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Lecoquierre F, Cassinari K, Chambon P, Nicolas G, Malsa S, Marlin R, Assouline Y, Fléjou JF, Frebourg T, Houdayer C, Bera O, Baert-Desurmont S. Patients with 10q22.3q23.1 recurrent deletion syndrome are at risk for juvenile polyposis. Eur J Med Genet 2019; 63:103773. [PMID: 31561016 DOI: 10.1016/j.ejmg.2019.103773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/16/2019] [Accepted: 09/22/2019] [Indexed: 01/10/2023]
Abstract
Juvenile polyposis syndrome (JPS) is a rare autosomal dominant predisposition to hamartomatous polyps within the gastrointestinal tract, at high risk for malignant transformation. BMPR1A and SMAD4 loss-of-function variants account for 50% of the cases. More specifically, point mutations and structural abnormalities in BMPR1A lead to a highly penetrant yet variable phenotype of JPS. Intriguingly, in the developmental disorder caused by a recurrent 10q22.3q23.1 7 Mb deletion which includes BMPR1A, juvenile polyps have never been reported. We present the case of a young adult harboring this recurrent deletion, in a context of intellectual disability, ventricular septal defect and severe juvenile polyposis syndrome diagnosed at the age of 25 years, requiring a surgical preventive colectomy. She developed a gastric adenocarcinoma from which she died at the age of 32. We hypothesize that with the current available pangenomic CNV arrays, the diagnosis of 10q22.3q23.1 deletion is often made several years before the onset of the digestive phenotype, which could explain the absence of reports for juvenile polyps. This observation highlights the importance of an active digestive surveillance of patients with 10q22.3q23.1 deletion.
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Affiliation(s)
- François Lecoquierre
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, F76000, Rouen, France.
| | - Kévin Cassinari
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, F76000, Rouen, France
| | - Pascal Chambon
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, F76000, Rouen, France
| | - Gaël Nicolas
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, F76000, Rouen, France
| | - Sarah Malsa
- Department of Cancer Genetics, Martinique University Hospital, Fort-de-France, Martinique, France
| | - Régine Marlin
- Department of Cancer Genetics, Martinique University Hospital, Fort-de-France, Martinique, France
| | - Yvon Assouline
- Departement of Gastro-Enterology, Clinique Saint Paul, Fort-de-France, Martinique, France
| | - Jean-François Fléjou
- Pathology Department, AP-HP, Hôpital Saint-Antoine, Faculté de Médecine Sorbonne Université, Paris, France
| | - Thierry Frebourg
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, F76000, Rouen, France
| | - Claude Houdayer
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, F76000, Rouen, France
| | - Odile Bera
- Department of Cancer Genetics, Martinique University Hospital, Fort-de-France, Martinique, France
| | - Stéphanie Baert-Desurmont
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, F76000, Rouen, France
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2
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Yao R, Yu T, Xu Y, Li G, Yin L, Zhou Y, Wang J, Yan Z. Concurrent somatic KRAS mutation and germline 10q22.3-q23.2 deletion in a patient with juvenile myelomonocytic leukemia, developmental delay, and multiple malformations: a case report. BMC Med Genomics 2018; 11:60. [PMID: 30012129 PMCID: PMC6048798 DOI: 10.1186/s12920-018-0377-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 07/03/2018] [Indexed: 11/10/2022] Open
Abstract
Background The proto-oncogene KRAS performs an essential function in normal tissue signaling, and the mutation of KRAS gene is a key step in the development of many cancers. Somatic KRAS mutations are often detected in patients with solid and non-solid tumors, whereas germline KRAS mutations are implicated in patients with the Noonan syndrome, cardio-facio-cutaneous (CFC) syndrome and Costello syndrome. The deletion of chromosome 10q22.3-q23.2 is a rare cytogenetic abnormality, which often leads to distinct facial appearance and delays in speech and global development. Case presentation Herein, we report the case of a 4-year-old boy diagnosed with juvenile myelomonocytic leukemia. The boy also had syndromic features, such as speech and motor developmental delay, multiple congenital malformations, including distinct facial features, club feet, and cryptorchidism. Using whole-exome sequencing, we identified a pathogenic mutation in KRAS [c.34G > A, p.Gly12Ser] isolated from peripheral blood DNA. Sanger sequencing confirmed the wild-type sequence in the parents and patient’s salivary cell DNA indicating its somatic state. A 7311-kb deletion in 10q22.3-q23.2 was also revealed by chromosomal microarray analysis, which was later proved as a germline de novo variant. Conclusion Juvenile myelomonocytic leukemia in the patient was attributed to a somatic KRAS mutation, whereas the syndromic features of the patient were considered a consequence of germline chromosome 10q22.3-q23.2 deletion. Genetic testing for patients with complicated phenotypes can be valuable in detecting multiple pathogenic variants.
