
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
| | - Christian Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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165
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Wang T, Hoekzema K, Vecchio D, Wu H, Sulovari A, Coe BP, Gillentine MA, Wilfert AB, Perez-Jurado LA, Kvarnung M, Sleyp Y, Earl RK, Rosenfeld JA, Geisheker MR, Han L, Du B, Barnett C, Thompson E, Shaw M, Carroll R, Friend K, Catford R, Palmer EE, Zou X, Ou J, Li H, Guo H, Gerdts J, Avola E, Calabrese G, Elia M, Greco D, Lindstrand A, Nordgren A, Anderlid BM, Vandeweyer G, Van Dijck A, Van der Aa N, McKenna B, Hancarova M, Bendova S, Havlovicova M, Malerba G, Bernardina BD, Muglia P, van Haeringen A, Hoffer MJV, Franke B, Cappuccio G, Delatycki M, Lockhart PJ, Manning MA, Liu P, Scheffer IE, Brunetti-Pierri N, Rommelse N, Amaral DG, Santen GWE, Trabetti E, Sedláček Z, Michaelson JJ, Pierce K, Courchesne E, Kooy RF, Nordenskjöld M, Romano C, Peeters H, Bernier RA, Gecz J, Xia K, Eichler EE. Large-scale targeted sequencing identifies risk genes for neurodevelopmental disorders. Nat Commun 2020; 11:4932. [PMID: 33004838 PMCID: PMC7530681 DOI: 10.1038/s41467-020-18723-y] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 09/04/2020] [Indexed: 02/08/2023] Open
Abstract
Most genes associated with neurodevelopmental disorders (NDDs) were identified with an excess of de novo mutations (DNMs) but the significance in case-control mutation burden analysis is unestablished. Here, we sequence 63 genes in 16,294 NDD cases and an additional 62 genes in 6,211 NDD cases. By combining these with published data, we assess a total of 125 genes in over 16,000 NDD cases and compare the mutation burden to nonpsychiatric controls from ExAC. We identify 48 genes (25 newly reported) showing significant burden of ultra-rare (MAF < 0.01%) gene-disruptive mutations (FDR 5%), six of which reach family-wise error rate (FWER) significance (p < 1.25E-06). Among these 125 targeted genes, we also reevaluate DNM excess in 17,426 NDD trios with 6,499 new autism trios. We identify 90 genes enriched for DNMs (FDR 5%; e.g., GABRG2 and UIMC1); of which, 61 reach FWER significance (p < 3.64E-07; e.g., CASZ1). In addition to doubling the number of patients for many NDD risk genes, we present phenotype-genotype correlations for seven risk genes (CTCF, HNRNPU, KCNQ3, ZBTB18, TCF12, SPEN, and LEO1) based on this large-scale targeted sequencing effort.
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Affiliation(s)
- Tianyun Wang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Davide Vecchio
- Rare Disease and Medical Genetics, Academic Department of Pediatrics, Bambino Gesù Children's Hospital, Rome, Italy
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, Rome, Italy
| | - Huidan Wu
- Center for Medical Genetics & Hunan Provincial Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Arvis Sulovari
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Bradley P Coe
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Amy B Wilfert
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Luis A Perez-Jurado
- Paediatric and Reproductive Genetics unit, Women's and Children's Hospital, Adelaide, SA, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
- Genetics Unit, Universitat Pompeu Fabra, Hospital del Mar Research Institute (IMIM) and CIBERER, Barcelona, Spain
| | - Malin Kvarnung
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Yoeri Sleyp
- Centre for Human Genetics, KU Leuven and Leuven Autism Research (LAuRes), Leuven, Belgium
| | - Rachel K Earl
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Jill A Rosenfeld
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics, Houston, TX, USA
| | | | - Lin Han
- Center for Medical Genetics & Hunan Provincial Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Bing Du
- Center for Medical Genetics & Hunan Provincial Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Chris Barnett
- Paediatric and Reproductive Genetics unit, Women's and Children's Hospital, Adelaide, SA, Australia
- Adelaide Medical School and the Robinson Research Institute, the University of Adelaide, Adelaide, SA, Australia
| | - Elizabeth Thompson
- Paediatric and Reproductive Genetics unit, Women's and Children's Hospital, Adelaide, SA, Australia
| | - Marie Shaw
- Adelaide Medical School and the Robinson Research Institute, the University of Adelaide, Adelaide, SA, Australia
| | - Renee Carroll
- Adelaide Medical School and the Robinson Research Institute, the University of Adelaide, Adelaide, SA, Australia
| | - Kathryn Friend
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Rachael Catford
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Elizabeth E Palmer
- Genetics of Learning Disability Service, Hunter New England Health Service, Waratah, NSW, Australia
- School of Women's and Children's Health, University of New South Wales, Randwick, NSW, Australia
| | - Xiaobing Zou
- Children Development Behavior Center, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Jianjun Ou
- Mental Health Institute of the Second Xiangya Hospital, Central South University, Changsha, China
| | - Honghui Li
- Key Laboratory of Developmental Disorders in Children, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, China
| | - Hui Guo
- Center for Medical Genetics & Hunan Provincial Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Jennifer Gerdts
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | | | | | | | | | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Britt-Marie Anderlid
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Geert Vandeweyer
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Anke Van Dijck
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | | | - Brooke McKenna
- Department of Psychology, Emory University, Atlanta, GA, USA
| | - Miroslava Hancarova
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Sarka Bendova
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Marketa Havlovicova
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Giovanni Malerba
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | | | | | - Arie van Haeringen
- Department of Clinical Genetics, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Mariette J V Hoffer
- Department of Clinical Genetics, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Barbara Franke
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
- Department of Psychiatry, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Gerarda Cappuccio
- Department of Translational Medicine, Federico II University, Naples, Italy
- Telethon Institute of Genetics and Medicine, Pozzuoli, Naples, Italy
| | | | - Paul J Lockhart
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Melanie A Manning
- Division of Medical Genetics, Department of Pediatrics, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Pengfei Liu
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics, Houston, TX, USA
| | - Ingrid E Scheffer
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, VIC, Australia
- Department of Medicine, University of Melbourne, Austin Health, Melbourne, Australia
- The Florey Institute of Neuroscience and Mental Health, Parkville, VIC, Australia
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Federico II University, Naples, Italy
- Telethon Institute of Genetics and Medicine, Pozzuoli, Naples, Italy
| | - Nanda Rommelse
- Department of Psychiatry, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
- Karakter Child and Adolescent Psychiatry Center, Nijmegen, Netherlands
| | - David G Amaral
- Department of Psychiatry and Behavioral Sciences and the MIND Institute, University of California, Davis, Sacramento, CA, USA
| | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Elisabetta Trabetti
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Zdeněk Sedláček
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Jacob J Michaelson
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Karen Pierce
- Department of Neurosciences, UC San Diego Autism Center, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Eric Courchesne
- Department of Neurosciences, UC San Diego Autism Center, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Magnus Nordenskjöld
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | | | - Hilde Peeters
- Centre for Human Genetics, KU Leuven and Leuven Autism Research (LAuRes), Leuven, Belgium
| | - Raphael A Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Jozef Gecz
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
- Adelaide Medical School and the Robinson Research Institute, the University of Adelaide, Adelaide, SA, Australia
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Kun Xia
- Center for Medical Genetics & Hunan Provincial Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
- CAS Center for Excellence in Brain Science and Intelligences Technology (CEBSIT), Chinese Academy of Sciences, Shanghai, China
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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166
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Alsubaie LM, Alsuwat HS, Almandil NB, AlSulaiman A, AbdulAzeez S, Borgio JF. Risk Y-haplotypes and pathogenic variants of Arab-ancestry boys with autism by an exome-wide association study. Mol Biol Rep 2020; 47:7623-7632. [DOI: 10.1007/s11033-020-05832-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 09/07/2020] [Indexed: 12/20/2022]
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167
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Maya I, Smirin-Yosef P, Kahana S, Morag S, Yacobson S, Agmon-Fishman I, Matar R, Bitton E, Shohat M, Basel-Salmon L, Salmon-Divon M. A study of normal copy number variations in Israeli population. Hum Genet 2020; 140:553-563. [PMID: 32980975 DOI: 10.1007/s00439-020-02225-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 09/19/2020] [Indexed: 10/23/2022]
Abstract
The population of Israel is ethnically diverse, and individuals from different ethnic groups share specific genetic variations. These variations, which have been passed on from common ancestors, are usually reported in public databases as rare variants. Here, we aimed to identify ethnicity-based benign copy number variants (CNVs) and generate the first Israeli CNV database. We applied a data-mining approach to the results of 10,193 chromosomal microarray tests, of which 2150 tests were from individuals of 13 common ethnic backgrounds (n ≥ 10). We found 165 CNV regions (> 50 kbp) that are unique to specific ethnic groups (uCNVRs). The frequency of more than 19% of these uCNVRs is between 1 and 20% of the common ethnic origin, while their frequency in the overall cohort is between 0.5 and 1.6%. Of these 165 uCNVRs, 98 are reported as variants of unknown significance or as not available in dbVar; we postulate that these uCNVRs should be annotated as either "likely benign" or "benign". The ethnic-specific CNVs extracted in this study will allow geneticists to distinguish between relevant pathogenic genomic aberrations and benign ethnicity-related variations, thus preventing variant misinterpretation that may lead to unnecessary pregnancy terminations.
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Affiliation(s)
- Idit Maya
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel
| | - Pola Smirin-Yosef
- Genomic Bioinformatics Laboratory, Department of Molecular Biology, Ariel University, Ariel, Israel.,Felsenstein Medical Research Center, Rabin Medical Center, Petah Tikva, Israel
| | - Sarit Kahana
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel
| | - Sne Morag
- Genomic Bioinformatics Laboratory, Department of Molecular Biology, Ariel University, Ariel, Israel
| | - Shiri Yacobson
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel
| | - Ifaat Agmon-Fishman
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel
| | - Reut Matar
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel
| | - Elisheva Bitton
- Genomic Bioinformatics Laboratory, Department of Molecular Biology, Ariel University, Ariel, Israel
| | - Mordechai Shohat
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Genomic Unit, Sheba Cancer Research Center, Sheba Medical Center, Tel-Hashomer, Israel.,Maccabi Health Services, Rehovot, Israel
| | - Lina Basel-Salmon
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel.,Felsenstein Medical Research Center, Rabin Medical Center, Petah Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petah Tikva, Israel
| | - Mali Salmon-Divon
- Genomic Bioinformatics Laboratory, Department of Molecular Biology, Ariel University, Ariel, Israel. .,The Adelson School of Medicine, Ariel University, Ariel, Israel.
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168
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Interpreting the impact of noncoding structural variation in neurodevelopmental disorders. Genet Med 2020; 23:34-46. [PMID: 32973355 PMCID: PMC7790743 DOI: 10.1038/s41436-020-00974-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/03/2020] [Accepted: 09/14/2020] [Indexed: 12/21/2022] Open
Abstract
The emergence of novel sequencing technologies has greatly improved the identification of structural variation, revealing that a human genome harbors tens of thousands of structural variants (SVs). Since these SVs primarily impact noncoding DNA sequences, the next challenge is one of interpretation, not least to improve our understanding of human disease etiology. However, this task is severely complicated by the intricacy of the gene regulatory landscapes embedded within these noncoding regions, their incomplete annotation, as well as their dependence on the three-dimensional (3D) conformation of the genome. Also in the context of neurodevelopmental disorders (NDDs), reports of putatively causal, noncoding SVs are accumulating and understanding their impact on transcriptional regulation is presenting itself as the next step toward improved genetic diagnosis.
