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Tschigg K, Consoli L, Brüggemann N, Hicks AA, Staunton C, Mascalzoni D, Biasiotto R. How to communicate and what to disclose to participants in a recall-by-genotype research approach: a multistep empirical study. J Community Genet 2024:10.1007/s12687-024-00733-8. [PMID: 39325315 DOI: 10.1007/s12687-024-00733-8] [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: 04/30/2024] [Accepted: 09/04/2024] [Indexed: 09/27/2024] Open
Abstract
Recall-by-genotype (RbG) is a bottom-up approach using existing genetic data to design follow-up stratified studies. Genetic information may be partially disclosed at invitation, thus raising ethical issues which call for defined best practices for disclosure and communication in RbG approaches. Within the context of the ProtectMove sub-project of the Cooperative Health Research in South Tyrol (CHRIS) study, we investigated research participant perspectives on RbG communication strategies (Step 1 and 4, questionnaire with a subsample of CHRIS participants with and without previous experience of RbG, respectively). Additionally, we explored researchers' and study personnel's experience with RbG (Step 2 and 3, focus group discussion). In step 1 (N = 95), participants were generally satisfied with the study process. Most (71.6%) wanted to know their carrier status for personal and collective benefit. Tailored disclosure strategies and transparent, effective, and well-thought-out communication approaches were advocated by study personnel (Step 2, N = 6) and researchers (Step 3, N = 7). Challenges in dealing with uncertainty, concerns caused by RbG invitations, and the possibility of misunderstanding were also raised. In step 4 (N = 369), participants valued being informed of study details at the first invitation stage, and generally felt comfortable towards RbG study invitations (58.5%) and to receiving genetic information after the study (58.5-81.6%). Comfort and perceived impact of disclosure of genetic information varied according to the type of variant being potentially disclosed. This study suggested designing communication strategies, based on clear and understandable explanations, sensitive to participant expectations and preferences, developing case-by-case solutions for disclosure.
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Affiliation(s)
- Katharina Tschigg
- Department of Cellular, Computational, and Integrative Biology, University of Trento, Trento, Italy
- Institute for Biomedicine, Eurac Research, Bolzano, Italy
| | - Luca Consoli
- Institute for Science in Society, Radboud University, Nijmegen, Netherlands
| | - Norbert Brüggemann
- Department of Neurology, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
- Institute of Neurogenetics, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Andrew A Hicks
- Institute for Biomedicine, Eurac Research, Bolzano, Italy
| | - Ciara Staunton
- Institute for Biomedicine, Eurac Research, Bolzano, Italy
- School of Law, University of KwaZulu-Natal, Durban, South Africa
| | - Deborah Mascalzoni
- Institute for Biomedicine, Eurac Research, Bolzano, Italy.
- Center for Research Ethics and Bioethics, Department of Public Health and Caring Sciences, Uppsala University, Uppsala, Sweden.
| | - Roberta Biasiotto
- Institute for Biomedicine, Eurac Research, Bolzano, Italy
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
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2
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Das S, Samarasinghe L, Deva S, Fernandez Co EM, Poudel S, Dave T, Prasad S, Sarangi A. Complex neuropsychiatric presentation of 17q12 duplication syndrome: A case report. SAGE Open Med Case Rep 2024; 12:2050313X241233184. [PMID: 38379631 PMCID: PMC10878203 DOI: 10.1177/2050313x241233184] [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: 10/11/2023] [Accepted: 01/29/2024] [Indexed: 02/22/2024] Open
Abstract
The chromosomal band 17q12 is characterized by a high density of genes and is bordered by segmental duplications, the structural arrangement of which increases the susceptibility of the region to deletions and duplications. Duplication of 17q12 is a rare genetic condition associated with variable characteristics from clinically asymptomatic to intellectual disabilities, seizures, and behavioral problems. The variability in phenotype is primarily due to variable expressivity and incomplete penetrance. Diagnosis is mostly established by chromosomal microarray. Treatment involves a multidisciplinary approach. We present a case of a 43-year-old female who initially presented with hyperphagia and was eventually diagnosed with bulimia nervosa, anxiety, mood disorder, and personality disorder. Additional research is required to better understand the impact of 17q12 duplication syndrome on the development of bulimia nervosa since its pathogenesis has not been adequately described in the current literature.
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Affiliation(s)
- Soumitra Das
- Department of Psychiatry, Western Health, Footscray, VIC, Australia
| | | | - Sheryl Deva
- Kamineni Academy of Medical Sciences and Research Center, Hyderabad, Telangana, India
| | | | | | - Tirth Dave
- Bukovinian State Medical University, Chernivtsi, Ukraine
| | - Sakshi Prasad
- Vinnytsia National Pirogov Memorial Medical University, Vinnitsya, Ukraine
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3
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The Genetics of Intellectual Disability. Brain Sci 2023; 13:brainsci13020231. [PMID: 36831774 PMCID: PMC9953898 DOI: 10.3390/brainsci13020231] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/23/2022] [Accepted: 01/16/2023] [Indexed: 02/03/2023] Open
Abstract
Intellectual disability (ID) has a prevalence of ~2-3% in the general population, having a large societal impact. The underlying cause of ID is largely of genetic origin; however, identifying this genetic cause has in the past often led to long diagnostic Odysseys. Over the past decades, improvements in genetic diagnostic technologies and strategies have led to these causes being more and more detectable: from cytogenetic analysis in 1959, we moved in the first decade of the 21st century from genomic microarrays with a diagnostic yield of ~20% to next-generation sequencing platforms with a yield of up to 60%. In this review, we discuss these various developments, as well as their associated challenges and implications for the field of ID, which highlight the revolutionizing shift in clinical practice from a phenotype-first into genotype-first approach.
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4
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Kang J, Zhou Q, Chen N, Liu Z, Zhang Y, Sun J, Ma C, Chen F, Ma Y, Wang L, Zhu L, Wang W. Clinical and Genetic Characteristics of a Cohort with Distal Vaginal Atresia. Int J Mol Sci 2022; 23:12853. [PMID: 36361644 PMCID: PMC9655474 DOI: 10.3390/ijms232112853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/20/2022] [Accepted: 10/20/2022] [Indexed: 01/09/2024] Open
Abstract
Distal vaginal atresia is a rare abnormality of female reproductive tract in which the vagina is closed or absent. The distal vagina may be replaced by fibrous tissue and the condition is often not diagnosed until a girl fails to begin having periods at puberty. Although it is a congenital disorder, potential genetic causes of distal vaginal atresia are still unknown. We recruited a cohort of 39 patients with distal vaginal atresia and analyzed their phenotypic and genetic features. In addition to the complaint of distal vaginal atresia, approximately 17.9% (7/39) of the patients had other Müllerian anomalies, and 17.9% (7/39) of the patients had other structural abnormalities, including renal-tract, skeletal and cardiac anomalies. Using genome sequencing, we identified two fragment duplications on 17q12 encompassing HNF1B and LHX1, two dosage-sensitive genes with candidate pathogenic variants, in two unrelated patients. A large fragment of uniparental disomy was detected in another patient, affecting genes involved in cell morphogenesis and connective tissue development. Additionally, we reported two variants on TBX3 and AXL, leading to distal vaginal atresia in mutated mouse model, in our clinical subjects for the first time. Essential biological functions of these detected genes with pathogenic variants included regulating reproductive development and cell fate and patterning during embryogenesis. We displayed the comprehensive clinical and genetic characteristic of a cohort with distal vaginal atresia and they were highly heterogeneous both phenotypically and genetically. The duplication of 17q12 in our cohort could help to expand its phenotypic spectrum and potential contribution to the distal vaginal atresia. Our findings of pathogenic genetic variants and associated phenotypes in our cohort could provide evidence and new insight for further research attempting to reveal genetic causes of distal vaginal atresia.