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Affiliation(s)
- Ruen Yao
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, People's Republic of China.,Institute for Pediatric Translational Medicine, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, People's Republic of China
| | - Tingting Yu
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, People's Republic of China. .,Institute for Pediatric Translational Medicine, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, People's Republic of China.
| | - Yufei Xu
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, People's Republic of China.,Institute for Pediatric Translational Medicine, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, People's Republic of China
| | - Guoqiang Li
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, People's Republic of China.,Institute for Pediatric Translational Medicine, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, People's Republic of China
| | - Lei Yin
- Department of Internal Medicine, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, People's Republic of China.,Rare Diseases Outpatient Clinic, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, People's Republic of China
| | - Yunfang Zhou
- Rare Diseases Outpatient Clinic, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, People's Republic of China
| | - Jian Wang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, People's Republic of China.,Institute for Pediatric Translational Medicine, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, People's Republic of China
| | - Zhilong Yan
- Department of Pediatric Surgery, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, People's Republic of China.
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3
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Coelho Molck M, Simioni M, Vieira TP, Sgardioli IC, Monteiro FP, Souza J, Fett‐Conte AC, Félix TM, Monlléo IL, Gil‐da‐Silva‐Lopes VL. Genomic imbalances in syndromic congenital heart disease. JORNAL DE PEDIATRIA (VERSÃO EM PORTUGUÊS) 2017. [DOI: 10.1016/j.jpedp.2017.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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4
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Molck MC, Simioni M, Paiva Vieira T, Sgardioli IC, Paoli Monteiro F, Souza J, Fett-Conte AC, Félix TM, Lopes Monlléo I, Gil-da-Silva-Lopes VL. Genomic imbalances in syndromic congenital heart disease. J Pediatr (Rio J) 2017; 93:497-507. [PMID: 28336264 DOI: 10.1016/j.jped.2016.11.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 11/21/2016] [Accepted: 11/21/2016] [Indexed: 12/27/2022] Open
Abstract
OBJECTIVE To identify pathogenic genomic imbalances in patients presenting congenital heart disease (CHD) with extra cardiac anomalies and exclusion of 22q11.2 deletion syndrome (22q11.2 DS). METHODS 78 patients negative for the 22q11.2 deletion, previously screened by fluorescence in situ hybridization (FISH) and/or multiplex ligation probe amplification (MLPA) were tested by chromosomal microarray analysis (CMA). RESULTS Clinically significant copy number variations (CNVs ≥300kb) were identified in 10% (8/78) of cases. In addition, potentially relevant CNVs were detected in two cases (993kb duplication in 15q21.1 and 706kb duplication in 2p22.3). Genes inside the CNV regions found in this study, such as IRX4, BMPR1A, SORBS2, ID2, ROCK2, E2F6, GATA4, SOX7, SEMAD6D, FBN1, and LTPB1 are known to participate in cardiac development and could be candidate genes for CHD. CONCLUSION These data showed that patients presenting CHD with extra cardiac anomalies and exclusion of 22q11.2 DS should be investigated by CMA. The present study emphasizes the possible role of CNVs in CHD.