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169
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Libero LE, Schaer M, Li DD, Amaral DG, Nordahl CW. A Longitudinal Study of Local Gyrification Index in Young Boys With Autism Spectrum Disorder. Cereb Cortex 2020; 29:2575-2587. [PMID: 29850803 DOI: 10.1093/cercor/bhy126] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Indexed: 12/31/2022] Open
Abstract
Local gyrification index (LGI), a metric quantifying cortical folding, was evaluated in 105 boys with autism spectrum disorder (ASD) and 49 typically developing (TD) boys at 3 and 5 years-of-age. At 3 years-of-age, boys with ASD had reduced gyrification in the fusiform gyrus compared with TD boys. A longitudinal evaluation from 3 to 5 years revealed that while TD boys had stable/decreasing LGI, boys with ASD had increasing LGI in right inferior temporal gyrus, right inferior frontal gyrus, right inferior parietal lobule, and stable LGI in left lingual gyrus. LGI was also examined in a previously defined neurophenotype of boys with ASD and disproportionate megalencephaly. At 3 years-of-age, this subgroup exhibited increased LGI in right dorsomedial prefrontal cortex, cingulate cortex, and paracentral cortex, and left cingulate cortex and superior frontal gyrus relative to TD boys and increased LGI in right paracentral lobule and parahippocampal gyrus, and left precentral gyrus compared with boys with ASD and normal brain size. In summary, this study identified alterations in the pattern and development of LGI during early childhood in ASD. Distinct patterns of alterations in subgroups of boys with ASD suggests that multiple neurophenotypes exist and boys with ASD and disproportionate megalencephaly should be evaluated separately.
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Affiliation(s)
- Lauren E Libero
- UC Davis MIND Institute and the UC Davis Department of Psychiatry and Behavioral Sciences, School of Medicine, 2230 Stockton Blvd., Sacramento, CA, USA
| | - Marie Schaer
- Office Medico-Pedagogique, Universite de Geneve, Rue David Dafour 1, Geneva 8, Switzerland
| | - Deana D Li
- UC Davis MIND Institute and the UC Davis Department of Psychiatry and Behavioral Sciences, School of Medicine, 2230 Stockton Blvd., Sacramento, CA, USA
| | - David G Amaral
- UC Davis MIND Institute and the UC Davis Department of Psychiatry and Behavioral Sciences, School of Medicine, 2230 Stockton Blvd., Sacramento, CA, USA
| | - Christine Wu Nordahl
- UC Davis MIND Institute and the UC Davis Department of Psychiatry and Behavioral Sciences, School of Medicine, 2230 Stockton Blvd., Sacramento, CA, USA
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170
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Co M, Anderson AG, Konopka G. FOXP transcription factors in vertebrate brain development, function, and disorders. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2020; 9:e375. [PMID: 31999079 PMCID: PMC8286808 DOI: 10.1002/wdev.375] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 12/17/2019] [Accepted: 01/08/2020] [Indexed: 12/22/2022]
Abstract
FOXP transcription factors are an evolutionarily ancient protein subfamily coordinating the development of several organ systems in the vertebrate body. Association of their genes with neurodevelopmental disorders has sparked particular interest in their expression patterns and functions in the brain. Here, FOXP1, FOXP2, and FOXP4 are expressed in distinct cell type-specific spatiotemporal patterns in multiple regions, including the cortex, hippocampus, amygdala, basal ganglia, thalamus, and cerebellum. These varied sites and timepoints of expression have complicated efforts to link FOXP1 and FOXP2 mutations to their respective developmental disorders, the former affecting global neural functions and the latter specifically affecting speech and language. However, the use of animal models, particularly those with brain region- and cell type-specific manipulations, has greatly advanced our understanding of how FOXP expression patterns could underlie disorder-related phenotypes. While many questions remain regarding FOXP expression and function in the brain, studies to date have illuminated the roles of these transcription factors in vertebrate brain development and have greatly informed our understanding of human development and disorders. This article is categorized under: Nervous System Development > Vertebrates: General Principles Gene Expression and Transcriptional Hierarchies > Gene Networks and Genomics Nervous System Development > Vertebrates: Regional Development.
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Affiliation(s)
- Marissa Co
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon
| | - Ashley G Anderson
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Genevieve Konopka
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas
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171
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Costain G, Walker S, Marano M, Veenma D, Snell M, Curtis M, Luca S, Buera J, Arje D, Reuter MS, Thiruvahindrapuram B, Trost B, Sung WWL, Yuen RKC, Chitayat D, Mendoza-Londono R, Stavropoulos DJ, Scherer SW, Marshall CR, Cohn RD, Cohen E, Orkin J, Meyn MS, Hayeems RZ. Genome Sequencing as a Diagnostic Test in Children With Unexplained Medical Complexity. JAMA Netw Open 2020; 3:e2018109. [PMID: 32960281 PMCID: PMC7509619 DOI: 10.1001/jamanetworkopen.2020.18109] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 07/12/2020] [Indexed: 12/16/2022] Open
Abstract
Importance Children with medical complexity (CMC) represent a growing population in the pediatric health care system, with high resource use and associated health care costs. A genetic diagnosis can inform prognosis, anticipatory care, management, and reproductive planning. Conventional genetic testing strategies for CMC are often costly, time consuming, and ultimately unsuccessful. Objective To evaluate the analytical and clinical validity of genome sequencing as a comprehensive diagnostic genetic test for CMC. Design, Setting, and Participants In this cohort study of the prospective use of genome sequencing and comparison with standard-of-care genetic testing, CMC were recruited from May 1, 2017, to November 30, 2018, from a structured complex care program based at a tertiary care pediatric hospital in Toronto, Canada. Recruited CMC had at least 1 chronic condition, technology dependence (child is dependent at least part of each day on mechanical ventilators, and/or child requires prolonged intravenous administration of nutritional substances or drugs, and/or child is expected to have prolonged dependence on other device-based support), multiple subspecialist involvement, and substantial health care use. Review of the care plans for 545 CMC identified 143 suspected of having an undiagnosed genetic condition. Fifty-four families met inclusion criteria and were interested in participating, and 49 completed the study. Probands, similarly affected siblings, and biological parents were eligible for genome sequencing. Exposures Genome sequencing was performed using blood-derived DNA from probands and family members using established methods and a bioinformatics pipeline for clinical genome annotation. Main Outcomes and Measures The primary study outcome was the diagnostic yield of genome sequencing (proportion of CMC for whom the test result yielded a new diagnosis). Results Genome sequencing was performed for 138 individuals from 49 families of CMC (29 male and 20 female probands; mean [SD] age, 7.0 [4.5] years). Genome sequencing detected all genomic variation previously identified by conventional genetic testing. A total of 15 probands (30.6%; 95% CI 19.5%-44.6%) received a new primary molecular genetic diagnosis after genome sequencing. Three individuals had novel diseases and an additional 9 had either ultrarare genetic conditions or rare genetic conditions with atypical features. At least 11 families received diagnostic information that had clinical management implications beyond genetic and reproductive counseling. Conclusions and Relevance This study suggests that genome sequencing has high analytical and clinical validity and can result in new diagnoses in CMC even in the setting of extensive prior investigations. This clinical population may be enriched for ultrarare and novel genetic disorders. Genome sequencing is a potentially first-tier genetic test for CMC.
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Affiliation(s)
- Gregory Costain
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Susan Walker
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Maria Marano
- Division of Paediatric Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Danielle Veenma
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Meaghan Snell
- Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Meredith Curtis
- Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Stephanie Luca
- Child Health Evaluative Sciences, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jason Buera
- Division of Paediatric Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Danielle Arje
- Division of Paediatric Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Miriam S. Reuter
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Brett Trost
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Wilson W. L. Sung
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ryan K. C. Yuen
- Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - David Chitayat
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Prenatal Diagnosis and Medical Genetics Program, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Roberto Mendoza-Londono
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - D. James Stavropoulos
- Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Stephen W. Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Paediatric Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Christian R. Marshall
- Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Ronald D. Cohn
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Paediatric Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Eyal Cohen
- Division of Paediatric Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Child Health Evaluative Sciences, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
- Institute of Health Policy Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Julia Orkin
- Division of Paediatric Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Child Health Evaluative Sciences, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - M. Stephen Meyn
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
- Center for Human Genomics and Precision Medicine, University of Wisconsin, Madison
| | - Robin Z. Hayeems
- Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Child Health Evaluative Sciences, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Health Policy Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
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172
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Vrkić Boban I, Sekiguchi F, Lozić M, Miyake N, Matsumoto N, Lozić B. A Novel SETBP1 Gene Disruption by a De Novo Balanced Translocation in a Patient with Speech Impairment, Intellectual, and Behavioral Disorder. J Pediatr Genet 2020; 11:135-138. [DOI: 10.1055/s-0040-1715639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 07/10/2020] [Indexed: 10/23/2022]
Abstract
AbstractBalanced chromosomal abnormalities (BCAs) can disrupt gene function resulting in disease. To date, BCA disrupting the SET binding protein 1 (SETBP1) gene has not been reported. On the other hand, de novo heterozygous variants in the highly conserved 11-bp region in SETBP1 can result in the Schinzel–Giedion syndrome. This condition is characterized by severe intellectual disability, a characteristic face, and multiple-system anomalies. Further other types of mutations involving SETBP1 are associated with a different phenotype, mental retardation, autosomal dominant 29 (MRD29), which has mild dysmorphic features, developmental delay, and behavioral disorders. Here we report a male patient who has moderate intellectual disability, mild behavioral difficulties, and severe expressive speech impairment resulting from a de novo balanced chromosome translocation, t(12;18)(q22;q12.3). By whole genome sequencing, we determined the breakpoints at the nucleotide level. The 18q12.3 breakpoint was located between exons 2 and 3 of SETBP1. Phenotypic features of our patient are compatible with those with MRD29. This is the first reported BCA disrupting SETBP1.
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Affiliation(s)
- Ivona Vrkić Boban
- Department of Pediatrics, University Hospital of Split, Split, Croatia
| | - Futoshi Sekiguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Kanazawa-ku, Yokohama, Japan
| | - Mirela Lozić
- School of Medicine, University of Split, Split, Croatia
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Kanazawa-ku, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Kanazawa-ku, Yokohama, Japan
| | - Bernarda Lozić
- Department of Pediatrics, University Hospital of Split, Split, Croatia
- School of Medicine, University of Split, Split, Croatia
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173
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Boscher E, Husson T, Quenez O, Laquerrière A, Marguet F, Cassinari K, Wallon D, Martinaud O, Charbonnier C, Nicolas G, Deleuze JF, Boland A, Lathrop M, Frébourg T, Campion D, Hébert SS, Rovelet-Lecrux A. Copy Number Variants in miR-138 as a Potential Risk Factor for Early-Onset Alzheimer's Disease. J Alzheimers Dis 2020; 68:1243-1255. [PMID: 30909216 DOI: 10.3233/jad-180940] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Early-onset Alzheimer's disease (EOAD) accounts for 5-10% of all AD cases, with a heritability ranging between 92% to 100%. With the exception of rare mutations in APP, PSEN1, and PSEN2 genes causing autosomal dominant EOAD, little is known about the genetic factors underlying most of the EOAD cases. In this study, we hypothesized that copy number variations (CNVs) in microRNA (miR) genes could contribute to risk for EOAD. miRs are short non-coding RNAs previously implicated in the regulation of AD-related genes and phenotypes. Using whole exome sequencing, we screened a series of 546 EOAD patients negative for autosomal dominant EOAD mutations and 597 controls. We identified 86 CNVs in miR genes of which 31 were exclusive to EOAD cases, including a duplication of the MIR138-2 locus. In functional studies in human cultured cells, we could demonstrate that miR-138 overexpression leads to higher Aβ production as well as tau phosphorylation, both implicated in AD pathophysiology. These changes were mediated in part by GSK-3β and FERMT2, a potential risk factor for AD. Additional disease-related genes were also prone to miR-138 regulation including APP and BACE1. This study suggests that increased gene dosage of MIR138-2 could contribute to risk for EOAD by regulating different biological pathways implicated in amyloid and tau metabolism. Additional studies are now required to better understand the role of miR-CNVs in EOAD.