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Affiliation(s)
- Jia Kang
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Qing Zhou
- BGI-Shenzhen, Shenzhen 518083, China
| | - Na Chen
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | | | - Ye Zhang
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Jinghua Sun
- BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Congcong Ma
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Fang Chen
- BGI-Shenzhen, Shenzhen 518083, China
- Shenzhen Engineering Laboratory for Birth Defects Screening, BGI-Shenzhen, Shenzhen 518083, China
| | - Yidi Ma
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Lin Wang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Lan Zhu
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
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5
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Freeth M, Al-Jawahiri R, Smith H, Stokes L. Speech, language and communication phenotyping in rare genetic syndromes: Commentary on Speech and language deficits are central to SETBP1 haploinsufficiency disorder. Eur J Hum Genet 2021; 29:1166-1167. [PMID: 34413496 DOI: 10.1038/s41431-021-00942-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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6
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Mosley TJ, Johnston HR, Cutler DJ, Zwick ME, Mulle JG. Sex-specific recombination patterns predict parent of origin for recurrent genomic disorders. BMC Med Genomics 2021; 14:154. [PMID: 34107974 PMCID: PMC8190997 DOI: 10.1186/s12920-021-00999-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 06/02/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Structural rearrangements of the genome, which generally occur during meiosis and result in large-scale (> 1 kb) copy number variants (CNV; deletions or duplications ≥ 1 kb), underlie genomic disorders. Recurrent pathogenic CNVs harbor similar breakpoints in multiple unrelated individuals and are primarily formed via non-allelic homologous recombination (NAHR). Several pathogenic NAHR-mediated recurrent CNV loci demonstrate biases for parental origin of de novo CNVs. However, the mechanism underlying these biases is not well understood. METHODS We performed a systematic, comprehensive literature search to curate parent of origin data for multiple pathogenic CNV loci. Using a regression framework, we assessed the relationship between parental CNV origin and the male to female recombination rate ratio. RESULTS We demonstrate significant association between sex-specific differences in meiotic recombination and parental origin biases at these loci (p = 1.07 × 10-14). CONCLUSIONS Our results suggest that parental origin of CNVs is largely influenced by sex-specific recombination rates and highlight the need to consider these differences when investigating mechanisms that cause structural variation.
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Affiliation(s)
- Trenell J Mosley
- Graduate Program in Genetics and Molecular Biology, Laney Graduate School, Emory University, 201 Dowman Drive, Atlanta, GA, 30322, USA
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA
| | - H Richard Johnston
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA
- Emory Integrated Computational Core, Emory University, 101 Woodruff Circle, Atlanta, GA, 30322, USA
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA
| | - Michael E Zwick
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA
- Department of Pediatrics, Emory University School of Medicine, 2015 Uppergate Drive, Atlanta, GA, 30322, USA
| | - Jennifer G Mulle
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA.
- Department of Epidemiology, Rollins School of Public Health, Emory University, 1518 Clifton Road NE, Atlanta, GA, 30322, USA.
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7
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Corrêa T, Feltes BC, Schinzel A, Riegel M. Network-based analysis using chromosomal microdeletion syndromes as a model. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2021; 187:337-348. [PMID: 33754460 DOI: 10.1002/ajmg.c.31900] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/15/2020] [Accepted: 03/05/2021] [Indexed: 12/13/2022]
Abstract
Microdeletion syndromes (MSs) are a heterogeneous group of genetic diseases that can virtually affect all functions and organs in humans. Although systems biology approaches integrating multiomics and database information into biological networks have expanded our knowledge of genetic disorders, cytogenomic network-based analysis has rarely been applied to study MSs. In this study, we analyzed data of 28 MSs, using network-based approaches, to investigate the associations between the critical chromosome regions and the respective underlying biological network systems. We identified MSs-associated proteins that were organized in a network of linked modules within the human interactome. Certain MSs formed highly interlinked self-contained disease modules. Furthermore, we observed disease modules involving proteins from other disease groups in the MSs interactome. Moreover, analysis of integrated data from 564 genes located in known chromosomal critical regions, including those contributing to topological parameters, shared pathways, and gene-disease associations, indicated that complex biological systems and cellular networks may underlie many genotype to phenotype associations in MSs. In conclusion, we used a network-based analysis to provide resources that may contribute to better understanding of the molecular pathways involved in MSs.
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Affiliation(s)
- Thiago Corrêa
- Post-Graduate Program in Genetics and Molecular Biology, Genetics Department, UFRGS, Porto Alegre, Brazil
| | - Bruno César Feltes
- Laboratory of Structural Bioinformatics, Institute of Informatics, UFRGS, Porto Alegre, Brazil.,Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Institute of Biosciences, UFRGS, Porto Alegre, Brazil
| | - Albert Schinzel
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Mariluce Riegel
- Post-Graduate Program in Genetics and Molecular Biology, Genetics Department, UFRGS, Porto Alegre, Brazil.,Medical Genetics Service, HCPA, Porto Alegre, Brazil
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8
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Eisenberg DP, Gregory MD, Berman KF. Subcortical Signatures of Hemizygosity and Psychosis in 22q11.2 Deletion Syndrome: Finding Common Ground in Rare Genetic Variation. Am J Psychiatry 2020; 177:564-566. [PMID: 32605438 PMCID: PMC9583700 DOI: 10.1176/appi.ajp.2020.20050598] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daniel P. Eisenberg
- Clinical and Translational Neuroscience Branch, NIMH, Intramural Research Program, Bethesda, Md
| | - Michael D. Gregory
- Clinical and Translational Neuroscience Branch, NIMH, Intramural Research Program, Bethesda, Md
| | - Karen F. Berman
- Clinical and Translational Neuroscience Branch, NIMH, Intramural Research Program, Bethesda, Md
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9
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Riggs ER, Nelson T, Merz A, Ackley T, Bunke B, Collins CD, Collinson MN, Fan YS, Goodenberger ML, Golden DM, Haglund-Hazy L, Krgovic D, Lamb AN, Lewis Z, Li G, Liu Y, Meck J, Neufeld-Kaiser W, Runke CK, Sanmann JN, Stavropoulos DJ, Strong E, Su M, Tayeh MK, Kokalj Vokac N, Thorland EC, Andersen E, Martin CL. Copy number variant discrepancy resolution using the ClinGen dosage sensitivity map results in updated clinical interpretations in ClinVar. Hum Mutat 2019; 39:1650-1659. [PMID: 30095202 DOI: 10.1002/humu.23610] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/16/2018] [Accepted: 08/03/2018] [Indexed: 11/07/2022]
Abstract
Conflict resolution in genomic variant interpretation is a critical step toward improving patient care. Evaluating interpretation discrepancies in copy number variants (CNVs) typically involves assessing overlapping genomic content with focus on genes/regions that may be subject to dosage sensitivity (haploinsufficiency (HI) and/or triplosensitivity (TS)). CNVs containing dosage sensitive genes/regions are generally interpreted as "likely pathogenic" (LP) or "pathogenic" (P), and CNVs involving the same known dosage sensitive gene(s) should receive the same clinical interpretation. We compared the Clinical Genome Resource (ClinGen) Dosage Map, a publicly available resource documenting known HI and TS genes/regions, against germline, clinical CNV interpretations within the ClinVar database. We identified 251 CNVs overlapping known dosage sensitive genes/regions but not classified as LP or P; these were sent back to their original submitting laboratories for re-evaluation. Of 246 CNVs re-evaluated, an updated clinical classification was warranted in 157 cases (63.8%); no change was made to the current classification in 79 cases (32.1%); and 10 cases (4.1%) resulted in other types of updates to ClinVar records. This effort will add curated interpretation data into the public domain and allow laboratories to focus attention on more complex discrepancies.