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Affiliation(s)
- Miriam Coelho Molck
- Universidade Estadual de Campinas (UNICAMP), Departamento de Genética Médica, Campinas, SP, Brazil
| | - Milena Simioni
- Universidade Estadual de Campinas (UNICAMP), Departamento de Genética Médica, Campinas, SP, Brazil
| | - Társis Paiva Vieira
- Universidade Estadual de Campinas (UNICAMP), Departamento de Genética Médica, Campinas, SP, Brazil
| | | | - Fabíola Paoli Monteiro
- Universidade Estadual de Campinas (UNICAMP), Departamento de Genética Médica, Campinas, SP, Brazil
| | - Josiane Souza
- Centro de Atendimento Integral ao Fissurado Lábio Palatal (CAIF), Curitiba, PR, Brazil
| | - Agnes Cristina Fett-Conte
- Faculdade de Medicina de São José do Rio Preto, Departamento de Biologia Molecular, São José do Rio Preto, SP, Brazil
| | - Têmis Maria Félix
- Hospital de Clínicas de Porto Alegre, Serviço de Genética Médica, Porto Alegre, RS, Brazil
| | - Isabella Lopes Monlléo
- Universidade Federal de Alagoas (UFAL), Hospital Universitário, Faculdade de Medicina, Serviço de Genética Clínica, Maceió, AL, Brazil
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5
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Topa A, Samuelsson L, Lovmar L, Stenman G, Kölby L. On the significance of craniosynostosis in a case of Kabuki syndrome with a concomitant KMT2D mutation and 3.2 Mbp de novo 10q22.3q23.1 deletion. Am J Med Genet A 2017; 173:2219-2225. [PMID: 28590022 DOI: 10.1002/ajmg.a.38296] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 03/29/2017] [Accepted: 04/29/2017] [Indexed: 11/08/2022]
Abstract
Craniosynostosis has rarely been described in patients with Kabuki syndrome. We report here a boy with facial asymmetry due to combined premature synostosis of the right coronal and sagittal sutures as well as several symptoms reminiscent of Kabuki syndrome (KS). Our case supports previous observations and suggests that craniosynostosis is a part of the KS phenotype. The uniqueness of our case is the sporadic co-occurrence of two genetic disorders, that is, a de novo frameshift variant in the KMT2D gene and a de novo 3.2 Mbp 10q22.3q23.1 deletion. Our findings emphasize the importance of the initial clinical assessment of children with craniosynostosis and that genomic and monogenic disorders, such as Kabuki syndrome, should be considered among the differential diagnoses of syndromic forms of craniosynostosis.
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Affiliation(s)
- Alexandra Topa
- Department of Pathology and Genetics, University of Gothenburg, The Sahlgrenska Academy, Gothenburg, Sweden.,Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Lena Samuelsson
- Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Lovisa Lovmar
- Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Göran Stenman
- Department of Pathology and Genetics, University of Gothenburg, The Sahlgrenska Academy, Gothenburg, Sweden.,Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Lars Kölby
- Department of Plastic Surgery, University of Gothenburg, The Sahlgrenska Academy, Gothenburg, Sweden
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6
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Coelho Molck M, Simioni M, Paiva Vieira T, Paoli Monteiro F, Gil-da-Silva-Lopes VL. A New Case of the Rare 10q22.3q23.2 Microdeletion Flanked by Low-Copy Repeats 3/4. Mol Syndromol 2017; 8:161-167. [PMID: 28588438 DOI: 10.1159/000469965] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2017] [Indexed: 01/07/2023] Open
Abstract
Deletions in the 10q22.3q23.2 region are rare and mediated by 2 low-copy repeats (LCRs 3 and 4). These deletions have already been recognized as the 10q22q23 deletion syndrome. The phenotype associated with this condition is rather uncharacteristic, and most common features are craniofacial dysmorphisms and developmental delay. We describe a boy with craniofacial dysmorphic features, developmental delay, tetralogy of Fallot, hand/foot abnormalities, and recurrent respiratory tract infections. Chromosomal microarray analysis disclosed a 7.8-Mb microdeletion at 10q22.3q23.2, flanked by LCRs 3/4, and an additional 16q12.1 microdeletion of 189 kb. This article reviews the clinical signs of reported cases with similar deletions and compares them with our patient, contributing to a better understanding of genotype-phenotype correlation.
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Affiliation(s)
- Miriam Coelho Molck
- Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Milena Simioni
- Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Társis Paiva Vieira
- Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Fabíola Paoli Monteiro
- Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Vera L Gil-da-Silva-Lopes
- Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
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7
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Lei TY, Wang HT, Li F, Cui YQ, Fu F, Li R, Liao C. De Novo 1.77-Mb Microdeletion of 10q22.2q22.3 in a Girl With Developmental Delay, Speech Delay, Congenital Cleft Palate, and Bilateral Hearing Impairment. Cleft Palate Craniofac J 2016; 54:343-350. [PMID: 27031267 DOI: 10.1597/15-171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Interstitial deletions of chromosome band 10q22.1q22.3 are rare. We here report a 2.5-year-old female patient with developmental delay, speech delay, congenital cleft palate, and bilateral hearing impairment. The girl's karyotype was normal. Chromosome microarray analysis (CMA) revealed a 1.77-Mb de novo interstitial deletion in 10q22.2q22.3. The deletion harbors 9 genes, including KAT6B, DUPD1, DUSP13, SAMD8, VDAC2, COMTD1, ZNF503, NCRNA00245, and C10orf11. This is the first patient with a deletion of the smallest size in 10q22.2q22.3 as detected using single nucleotide polymorphism (SNP) arrays. Comparisons with patients with overlapping deletions and in neighboring regions demonstrate the clinical impact of each deletion and in the context of other deletions within the 10q22q23 region. Additionally, KAT6B and C10orf11 could represent disease-associated genes that contribute to developmental delay, speech and language delay, and congenital cleft palate.