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Affiliation(s)
- Emmanuelle Boscher
- Centre de recherche du CHU de Québec-Université Laval, CHUL, Axe Neurosciences, Québec, Canada.,Faculté de médecine, Département de psychiatrie et de neurosciences, Université Laval, Québec, Canada
| | - Thomas Husson
- Department of Genetics and CNR-MAJ, Normandie Univ, UNIROUEN, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Olivier Quenez
- Department of Genetics and CNR-MAJ, Normandie Univ, UNIROUEN, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Annie Laquerrière
- Department of Pathology, Normandie Univ, UNIROUEN, Rouen University Hospital, Rouen, France
| | - Florent Marguet
- Department of Pathology, Normandie Univ, UNIROUEN, Rouen University Hospital, Rouen, France
| | - Kevin Cassinari
- Department of Genetics and CNR-MAJ, Normandie Univ, UNIROUEN, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - David Wallon
- Department of Neurology and CNR-MAJ, Normandie Univ, UNIROUEN, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Olivier Martinaud
- Normandie Univ, UNICAEN, EPHE, INSERM, U1077, CHU de Caen, Neuropsychologie et Imagerie de la Mémoire Humaine, Caen, France
| | - Camille Charbonnier
- Department of Genetics and CNR-MAJ, Normandie Univ, UNIROUEN, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Gaël Nicolas
- Department of Genetics and CNR-MAJ, Normandie Univ, UNIROUEN, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Jean-François Deleuze
- Centre National de recherche en Génomique Humaine, Institut de Génomique, CEA, Evry, France
| | - Anne Boland
- Centre National de recherche en Génomique Humaine, Institut de Génomique, CEA, Evry, France
| | - Mark Lathrop
- McGill University and Génome Québec Innovation Centre, Montréal, Canada
| | - Thierry Frébourg
- Department of Genetics and CNR-MAJ, Normandie Univ, UNIROUEN, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | | | - Dominique Campion
- Department of Genetics and CNR-MAJ, Normandie Univ, UNIROUEN, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Sébastien S Hébert
- Centre de recherche du CHU de Québec-Université Laval, CHUL, Axe Neurosciences, Québec, Canada.,Faculté de médecine, Département de psychiatrie et de neurosciences, Université Laval, Québec, Canada
| | - Anne Rovelet-Lecrux
- Department of Genetics and CNR-MAJ, Normandie Univ, UNIROUEN, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine, Rouen, France
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174
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Jiang L, Huguet G, Schramm C, Ciampi A, Main A, Passo C, Jean‐Louis M, Auger M, Schumann G, Porteous D, Jacquemont S, Greenwood CMT. Estimating the effects of copy‐number variants on intelligence using hierarchical Bayesian models. Genet Epidemiol 2020; 44:825-840. [DOI: 10.1002/gepi.22344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 06/24/2020] [Accepted: 07/21/2020] [Indexed: 01/01/2023]
Affiliation(s)
- Lai Jiang
- Lady Davis Institute Jewish General Hospital Montreal Canada
- Department of Epidemiology, Biostatistics and Occupational Health McGill University Montreal Canada
- Centre Hospitalier Universitaire (CHU) Sainte‐Justine Montreal Canada
| | - Guillaume Huguet
- Centre Hospitalier Universitaire (CHU) Sainte‐Justine Montreal Canada
- Universite de Montreal Montreal Canada
| | - Catherine Schramm
- Lady Davis Institute Jewish General Hospital Montreal Canada
- Centre Hospitalier Universitaire (CHU) Sainte‐Justine Montreal Canada
- Universite de Montreal Montreal Canada
| | - Antonio Ciampi
- Department of Epidemiology, Biostatistics and Occupational Health McGill University Montreal Canada
| | - Antoine Main
- Centre Hospitalier Universitaire (CHU) Sainte‐Justine Montreal Canada
- Universite de Montreal Montreal Canada
- Department of Decision Sciences Hautes etudes commerciales de Montreal (HEC) Montreal Canada
| | - Claudine Passo
- Centre Hospitalier Universitaire (CHU) Sainte‐Justine Montreal Canada
- Universite de Montreal Montreal Canada
| | - Martineau Jean‐Louis
- Centre Hospitalier Universitaire (CHU) Sainte‐Justine Montreal Canada
- Universite de Montreal Montreal Canada
| | - Maude Auger
- Centre Hospitalier Universitaire (CHU) Sainte‐Justine Montreal Canada
- Universite de Montreal Montreal Canada
| | - Gunter Schumann
- Institute of Psychiatry, Psychology, and Neuroscience King's College London London UK
| | - David Porteous
- Department of Psychology, Lothian Birth Cohorts Group, School of Philosophy, Psychology and Language Sciences The University of Edinburgh Edinburgh UK
- Medical Genetics Section, Centre for Genomic Experimental Medicine, MRC Institute of Genetics Molecular Medicine, Western General Hospital The University of Edinburgh Edinburgh UK
- Generation Scotland, Centre for Genomic and Experimental Medicine University of Edinburgh Edinburgh UK
| | - Sébastien Jacquemont
- Centre Hospitalier Universitaire (CHU) Sainte‐Justine Montreal Canada
- Universite de Montreal Montreal Canada
| | - Celia M. T. Greenwood
- Lady Davis Institute Jewish General Hospital Montreal Canada
- Department of Epidemiology, Biostatistics and Occupational Health McGill University Montreal Canada
- Gerald Bronfman Department of Oncology McGill University Montreal Canada
- Department of Human Genetics McGill University Montreal Canada
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175
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The Role of Alpha-Synuclein and Other Parkinson's Genes in Neurodevelopmental and Neurodegenerative Disorders. Int J Mol Sci 2020; 21:ijms21165724. [PMID: 32785033 PMCID: PMC7460874 DOI: 10.3390/ijms21165724] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 07/29/2020] [Accepted: 08/08/2020] [Indexed: 12/13/2022] Open
Abstract
Neurodevelopmental and late-onset neurodegenerative disorders present as separate entities that are clinically and neuropathologically quite distinct. However, recent evidence has highlighted surprising commonalities and converging features at the clinical, genomic, and molecular level between these two disease spectra. This is particularly striking in the context of autism spectrum disorder (ASD) and Parkinson's disease (PD). Genetic causes and risk factors play a central role in disease pathophysiology and enable the identification of overlapping mechanisms and pathways. Here, we focus on clinico-genetic studies of causal variants and overlapping clinical and cellular features of ASD and PD. Several genes and genomic regions were selected for our review, including SNCA (alpha-synuclein), PARK2 (parkin RBR E3 ubiquitin protein ligase), chromosome 22q11 deletion/DiGeorge region, and FMR1 (fragile X mental retardation 1) repeat expansion, which influence the development of both ASD and PD, with converging features related to synaptic function and neurogenesis. Both PD and ASD display alterations and impairments at the synaptic level, representing early and key disease phenotypes, which support the hypothesis of converging mechanisms between the two types of diseases. Therefore, understanding the underlying molecular mechanisms might inform on common targets and therapeutic approaches. We propose to re-conceptualize how we understand these disorders and provide a new angle into disease targets and mechanisms linking neurodevelopmental disorders and neurodegeneration.
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Tuke M, Tyrrell J, Ruth KS, Beaumont RN, Wood AR, Murray A, Frayling TM, Weedon MN, Wright CF. Large Copy-Number Variants in UK Biobank Caused by Clonal Hematopoiesis May Confound Penetrance Estimates. Am J Hum Genet 2020; 107:325-329. [PMID: 32574563 DOI: 10.1016/j.ajhg.2020.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 06/02/2020] [Indexed: 12/20/2022] Open
Abstract
Large copy-number variants (CNVs) are strongly associated with both developmental delay and cancer, but the type of disease depends strongly on when and where the mutation occurred, i.e., germline versus somatic. We used microarray data from UK Biobank to investigate the prevalence and penetrance of large autosomal CNVs and chromosomal aneuploidies using a standard CNV detection algorithm not designed for detecting mosaic variants. We found 160 individuals that carry >10 Mb copy number changes, including 56 with whole chromosome aneuploidies. Nineteen (12%) individuals had a diagnosis of Down syndrome or other developmental disorder, while 84 (52.5%) individuals had a diagnosis of hematological malignancies or chronic myeloproliferative disorders. Notably, there was no evidence of mosaicism in the blood for many of these large CNVs, so they could easily be mistaken for germline alleles even when caused by somatic mutations. We therefore suggest that somatic mutations associated with blood cancers may result in false estimates of rare variant penetrance from population biobanks.
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Affiliation(s)
- Marcus Tuke
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Jessica Tyrrell
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Katherine S Ruth
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Robin N Beaumont
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Andrew R Wood
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Anna Murray
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Timothy M Frayling
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Michael N Weedon
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Caroline F Wright
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK.
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177
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Schut PC, Brosens E, Van Dooren TJM, Galis F, Ten Broek CMA, Baijens IMM, Dremmen MHG, Tibboel D, Schol MP, de Klein A, Eggink AJ, Cohen-Overbeek TE. Exploring copy number variants in deceased fetuses and neonates with abnormal vertebral patterns and cervical ribs. Birth Defects Res 2020; 112:1513-1525. [PMID: 32755042 PMCID: PMC7689732 DOI: 10.1002/bdr2.1786] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 07/03/2020] [Accepted: 07/21/2020] [Indexed: 12/13/2022]
Abstract
Background Cervical patterning abnormalities are rare in the general population, but one variant, cervical ribs, is particularly common in deceased fetuses and neonates. The discrepancy between the incidence in the general population and early mortality is likely due to indirect selection against cervical ribs. The cause for the co‐occurrence of cervical ribs and adverse outcome remains unidentified. Copy number variations resulting in gain or loss of specific genes involved in development and patterning could play a causative role. Methods Radiographs of 374 deceased fetuses and infants, including terminations of pregnancies, stillbirths and neonatal deaths, were assessed. Copy number profiles of 265 patients were determined using single nucleotide polymorphism array. Results 274/374 patients (73.3%) had an abnormal vertebral pattern, which was associated with congenital abnormalities. Cervical ribs were present in 188/374 (50.3%) and were more common in stillbirths (69/128 [53.9%]) and terminations of pregnancies (101/188 [53.7%]), compared to live births (18/58, 31.0%). Large (likely) deleterious copy number variants and aneuploidies were prevalent in these patients. None of the rare copy number variants were recurrent or overlapped with candidate genes for vertebral patterning. Conclusions The large variety of copy number variants in deceased fetuses and neonates with similar abnormalities of the vertebral pattern probably reflects the etiological heterogeneity of vertebral patterning abnormalities. This genetic heterogeneity corresponds with the hypothesis that cervical ribs can be regarded as a sign of disruption of critical, highly interactive stages of embryogenesis. The vertebral pattern can probably provide valuable information regarding fetal and neonatal outcome.