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Affiliation(s)
- Erin R Riggs
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, USA
| | - Tristan Nelson
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, USA
| | - Andrew Merz
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, USA
| | - Todd Ackley
- Michigan Medical Genetics Laboratories (MMGL), University of Michigan, Ann Arbor, MI, USA
| | | | | | - Morag N Collinson
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, Wiltshire, UK
| | - Yao-Shan Fan
- University of Miami Miller School of Medicine, Miami, FL, USA
| | - McKinsey L Goodenberger
- Genomics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Denae M Golden
- Human Genetics Laboratory, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE, USA
| | - Linda Haglund-Hazy
- Michigan Medical Genetics Laboratories (MMGL), University of Michigan, Ann Arbor, MI, USA
| | - Danijela Krgovic
- University Medical Centre Maribor, Laboratory of Medical Genetics, Maribor, Slovenia.,Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Allen N Lamb
- ARUP Laboratories, Salt Lake City, UT, USA.,University of Utah, Salt Lake City, UT, USA
| | - Zoe Lewis
- ARUP Laboratories, Salt Lake City, UT, USA
| | | | - Yajuan Liu
- Clinical Cytogenomics Laboratory, Department of Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Whitney Neufeld-Kaiser
- Clinical Cytogenomics Laboratory, Department of Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Cassandra K Runke
- Genomics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Jennifer N Sanmann
- Human Genetics Laboratory, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE, USA
| | | | - Emma Strong
- Genome Diagnostics, The Hospital for Sick Children, University of Toronto, Canada
| | - Meng Su
- University of Miami Miller School of Medicine, Miami, FL, USA
| | - Marwan K Tayeh
- Michigan Medical Genetics Laboratories (MMGL), University of Michigan, Ann Arbor, MI, USA
| | - Nadja Kokalj Vokac
- University Medical Centre Maribor, Laboratory of Medical Genetics, Maribor, Slovenia.,Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Erik C Thorland
- Genomics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Erica Andersen
- ARUP Laboratories, Salt Lake City, UT, USA.,University of Utah, Salt Lake City, UT, USA
| | - Christa L Martin
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, USA
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10
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Park J, Levin MG, Haggerty CM, Hartzel DN, Judy R, Kember RL, Reza N, Ritchie MD, Owens AT, Damrauer SM, Rader DJ. A genome-first approach to aggregating rare genetic variants in LMNA for association with electronic health record phenotypes. Genet Med 2019; 22:102-111. [PMID: 31383942 DOI: 10.1038/s41436-019-0625-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 07/18/2019] [Indexed: 01/21/2023] Open
Abstract
PURPOSE "Genome-first" approaches, in which genetic sequencing is agnostically linked to associated phenotypes, can enhance our understanding of rare variants' contributions to disease. Loss-of-function variants in LMNA cause a range of rare diseases, including cardiomyopathy. METHODS We leveraged exome sequencing from 11,451 unselected individuals in the Penn Medicine Biobank to associate rare variants in LMNA with diverse electronic health record (EHR)-derived phenotypes. We used Rare Exome Variant Ensemble Learner (REVEL) to annotate rare missense variants, clustered predicted deleterious and loss-of-function variants into a "gene burden" (N = 72 individuals), and performed a phenome-wide association study (PheWAS). Major findings were replicated in DiscovEHR. RESULTS The LMNA gene burden was significantly associated with primary cardiomyopathy (p = 1.78E-11) and cardiac conduction disorders (p = 5.27E-07). Most patients had not been clinically diagnosed with LMNA cardiomyopathy. We also noted an association with chronic kidney disease (p = 1.13E-06). Regression analyses on echocardiography and serum labs revealed that LMNA variant carriers had dilated cardiomyopathy and primary renal disease. CONCLUSION Pathogenic LMNA variants are an underdiagnosed cause of cardiomyopathy. We also find that LMNA loss of function may be a primary cause of renal disease. Finally, we show the value of aggregating rare, annotated variants into a gene burden and using PheWAS to identify novel ontologies for pleiotropic human genes.