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8
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Szabo-Rogers H, Yakob W, Liu KJ. Frontal Bone Insufficiency in Gsk3β Mutant Mice. PLoS One 2016; 11:e0149604. [PMID: 26886780 PMCID: PMC4757545 DOI: 10.1371/journal.pone.0149604] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 02/03/2016] [Indexed: 12/17/2022] Open
Abstract
The development of the mammalian skull is a complex process that requires multiple tissue interactions and a balance of growth and differentiation. Disrupting this balance can lead to changes in the shape and size of skull bones, which can have serious clinical implications. For example, insufficient ossification of the bony elements leads to enlarged anterior fontanelles and reduced mechanical protection of the brain. In this report, we find that loss of Gsk3β leads to a fully penetrant reduction of frontal bone size and subsequent enlarged frontal fontanelle. In the absence of Gsk3β the frontal bone primordium undergoes increased cell death and reduced proliferation with a concomitant increase in Fgfr2-IIIc and Twist1 expression. This leads to a smaller condensation and premature differentiation. This phenotype appears to be Wnt-independent and is not rescued by decreasing the genetic dose of β-catenin/Ctnnb1. Taken together, our work defines a novel role for Gsk3β in skull development.
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Affiliation(s)
- Heather Szabo-Rogers
- Craniofacial Development and Stem Cell Biology, Floor 27, Tower Wing, Guy’s Campus, King’s College London, London, United Kingdom SE1 9RT
| | - Wardati Yakob
- Craniofacial Development and Stem Cell Biology, Floor 27, Tower Wing, Guy’s Campus, King’s College London, London, United Kingdom SE1 9RT
| | - Karen J. Liu
- Craniofacial Development and Stem Cell Biology, Floor 27, Tower Wing, Guy’s Campus, King’s College London, London, United Kingdom SE1 9RT
- * E-mail:
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9
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Barnett CP, van Bon BWM. Monogenic and chromosomal causes of isolated speech and language impairment. J Med Genet 2015; 52:719-29. [DOI: 10.1136/jmedgenet-2015-103161] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 06/11/2015] [Indexed: 12/26/2022]
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10
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Coe BP, Witherspoon K, Rosenfeld JA, van Bon BWM, Vulto-van Silfhout AT, Bosco P, Friend KL, Baker C, Buono S, Vissers LELM, Schuurs-Hoeijmakers JH, Hoischen A, Pfundt R, Krumm N, Carvill GL, Li D, Amaral D, Brown N, Lockhart PJ, Scheffer IE, Alberti A, Shaw M, Pettinato R, Tervo R, de Leeuw N, Reijnders MRF, Torchia BS, Peeters H, O'Roak BJ, Fichera M, Hehir-Kwa JY, Shendure J, Mefford HC, Haan E, Gécz J, de Vries BBA, Romano C, Eichler EE. Refining analyses of copy number variation identifies specific genes associated with developmental delay. Nat Genet 2014; 46:1063-71. [PMID: 25217958 PMCID: PMC4177294 DOI: 10.1038/ng.3092] [Citation(s) in RCA: 427] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 08/20/2014] [Indexed: 12/16/2022]
Abstract
Copy number variants (CNVs) are associated with many neurocognitive disorders; however, these events are typically large and the underlying causative gene is unclear. We created an expanded CNV morbidity map from 29,085 children with developmental delay versus 19,584 healthy controls, identifying 70 significant CNVs. We resequenced 26 candidate genes in 4,716 additional cases with developmental delay or autism and 2,193 controls. An integrated analysis of CNV and single-nucleotide variant (SNV) data pinpointed ten genes enriched for putative loss of function. Patient follow-up on a subset identified new clinical subtypes of pediatric disease and the genes responsible for disease-associated CNVs. This includes haploinsufficiency of SETBP1 associated with intellectual disability and loss of expressive language and truncations of ZMYND11 in patients with autism, aggression and complex neuropsychiatric features. This combined CNV and SNV approach facilitates the rapid discovery of new syndromes and neuropsychiatric disease genes despite extensive genetic heterogeneity.