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Affiliation(s)
- Pauline C Schut
- Department of Obstetrics and Gynecology, Division of Obstetrics and Fetal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Tom J M Van Dooren
- Naturalis Biodiversity Center, Leiden, The Netherlands.,CNRS, Institute of Ecology and Environmental Sciences iEES Paris, Sorbonne University, Paris, France
| | | | | | - Inge M M Baijens
- Department of Obstetrics and Gynecology, Division of Obstetrics and Fetal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Marjolein H G Dremmen
- Department of Radiology, Division of Paediatric Radiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Dick Tibboel
- Department of Paediatric Surgery, Erasmus MC, Erasmus University Medical Center Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Martin P Schol
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Alex J Eggink
- Department of Obstetrics and Gynecology, Division of Obstetrics and Fetal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Titia E Cohen-Overbeek
- Department of Obstetrics and Gynecology, Division of Obstetrics and Fetal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
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178
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Recurrent inversion toggling and great ape genome evolution. Nat Genet 2020; 52:849-858. [PMID: 32541924 PMCID: PMC7415573 DOI: 10.1038/s41588-020-0646-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 05/15/2020] [Indexed: 01/14/2023]
Abstract
Inversions play an important role in disease and evolution but are difficult to characterize because their breakpoints map to large repeats. We increased by sixfold the number (n = 1,069) of previously reported great ape inversions by using single-cell DNA template strand and long-read sequencing. We find that the X chromosome is most enriched (2.5-fold) for inversions, on the basis of its size and duplication content. There is an excess of differentially expressed primate genes near the breakpoints of large (>100 kilobases (kb)) inversions but not smaller events. We show that when great ape lineage-specific duplications emerge, they preferentially (approximately 75%) occur in an inverted orientation compared to that at their ancestral locus. We construct megabase-pair scale haplotypes for individual chromosomes and identify 23 genomic regions that have recurrently toggled between a direct and an inverted state over 15 million years. The direct orientation is most frequently the derived state for human polymorphisms that predispose to recurrent copy number variants associated with neurodevelopmental disease.
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179
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Cody JD. The Consequences of Abnormal Gene Dosage: Lessons from Chromosome 18. Trends Genet 2020; 36:764-776. [PMID: 32660784 DOI: 10.1016/j.tig.2020.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 12/18/2022]
Abstract
Accurate interpretation of genomic copy number variation (CNV) remains a challenge and has important consequences for both congenital and late-onset disease. Hemizygosity dosage characterization of the genes on chromosome 18 reveals a spectrum of outcomes ranging from no clinical effect, to risk factors for disease, to both low- and high-penetrance disease. These data are important for accurate and predictive clinical management. Additionally, the potential mechanisms of reduced penetrance due to dosage compensation are discussed as a key to understanding avenues for potential treatment. This review describes the chromosome 18 findings, and discusses the molecular mechanisms that allow haploinsufficiency, reduced penetrance, and dosage compensation.
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Affiliation(s)
- Jannine DeMars Cody
- Department of Pediatrics, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Chromosome 18 Registry and Research Society, San Antonio, TX 78229, USA.
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180
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Ashitha SNM, Ramachandra NB. Integrated Functional Analysis Implicates Syndromic and Rare Copy Number Variation Genes as Prominent Molecular Players in Pathogenesis of Autism Spectrum Disorders. Neuroscience 2020; 438:25-40. [DOI: 10.1016/j.neuroscience.2020.04.051] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 01/05/2023]
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181
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Muys J, Jacquemyn Y, Blaumeiser B, Bourlard L, Brison N, Bulk S, Chiarappa P, De Leener A, De Rademaeker M, Désir J, Destrée A, Devriendt K, Dheedene A, Duquenne A, Fieuw A, Fransen E, Gatot J, Jamar M, Janssens S, Kerstjens J, Keymolen K, Lederer D, Menten B, Pichon B, Rombout S, Sznajer Y, Van Den Bogaert A, Van Den Bogaert K, Vermeesch J, Janssens K. Prenatally detected copy number variants in a national cohort: A postnatal follow‐up study. Prenat Diagn 2020; 40:1272-1283. [DOI: 10.1002/pd.5751] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 05/13/2020] [Accepted: 05/16/2020] [Indexed: 01/17/2023]
Affiliation(s)
- Joke Muys
- Department of Gynaecology University Hospital Antwerp Edegem Belgium
- Center for Medical Genetics, Universiteit Antwerpen Antwerpen Belgium
| | - Yves Jacquemyn
- Department of Gynaecology University Hospital Antwerp Edegem Belgium
- ASTARC and Global Health Institute Universiteit Antwerpen Antwerpen Belgium
| | - Bettina Blaumeiser
- Department of Gynaecology University Hospital Antwerp Edegem Belgium
- Center for Medical Genetics, Universiteit Antwerpen Antwerpen Belgium
| | - Laura Bourlard
- Center for Medical Genetics Université Libre de Bruxelles Bruxelles Belgium
| | - Nathalie Brison
- Center for Medical Genetics Katholieke Universiteit Leuven Leuven Belgium
| | - Saskia Bulk
- Center for Medical Genetics Centre Hospitalier Universitaire de Liège Liege Belgium
| | - Patrizia Chiarappa
- Center for Medical Genetics Université Catholique de Louvain Louvain‐la‐Neuve Belgium
| | - Anne De Leener
- Center for Medical Genetics Université Catholique de Louvain Louvain‐la‐Neuve Belgium
| | | | - Julie Désir
- Center for Medical Genetics Université Libre de Bruxelles Bruxelles Belgium
| | - Anne Destrée
- Center for Medical Genetics Institut de Pathologie et de Génétique Gosselies Gosselies Belgium
| | - Koenraad Devriendt
- Center for Medical Genetics Katholieke Universiteit Leuven Leuven Belgium
| | | | - Armelle Duquenne
- Center for Medical Genetics Université Catholique de Louvain Louvain‐la‐Neuve Belgium
| | - Annelies Fieuw
- Center for Medical Genetics Vrije Universiteit Brussel Brussel Belgium
| | - Erik Fransen
- Center for Medical Genetics, Universiteit Antwerpen Antwerpen Belgium
| | - Jean‐Stéphane Gatot
- Center for Medical Genetics Centre Hospitalier Universitaire de Liège Liege Belgium
| | - Mauricette Jamar
- Center for Medical Genetics Centre Hospitalier Universitaire de Liège Liege Belgium
| | | | - Jorien Kerstjens
- Faculty for Medical Sciences Rijksuniversteit Groningen Groningen The Netherlands
| | | | - Damien Lederer
- Center for Medical Genetics Institut de Pathologie et de Génétique Gosselies Gosselies Belgium
| | - Björn Menten
- Center for Medical Genetics Universiteit Gent Gent Belgium
| | - Bruno Pichon
- Center for Medical Genetics Université Libre de Bruxelles Bruxelles Belgium
| | - Sonia Rombout
- Center for Medical Genetics Institut de Pathologie et de Génétique Gosselies Gosselies Belgium
| | - Yves Sznajer
- Center for Medical Genetics Université Catholique de Louvain Louvain‐la‐Neuve Belgium
| | | | | | - Joris Vermeesch
- Center for Medical Genetics Katholieke Universiteit Leuven Leuven Belgium
| | - Katrien Janssens
- Center for Medical Genetics, Universiteit Antwerpen Antwerpen Belgium
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182
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Sadler B, Haller G, Antunes L, Nikolov M, Amarillo I, Coe B, Dobbs MB, Gurnett CA. Rare and de novo duplications containing SHOX in clubfoot. J Med Genet 2020; 57:851-857. [PMID: 32518174 PMCID: PMC7688552 DOI: 10.1136/jmedgenet-2020-106842] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/04/2020] [Accepted: 03/05/2020] [Indexed: 11/12/2022]
Abstract
Introduction Congenital clubfoot is a common birth defect that affects at least 0.1% of all births. Nearly 25% cases are familial and the remaining are sporadic in inheritance. Copy number variants (CNVs) involving transcriptional regulators of limb development, including PITX1 and TBX4, have previously been shown to cause familial clubfoot, but much of the heritability remains unexplained. Methods Exome sequence data from 816 unrelated clubfoot cases and 2645 in-house controls were analysed using coverage data to identify rare CNVs. The precise size and location of duplications were then determined using high-density Affymetrix Cytoscan chromosomal microarray (CMA). Segregation in families and de novo status were determined using qantitative PCR. Results Chromosome Xp22.33 duplications involving SHOX were identified in 1.1% of cases (9/816) compared with 0.07% of in-house controls (2/2645) (p=7.98×10−5, OR=14.57) and 0.27% (38/13592) of Atherosclerosis Risk in Communities/the Wellcome Trust Case Control Consortium 2 controls (p=0.001, OR=3.97). CMA validation confirmed an overlapping 180.28 kb duplicated region that included SHOX exons as well as downstream non-coding regions. In four of six sporadic cases where DNA was available for unaffected parents, the duplication was de novo. The probability of four de novo mutations in SHOX by chance in a cohort of 450 sporadic clubfoot cases is 5.4×10–10. Conclusions Microduplications of the pseudoautosomal chromosome Xp22.33 region (PAR1) containing SHOX and downstream enhancer elements occur in ~1% of patients with clubfoot. SHOX and regulatory regions have previously been implicated in skeletal dysplasia as well as idiopathic short stature, but have not yet been reported in clubfoot. SHOX duplications likely contribute to clubfoot pathogenesis by altering early limb development.