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Affiliation(s)
- Joseph Park
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael G Levin
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Christopher M Haggerty
- Department of Imaging Science and Innovation and The Heart Institute, Geisinger, Danville, PA, USA.,Biomedical and Translational Informatics Institute, Geisinger, Danville, PA, USA
| | - Dustin N Hartzel
- Biomedical and Translational Informatics Institute, Geisinger, Danville, PA, USA
| | - Renae Judy
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rachel L Kember
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nosheen Reza
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | | | - Marylyn D Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anjali T Owens
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Scott M Damrauer
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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11
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Minnerop M, Kurzwelly D, Wagner H, Schüle R, Ramirez A. Reply: Biallelic POLR3A variants confirmed as a frequent cause of hereditary ataxia and spastic paraparesis. Brain 2019; 142:e13. [PMID: 30847463 DOI: 10.1093/brain/awz042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Martina Minnerop
- Institute of Neuroscience and Medicine (INM-1), Research Centre Juelich, Jülich, Germany.,Center for Movement Disorders and Neuromodulation, Department of Neurology and Institute of Clinical Neuroscience and Medical Psychology, Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany
| | | | - Holger Wagner
- Division for Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, Medical Faculty, University of Cologne, Cologne, Germany
| | - Rebecca Schüle
- Center for Neurology and Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center of Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Alfredo Ramirez
- Division for Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, Medical Faculty, University of Cologne, Cologne, Germany.,Department for Neurodegenerative Diseases and Geriatric Psychiatry, University of Bonn, Bonn, Germany
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12
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Kamath A, Linden SC, Evans FM, Hall J, Jose SF, Spillane SA, Hardie ADR, Morgan SM, Pilz DT. Chromosome 17q12 duplications: Further delineation of the range of psychiatric and clinical phenotypes. Am J Med Genet B Neuropsychiatr Genet 2018; 177:520-528. [PMID: 30134084 DOI: 10.1002/ajmg.b.32643] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 01/22/2018] [Accepted: 04/23/2018] [Indexed: 11/06/2022]
Abstract
Copy number variants at chromosome 17q12 have been associated with a spectrum of phenotypes. Deletions of 17q12 are well described and associated with maturity onset diabetes of the young type 5 (MODY5) and cystic renal disease (HNF1β) as well as cognitive impairment and seizures. Duplication of 17q12 is emerging as a new genetic syndrome, associated with learning disability, seizures, and behavioral problems. The duplication is often inherited from an apparently unaffected parent. Here, we describe a three-generation family with multiple individuals carrying a17q12 microduplication with varying clinical features, consistent with variable penetrance. The proband who inherited a 1.8 Mb interstitial 17q12 duplication from his mother presented with developmental delay, behavioral problems, and mild dysmorphism. One of his sisters, his maternal uncle, and his maternal grandmother also carry the 17q12 microduplication. Clinical features of the carriers include renal problems, diabetes mellitus, learning difficulties, epilepsy and mental illness. Cognitive abilities range from normal function to moderate impairment (full-scale IQ range: 52-99). In light of recent reports of association of this locus with schizophrenia, we performed a detailed psychiatric assessment and confirmed that one family member has symptoms consistent with a diagnosis of schizophrenia and another has a prodromal syndrome with attenuated positive symptoms of psychosis. This report extends the clinical phenotype associated with the 17q12 microduplication and highlights the phenotypic variability.
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Affiliation(s)
- Arveen Kamath
- Institute of Medical Genetics, All Wales Medical Genetics Service, University Hospital of Wales, Cardiff, United Kingdom
| | - Stefanie C Linden
- Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, United Kingdom
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Ffion M Evans
- Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, United Kingdom
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Jeremy Hall
- Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, United Kingdom
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Sian F Jose
- Institute of Medical Genetics, All Wales Medical Genetics Service, University Hospital of Wales, Cardiff, United Kingdom
| | - Sally A Spillane
- Institute of Medical Genetics, All Wales Medical Genetics Service, University Hospital of Wales, Cardiff, United Kingdom
| | - Alan D R Hardie
- Institute of Medical Genetics, All Wales Medical Genetics Service, University Hospital of Wales, Cardiff, United Kingdom
| | - Sian M Morgan
- Institute of Medical Genetics, All Wales Medical Genetics Service, University Hospital of Wales, Cardiff, United Kingdom
| | - Daniela T Pilz
- Institute of Medical Genetics, All Wales Medical Genetics Service, University Hospital of Wales, Cardiff, United Kingdom
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13
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Affiliation(s)
- Kevin J. Mitchell
- Institutes of Genetics and Neuroscience; Trinity College Dublin; Dublin 2 Ireland
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14
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Renaud M, Tranchant C, Martin JVT, Mochel F, Synofzik M, van de Warrenburg B, Pandolfo M, Koenig M, Kolb SA, Anheim M, Alonso I, Azzedine H, Barbot C, Bereau M, Berkovic S, Bernard G, Bindoff LA, Bompaire F, Bonneau D, Bonneau P, Boycott KM, Bras J, Brais B, Brigatti KW, Cameron J, Chamova T, Choquet K, Delague V, Denizeau P, Dotti MT, El‐Euch G, Elmalik SA, Federico A, Fiskerstrand T, Gagnon C, Guerreiro R, Guissart C, Hassin‐Baer S, Heimdal KR, Héron B, Isohanni P, Kalaydijeva L, Kawarai T, Koht JA, Lai S, Piana RL, Lecocq C, Linnankivi T, Lönnqvist T, Lu C, Maas R, Mahlaoui N, Mallaret M, Marelli C, Mariotti C, Mathieu J, Méneret A, Mignarri A, Monin ML, Montaut S, Nanetti L, Nadjar Y, Poujois A, Salih MA, Sousa S, Stanier P, Stoppa‐Lyonnet D, Strauss K, Tallaksen C, Tarnopolsky M, Tinant N, Tournev I, Topaloglu H, Varhaug KN, Woimant F, Wolf NI, Yahalom G, Yoon G, Young M. A recessive ataxia diagnosis algorithm for the next generation sequencing era. Ann Neurol 2017; 82:892-899. [DOI: 10.1002/ana.25084] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 10/12/2017] [Accepted: 10/17/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Mathilde Renaud
- Department of Neurology, Hautepierre HospitalUniversity Hospitals of StrasbourgStrasbourg France
- Institute of Genetics and Molecular and Cellular Biology, INSERM‐U964/CNRS‐UMR7104University of StrasbourgIllkirch France
- Strasbourg Federation of Translational MedicineUniversity of StrasbourgStrasbourg France
| | - Christine Tranchant
- Department of Neurology, Hautepierre HospitalUniversity Hospitals of StrasbourgStrasbourg France
- Institute of Genetics and Molecular and Cellular Biology, INSERM‐U964/CNRS‐UMR7104University of StrasbourgIllkirch France
- Strasbourg Federation of Translational MedicineUniversity of StrasbourgStrasbourg France
| | | | - Fanny Mochel
- Department of GeneticsPitié‐Salpêtrière University HospitalParis France
- Neurometabolic GRCPierre and Marie Curie UniversityParis France
- Neurometabolic Research GroupPierre and Marie Curie UniversityParis France
| | - Matthis Synofzik
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain ResearchUniversity of TübingenTübingen Germany
- German Center for Neurodegenerative DiseasesTübingen Germany
| | - Bart van de Warrenburg
- Department of NeurologyRadboud University Medical Center, Donders Institute for Brain, Cognition, and BehaviorNijmegen the Netherlands
| | - Massimo Pandolfo
- Department of NeurologyFree University of Brussels, Erasme HospitalBrussels Belgium
| | - Michel Koenig
- Rare Disease Genetics LaboratoryUniversity Institute of Clinical Research, University of Montpellier, Montpellier University Hospital CenterMontpellier France
| | | | - Mathieu Anheim
- Department of Neurology, Hautepierre HospitalUniversity Hospitals of StrasbourgStrasbourg France
- Institute of Genetics and Molecular and Cellular Biology, INSERM‐U964/CNRS‐UMR7104University of StrasbourgIllkirch France