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Affiliation(s)
- Bradley P Coe
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Kali Witherspoon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Jill A Rosenfeld
- Signature Genomics Laboratories, LLC, PerkinElmer, Inc., Spokane, Washington, USA
| | - Bregje W M van Bon
- 1] Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands. [2] SA Pathology, North Adelaide, South Australia, Australia
| | | | - Paolo Bosco
- IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Associazione Oasi Maria Santissima, Troina, Italy
| | | | - Carl Baker
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Serafino Buono
- IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Associazione Oasi Maria Santissima, Troina, Italy
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Alex Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Nik Krumm
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Gemma L Carvill
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Deana Li
- Representing the Autism Phenome Project, MIND Institute, University of California, Davis, Sacramento, California, USA
| | - David Amaral
- Representing the Autism Phenome Project, MIND Institute, University of California, Davis, Sacramento, California, USA
| | - Natasha Brown
- 1] Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, Victoria, Australia. [2] Barwon Child Health Unit, Barwon Health, Geelong, Victoria, Australia
| | - Paul J Lockhart
- 1] Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, Victoria, Australia. [2] Murdoch Childrens Research Institute, University of Melbourne, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Ingrid E Scheffer
- Florey Institute, University of Melbourne, Austin Health and Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Antonino Alberti
- IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Associazione Oasi Maria Santissima, Troina, Italy
| | - Marie Shaw
- SA Pathology, North Adelaide, South Australia, Australia
| | - Rosa Pettinato
- IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Associazione Oasi Maria Santissima, Troina, Italy
| | - Raymond Tervo
- Division of Developmental and Behavioral Pediatrics, Mayo Clinic, Rochester, Minnesota, USA
| | - Nicole de Leeuw
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Margot R F Reijnders
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Beth S Torchia
- Signature Genomics Laboratories, LLC, PerkinElmer, Inc., Spokane, Washington, USA
| | - Hilde Peeters
- 1] Center for Human Genetics, University Hospitals Leuven, KU Leuven, Leuven, Belgium. [2] Leuven Autism Research (LAuRes), Leuven, Belgium
| | - Brian J O'Roak
- 1] Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA. [2]
| | - Marco Fichera
- 1] IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Associazione Oasi Maria Santissima, Troina, Italy. [2]
| | - Jayne Y Hehir-Kwa
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jay Shendure
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Heather C Mefford
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Eric Haan
- 1] SA Pathology, North Adelaide, South Australia, Australia. [2] School of Paediatrics and Reproductive Health, University of Adelaide, Adelaide, South Australia, Australia
| | - Jozef Gécz
- 1] SA Pathology, North Adelaide, South Australia, Australia. [2] Robinson Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Bert B A de Vries
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Corrado Romano
- IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Associazione Oasi Maria Santissima, Troina, Italy
| | - Evan E Eichler
- 1] Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA. [2] Howard Hughes Medical Institute, Seattle, Washington, USA
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11
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Petrova E, Neuner C, Haaf T, Schmid M, Wirbelauer J, Jurkutat A, Wermke K, Nanda I, Kunstmann E. A Boy with an LCR3/4-Flanked 10q22.3q23.2 Microdeletion and Uncommon Phenotypic Features. Mol Syndromol 2014; 5:19-24. [PMID: 24550761 DOI: 10.1159/000355847] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2013] [Indexed: 11/19/2022] Open
Abstract
The recurrent 10q22.3q23.2 deletion with breakpoints within low copy repeats 3 and 4 is a rare genomic disorder, reported in only 13 patients to date. The phenotype is rather uncharacteristic, which makes a clinical diagnosis difficult. A phenotypic feature described in almost all patients is a delay in speech development, albeit systematic studies are still pending. In this study, we report on a boy with an LCR3/4-flanked 10q22.3q23.2 deletion exhibiting an age-appropriate language development evaluated by a standardized test at an age of 2 years and 3 months. The boy was born with a cleft palate - a feature not present in any of the patients described before. Previously reported cases are reviewed, and the role of the BMPR1A gene is discussed. The phenotype of patients with an LCR3/4-flanked 10q22.3q23.2 deletion can be rather variable, so counseling the families regarding the prognosis of an affected child should be done with caution. Long-term studies of affected children are needed to delineate the natural history of this rare disorder.
