Molecular characterization of NRXN1 deletions from 19,263 clinical microarray cases identifies exons important for neurodevelopmental disease expression
The purpose of the current study was to assess the penetrance of NRXN1 deletions. We compared the prevalence and genomic extent of NRXN1 deletions identified among 19,263 clinically referred cases to that of 15,264 controls. The burden of additional clinically relevant copy-number variations (CNVs)...
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| Published in | Genetics in medicine Vol. 19; no. 1; pp. 53 - 61 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
New York
Elsevier Inc
01.01.2017
Nature Publishing Group US Elsevier Limited |
| Subjects | |
| Online Access | Get full text |
| ISSN | 1098-3600 1530-0366 1530-0366 |
| DOI | 10.1038/gim.2016.54 |
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| Abstract | The purpose of the current study was to assess the penetrance of NRXN1 deletions.
We compared the prevalence and genomic extent of NRXN1 deletions identified among 19,263 clinically referred cases to that of 15,264 controls. The burden of additional clinically relevant copy-number variations (CNVs) was used as a proxy to estimate the relative penetrance of NRXN1 deletions.
We identified 41 (0.21%) previously unreported exonic NRXN1 deletions ascertained for developmental delay/intellectual disability that were significantly greater than in controls (odds ratio (OR) = 8.14; 95% confidence interval (CI): 2.91–22.72; P < 0.0001). Ten (22.7%) of these had a second clinically relevant CNV. Subjects with a deletion near the 3ʹ end of NRXN1 were significantly more likely to have a second rare CNV than subjects with a 5ʹ NRXN1 deletion (OR = 7.47; 95% CI: 2.36–23.61; P = 0.0006). The prevalence of intronic NRXN1 deletions was not statistically different between cases and controls (P = 0.618). The majority (63.2%) of intronic NRXN1 deletion cases had a second rare CNV at a prevalence twice as high as that for exonic NRXN1 deletion cases (P = 0.0035).
The results support the importance of exons near the 5ʹ end of NRXN1 in the expression of neurodevelopmental disorders. Intronic NRXN1 deletions do not appear to substantially increase the risk for clinical phenotypes. |
|---|---|
| AbstractList | Purpose:
The purpose of the current study was to assess the penetrance of
NRXN1
deletions.
Methods:
We compared the prevalence and genomic extent of
NRXN1
deletions identified among 19,263 clinically referred cases to that of 15,264 controls. The burden of additional clinically relevant copy-number variations (CNVs) was used as a proxy to estimate the relative penetrance of
NRXN1
deletions.
Results:
We identified 41 (0.21%) previously unreported exonic
NRXN1
deletions ascertained for developmental delay/intellectual disability that were significantly greater than in controls (odds ratio (OR) = 8.14; 95% confidence interval (CI): 2.91–22.72;
P
< 0.0001). Ten (22.7%) of these had a second clinically relevant CNV. Subjects with a deletion near the 3ʹ end of
NRXN1
were significantly more likely to have a second rare CNV than subjects with a 5ʹ
NRXN1
deletion (OR = 7.47; 95% CI: 2.36–23.61;
P
= 0.0006). The prevalence of intronic
NRXN1
deletions was not statistically different between cases and controls (
P
= 0.618). The majority (63.2%) of intronic
NRXN1
deletion cases had a second rare CNV at a prevalence twice as high as that for exonic
NRXN1
deletion cases (
P
= 0.0035).
Conclusions:
The results support the importance of exons near the 5ʹ end of
NRXN1
in the expression of neurodevelopmental disorders. Intronic
NRXN1
deletions do not appear to substantially increase the risk for clinical phenotypes.