- Strasbourg Federation of Translational MedicineUniversity of StrasbourgStrasbourg France
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15
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Dennert N, Engels H, Cremer K, Becker J, Wohlleber E, Albrecht B, Ehret JK, Lüdecke HJ, Suri M, Carignani G, Renieri A, Kukuk GM, Wieland T, Andrieux J, Strom TM, Wieczorek D, Dieux-Coëslier A, Zink AM. De novo microdeletions and point mutations affecting SOX2 in three individuals with intellectual disability but without major eye malformations. Am J Med Genet A 2016; 173:435-443. [PMID: 27862890 DOI: 10.1002/ajmg.a.38034] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 10/10/2016] [Indexed: 01/04/2023]
Abstract
Loss-of-function mutations and deletions of the SOX2 gene are known to cause uni- and bilateral anophthalmia and microphthalmia as well as related disorders such as anophthalmia-esophageal-genital syndrome. Thus, anophthalmia/microphthalmia is the primary indication for targeted, "phenotype first" analyses of SOX2. However, SOX2 mutations are also associated with a wide range of non-ocular abnormalities, such as postnatal growth retardation, structural brain anomalies, hypogenitalism, and developmental delay. The present report describes three patients without anophthalmia/microphthalmia and loss-of-function mutations or microdeletions of SOX2 who had been investigated in a "genotype first" manner due to intellectual disability/developmental delay using whole exome sequencing or chromosomal microarray analyses. This result prompted us to perform SOX2 Sanger sequencing in 192 developmental delay/intellectual disability patients without anophthalmia or microphthalmia. No additional SOX2 loss-of-function mutations were detected in this cohort, showing that SOX2 is clearly not a major cause of intellectual disability without anophthalmia/microphthalmia. In our three patients and four further, reported "genotype first" SOX2 microdeletion patients, anophthalmia/microphthalmia was present in less than half of the patients. Thus, SOX2 is another example of a gene whose clinical spectrum is broadened by the generation of "genotype first" findings using hypothesis-free, genome-wide methods. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Nicola Dennert
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Hartmut Engels
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Kirsten Cremer
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Jessica Becker
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Eva Wohlleber
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Beate Albrecht
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Julia K Ehret
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Hermann-Josef Lüdecke
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany.,Institute of Human Genetics, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Mohnish Suri
- Nottingham Clinical Genetics Service, Nottingham University Hospitals NHS Trust, City Hospital Campus, Nottingham, United Kingdom
| | | | | | - Guido M Kukuk
- Department of Radiology, University of Bonn, Bonn, Germany
| | - Thomas Wieland
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Joris Andrieux
- Laboratory of Medical Genetics, Hôpital Jeanne de Flandre University Hospital, Lille, France
| | - Tim M Strom
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Dagmar Wieczorek
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany.,Institute of Human Genetics, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Anne Dieux-Coëslier
- Clinical Genetics, Hôpital Jeanne de France University Hospital, Lille, France
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16
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Rogdaki M, Jauhar S, McCutcheon R, Howes O. Treatment-Resistant Schizophrenia in a Patient With 17q12 Duplication. Biol Psychiatry 2016; 80:e19-e20. [PMID: 26582588 DOI: 10.1016/j.biopsych.2015.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 09/30/2015] [Accepted: 10/01/2015] [Indexed: 11/26/2022]
Affiliation(s)
- Maria Rogdaki
- Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, King's College.
| | - Sameer Jauhar
- Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, King's College
| | - Robert McCutcheon
- Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, King's College
| | - Oliver Howes
- Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, King's College; Psychiatric Imaging, MRC Clinical Sciences Centre, Hammersmith Hospital, London, United Kingdom
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17
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Reiff M, Mueller R, Mulchandani S, Spinner NB, Pyeritz RE, Bernhardt BA. A qualitative study of healthcare providers' perspectives on the implications of genome-wide testing in pediatric clinical practice. J Genet Couns 2014; 23:474-88. [PMID: 24037030 PMCID: PMC3955216 DOI: 10.1007/s10897-013-9653-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 08/22/2013] [Indexed: 12/20/2022]
Abstract
The utilization of genome-wide chromosomal microarray analysis (CMA) in pediatric clinical practice provides an opportunity to consider how genetic diagnostics is evolving, and to prepare for the clinical integration of genome-wide sequencing technologies. We conducted semi-structured interviews with 15 healthcare providers (7 genetic counselors, 4 medical geneticists, and 4 non-genetics providers) to investigate the impact of CMA on clinical practice, and implications for providers, patients and families. Interviews were analyzed qualitatively using content analysis. Most providers reported that genomic testing enhanced their professional experience and was beneficial to patients, primarily due to the improved diagnostic rate compared with earlier chromosomal studies. Other effects on practice included moving towards genotype-first diagnosis and broadening indications for chromosomal testing. Opinions varied concerning informed consent and disclosure of results. The duty to disclose incidental findings (IFs) was noted; however concerns were raised about potential psychosocial harms of disclosing pre-symptomatic findings. Tensions were revealed between the need for comprehensive informed consent for all families and the challenges of communicating time-consuming and potentially anxiety-provoking information regarding uncertain and incidental findings that may be relevant only in rare cases. Genetic counselors can play an important role in liaising with families, health professionals and testing laboratories, providing education and guidance to non-genetics providers, and enabling families to receive adequate pre-and post-test information and follow-up care.
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Affiliation(s)
- Marian Reiff
- Center for the Integration of Genetic Health Care Technologies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA,
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18
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Stevens SJC, Blom EW, Siegelaer ITJ, Smeets EEJGL. A recurrent deletion syndrome at chromosome bands 2p11.2-2p12 flanked by segmental duplications at the breakpoints and including REEP1. Eur J Hum Genet 2014; 23:543-6. [PMID: 24986827 DOI: 10.1038/ejhg.2014.124] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 05/12/2014] [Accepted: 06/03/2014] [Indexed: 01/26/2023] Open
Abstract
We identified an identical and recurrent 9.4-Mbp deletion at chromosome bands 2p11.2-2p12, which occurred de novo in two unrelated patients. It is flanked at the distal and proximal breakpoints by two homologous segmental duplications consisting of low copy repeat (LCR) blocks in direct orientation, which have >99% sequence identity. Despite the fact that the deletion was almost 10 Mbp in size, the patients showed a relatively mild clinical phenotype, that is, mild-to-moderate intellectual disability, a happy disposition, speech delay and delayed motor development. Their phenotype matches with that of previously described patients. The 2p11.2-2p12 deletion includes the REEP1 gene that is associated with spastic paraplegia and phenotypic features related to this are apparent in most 2p11.2-2p12 deletion patients, but not in all. Other hemizygous genes that may contribute to the clinical phenotype include LRRTM1 and CTNNA2. We propose a recurrent but rare 2p11.2-2p12 deletion syndrome based on (1) the identical, non-random localisation of the de novo deletion breakpoints in two unrelated patients and a patient from literature, (2) the patients' phenotypic similarity and their phenotypic overlap with other 2p deletions and (3) the presence of highly identical LCR blocks flanking both breakpoints, consistent with a non-allelic homologous recombination (NAHR)-mediated rearrangement.