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Affiliation(s)
- Brooke Sadler
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, Missouri, USA
| | - Gabe Haller
- Department of Orthopedic Surgery, Washington University in Saint Louis School of Medicine, Saint Louis, Missouri, USA
| | - Lilian Antunes
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, Missouri, USA
| | - Momchil Nikolov
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, Missouri, USA
| | - Ina Amarillo
- Department of Pathology and Immunology, Washington University in Saint Louis School of Medicine, Saint Louis, Missouri, USA
| | - Bradley Coe
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA.,Department of Pathology & Laboratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Matthew B Dobbs
- Department of Orthopedic Surgery, Washington University in Saint Louis School of Medicine, Saint Louis, Missouri, USA
| | - Christina A Gurnett
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, Missouri, USA
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183
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Oneda B, Sirleto P, Baldinger R, Taralczak M, Joset P, Zweier M, Niedrist D, Azzarello-Burri S, Britschgi C, Breymann C, Ochsenbein-Kölble N, Burkhardt T, Wisser J, Zimmermann R, Steindl K, Rauch A. Genome-wide non-invasive prenatal testing in single- and multiple-pregnancies at any risk: Identification of maternal polymorphisms to reduce the number of unnecessary invasive confirmation testing. Eur J Obstet Gynecol Reprod Biol 2020; 252:19-29. [PMID: 32619881 DOI: 10.1016/j.ejogrb.2020.05.070] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 05/29/2020] [Accepted: 05/31/2020] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Non-invasive prenatal testing by targeted or genome-wide copy number profiling (cnNIPT) has the potential to outperform standard NIPT targeting the common trisomies 13, 18, and 21, only. Nevertheless, prospective results and outcome data on cnNIPT are still scarce and there is increasing evidence for maternal copy number variants (CNVs) interfering with results of both, standard and cnNIPT. STUDY DESIGN We assessed the performance of cnNIPT in 3053 prospective and 116 retrospective cases with special consideration of maternal CNVs in singleton and multiple gestational pregnancies at any risk, as well as comprehensive follow-up. RESULTS A result was achieved in 2998 (98.2%) of total prospective cases (89.2% analyzed genome-wide). Confirmed fetal chromosomal abnormalities were detected in 45 (1.5%) cases, of which five (11%) would have remained undetected in standard NIPTs. Additionally, we observed 4 likely fetal trisomies without follow-up and a likely phenotype associated placental partial trisomy 16. Moreover, we observed clinically relevant confirmed maternal CNVs in 9 (0.3%) cases and likely maternal clonal hematopoiesis in 3 (0.1%). For common fetal trisomies we prospectively observed a very high sensitivity (100% [95% CI: 91.96-100%]) and specificity (>99.9% [95% CI: 99.8-100%]), and positive predictive value (PPV) (97.8% [95% CI: 86.1-99.7%]), but our retrospective control cases demonstrated that due to cases of fetal restricted mosaicism the true sensitivity of NIPT is lower. After showing that 97.3% of small CNVs prospectively observed in 8.3% of genome-wide tests were mostly benign maternal variants, sensitivity (75.0% [95% CI: 19.4%-99.4%]), specificity (99.7% [99.5%-99.9%]) and PPV (30.0% [14.5%-52.1%]) for relevant fetal CNVs were relatively high, too. Maternal autoimmune disorders and medication, such as dalteparin, seem to impair assay quality. CONCLUSION When maternal CNVs are recognized as such, cnNIPT showed a very high sensitivity, specificity and PPV for common trisomies in single and multiple pregnancies at any risk and very good values genome-wide. We found that the resolution for segmental aberrations is generally comparable to standard karyotyping, and exceeds the latter if the fetal fraction is above 10%, which allows detection of the 2.5 Mb 22q11.2 microdeletion associated with the velocardiofacial syndrome, even if the mother is not a carrier.
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Affiliation(s)
- Beatrice Oneda
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland.
| | - Pietro Sirleto
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Rosa Baldinger
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | | | - Pascal Joset
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Markus Zweier
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Dunja Niedrist
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | | | - Christian Britschgi
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | | | - Nicole Ochsenbein-Kölble
- Division of Obstetrics, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Tilo Burkhardt
- Division of Obstetrics, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Josef Wisser
- Division of Obstetrics, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Roland Zimmermann
- Division of Obstetrics, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
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184
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Mansfield P, Constantino JN, Baldridge D. MYT1L: A systematic review of genetic variation encompassing schizophrenia and autism. Am J Med Genet B Neuropsychiatr Genet 2020; 183:227-233. [PMID: 32267091 PMCID: PMC7605444 DOI: 10.1002/ajmg.b.32781] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 01/23/2020] [Accepted: 02/03/2020] [Indexed: 02/03/2023]
Abstract
Variations in MYT1L, a gene encoding a transcription factor expressed in the brain, have been associated with autism, intellectual disability, and schizophrenia. Here we provide an updated review of published reports of neuropsychiatric correlates of loss of function and duplication of MYT1L. Of 27 duplications all were partial; 33% were associated exclusively with schizophrenia, and the chromosomal locations of schizophrenia-associated duplications exhibited a distinct difference in pattern-of-location from those associated with autism and/or intellectual disability. Of 51 published heterozygous loss of function variants, all but one were associated with intellectual disability, autism, or both, and one resulted in no neuropsychiatric diagnosis. There were no reports of schizophrenia associated with loss of function variants of MYT1L (Fisher's exact p < .00001, for contrast with all reported duplications). Although the precise function of the various mutations remains unspecified, these data collectively establish the candidacy of MYT1L as a reciprocal mutation, in which schizophrenia may be engendered by partial duplications, typically involving the 3' end of the gene, while developmental disability-notably autism-is associated with both loss of function and partial duplication. Future research on the specific effects of contrasting mutations in MYT1L may provide insight into the causal origins of autism and schizophrenia.
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Affiliation(s)
| | - John N. Constantino
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, Missouri,Department of Pediatrics, Washington University School of Medicine, Saint Louis, Missouri
| | - Dustin Baldridge
- Department of Pediatrics, Washington University School of Medicine, Saint Louis, Missouri
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185
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Singer A, Maya I, Banne E, Baris Feldman H, Vinkler C, Ben Shachar S, Sagi-Dain L. Prenatal clubfoot increases the risk for clinically significant chromosomal microarray results - Analysis of 269 singleton pregnancies. Early Hum Dev 2020; 145:105047. [PMID: 32339917 DOI: 10.1016/j.earlhumdev.2020.105047] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/05/2020] [Accepted: 04/17/2020] [Indexed: 11/16/2022]
Abstract
OBJECTIVE To examine the detection rate of clinically significant chromosomal microarray analysis (CMA) results in singleton pregnancies with clubfoot. METHODS Data from all CMA tests in singleton pregnancies with sonographic diagnosis of clubfoot (talipes equinovarus) performed between January 2013 and September 2017 were retrospectively obtained from the Israeli Ministry of Health computerized database. The rates of clinically significant CMA results in fetuses with clubfoot were compared to the general population risk, based on a local cohort of 5541 pregnancies with no major sonographic anomalies. RESULTS Of the 5750 CMA tests, a total of 269 (4.7%) were performed due to demonstration of fetal clubfoot. Of the 229 cases with isolated deformity, nine (3.9%) clinically significant CMA results were detected. This detection rate is significantly increased compared to the control population (RR 2.7 (95% CI 1.4-5.0)). In the 40 pregnancies with non-isolated clubfoot, seven (17.5%) clinically significant CMA results were detected, a significantly higher frequency compared to the control population and to isolated clubfoot cases. DISCUSSION Sonographic diagnosis of clubfoot, whether isolated or associated with additional sonographic defects, increases the risk for abnormal CMA findings. Thus, CMA analysis, in conjunction with thorough sonographic anatomic survey, should be recommended in such pregnancies.
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Affiliation(s)
- Amihood Singer
- Community Genetics, Public Health Services, Ministry of Health, Jerusalem, Israel
| | - Idit Maya
- Recanati Genetics Institute, Beilinson Hospital, Rabin Medical Center, Petach Tikva, Israel
| | - Ehud Banne
- Department of Genetics and Metabolic Diseases, Hadassah, Hebrew University Medical Center, Jerusalem, Israel
| | - Hagit Baris Feldman
- Genetic Institute, Tel Aviv Sourasky Medical Center, and the Technion - Israel Institute of Technology, Haifa, Israel
| | - Chana Vinkler
- Institute of Medical Genetics, Metabolic Neurogenetic Service, Wolfson Medical Center, Holon, Israel
| | - Shay Ben Shachar
- Genetics Institute, Tel Aviv Sourasky Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Lena Sagi-Dain
- Genetics Institute, Carmel Medical Center, affiliated to the Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel.
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186
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Simpson JL, Rechitsky S, Kuliev A. Before the beginning: the genetic risk of a couple aiming to conceive. Fertil Steril 2020; 112:622-630. [PMID: 31561864 DOI: 10.1016/j.fertnstert.2019.08.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/02/2019] [Accepted: 08/05/2019] [Indexed: 11/17/2022]
Abstract
Disorders of genetic etiology exist in 2%-3% of live-born infants. Identifying couples with increased susceptibility for offspring with anomalies or genetic disorders is increasingly effective as a result of molecular advances. Preimplantation genetic testing (PGT) with the use of trophectoderm biopsy, 24-chromosome testing, and molecular testing have allowed wider applicability for avoiding a clinical pregnancy termination. Cell-free DNA in maternal blood is another targeted option, although invasive prenatal genetic diagnosis provides the greatest amount of genetic information. DNA-based methods to detect subtle chromosomal abnormalities are much more sensitive than traditional karyotypes and do not require cultured cells. Aneuploidy and structural chromosomal abnormalities can be readily detected with the use of small amounts of DNA, if necessary amplified, as in PGT. Novel approaches exist for detecting perturbations in single-gene disorders. Not only has the molecular basis for many monogenic disorders been elucidated, but modest costs for DNA sequencing has made testing feasible. As the number of testable genetic disorders has increased, principles underlying screening have advanced. Genetic screening for disorders of high incidence in certain ethnic groups was initiated decades ago; however, limitations exist, and reduction in live-born incidence is not infrequently small. Expanded carrier screening is now offered in panethnic fashion, extending surveillance to couples of mixed ethnicities and involving many more genetic conditions. Targeted gene panels (e.g., adult-onset cancer genes) further increase the number of genetic disorders amenable to screening, often leading to PGT.
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Affiliation(s)
- Joe Leigh Simpson
- Department of Human and Medical Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida; Reproductive Genetic Innovation, Northbrook, Illinois.
| | - Svetlana Rechitsky
- Department of Human and Medical Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida; Reproductive Genetic Innovation, Northbrook, Illinois
| | - Anver Kuliev
- Department of Human and Medical Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida; Reproductive Genetic Innovation, Northbrook, Illinois
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187
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Tevzadze G, Zhuravliova E, Barbakadze T, Shanshiashvili L, Dzneladze D, Nanobashvili Z, Lordkipanidze T, Mikeladze D. Gut neurotoxin p-cresol induces differential expression of GLUN2B and GLUN2A subunits of the NMDA receptor in the hippocampus and nucleus accumbens in healthy and audiogenic seizure-prone rats. AIMS Neurosci 2020; 7:30-42. [PMID: 32455164 PMCID: PMC7242059 DOI: 10.3934/neuroscience.2020003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/17/2020] [Indexed: 01/18/2023] Open
Abstract
Mislocalization and abnormal expression of N-methyl-D-aspartate glutamate receptor (NMDAR) subunits is observed in several brain disorders and pathological conditions. Recently, we have shown that intraperitoneal injection of the gut neurotoxin p-cresol induces autism-like behavior and accelerates seizure reactions in healthy and epilepsy-prone rats, respectively. In this study, we evaluated the expression of GLUN2B and GLUN2A NMDAR subunits, and assessed the activity of cAMP-response element binding protein (CREB) and Rac1 in the hippocampi and nucleus accumbens of healthy and epilepsy-prone rats following p-cresol administration. We have found that subchronic intraperitoneal injection of p-cresol induced differential expression of GLUN2B and GLUN2A between the two brain regions, and altered the GLUN2B/GLUN2A ratio, in rats in both groups. Moreover, p-cresol impaired CREB phosphorylation in both brain structures and stimulated Rac activity in the hippocampus. These data indicate that p-cresol differently modulates the expression of NMDAR subunits in the nucleus accumbens and hippocampi of healthy and epilepsy-prone rats. We propose that these differences are due to the specificity of interactions between dopaminergic and glutamatergic pathways in these structures.