Genet Med
19
1, 53–61. Purpose:The purpose of the current study was to assess the penetrance of NRXN1 deletions.Methods:We compared the prevalence and genomic extent of NRXN1 deletions identified among 19,263 clinically referred cases to that of 15,264 controls. The burden of additional clinically relevant copy-number variations (CNVs) was used as a proxy to estimate the relative penetrance of NRXN1 deletions.Results:We identified 41 (0.21%) previously unreported exonic NRXN1 deletions ascertained for developmental delay/intellectual disability that were significantly greater than in controls (odds ratio (OR) = 8.14; 95% confidence interval (CI): 2.91-22.72; P < 0.0001). Ten (22.7%) of these had a second clinically relevant CNV. Subjects with a deletion near the 3' end of NRXN1 were significantly more likely to have a second rare CNV than subjects with a 5' NRXN1 deletion (OR = 7.47; 95% CI: 2.36-23.61; P = 0.0006). The prevalence of intronic NRXN1 deletions was not statistically different between cases and controls (P = 0.618). The majority (63.2%) of intronic NRXN1 deletion cases had a second rare CNV at a prevalence twice as high as that for exonic NRXN1 deletion cases (P = 0.0035).Conclusions:The results support the importance of exons near the 5' end of NRXN1 in the expression of neurodevelopmental disorders. Intronic NRXN1 deletions do not appear to substantially increase the risk for clinical phenotypes.Genet Med 19 1, 53-61. The purpose of the current study was to assess the penetrance of NRXN1 deletions. We compared the prevalence and genomic extent of NRXN1 deletions identified among 19,263 clinically referred cases to that of 15,264 controls. The burden of additional clinically relevant copy-number variations (CNVs) was used as a proxy to estimate the relative penetrance of NRXN1 deletions. We identified 41 (0.21%) previously unreported exonic NRXN1 deletions ascertained for developmental delay/intellectual disability that were significantly greater than in controls (odds ratio (OR) = 8.14; 95% confidence interval (CI): 2.91–22.72; P < 0.0001). Ten (22.7%) of these had a second clinically relevant CNV. Subjects with a deletion near the 3ʹ end of NRXN1 were significantly more likely to have a second rare CNV than subjects with a 5ʹ NRXN1 deletion (OR = 7.47; 95% CI: 2.36–23.61; P = 0.0006). The prevalence of intronic NRXN1 deletions was not statistically different between cases and controls (P = 0.618). The majority (63.2%) of intronic NRXN1 deletion cases had a second rare CNV at a prevalence twice as high as that for exonic NRXN1 deletion cases (P = 0.0035). The results support the importance of exons near the 5ʹ end of NRXN1 in the expression of neurodevelopmental disorders. Intronic NRXN1 deletions do not appear to substantially increase the risk for clinical phenotypes. The purpose of the current study was to assess the penetrance of NRXN1 deletions. We compared the prevalence and genomic extent of NRXN1 deletions identified among 19,263 clinically referred cases to that of 15,264 controls. The burden of additional clinically relevant copy-number variations (CNVs) was used as a proxy to estimate the relative penetrance of NRXN1 deletions. We identified 41 (0.21%) previously unreported exonic NRXN1 deletions ascertained for developmental delay/intellectual disability that were significantly greater than in controls (odds ratio (OR) = 8.14; 95% confidence interval (CI): 2.91-22.72; P < 0.0001). Ten (22.7%) of these had a second clinically relevant CNV. Subjects with a deletion near the 3' end of NRXN1 were significantly more likely to have a second rare CNV than subjects with a 5' NRXN1 deletion (OR = 7.47; 95% CI: 2.36-23.61; P = 0.0006). The prevalence of intronic NRXN1 deletions was not statistically different between cases and controls (P = 0.618). The majority (63.2%) of intronic NRXN1 deletion cases had a second rare CNV at a prevalence twice as high as that for exonic NRXN1 deletion cases (P = 0.0035). The results support the importance of exons near the 5' end of NRXN1 in the expression of neurodevelopmental disorders. Intronic NRXN1 deletions do not appear to substantially increase the risk for clinical phenotypes.Genet Med 19 1, 53-61. |
| Author | Schultz, Lee-Anne Walinga, Margreet Gazzellone, Matthew Graham, Gail E. Marshall, Christian R. Rajguru, Manjulata Armour, Christine M. Morra, Antonella Boyd, Kerry Li, Chumei Jung, Jack H. McCready, Elizabeth Bassett, Anne S. Siu, Victoria Scherer, Stephen W. Lowther, Chelsea Nowaczyk, Malgorzata J.M. Dick, Paul T. Stavropoulos, Dimitri J. Samdup, Dawa Bikangaga, Peter Zaazou, Mostafa Zeesman, Susan Lionel, Anath C. Goh, Elaine S. Goobie, Sharan Prasad, Chitra Nicolson, Rob Hussain, Asmaa S. Speevak, Marsha Tarnopolsky, Mark A. Reijenga, Renske G. |