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Affiliation(s)
- Servi J C Stevens
- Department Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Eveline W Blom
- Department Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Ingrid T J Siegelaer
- Department Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Eric E J G L Smeets
- Department Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
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19
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Dittwald P, Gambin T, Szafranski P, Li J, Amato S, Divon MY, Rodríguez Rojas LX, Elton LE, Scott DA, Schaaf CP, Torres-Martinez W, Stevens AK, Rosenfeld JA, Agadi S, Francis D, Kang SHL, Breman A, Lalani SR, Bacino CA, Bi W, Milosavljevic A, Beaudet AL, Patel A, Shaw CA, Lupski JR, Gambin A, Cheung SW, Stankiewicz P. NAHR-mediated copy-number variants in a clinical population: mechanistic insights into both genomic disorders and Mendelizing traits. Genome Res 2013; 23:1395-409. [PMID: 23657883 PMCID: PMC3759717 DOI: 10.1101/gr.152454.112] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 04/30/2013] [Indexed: 12/30/2022]
Abstract
We delineated and analyzed directly oriented paralogous low-copy repeats (DP-LCRs) in the most recent version of the human haploid reference genome. The computationally defined DP-LCRs were cross-referenced with our chromosomal microarray analysis (CMA) database of 25,144 patients subjected to genome-wide assays. This computationally guided approach to the empirically derived large data set allowed us to investigate genomic rearrangement relative frequencies and identify new loci for recurrent nonallelic homologous recombination (NAHR)-mediated copy-number variants (CNVs). The most commonly observed recurrent CNVs were NPHP1 duplications (233), CHRNA7 duplications (175), and 22q11.21 deletions (DiGeorge/velocardiofacial syndrome, 166). In the ∼25% of CMA cases for which parental studies were available, we identified 190 de novo recurrent CNVs. In this group, the most frequently observed events were deletions of 22q11.21 (48), 16p11.2 (autism, 34), and 7q11.23 (Williams-Beuren syndrome, 11). Several features of DP-LCRs, including length, distance between NAHR substrate elements, DNA sequence identity (fraction matching), GC content, and concentration of the homologous recombination (HR) hot spot motif 5'-CCNCCNTNNCCNC-3', correlate with the frequencies of the recurrent CNVs events. Four novel adjacent DP-LCR-flanked and NAHR-prone regions, involving 2q12.2q13, were elucidated in association with novel genomic disorders. Our study quantitates genome architectural features responsible for NAHR-mediated genomic instability and further elucidates the role of NAHR in human disease.
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Affiliation(s)
- Piotr Dittwald
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Institute of Informatics, University of Warsaw, 02-097 Warsaw, Poland
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Institute of Computer Science, Warsaw University of Technology, 02-665 Warsaw, Poland
| | - Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jian Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Stephen Amato
- Genetics and Metabolism, Phoenix Children's Hospital, Phoenix, Arizona 85006, USA
| | | | | | - Lindsay E. Elton
- Child Neurology, Pediatric Specialty Services, Austin, Texas 78723, USA
| | - Daryl A. Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Christian P. Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Wilfredo Torres-Martinez
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | - Abby K. Stevens
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | - Jill A. Rosenfeld
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, Washington 99207, USA
| | - Satish Agadi
- Department of Pediatrics and Neurology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - David Francis
- Cytogenetics Department, Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria 3052, Australia
| | - Sung-Hae L. Kang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Amy Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Seema R. Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Carlos A. Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Aleksandar Milosavljevic
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Arthur L. Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Chad A. Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
- Texas Children's Hospital, Houston, Texas 77030, USA
| | - Anna Gambin
- Institute of Informatics, University of Warsaw, 02-097 Warsaw, Poland
- Mossakowski Medical Research Centre, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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Rigter T, Henneman L, Kristoffersson U, Hall A, Yntema HG, Borry P, Tönnies H, Waisfisz Q, Elting MW, Dondorp WJ, Cornel MC. Reflecting on earlier experiences with unsolicited findings: points to consider for next-generation sequencing and informed consent in diagnostics. Hum Mutat 2013; 34:1322-8. [PMID: 23784691 PMCID: PMC4285964 DOI: 10.1002/humu.22370] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 06/13/2013] [Indexed: 12/13/2022]
Abstract
High-throughput nucleotide sequencing (often referred to as next-generation sequencing; NGS) is increasingly being chosen as a diagnostic tool for cases of expected but unresolved genetic origin. When exploring a higher number of genetic variants, there is a higher chance of detecting unsolicited findings. The consequential increased need for decisions on disclosure of these unsolicited findings poses a challenge for the informed consent procedure. This article discusses the ethical and practical dilemmas encountered when contemplating informed consent for NGS in diagnostics from a multidisciplinary point of view. By exploring recent similar experiences with unsolicited findings in other settings, an attempt is made to describe what can be learned so far for implementing NGS in standard genetic diagnostics. The article concludes with a set of points to consider in order to guide decision-making on the extent of return of results in relation to the mode of informed consent. We hereby aim to provide a sound basis for developing guidelines for optimizing the informed consent procedure.
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Affiliation(s)
- Tessel Rigter
- Department of Clinical Genetics, Section of Community Genetics and the EMGO Institute for Health and Care Research, VU University Medical Center, Amsterdam, The Netherlands
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21
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Bierhals T, Maddukuri SB, Kutsche K, Girisha KM. Expanding the phenotype associated with 17q12 duplication: Case report and review of the literature. Am J Med Genet A 2013; 161A:352-9. [DOI: 10.1002/ajmg.a.35730] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Accepted: 10/01/2012] [Indexed: 12/29/2022]
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Abstract
Children have been identified as uniquely vulnerable clinical research subjects since the early 1970s. This article reviews the historical underpinnings of this designation, the current regulatory framework for pediatric and neonatal research, and common problems in pediatric research oversight. It also presents 3 areas of pediatric and neonatal research (genomic screening, healthy children donating stem cells, and therapeutic hypothermia for neonates with hypoxic-ischemic encephalopathy) that highlight contemporary challenges in pediatric research ethics, including balancing risk and benefit, informed consent and assent, and clinical equipoise.