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Affiliation(s)
- Gigi Tevzadze
- 4-D Research Institute, Ilia State University, 3/5 Cholokashvili av, Tbilisi, 0162, Georgia
| | - Elene Zhuravliova
- Institute of Chemical Biology, Ilia State University, 3/5 Cholokashvili av, Tbilisi, 0162, Georgia.,I. Beritashvili Center of Experimental Biomedicine 14, Gotua Str., Tbilisi 0160, Georgia
| | - Tamar Barbakadze
- Institute of Chemical Biology, Ilia State University, 3/5 Cholokashvili av, Tbilisi, 0162, Georgia.,I. Beritashvili Center of Experimental Biomedicine 14, Gotua Str., Tbilisi 0160, Georgia
| | - Lali Shanshiashvili
- Institute of Chemical Biology, Ilia State University, 3/5 Cholokashvili av, Tbilisi, 0162, Georgia.,I. Beritashvili Center of Experimental Biomedicine 14, Gotua Str., Tbilisi 0160, Georgia
| | - Davit Dzneladze
- I. Beritashvili Center of Experimental Biomedicine 14, Gotua Str., Tbilisi 0160, Georgia
| | - Zaqaria Nanobashvili
- I. Beritashvili Center of Experimental Biomedicine 14, Gotua Str., Tbilisi 0160, Georgia
| | - Tamar Lordkipanidze
- Institute of Chemical Biology, Ilia State University, 3/5 Cholokashvili av, Tbilisi, 0162, Georgia.,I. Beritashvili Center of Experimental Biomedicine 14, Gotua Str., Tbilisi 0160, Georgia
| | - David Mikeladze
- Institute of Chemical Biology, Ilia State University, 3/5 Cholokashvili av, Tbilisi, 0162, Georgia.,I. Beritashvili Center of Experimental Biomedicine 14, Gotua Str., Tbilisi 0160, Georgia
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188
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Mountford HS, Bishop DVM, Thompson PA, Simpson NH, Newbury DF. Copy number variation burden does not predict severity of neurodevelopmental phenotype in children with a sex chromosome trisomy. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:256-266. [PMID: 32452638 DOI: 10.1002/ajmg.c.31791] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 12/14/2022]
Abstract
Sex chromosome trisomies (SCTs) (XXX, XXY, and XYY karyotypes) are associated with an elevated risk of neurodevelopmental disorders. The range of severity of the phenotype is substantial. We considered whether this variable outcome was related to the presence of copy number variants (CNVs)-stretches of duplicated or deleted DNA. A sample of 125 children with an SCT were compared with 181 children of normal karyotype who had been given the same assessments. First, we compared the groups on measures of overall CNV burden: number of CNVs, total span of CNVs, and likely functional impact (probability of loss-of-function intolerance, pLI, summed over CNVs). Differences between groups were small relative to within-group variance and not statistically significant on overall test. Next, we considered whether a measure of general neurodevelopmental impairment was predicted by pLI summed score, SCT versus comparison group, or the interaction between them. There was a substantial effect of SCT/comparison status but the pLI score was not predictive of outcomes in either group. We conclude that variable presence of CNVs is not a likely explanation for the wide phenotypic variation in children with SCTs. We discuss methodological challenges of testing whether CNVs are implicated in causing neurodevelopmental problems.
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Affiliation(s)
- Hayley S Mountford
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, Oxfordshire, UK
| | - Dorothy V M Bishop
- Department of Experimental Psychology, University of Oxford, Oxford, Oxfordshire, UK
| | - Paul A Thompson
- Department of Experimental Psychology, University of Oxford, Oxford, Oxfordshire, UK
| | - Nuala H Simpson
- Department of Experimental Psychology, University of Oxford, Oxford, Oxfordshire, UK
| | - Dianne F Newbury
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, Oxfordshire, UK
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189
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Sullivan JA, Stong N, Baugh EH, McDonald MT, Takeuchi A, Shashi V. A pathogenic variant in the SETBP1 hotspot results in a forme-fruste Schinzel-Giedion syndrome. Am J Med Genet A 2020; 182:1947-1951. [PMID: 32445275 DOI: 10.1002/ajmg.a.61630] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/25/2020] [Accepted: 04/28/2020] [Indexed: 12/12/2022]
Abstract
Schinzel-Giedion syndrome (SGS; OMIM 269150) is an ultra-rare genetic disorder associated with a distinctive facial gestalt, congenital malformations, severe intellectual disability, and a progressive neurological course. The prognosis for SGS is poor, with survival beyond the first decade rare. Germline, de novo heterozygous variants in the SETBP1 gene cause SGS with the pathogenic variants associated with the SGS phenotype missense and confined to exon 4 of the gene, clustered in a four amino acid (12 bp) hotspot in the SKI homologous region of the SETBP1 protein. We report a patient with a de novo I871S variant within the SKI homologous region, which has been associated with the severe phenotype previously; but our patient has fewer features of SGS and a milder course. This is the first report of a forme-fruste phenotype in a patient with a pathogenic variant within the SGS hotspot on the SETBP1 gene and it highlights the importance of considering atypical clinical presentations in the context of severe ultra-rare genetic disorders.
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Affiliation(s)
- Jennifer A Sullivan
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Evan H Baugh
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Marie T McDonald
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Akihito Takeuchi
- Department of Neonatology, Okayama Medical Center, National Hospital Organization, Okayama, Japan
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
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190
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Golicz AA, Bhalla PL, Edwards D, Singh MB. Rice 3D chromatin structure correlates with sequence variation and meiotic recombination rate. Commun Biol 2020; 3:235. [PMID: 32398676 PMCID: PMC7217851 DOI: 10.1038/s42003-020-0932-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 03/31/2020] [Indexed: 11/30/2022] Open
Abstract
Genomes of many eukaryotic species have a defined three-dimensional architecture critical for cellular processes. They are partitioned into topologically associated domains (TADs), defined as regions of high chromatin inter-connectivity. While TADs are not a prominent feature of A. thaliana genome organization, they have been reported for other plants including rice, maize, tomato and cotton and for which TAD formation appears to be linked to transcription and chromatin epigenetic status. Here we show that in the rice genome, sequence variation and meiotic recombination rate correlate with the 3D genome structure. TADs display increased SNP and SV density and higher recombination rate compared to inter-TAD regions. We associate the observed differences with the TAD epigenetic landscape, TE composition and an increased incidence of meiotic crossovers. Golicz et al. report an increase in single nucleotide polymorphisms and structural variations across and within Topologically Associated Domains (TADs) in the rice genome, which is different to the pattern observed in the human genome. They show that this may be due to epigenetic modifications, transposable elements composition, and meiotic crossovers in the TAD regions.
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Affiliation(s)
- Agnieszka A Golicz
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Prem L Bhalla
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Mohan B Singh
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
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191
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A brief report: de novo copy number variants in children with attention deficit hyperactivity disorder. Transl Psychiatry 2020; 10:135. [PMID: 32398668 PMCID: PMC7217839 DOI: 10.1038/s41398-020-0821-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/06/2020] [Accepted: 04/21/2020] [Indexed: 01/09/2023] Open
Abstract
Recent case-control genetic studies of attention deficit hyperactivity disorder (ADHD) have implicated common and rare genetic risk alleles, highlighting the polygenic and complex aetiology of this neurodevelopmental disorder. Studies of other neurodevelopmental disorders, such as autism spectrum disorder (ASD), Tourette disorder, developmental delay/intellectual disability and schizophrenia indicate that identification of specific risk alleles and additional insights into disorder biology can be gained by studying non-inherited de novo variation. In this study, we aimed to identify large de novo copy number variants (CNVs) in children with ADHD. Children with a confirmed diagnosis of ADHD and their parents were genotyped and included in this sample. We used PennCNV to call large (>200 kb) CNVs and identified those calls that were present in the proband and absent in both biological parents. In 305 parent-offspring trios, we detected 14 de novo CNVs in 13 probands, giving a mutation rate of 4.6% and a per individual rate of 4.3%. This rate is higher than published reports in controls and similar to those observed for ASD, schizophrenia and Tourette disorder. We also identified de novo mutations at four genomic loci (15q13.1-13.2 duplication, 16p13.11 duplication, 16p12.2 deletion and 22q11.21 duplication) that have previously been implicated in other neurodevelopmental disorders, two of which (16p13.11 and 22q11.21) have also been implicated in case-control ADHD studies. Our study complements ADHD case-control genomic analyses and demonstrates the need for larger parent-offspring trio genetic studies to gain further insights into the complex aetiology of ADHD.
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192
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Legge SE, Dennison CA, Pardiñas AF, Rees E, Lynham AJ, Hopkins L, Bates L, Kirov G, Owen MJ, O'Donovan MC, Walters JTR. Clinical indicators of treatment-resistant psychosis. Br J Psychiatry 2020; 216:259-266. [PMID: 31155017 DOI: 10.1192/bjp.2019.120] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
BACKGROUND Around 30% of individuals with schizophrenia remain symptomatic and significantly impaired despite antipsychotic treatment and are considered to be treatment resistant. Clinicians are currently unable to predict which patients are at higher risk of treatment resistance. AIMS To determine whether genetic liability for schizophrenia and/or clinical characteristics measurable at illness onset can prospectively indicate a higher risk of treatment-resistant psychosis (TRP). METHOD In 1070 individuals with schizophrenia or related psychotic disorders, schizophrenia polygenic risk scores (PRS) and large copy number variations (CNVs) were assessed for enrichment in TRP. Regression and machine-learning approaches were used to investigate the association of phenotypes related to demographics, family history, premorbid factors and illness onset with TRP. RESULTS Younger age at onset (odds ratio 0.94, P = 7.79 × 10-13) and poor premorbid social adjustment (odds ratio 1.64, P = 2.41 × 10-4) increased risk of TRP in univariate regression analyses. These factors remained associated in multivariate regression analyses, which also found lower premorbid IQ (odds ratio 0.98, P = 7.76 × 10-3), younger father's age at birth (odds ratio 0.97, P = 0.015) and cannabis use (odds ratio 1.60, P = 0.025) increased the risk of TRP. Machine-learning approaches found age at onset to be the most important predictor and also identified premorbid IQ and poor social adjustment as predictors of TRP, mirroring findings from regression analyses. Genetic liability for schizophrenia was not associated with TRP. CONCLUSIONS People with an earlier age at onset of psychosis and poor premorbid functioning are more likely to be treatment resistant. The genetic architecture of susceptibility to schizophrenia may be distinct from that of treatment outcomes.