| AuthorAffiliation | 12 Department of Pediatrics, Schulich School of Medicine and Dentistry, London, ON, Canada 14 Department of Pediatrics, McMaster University, Hamilton, ON, Canada 1 Institute of Medical Science, University of Toronto, Toronto, ON, Canada 6 Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada 8 William Osler Health Centre, Brampton, ON, Canada 17 Ipse de Bruggen, Zwammerdam, the Netherlands 16 Vanboeijen, Assen, the Netherlands 2 Trillium Health Partners Credit Valley Site, Toronto, ON, Canada 11 London Health Sciences Centre, Children’s Hospital of Western Ontario, London, ON, Canada 15 Grey Bruce Health Services, Owen Sound, ON, Canada 13 Cambridge Memorial Hospital, Cambridge, ON, Canada 21 Department of Psychiatry, Faculty of Medicine, University of Toronto, Toronto, ON, Canada 9 Hotel Dieu Hospital, Child Development Centre, Kingston, ON, Canada 19 McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada 7 Departments |
| AuthorAffiliation_xml | – name: 2 Trillium Health Partners Credit Valley Site, Toronto, ON, Canada – name: 3 Regional Genetics Program, Children’s Hospital of Eastern Ontario, ON, Canada – name: 15 Grey Bruce Health Services, Owen Sound, ON, Canada – name: 17 Ipse de Bruggen, Zwammerdam, the Netherlands – name: 21 Department of Psychiatry, Faculty of Medicine, University of Toronto, Toronto, ON, Canada – name: 7 Departments of Psychiatry, Western University, London, ON, Canada – name: 9 Hotel Dieu Hospital, Child Development Centre, Kingston, ON, Canada – name: 6 Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada – name: 20 Cytogenetics Laboratory, Department of Pediatric Laboratory Medicine, the Hospital for Sick Children, Toronto, ON, Canada – name: 13 Cambridge Memorial Hospital, Cambridge, ON, Canada – name: 18 The Centre for Applied Genomics, the Hospital for Sick Children, Toronto, ON, Canada – name: 10 Bethesda Services, Thorold, ON, Canada – name: 19 McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada – name: 8 William Osler Health Centre, Brampton, ON, Canada – name: 5 McMaster Children’s Hospital, Department of Pediatrics and Clinical Genetics Program, Hamilton, ON, Canada – name: 1 Institute of Medical Science, University of Toronto, Toronto, ON, Canada – name: 16 Vanboeijen, Assen, the Netherlands – name: 14 Department of Pediatrics, McMaster University, Hamilton, ON, Canada – name: 4 Department of Pediatrics, University of Ottawa, Ottawa, ON, Canada – name: 11 London Health Sciences Centre, Children’s Hospital of Western Ontario, London, ON, Canada – name: 12 Department of Pediatrics, Schulich School of Medicine and Dentistry, London, ON, Canada |
| Author_xml | – sequence: 1 givenname: Chelsea surname: Lowther fullname: Lowther, Chelsea organization: Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada – sequence: 2 givenname: Marsha surname: Speevak fullname: Speevak, Marsha organization: Trillium Health Partners Credit Valley Site, Toronto, Ontario, Canada – sequence: 3 givenname: Christine M. surname: Armour fullname: Armour, Christine M. organization: Regional Genetics Program, Children’s Hospital of Eastern Ontario, Toronto, ON, Canada – sequence: 4 givenname: Elaine S. surname: Goh fullname: Goh, Elaine S. organization: Trillium Health Partners Credit Valley Site, Toronto, Ontario, Canada – sequence: 5 givenname: Gail E. surname: Graham fullname: Graham, Gail E. organization: Department of Pediatrics, University of Ottawa, Ottawa, Ontario, Canada – sequence: 6 givenname: Chumei surname: Li fullname: Li, Chumei organization: Department of Pediatrics, University of Ottawa, Ottawa, Ontario, Canada – 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fullname: Bikangaga, Peter organization: William Osler Health Centre, Brampton, Ontario, Canada – sequence: 13 givenname: Dawa surname: Samdup fullname: Samdup, Dawa organization: Hotel Dieu Hospital, Child Development Centre, Kingston, Ontario, Canada – sequence: 14 givenname: Mostafa surname: Zaazou fullname: Zaazou, Mostafa organization: Trillium Health Partners Credit Valley Site, Toronto, Ontario, Canada – sequence: 15 givenname: Kerry surname: Boyd fullname: Boyd, Kerry organization: Department of Psychiatry, McMaster University, Hamilton, Ontario, Canada – sequence: 16 givenname: Jack H. surname: Jung fullname: Jung, Jack H. organization: London Health Sciences Centre, Children’s Hospital of Western Ontario, London, Ontario, Canada – sequence: 17 givenname: Victoria surname: Siu fullname: Siu, Victoria organization: Department of Pediatrics, Schulich School of Medicine and Dentistry, London, Ontario, Canada – sequence: 18 givenname: Manjulata surname: Rajguru fullname: Rajguru, 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fullname: Walinga, Margreet organization: Vanboeijen, Assen, The Netherlands – sequence: 25 givenname: Renske G. surname: Reijenga fullname: Reijenga, Renske G. organization: Ipse de Bruggen, Zwammerdam, The Netherlands – sequence: 26 givenname: Matthew surname: Gazzellone fullname: Gazzellone, Matthew organization: The Centre for Applied Genomics, the Hospital for Sick Children, Toronto, Ontario, Canada – sequence: 27 givenname: Anath C. surname: Lionel fullname: Lionel, Anath C. organization: The Centre for Applied Genomics, the Hospital for Sick Children, Toronto, Ontario, Canada – sequence: 28 givenname: Christian R. surname: Marshall fullname: Marshall, Christian R. organization: The Centre for Applied Genomics, the Hospital for Sick Children, Toronto, Ontario, Canada – sequence: 29 givenname: Stephen W. surname: Scherer fullname: Scherer, Stephen W. organization: The Centre for Applied Genomics, the Hospital for Sick Children, Toronto, Ontario, Canada – sequence: 30 givenname: Dimitri J. surname: Stavropoulos fullname: Stavropoulos, Dimitri J. organization: Cytogenetics Laboratory, Department of Pediatric Laboratory Medicine, the Hospital for Sick Children, Toronto, Ontario, Canada – sequence: 31 givenname: Elizabeth surname: McCready fullname: McCready, Elizabeth organization: Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada – sequence: 32 givenname: Anne S. surname: Bassett fullname: Bassett, Anne S. email: anne.bassett@utoronto.ca organization: Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/27195815$$D View this record in MEDLINE/PubMed |
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| Keywords | genotype–phenotype variable expression NRXN1 copy-number variation penetrance |
| Language | English |
| License | This article is made available under the Elsevier license. Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms publisher-specific-oa |
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| PublicationTitle | Genetics in medicine |
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46 Boucard, Chubykin, Comoletti, Taylor, Südhof (CR7) 2005; 48 Kearney, Thorland, Brown, Quintero-Rivera, South (CR29) 2011; 13 Siddiqui, Pancaroglu, Kang, Rooyakkers, Craig (CR1) 2010; 30 Szatmari, Paterson, Zwaigenbaum (CR11) 2007; 39 McGrath, Yu, Marshall (CR18) 2014; 53 Brzustowicz, Bassett (CR25) 2012; 3 Dabell, Rosenfeld, Bader (CR31) 2013; 161A Pedrosa, Kaushik, Lachman (CR33) 2010; 24 Liu, Cheng, Ye (CR20) 2013; 1 Hayden (CR27) 2014; 507 Zarrei, MacDonald, Merico, Scherer (CR38) 2015; 16 Uddin (10.1038/gim.2016.54_bb0120) Rosenfeld (10.1038/gim.2016.54_bb0180) Girirajan (10.1038/gim.2016.54_bb0145) Ushkaryov (10.1038/gim.2016.54_bb0030) EPICURE Consortium (10.1038/gim.2016.54_bb0085) Duong (10.1038/gim.2016.54_bb0165) Sugita (10.1038/gim.2016.54_bb0050) Liu (10.1038/gim.2016.54_bb0105) Siddiqui (10.1038/gim.2016.54_bb0010) MacDonald (10.1038/gim.2016.54_bb0190) Tourette Syndrome Association International Consortium for Genetics (10.1038/gim.2016.54_bb0080) Autism Genome Project Consortium (10.1038/gim.2016.54_bb0125) Briggs (10.1038/gim.2016.54_bb0175) Marshall (10.1038/gim.2016.54_bb0065) Püschel (10.1038/gim.2016.54_bb0020) Boucard (10.1038/gim.2016.54_bb0040) Alzheimer’s Disease Neuroimaging Initiative; 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| Snippet | The purpose of the current study was to assess the penetrance of NRXN1 deletions.
We compared the prevalence and genomic extent of NRXN1 deletions identified... Purpose: The purpose of the current study was to assess the penetrance of NRXN1 deletions. Methods: We compared the prevalence and genomic extent of NRXN1... Purpose:The purpose of the current study was to assess the penetrance of NRXN1 deletions.Methods:We compared the prevalence and genomic extent of NRXN1... |
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| SubjectTerms | 631/1647/2017/2079 631/208/2489 631/208/457/649 692/699/375/366 Biomedicine Calcium-Binding Proteins Cell Adhesion Molecules, Neuronal - genetics Child copy-number variation DNA Copy Number Variations Exons - genetics Female Genetic Predisposition to Disease Genotype genotype–phenotype Human Genetics Humans Introns - genetics Laboratory Medicine Male Microarray Analysis Nerve Tissue Proteins - genetics Neural Cell Adhesion Molecules Neurodevelopmental Disorders - epidemiology Neurodevelopmental Disorders - genetics Neurodevelopmental Disorders - physiopathology NRXN1 original-research-article Penetrance Phenotype Sequence Deletion variable expression |
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| Title | Molecular characterization of NRXN1 deletions from 19,263 clinical microarray cases identifies exons important for neurodevelopmental disease expression |
| URI | https://dx.doi.org/10.1038/gim.2016.54 https://link.springer.com/article/10.1038/gim.2016.54 https://www.ncbi.nlm.nih.gov/pubmed/27195815 https://www.proquest.com/docview/1903486647 https://pubmed.ncbi.nlm.nih.gov/PMC4980119 https://www.nature.com/articles/gim201654.pdf |
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