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Affiliation(s)
- Naomi Laventhal
- Department of Pediatrics and Communicable Diseases, Division of Neonatal-Perinatal Medicine, University of Michigan School of Medicine, 8-621 C&W Mott Hospital, 1540 E. Hospital Drive, SPC 4254, Ann Arbor, MI 48109-4254, Phone: 734-763-4109, Fax: 734-763-7728,
| | - Beth Tarini
- Department of Pediatrics and Communicable Diseases, Child Health Evaluation and Research Unit, University of Michigan School of Medicine, 300 North Ingalls 6C11, Ann Arbor, Michigan 48109-5456, Phone: 734-615-8153, Fax: 734-264-2599,
| | - John Lantos
- Children’s Mercy Bioethics Center, Children’s Mercy Hospital, 2401 Gilham Rd., Kansas, City, MO 64108, Phone: 816-701-5283, Fax: 816-701-5286,
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23
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Mundhofir FE, Winarni TI, van Bon BW, Aminah S, Nillesen WM, Merkx G, Smeets D, Hamel BC, Faradz SM, Yntema HG. A Cytogenetic Study in a Large Population of Intellectually Disabled Indonesians. Genet Test Mol Biomarkers 2012; 16:412-7. [DOI: 10.1089/gtmb.2011.0157] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Farmaditya E.P. Mundhofir
- Division of Human Genetics, Center for Biomedical Research (CEBIOR), Faculty of Medicine, Diponegoro University GSG, Semarang, Indonesia
- Department of Human Genetics, Radboud University, Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Tri Indah Winarni
- Division of Human Genetics, Center for Biomedical Research (CEBIOR), Faculty of Medicine, Diponegoro University GSG, Semarang, Indonesia
| | - Bregje W. van Bon
- Department of Human Genetics, Radboud University, Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Siti Aminah
- Department of Neurology, Hasan Sadikin Central General Hospital, Bandung, Indonesia
| | - Willy M. Nillesen
- Department of Human Genetics, Radboud University, Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Gerard Merkx
- Department of Human Genetics, Radboud University, Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Dominique Smeets
- Department of Human Genetics, Radboud University, Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Ben C.J. Hamel
- Department of Human Genetics, Radboud University, Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Sultana M.H. Faradz
- Division of Human Genetics, Center for Biomedical Research (CEBIOR), Faculty of Medicine, Diponegoro University GSG, Semarang, Indonesia
| | - Helger G. Yntema
- Department of Human Genetics, Radboud University, Nijmegen Medical Centre, Nijmegen, The Netherlands
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24
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Galizia EC, Srikantha M, Palmer R, Waters JJ, Lench N, Ogilvie CM, Kasperavičiūtė D, Nashef L, Sisodiya SM. Array comparative genomic hybridization: results from an adult population with drug-resistant epilepsy and co-morbidities. Eur J Med Genet 2012; 55:342-8. [PMID: 22342432 PMCID: PMC3526772 DOI: 10.1016/j.ejmg.2011.12.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Accepted: 12/27/2011] [Indexed: 01/15/2023]
Abstract
Background The emergence of array comparative genomic hybridization (array CGH) as a diagnostic tool in molecular genetics has facilitated recognition of microdeletions and microduplications as risk factors for both generalised and focal epilepsies. Furthermore, there is evidence that some microdeletions/duplications, such as the 15q13.3 deletion predispose to a range of neuropsychiatric disorders, including intellectual disability (ID), autism, schizophrenia and epilepsy. We hypothesised that array CGH would reveal relevant findings in an adult patient group with epilepsy and complex phenotypes. Methods 82 patients (54 from the National Hospital for Neurology and Neurosurgery and 28 from King’s College Hospital) with drug-resistant epilepsy and co-morbidities had array CGH. Separate clinicians ordered array CGH and separate platforms were used at the two sites. Results In the two independent groups we identified copy number variants judged to be of pathogenic significance in 13.5% (7/52) and 20% (5/25) respectively, noting that slightly different selection criteria were used, giving an overall yield of 15.6%. Sixty-nine variants of unknown significance were also identified in the group from the National Hospital for Neurology and Neurosurgery and 5 from the King’s College Hospital patient group. Conclusion We conclude that array CGH be considered an important investigation in adults with complicated epilepsy and, at least at present for selected patients, should join the diagnostic repertoire of clinical history and examination, neuroimaging, electroencephalography and other indicated investigations in generating a more complete formulation of an individual’s epilepsy.
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Affiliation(s)
- Elizabeth C Galizia
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, Queen Square, London, United Kingdom
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Mefford HC, Yendle SC, Hsu C, Cook J, Geraghty E, McMahon JM, Eeg-Olofsson O, Sadleir LG, Gill D, Ben-Zeev B, Lerman-Sagie T, Mackay M, Freeman JL, Andermann E, Pelakanos JT, Andrews I, Wallace G, Eichler EE, Berkovic SF, Scheffer IE. Rare copy number variants are an important cause of epileptic encephalopathies. Ann Neurol 2011; 70:974-85. [PMID: 22190369 PMCID: PMC3245646 DOI: 10.1002/ana.22645] [Citation(s) in RCA: 179] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
OBJECTIVE Rare copy number variants (CNVs)--deletions and duplications--have recently been established as important risk factors for both generalized and focal epilepsies. A systematic assessment of the role of CNVs in epileptic encephalopathies, the most devastating and often etiologically obscure group of epilepsies, has not been performed. METHODS We evaluated 315 patients with epileptic encephalopathies characterized by epilepsy and progressive cognitive impairment for rare CNVs using a high-density, exon-focused, whole-genome oligonucleotide array. RESULTS We found that 25 of 315 (7.9%) of our patients carried rare CNVs that may contribute to their phenotype, with at least one-half being clearly or likely pathogenic. We identified 2 patients with overlapping deletions at 7q21 and 2 patients with identical duplications of 16p11.2. In our cohort, large deletions were enriched in affected individuals compared to controls, and 4 patients harbored 2 rare CNVs. We screened 2 novel candidate genes found within the rare CNVs in our cohort but found no mutations in our patients with epileptic encephalopathies. We highlight several additional novel candidate genes located in CNV regions. INTERPRETATION Our data highlight the significance of rare CNVs in the epileptic encephalopathies, and we suggest that CNV analysis should be considered in the genetic evaluation of these patients. Our findings also highlight novel candidate genes for further study.
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Affiliation(s)
- Heather C Mefford
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA, USA.
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Mulley JC, Dibbens LM. Genetic variations and associated pathophysiology in the management of epilepsy. APPLICATION OF CLINICAL GENETICS 2011; 4:113-25. [PMID: 23776372 PMCID: PMC3681183 DOI: 10.2147/tacg.s7407] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The genomic era has enabled the application of molecular tools to the solution of many of the genetic epilepsies, with and without comorbidities. Massively parallel sequencing has recently reinvigorated gene discovery for the monogenic epilepsies. Recurrent and novel copy number variants have given much-needed impetus to the advancement of our understanding of epilepsies with complex inheritance. Superimposed upon that is the phenotypic blurring by presumed genetic modifiers scattering the effects of the primary mutation. The genotype-first approach has uncovered associated syndrome constellations, of which epilepsy is only one of the syndromes. As the molecular genetic basis for the epilepsies unravels, it will increasingly influence the classification and diagnosis of the epilepsies. The ultimate goal of the molecular revolution has to be the design of treatment protocols based on genetic profiles, and cracking the 30% of epilepsies refractory to current medications, but that still lies well into the future. The current focus is on the scientific basis for epilepsy. Understanding its genetic causes and biophysical mechanisms is where we are currently positioned: prizing the causes of epilepsy "out of the shadows" and exposing its underlying mechanisms beyond even the ion-channels.