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Affiliation(s)
- Sophie E Legge
- Research Associate, Medical Research Council (MRC) Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, UK
| | - Charlotte A Dennison
- PhD Student, MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, UK
| | - Antonio F Pardiñas
- Lecturer, MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, UK
| | - Elliott Rees
- Research Associate, MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, UK
| | - Amy J Lynham
- Research Associate, MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, UK
| | - Lucinda Hopkins
- Sample and Governance Manager, MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, UK
| | - Lesley Bates
- Laboratory Manager, MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, UK
| | - George Kirov
- Professor, MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, UK
| | - Michael J Owen
- Director, MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, UK
| | - Michael C O'Donovan
- Professor, MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, UK
| | - James T R Walters
- Professor, MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, UK
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193
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Rees E, Owen MJ. Translating insights from neuropsychiatric genetics and genomics for precision psychiatry. Genome Med 2020; 12:43. [PMID: 32349784 PMCID: PMC7189552 DOI: 10.1186/s13073-020-00734-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 04/03/2020] [Indexed: 12/30/2022] Open
Abstract
The primary aim of precision medicine is to tailor healthcare more closely to the needs of individual patients. This requires progress in two areas: the development of more precise treatments and the ability to identify patients or groups of patients in the clinic for whom such treatments are likely to be the most effective. There is widespread optimism that advances in genomics will facilitate both of these endeavors. It can be argued that of all medical specialties psychiatry has most to gain in these respects, given its current reliance on syndromic diagnoses, the minimal foundation of existing mechanistic knowledge, and the substantial heritability of psychiatric phenotypes. Here, we review recent advances in psychiatric genomics and assess the likely impact of these findings on attempts to develop precision psychiatry. Emerging findings indicate a high degree of polygenicity and that genetic risk maps poorly onto the diagnostic categories used in the clinic. The highly polygenic and pleiotropic nature of psychiatric genetics will impact attempts to use genomic data for prediction and risk stratification, and also poses substantial challenges for conventional approaches to gaining biological insights from genetic findings. While there are many challenges to overcome, genomics is building an empirical platform upon which psychiatry can now progress towards better understanding of disease mechanisms, better treatments, and better ways of targeting treatments to the patients most likely to benefit, thus paving the way for precision psychiatry.
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Affiliation(s)
- Elliott Rees
- grid.5600.30000 0001 0807 5670MRC Centre for Neuropsychiatric Genetics and Genomics, Neuroscience and Mental Health Research Institute and Division of Psychological Medicine and Clinical Neuroscience, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ UK
| | - Michael J. Owen
- grid.5600.30000 0001 0807 5670MRC Centre for Neuropsychiatric Genetics and Genomics, Neuroscience and Mental Health Research Institute and Division of Psychological Medicine and Clinical Neuroscience, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ UK
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194
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Sjaarda CP, Kaiser B, McNaughton AJM, Hudson ML, Harris-Lowe L, Lou K, Guerin A, Ayub M, Liu X. De novo duplication on Chromosome 19 observed in nuclear family displaying neurodevelopmental disorders. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a004721. [PMID: 32321736 PMCID: PMC7304355 DOI: 10.1101/mcs.a004721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 04/06/2020] [Indexed: 11/25/2022] Open
Abstract
Pleiotropy and variable expressivity have been cited to explain the seemingly distinct neurodevelopmental disorders due to a common genetic etiology within the same family. Here we present a family with a de novo 1-Mb duplication involving 18 genes on Chromosome 19. Within the family there are multiple cases of neurodevelopmental disorders including autism spectrum disorder, attention deficit/hyperactivity disorder, intellectual disability, and psychiatric disease in individuals carrying this copy-number variant (CNV). Quantitative polymerase chain reaction (PCR) confirmed the CNV was de novo in the mother and inherited by both sons. Whole-exome sequencing did not uncover further genetic risk factors segregating within the family. Transcriptome analysis of peripheral blood demonstrated a ∼1.5-fold increase in RNA transcript abundance in 12 of the 15 detected genes within the CNV region for individuals carrying the CNV compared with their noncarrier relatives. Examination of transcript abundance across the rest of the transcriptome identified 407 differentially expressed genes (P-value < 0.05; adjusted P-value < 0.1) mapping to immune response, response to endoplasmic reticulum stress, and regulation of epithelial cell proliferation pathways. 16S microbiome profiling demonstrated compositional difference in the gut bacteria between the half-brothers. These results raise the possibility that the observed CNV may contribute to the varied phenotypic characteristics in family members through alterations in gene expression and/or dysbiosis of the gut microbiome. More broadly, there is growing evidence that different neurodevelopmental and psychiatric disorders can share the same genetic variant, which lays a framework for later neurodevelopmental and psychiatric manifestations.
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Affiliation(s)
- Calvin P Sjaarda
- Queen's Genomics Laboratory at Ongwanada (QGLO), Ongwanada Resource Center, Kingston, Ontario K7M 8A6, Canada.,Department of Psychiatry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Beatrice Kaiser
- Queen's Genomics Laboratory at Ongwanada (QGLO), Ongwanada Resource Center, Kingston, Ontario K7M 8A6, Canada.,Department of Psychiatry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Amy J M McNaughton
- Queen's Genomics Laboratory at Ongwanada (QGLO), Ongwanada Resource Center, Kingston, Ontario K7M 8A6, Canada.,Department of Psychiatry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Melissa L Hudson
- Queen's Genomics Laboratory at Ongwanada (QGLO), Ongwanada Resource Center, Kingston, Ontario K7M 8A6, Canada.,Department of Psychiatry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Liam Harris-Lowe
- Queen's Genomics Laboratory at Ongwanada (QGLO), Ongwanada Resource Center, Kingston, Ontario K7M 8A6, Canada.,School of Applied Science and Computing, St. Lawrence College, Kingston, Ontario K7L 5A6, Canada
| | - Kyle Lou
- Queen's Genomics Laboratory at Ongwanada (QGLO), Ongwanada Resource Center, Kingston, Ontario K7M 8A6, Canada.,Department of Psychiatry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Andrea Guerin
- Division of Medical Genetics, Department of Pediatrics, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Muhammad Ayub
- Department of Psychiatry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Xudong Liu
- Queen's Genomics Laboratory at Ongwanada (QGLO), Ongwanada Resource Center, Kingston, Ontario K7M 8A6, Canada.,Department of Psychiatry, Queen's University, Kingston, Ontario K7L 3N6, Canada
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195
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Kahila H, Marjonen H, Auvinen P, Avela K, Riikonen R, Kaminen‐Ahola N. 18q12.3-q21.1 microdeletion detected in the prenatally alcohol-exposed dizygotic twin with discordant fetal alcohol syndrome phenotype. Mol Genet Genomic Med 2020; 8:e1192. [PMID: 32096599 PMCID: PMC7196488 DOI: 10.1002/mgg3.1192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 11/21/2019] [Accepted: 12/10/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND A pair of dizygotic twins discordantly affected by heavy prenatal alcohol exposure (PAE) was reported previously by Riikonen, suggesting the role of genetic risk or protective factors in the etiology of alcohol-induced developmental disorders. Now, we have re-examined these 25-year-old twins and explored genetic origin of the phenotypic discordancy reminiscent with fetal alcohol syndrome (FAS). Furthermore, we explored alterations in DNA methylation profile of imprinting control region at growth-related insulin-like growth factor 2 (IGF2)/H19 locus in twins' white blood cells (WBC), which have been associated earlier with alcohol-induced genotype-specific changes in placental tissue. METHODS Microarray-based comparative genomic hybridization (aCGH) was used to detect potential submicroscopic chromosomal abnormalities, and developmental as well as phenotypic information about twins were collected. Traditional bisulfite sequencing was used for DNA methylation analysis. RESULTS Microarray-based comparative genomic hybridization revealed a microdeletion 18q12.3-q21.1. in affected twin, residing in a known 18q deletion syndrome region. This syndrome has been associated with growth restriction, developmental delay or intellectual deficiency, and abnormal facial features in previous studies, and thus likely explains the phenotypic discordancy between the twins. We did not observe association between WBCs' DNA methylation profile and PAE, but interestingly, a trend of decreased DNA methylation at the imprinting control region was seen in the twin with prenatal growth retardation at birth. CONCLUSIONS The microdeletion emphasizes the importance of adequate chromosomal testing in examining the etiology of complex alcohol-induced developmental disorders. Furthermore, the genotype-specific decreased DNA methylation at the IGF2/H19 locus cannot be considered as a biological mark for PAE in adult WBCs.
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Affiliation(s)
- Hanna Kahila
- Department of Obstetrics and GynecologyHelsinki University Hospital and University of HelsinkiHelsinkiFinland
| | - Heidi Marjonen
- Department of Medical and Clinical GeneticsMedicumUniversity of HelsinkiHelsinkiFinland
| | - Pauliina Auvinen
- Department of Medical and Clinical GeneticsMedicumUniversity of HelsinkiHelsinkiFinland
| | - Kristiina Avela
- Department of Clinical GeneticsHelsinki University HospitalHUSLABHelsinkiFinland
| | - Raili Riikonen
- Children's HospitalKuopio University HospitalUniversity of Eastern FinlandKuopioFinland
| | - Nina Kaminen‐Ahola
- Department of Medical and Clinical GeneticsMedicumUniversity of HelsinkiHelsinkiFinland
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196
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Botton MR, Lu X, Zhao G, Repnikova E, Seki Y, Gaedigk A, Schadt EE, Edelmann L, Scott SA. Structural variation at the CYP2C locus: Characterization of deletion and duplication alleles. Hum Mutat 2020; 40:e37-e51. [PMID: 31260137 DOI: 10.1002/humu.23855] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/11/2019] [Accepted: 06/25/2019] [Indexed: 12/27/2022]
Abstract
The human CYP2C locus harbors the polymorphic CYP2C18, CYP2C19, CYP2C9, and CYP2C8 genes, and of these, CYP2C19 and CYP2C9 are directly involved in the metabolism of ~15% of all medications. All variant CYP2C19 and CYP2C9 star (*) allele haplotypes currently cataloged by the Pharmacogene Variation (PharmVar) Consortium are defined by sequence variants. To determine if structural variation also occurs at the CYP2C locus, the 10q23.33 region was interrogated across deidentified clinical chromosomal microarray (CMA) data from 20,642 patients tested at two academic medical centers. Fourteen copy number variants that affected the coding region of CYP2C genes were detected in the clinical CMA cohorts, which ranged in size from 39.2 to 1,043.3 kb. Selected deletions and duplications were confirmed by MLPA or ddPCR. Analysis of the clinical CMA and an additional 78,839 cases from the Database of Genomic Variants (DGV) and ClinGen (total n = 99,481) indicated that the carrier frequency of a CYP2C structural variant is ~1 in 1,000, with ~1 in 2,000 being a CYP2C19 full gene or partial-gene deletion carrier, designated by PharmVar as CYP2C19*36 and *37, respectively. Although these structural variants are rare in the general population, their detection will likely improve metabolizer phenotype prediction when interrogated for research and/or clinical testing.