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Affiliation(s)
- E Petrova
- Institute for Human Genetics, University of Wuerzburg, Wuerzburg, Germany
| | - C Neuner
- Institute for Human Genetics, University of Wuerzburg, Wuerzburg, Germany
| | - T Haaf
- Institute for Human Genetics, University of Wuerzburg, Wuerzburg, Germany
| | - M Schmid
- Institute for Human Genetics, University of Wuerzburg, Wuerzburg, Germany
| | - J Wirbelauer
- University Children's Hospital, University of Wuerzburg, Wuerzburg, Germany
| | - A Jurkutat
- Department of Special Education, Speech and Language Pathology, University of Wuerzburg, Wuerzburg, Germany
| | - K Wermke
- Department of Orthodontics, Center for Pre-Speech Development and Developmental Disorders, University of Wuerzburg, Wuerzburg, Germany
| | - I Nanda
- Institute for Human Genetics, University of Wuerzburg, Wuerzburg, Germany
| | - E Kunstmann
- Institute for Human Genetics, University of Wuerzburg, Wuerzburg, Germany
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12
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Osoegawa K, Iovannisci DM, Lin B, Parodi C, Schultz K, Shaw GM, Lammer EJ. Identification of novel candidate gene loci and increased sex chromosome aneuploidy among infants with conotruncal heart defects. Am J Med Genet A 2013; 164A:397-406. [PMID: 24127225 DOI: 10.1002/ajmg.a.36291] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 09/10/2013] [Indexed: 12/17/2022]
Abstract
Congenital heart defects (CHDs) are common malformations, affecting four to eight per 1,000 total births. Conotruncal defects are an important pathogenetic subset of CHDs, comprising nearly 20% of the total. Although both environmental and genetic factors are known to contribute to the occurrence of conotruncal defects, the causes remain unknown for most. To identify novel candidate genes/loci, we used array comparative genomic hybridization to detect chromosomal microdeletions/duplications. From a population base of 974,579 total births born during 1999-2004, we screened 389 California infants born with tetralogy of Fallot or d-transposition of the great arteries. We found that 1.7% (5/288) of males with a conotruncal defect had sex chromosome aneuploidy, a sevenfold increased frequency (relative risk = 7.0; 95% confidence interval 2.9-16.9). We identified eight chromosomal microdeletions/duplications for conotruncal defects. From these duplications and deletions, we found five high priority candidate genes (GATA4, CRKL, BMPR1A, SNAI2, and ZFHX4). This is the initial report that sex chromosome aneuploidy is associated with conotruncal defects among boys. These chromosomal microduplications/deletions provide evidence that GATA4, SNAI2, and CRKL are highly dosage sensitive genes involved in outflow tract development. Genome wide screening for copy number variation can be productive for identifying novel genes/loci contributing to non-syndromic common malformations.
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Affiliation(s)
- Kazutoyo Osoegawa
- Center for Genetics, Children's Hospital Oakland Research Institute, Children's Hospital Research Center Oakland, Oakland, California
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13
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Septer S, Zhang L, Lawson CE, Cocjin J, Attard T, Ardinger HH. Aggressive juvenile polyposis in children with chromosome 10q23 deletion. World J Gastroenterol 2013; 19:2286-2292. [PMID: 23599658 PMCID: PMC3627896 DOI: 10.3748/wjg.v19.i14.2286] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Accepted: 02/07/2013] [Indexed: 02/06/2023] Open
Abstract
Juvenile polyps are relatively common findings in children, while juvenile polyposis syndrome (JPS) is a rare hereditary syndrome entailing an increased risk of colorectal cancer. Mutations in BMPR1A or SMAD4 are found in roughly half of patients diagnosed with JPS. Mutations in PTEN gene are also found in patients with juvenile polyps and in Bannayan-Riley-Ruvalcaba syndrome and Cowden syndrome. Several previous reports have described microdeletions in chromosome 10q23 encompassing both PTEN and BMPR1A causing aggressive polyposis and malignancy in childhood. These reports have also described extra-intestinal findings in most cases including cardiac anomalies, developmental delay and macrocephaly. In this report we describe a boy with a 5.75 Mb deletion of chromosome 10q23 and a 1.03 Mb deletion within chromosome band 1p31.3 who displayed aggressive juvenile polyposis and multiple extra-intestinal anomalies including macrocephaly, developmental delay, short stature, hypothyroidism, atrial septal defect, ventricular septal defect and hypospadias. He required colectomy at six years of age, and early colectomy was a common outcome in other children with similar deletions. Due to the aggressive polyposis and reports of dysplasia and even malignancy at a young age, we propose aggressive gastrointestinal surveillance in children with 10q23 microdeletions encompassing the BMPR1A and PTEN genes to include both the upper and lower gastrointestinal tracts, and also include a flowchart for an effective genetic testing strategy in children with juvenile polyposis.