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Affiliation(s)
- John C Mulley
- Department of Genetic Medicine, Directorate of Genetics and Molecular Pathology, SA Pathology at Women's and Children's Hospital, North Adelaide, Australia ; School of Paediatrics and Reproductive Health, and School of Molecular and Biomedical Sciences, The University of Adelaide, Adelaide, Australia
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Recurrent 200-kb deletions of 16p11.2 that include the SH2B1 gene are associated with developmental delay and obesity. Genet Med 2011; 12:641-7. [PMID: 20808231 DOI: 10.1097/gim.0b013e3181ef4286] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
PURPOSE The short arm of chromosome 16 is rich in segmental duplications, predisposing this region of the genome to a number of recurrent rearrangements. Genomic imbalances of an approximately 600-kb region in 16p11.2 (29.5-30.1 Mb) have been associated with autism, intellectual disability, congenital anomalies, and schizophrenia. However, a separate, distal 200-kb region in 16p11.2 (28.7-28.9 Mb) that includes the SH2B1 gene has been recently associated with isolated obesity. The purpose of this study was to better define the phenotype of this recurrent SH2B1-containing microdeletion in a cohort of phenotypically abnormal patients not selected for obesity. METHODS Array comparative hybridization was performed on a total of 23,084 patients in a clinical setting for a variety of indications, most commonly developmental delay. RESULTS Deletions of the SH2B1-containing region were identified in 31 patients. The deletion is enriched in the patient population when compared with controls (P = 0.003), with both inherited and de novo events. Detailed clinical information was available for six patients, who all had developmental delays of varying severity. Body mass index was ≥95th percentile in four of six patients, supporting the previously described association with obesity. The reciprocal duplication, found in 17 patients, does not seem to be significantly enriched in our patient population compared with controls. CONCLUSIONS Deletions of the 16p11.2 SH2B1-containing region are pathogenic and are associated with developmental delay in addition to obesity.
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Abstract
Epilepsy is one of the most common neurological disorders, with a prevalence of 1% and lifetime incidence of 3%. There are numerous epilepsy syndromes, most of which are considered to be genetic epilepsies. Despite the discovery of more than 20 genes for epilepsy to date, much of the genetic contribution to epilepsy is not yet known. Copy number variants have been established as an important source of mutation in other complex brain disorders, including intellectual disability, autism and schizophrenia. Recent advances in technology now facilitate genome-wide searches for copy number variants and are beginning to be applied to epilepsy. Here, we discuss what is currently known about the contribution of copy number variants to epilepsy, and how that knowledge is redefining classification of clinical and genetic syndromes.
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Cooper DN, Chen JM, Ball EV, Howells K, Mort M, Phillips AD, Chuzhanova N, Krawczak M, Kehrer-Sawatzki H, Stenson PD. Genes, mutations, and human inherited disease at the dawn of the age of personalized genomics. Hum Mutat 2010; 31:631-55. [PMID: 20506564 DOI: 10.1002/humu.21260] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The number of reported germline mutations in human nuclear genes, either underlying or associated with inherited disease, has now exceeded 100,000 in more than 3,700 different genes. The availability of these data has both revolutionized the study of the morbid anatomy of the human genome and facilitated "personalized genomics." With approximately 300 new "inherited disease genes" (and approximately 10,000 new mutations) being identified annually, it is pertinent to ask how many "inherited disease genes" there are in the human genome, how many mutations reside within them, and where such lesions are likely to be located? To address these questions, it is necessary not only to reconsider how we define human genes but also to explore notions of gene "essentiality" and "dispensability."Answers to these questions are now emerging from recent novel insights into genome structure and function and through complete genome sequence information derived from multiple individual human genomes. However, a change in focus toward screening functional genomic elements as opposed to genes sensu stricto will be required if we are to capitalize fully on recent technical and conceptual advances and identify new types of disease-associated mutation within noncoding regions remote from the genes whose function they disrupt.
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Affiliation(s)
- David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, United Kingdom.
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Epigenetics, copy number variation, and other molecular mechanisms underlying neurodevelopmental disabilities: new insights and diagnostic approaches. J Dev Behav Pediatr 2010; 31:582-91. [PMID: 20814257 DOI: 10.1097/dbp.0b013e3181ee384e] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The diagnostic evaluation of children with intellectual disability (ID) and other neurodevelopmental disabilities (NDD) has become increasingly complex in recent years owing to a number of newly recognized genetic mechanisms and sophisticated methods to diagnose them. Previous studies have attempted to address the diagnostic yield of finding a genetic cause in ID. The results have varied widely from 10% to 81%, with the highest percentage being found in studies using new array comparative genomic hybridization methodology especially in autism. Although many cases of ID/NDD result from chromosomal aneuploidy or structural rearrangements, single gene disorders and new categories of genome modification, including epigenetics and copy number variation play an increasingly important role in diagnosis and testing. Epigenetic mechanisms, such as DNA methylation and modifications to histone proteins, regulate high-order DNA structure and gene expression. Aberrant epigenetic and copy number variation mechanisms are involved in several neurodevelopmental and neurodegenerative disorders including Rett syndrome, fragile X syndrome, and microdeletion syndromes. This review will describe a number of the molecular genetic mechanisms that play a role in disorders leading to ID/NDD and will discuss the categories and technologies for diagnostic testing of these conditions.
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Copy number variations associated with autism spectrum disorders contribute to a spectrum of neurodevelopmental disorders. Genet Med 2010; 12:694-702. [DOI: 10.1097/gim.0b013e3181f0c5f3] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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Bedoyan JK, Kumar RA, Sudi J, Silverstein F, Ackley T, Iyer RK, Christian SL, Martin DM. Duplication 16p11.2 in a child with infantile seizure disorder. Am J Med Genet A 2010; 152A:1567-74. [PMID: 20503337 DOI: 10.1002/ajmg.a.33415] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Submicroscopic recurrent 16p11.2 rearrangements are associated with several neurodevelopmental disorders, including autism, mental retardation, and schizophrenia. The common 16p11.2 region includes 24 known genes, of which 22 are expressed in the developing human fetal nervous system. As yet, the mechanisms leading to neurodevelopmental abnormalities and the broader phenotypes associated with deletion or duplication of 16p11.2 have not been clarified. Here we report a child with spastic quadriparesis, refractory infantile seizures, severe global developmental delay, hypotonia, and microcephaly, and a de novo 598 kb 16p11.2 microduplication. Family history is negative for any of these features in parents and immediate family members. Sequencing analyses showed no mutations in DOC2A, QPRT, and SEZ6L2, genes within the duplicated 16p11.2 region that have been implicated in neuronal function and/or seizure related phenotypes. The child's clinical course is consistent with a rare seizure disorder called malignant migrating partial seizure disorder of infancy, raising the possibility that duplication or disruption of genes in the 16p11.2 interval may contribute to this severe disorder.
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Affiliation(s)
- Jirair K Bedoyan
- Department of Pediatrics, The University of Michigan, Ann Arbor, Michigan 48109-5652, USA
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