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Affiliation(s)
- Mariana R Botton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Sema4, A Mount Sinai venture, Stamford, Connecticut
| | - Xingwu Lu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Sema4, A Mount Sinai venture, Stamford, Connecticut
| | - Geping Zhao
- Sema4, A Mount Sinai venture, Stamford, Connecticut
| | - Elena Repnikova
- Clinical Genetics and Genomics Laboratories, Children's Mercy Hospital Kansas City, Kansas City, Missouri.,School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri
| | | | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Sema4, A Mount Sinai venture, Stamford, Connecticut
| | - Lisa Edelmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Sema4, A Mount Sinai venture, Stamford, Connecticut
| | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Sema4, A Mount Sinai venture, Stamford, Connecticut
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197
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Yates TM, Drucker M, Barnicoat A, Low K, Gerkes EH, Fry AE, Parker MJ, O'Driscoll M, Charles P, Cox H, Marey I, Keren B, Rinne T, McEntagart M, Ramachandran V, Drury S, Vansenne F, Sival DA, Herkert JC, Callewaert B, Tan W, Balasubramanian M. ZMYND11
‐related syndromic intellectual disability: 16 patients delineating and expanding the phenotypic spectrum. Hum Mutat 2020; 41:1042-1050. [PMID: 32097528 DOI: 10.1002/humu.24001] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 01/24/2020] [Accepted: 02/15/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Thabo M. Yates
- Sheffield Clinical Genetics ServiceSheffield Children's NHS Foundation TrustSheffield UK
| | - Morgan Drucker
- Department of PediatricsJohns Hopkins UniversityBaltimore Maryland
| | - Angela Barnicoat
- Northeast Thames Regional Genetics ServiceGreat Ormond Street Hospital for ChildrenLondon UK
| | - Karen Low
- Department of Clinical GeneticsSt Michael's HospitalBristol UK
| | - Erica H. Gerkes
- Department of Genetics, University of GroningenUniversity Medical Center GroningenGroningen The Netherlands
| | - Andrew E. Fry
- Institute of Medical GeneticsUniversity Hospital of WalesCardiff UK
| | - Michael J. Parker
- Sheffield Clinical Genetics ServiceSheffield Children's NHS Foundation TrustSheffield UK
| | - Mary O'Driscoll
- West Midlands Regional Clinical Genetics ServiceBirmingham Health Partners Birmingham Women's Hospital NHS Foundation TrustBirmingham UK
| | - Perrine Charles
- Département de GénétiqueAPHP, Hopital La Pitie SalpetriereParis France
| | - Helen Cox
- West Midlands Regional Clinical Genetics ServiceBirmingham Health Partners Birmingham Women's Hospital NHS Foundation TrustBirmingham UK
| | - Isabelle Marey
- Département de GénétiqueAPHP, Hopital La Pitie SalpetriereParis France
| | - Boris Keren
- Département de GénétiqueAPHP, Hopital La Pitie SalpetriereParis France
| | - Tuula Rinne
- Department of GeneticsRadboud University Medical CenterNijmegen The Netherlands
| | - Meriel McEntagart
- South West Thames Regional Genetics Centre, St. George's Healthcare NHS TrustSt. George's, University of LondonLondon UK
| | - Vijaya Ramachandran
- Congenica Limited, Biodata Innovation CentreWellcome Genome CampusCambridge UK
| | - Suzanne Drury
- Congenica Limited, Biodata Innovation CentreWellcome Genome CampusCambridge UK
| | - Fleur Vansenne
- Department of Genetics, University of GroningenUniversity Medical Center GroningenGroningen The Netherlands
| | - Deborah A. Sival
- Department of Pediatrics, Beatrix Children's HospitalUniversity Medical Center GroningenGroningen The Netherlands
| | - Johanna C. Herkert
- Department of Genetics, University of GroningenUniversity Medical Center GroningenGroningen The Netherlands
| | - Bert Callewaert
- Department of Biomolecular Medicine, Ghent University, Ghent University HospitalCenter for Medical GeneticsGhent Belgium
| | - Wen‐Hann Tan
- Division of Genetics and Genomics, Boston Children's HospitalHarvard Medical SchoolBoston Massachusetts
| | - Meena Balasubramanian
- Sheffield Clinical Genetics ServiceSheffield Children's NHS Foundation TrustSheffield UK
- Department of Oncology and Metabolism, Academic Unit of Child HealthUniversity of SheffieldSheffield UK
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198
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Chen CP, Ko TM, Wang LK, Chern SR, Wu PS, Chen SW, Wu FT, Chen LF, Wang W. Inv dup del(10p): Prenatal diagnosis and molecular cytogenetic characterization. Taiwan J Obstet Gynecol 2020; 58:698-703. [PMID: 31542096 DOI: 10.1016/j.tjog.2019.07.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2019] [Indexed: 10/26/2022] Open
Abstract
OBJECTIVE We present molecular cytogenetic characterization of prenatally detected inverted duplication and deletion of 10p [inv dup del(10p)]. CASE REPORT A 39-year-old, primigravid woman underwent amniocentesis at 17 weeks of gestation because of advanced maternal age. Amniocentesis revealed a derivative chromosome 10 with additional material at the end of the short arm of one chromosome 10. Simultaneous array comparative genomic hybridization (aCGH) analysis revealed the result of arr 10p15.3 (136,361-451,013) × 1, 10p15.3p12.1 (536,704-25,396,900) × 3 [GRCh37 (hg19)] with a 0.31-Mb deletion of 10p15.3 encompassing ZMYND11 and DIP2C, and a 24.86-Mb duplication of 10p15.3p12.1. The pregnancy was subsequently terminated, and a female fetus was delivered with facial dysmorphism. Postnatal aCGH analysis showed that the umbilical cord had the same result as that of amniotic fluid, whereas the placenta had only the deletion of 10p15.3. Fluorescence in situ hybridization (FISH) analysis of the cord blood confirmed inverted duplication and deletion of 10p. The cord blood had a karyotype of 46,XX,der(10) del(10) (p15.3)dup(10) (p15.3p12.1)dn. Polymorphic DNA marker analysis confirmed a maternal origin of the chromosome 10 aberration. CONCLUSION Prenatal diagnosis of inv dup del(10p) with haploinsufficiency of ZMYND11 should include a genetic counseling of mental retardation and chromosome 10p15.3 microdeletion syndrome. aCGH, FISH and polymorphic DNA marker analysis are useful for perinatal investigation of inv dup del(10p).
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Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; Department of Biotechnology, Asia University, Taichung, Taiwan; School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; Institute of Clinical and Community Health Nursing, National Yang-Ming University, Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, National Yang-Ming University, Taipei, Taiwan.
| | - Tsang-Ming Ko
- Genephile Bioscience Laboratory, Ko's Obstetrics and Gynecology, Taipei, Taiwan
| | - Liang-Kai Wang
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Schu-Rern Chern
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | | | - Shin-Wen Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Fang-Tzu Wu
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Li-Feng Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Wayseen Wang
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; Department of Bioengineering, Tatung University, Taipei, Taiwan
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199
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Abstract
BACKGROUND There is increasing evidence that certain genetic variants increase the risk of schizophrenia and other neurodevelopmental disorders. Exome sequencing has been shown to have a high diagnostic yield for developmental disability and testing for copy number variants has been advocated for schizophrenia. The diagnostic yield for exome sequencing in schizophrenia is unknown. METHOD A sample of 591 exome-sequenced schizophrenia cases and their parents were screened for disruptive and damaging variants in autosomal genes listed in the Genomics England panels for intellectual disability and other neurological disorders. RESULTS Previously reported disruptive de novo variants were noted in SETD1A, POGZ, SCN2A, and ZMYND11. Although the loss of function of ZMYND11 is a recognized cause of intellectual disability, it has not previously been noted as a risk factor for schizophrenia. A damaging de novo variant of uncertain significance was noted in NRXN1. A previously reported homozygous damaging variant in BLM is predicted to cause Bloom syndrome in 1 case and 1 case was homozygous for a damaging variant in MCPH1, a result of uncertain significance. There were more than 400 disruptive and damaging variants in the target genes in cases but similar numbers were seen among untransmitted parental alleles and none appeared to be clinically significant. CONCLUSIONS The diagnostic yield from exome sequencing in schizophrenia is low. Disruptive and damaging variants seen in known neuropsychiatric genes should not be automatically assumed to have an etiological role if observed in a patient with schizophrenia.
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Affiliation(s)
| | - David Curtis
- UCL Genetics Institute, University College London, UK
- Centre for Psychiatry, Barts and the London School of Medicine and Dentistry, UK
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200
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Satterstrom FK, Kosmicki JA, Wang J, Breen MS, De Rubeis S, An JY, Peng M, Collins R, Grove J, Klei L, Stevens C, Reichert J, Mulhern MS, Artomov M, Gerges S, Sheppard B, Xu X, Bhaduri A, Norman U, Brand H, Schwartz G, Nguyen R, Guerrero EE, Dias C, Betancur C, Cook EH, Gallagher L, Gill M, Sutcliffe JS, Thurm A, Zwick ME, Børglum AD, State MW, Cicek AE, Talkowski ME, Cutler DJ, Devlin B, Sanders SJ, Roeder K, Daly MJ, Buxbaum JD. Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism. Cell 2020; 180:568-584.e23. [PMID: 31981491 PMCID: PMC7250485 DOI: 10.1016/j.cell.2019.12.036] [Citation(s) in RCA: 1164] [Impact Index Per Article: 291.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 07/08/2019] [Accepted: 12/24/2019] [Indexed: 12/15/2022]
Abstract
We present the largest exome sequencing study of autism spectrum disorder (ASD) to date (n = 35,584 total samples, 11,986 with ASD). Using an enhanced analytical framework to integrate de novo and case-control rare variation, we identify 102 risk genes at a false discovery rate of 0.1 or less. Of these genes, 49 show higher frequencies of disruptive de novo variants in individuals ascertained to have severe neurodevelopmental delay, whereas 53 show higher frequencies in individuals ascertained to have ASD; comparing ASD cases with mutations in these groups reveals phenotypic differences. Expressed early in brain development, most risk genes have roles in regulation of gene expression or neuronal communication (i.e., mutations effect neurodevelopmental and neurophysiological changes), and 13 fall within loci recurrently hit by copy number variants. In cells from the human cortex, expression of risk genes is enriched in excitatory and inhibitory neuronal lineages, consistent with multiple paths to an excitatory-inhibitory imbalance underlying ASD.
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Affiliation(s)
- F Kyle Satterstrom
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jack A Kosmicki
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jiebiao Wang
- Department of Statistics, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Michael S Breen
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joon-Yong An
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, Republic of Korea
| | - Minshi Peng
- Department of Statistics, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Ryan Collins
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, USA
| | - Jakob Grove
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark; Center for Genomics and Personalized Medicine, Aarhus, Denmark; Department of Biomedicine - Human Genetics, Aarhus University, Aarhus, Denmark
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Christine Stevens
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jennifer Reichert
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Maureen S Mulhern
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mykyta Artomov
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Sherif Gerges
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Brooke Sheppard
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Xinyi Xu
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aparna Bhaduri
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Utku Norman
- Computer Engineering Department, Bilkent University, Ankara, Turkey
| | - Harrison Brand
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Grace Schwartz
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Rachel Nguyen
- Center for Autism Research and Translation, University of California, Irvine, Irvine, CA, USA
| | - Elizabeth E Guerrero
- MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California, Davis, Davis, CA, USA
| | - Caroline Dias
- Division of Genetics, Boston Children's Hospital, Boston, MA, USA; Division of Developmental Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Catalina Betancur
- Sorbonne Université, INSERM, CNRS, Neuroscience Paris Seine, Institut de Biologie Paris Seine, Paris, France
| | - Edwin H Cook
- Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA
| | - Louise Gallagher
- Department of Psychiatry, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Michael Gill
- Department of Psychiatry, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - James S Sutcliffe
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA; Department of Molecular Physiology and Biophysics and Psychiatry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Audrey Thurm
- National Institute of Mental Health, NIH, Bethesda, MD, USA
| | - Michael E Zwick
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Anders D Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark; Center for Genomics and Personalized Medicine, Aarhus, Denmark; Department of Biomedicine - Human Genetics, Aarhus University, Aarhus, Denmark; Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Matthew W State
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - A Ercument Cicek
- Department of Statistics, Carnegie Mellon University, Pittsburgh, PA, USA; Computer Engineering Department, Bilkent University, Ankara, Turkey
| | - Michael E Talkowski
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Stephan J Sanders
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
| | - Kathryn Roeder
- Department of Statistics, Carnegie Mellon University, Pittsburgh, PA, USA; Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA.
| | - Mark J Daly
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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