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14
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Copy number analysis of 413 isolated talipes equinovarus patients suggests role for transcriptional regulators of early limb development. Eur J Hum Genet 2012; 21:373-80. [PMID: 22892537 DOI: 10.1038/ejhg.2012.177] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Talipes equinovarus is one of the most common congenital musculoskeletal anomalies and has a worldwide incidence of 1 in 1000 births. A genetic predisposition to talipes equinovarus is evidenced by the high concordance rate in twin studies and the increased risk to first-degree relatives. Despite the frequency of isolated talipes equinovarus and the strong evidence of a genetic basis for the disorder, few causative genes have been identified. To identify rare and/or recurrent copy number variants, we performed a genome-wide screen for deletions and duplications in 413 isolated talipes equinovarus patients using the Affymetrix 6.0 array. Segregation analysis within families and gene expression in mouse E12.5 limb buds were used to determine the significance of copy number variants. We identified 74 rare, gene-containing copy number variants that were present in talipes equinovarus probands and not present in 759 controls or in the Database of Genomic Variants. The overall frequency of copy number variants was similar between talipes equinovarus patients compared with controls. Twelve rare copy number variants segregate with talipes equinovarus in multiplex pedigrees, and contain the developmentally expressed transcription factors and transcriptional regulators PITX1, TBX4, HOXC13, UTX, CHD (chromodomain protein)1, and RIPPLY2. Although our results do not support a major role for recurrent copy number variations in the etiology of isolated talipes equinovarus, they do suggest a role for genes involved in early embryonic patterning in some families that can now be tested with large-scale sequencing methods.
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Breckpot J, Tranchevent LC, Thienpont B, Bauters M, Troost E, Gewillig M, Vermeesch JR, Moreau Y, Devriendt K, Van Esch H. BMPR1A is a candidate gene for congenital heart defects associated with the recurrent 10q22q23 deletion syndrome. Eur J Med Genet 2012; 55:12-6. [DOI: 10.1016/j.ejmg.2011.10.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 10/03/2011] [Indexed: 12/17/2022]
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16
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Dasouki MJ, Youngs EL, Hovanes K. Structural Chromosome Abnormalities Associated with Obesity: Report of Four New subjects and Review of Literature. Curr Genomics 2011; 12:190-203. [PMID: 22043167 PMCID: PMC3137004 DOI: 10.2174/138920211795677930] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Revised: 03/29/2011] [Accepted: 03/30/2011] [Indexed: 11/22/2022] Open
Abstract
Obesity in humans is a complex polygenic trait with high inter-individual heritability estimated at 40-70%. Candidate gene, DNA linkage and genome-wide association studies (GWAS) have allowed for the identification of a large set of genes and genomic regions associated with obesity. Structural chromosome abnormalities usually result in congenital anomalies, growth retardation and developmental delay. Occasionally, they are associated with hyperphagia and obesity rather than growth delay. We report four new individuals with structural chromosome abnormalities involving 10q22.3-23.2, 16p11.2 and Xq27.1-q28 chromosomal regions with early childhood obesity and developmental delay. We also searched and summarized the literature for structural chromosome abnormalities reported in association with childhood obesity.
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Affiliation(s)
- Majed J Dasouki
- Departments of Pediatrics and Internal Medicine, Kansas University Medical Center, Kansas City, Kansas, USA
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Dahdaleh FS, Carr JC, Calva D, Howe JR. Juvenile polyposis and other intestinal polyposis syndromes with microdeletions of chromosome 10q22-23. Clin Genet 2011; 81:110-6. [PMID: 21834858 DOI: 10.1111/j.1399-0004.2011.01763.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Juvenile polyposis (JP) is an autosomal dominant hamartomatous polyposis syndrome that carries a significant risk for the development of colorectal cancer. Microdeletions of one of the two predisposing genes to JP, BMPR1A, have been associated with a severe form of JP called juvenile polyposis of infancy. Many of these deletions have also been found to contiguously include PTEN, which is the gene responsible for the development of Cowden syndrome. The advent of molecular techniques that localize genomic copy number variations and others that target specific genes such as multiplex-ligation probe analysis has allowed researchers to explore this area further for deletions. Here, we review the literature for microdeletions described on chromosome 10q22-23 in patients with JP and other intestinal polyposis syndromes.
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Affiliation(s)
- F S Dahdaleh
- Department of Surgery, University of Iowa Carver College of Medicine, Iowa City, IA, USA
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18
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van Bon BWM, Balciuniene J, Fruhman G, Nagamani SCS, Broome DL, Cameron E, Martinet D, Roulet E, Jacquemont S, Beckmann JS, Irons M, Potocki L, Lee B, Cheung SW, Patel A, Bellini M, Selicorni A, Ciccone R, Silengo M, Vetro A, Knoers NV, de Leeuw N, Pfundt R, Wolf B, Jira P, Aradhya S, Stankiewicz P, Brunner HG, Zuffardi O, Selleck SB, Lupski JR, de Vries BBA. The phenotype of recurrent 10q22q23 deletions and duplications. Eur J Hum Genet 2011; 19:400-8. [PMID: 21248748 DOI: 10.1038/ejhg.2010.211] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The genomic architecture of the 10q22q23 region is characterised by two low-copy repeats (LCRs3 and 4), and deletions in this region appear to be rare. We report the clinical and molecular characterisation of eight novel deletions and six duplications within the 10q22.3q23.3 region. Five deletions and three duplications occur between LCRs3 and 4, whereas three deletions and three duplications have unique breakpoints. Most of the individuals with the LCR3-4 deletion had developmental delay, mainly affecting speech. In addition, macrocephaly, mild facial dysmorphisms, cerebellar anomalies, cardiac defects and congenital breast aplasia were observed. For congenital breast aplasia, the NRG3 gene, known to be involved in early mammary gland development in mice, is a putative candidate gene. For cardiac defects, BMPR1A and GRID1 are putative candidate genes because of their association with cardiac structure and function. Duplications between LCRs3 and 4 are associated with variable phenotypic penetrance. Probands had speech and/or motor delays and dysmorphisms including a broad forehead, deep-set eyes, upslanting palpebral fissures, a smooth philtrum and a thin upper lip. In conclusion, duplications between LCRs3 and 4 on 10q22.3q23.2 may lead to a distinct facial appearance and delays in speech and motor development. However, the phenotypic spectrum is broad, and duplications have also been found in healthy family members of a proband. Reciprocal deletions lead to speech and language delay, mild facial dysmorphisms and, in some individuals, to cerebellar, breast developmental and cardiac defects.
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Affiliation(s)
- Bregje W M van Bon
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.
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Theisen A, Shaffer LG. Disorders caused by chromosome abnormalities. APPLICATION OF CLINICAL GENETICS 2010; 3:159-74. [PMID: 23776360 PMCID: PMC3681172 DOI: 10.2147/tacg.s8884] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Many human genetic disorders result from unbalanced chromosome abnormalities, in which there is a net gain or loss of genetic material. Such imbalances often disrupt large numbers of dosage-sensitive, developmentally important genes and result in specific and complex phenotypes. Alternately, some chromosomal syndromes may be caused by a deletion or duplication of a single gene with pleiotropic effects. Traditionally, chromosome abnormalities were identified by visual inspection of the chromosomes under a microscope. The use of molecular cytogenetic technologies, such as fluorescence in situ hybridization and microarrays, has allowed for the identification of cryptic or submicroscopic imbalances, which are not visible under the light microscope. Microarrays have allowed for the identification of numerous new syndromes through a genotype-first approach in which patients with the same or overlapping genomic alterations are identified and then the phenotypes are described. Because many chromosomal alterations are large and encompass numerous genes, the ascertainment of individuals with overlapping deletions and varying clinical features may allow researchers to narrow the region in which to search for candidate genes.
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Betancur C. Etiological heterogeneity in autism spectrum disorders: more than 100 genetic and genomic disorders and still counting. Brain Res 2010; 1380:42-77. [PMID: 21129364 DOI: 10.1016/j.brainres.2010.11.078] [Citation(s) in RCA: 578] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Revised: 11/22/2010] [Accepted: 11/23/2010] [Indexed: 12/31/2022]
Abstract
There is increasing evidence that autism spectrum disorders (ASDs) can arise from rare highly penetrant mutations and genomic imbalances. The rare nature of these variants, and the often differing orbits of clinical and research geneticists, can make it difficult to fully appreciate the extent to which we have made progress in understanding the genetic etiology of autism. In fact, there is a persistent view in the autism research community that there are only a modest number of autism loci known. We carried out an exhaustive review of the clinical genetics and research genetics literature in an attempt to collate all genes and recurrent genomic imbalances that have been implicated in the etiology of ASD. We provide data on 103 disease genes and 44 genomic loci reported in subjects with ASD or autistic behavior. These genes and loci have all been causally implicated in intellectual disability, indicating that these two neurodevelopmental disorders share common genetic bases. A genetic overlap between ASD and epilepsy is also apparent in many cases. Taken together, these findings clearly show that autism is not a single clinical entity but a behavioral manifestation of tens or perhaps hundreds of genetic and genomic disorders. Increased recognition of the etiological heterogeneity of ASD will greatly expand the number of target genes for neurobiological investigations and thereby provide additional avenues for the development of pathway-based pharmacotherapy. Finally, the data provide strong support for high-resolution DNA microarrays as well as whole-exome and whole-genome sequencing as critical approaches for identifying the genetic causes of ASDs.
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