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Copy number variation in the dosage-sensitive 16p11.2 interval accounts for only a small proportion of autism incidence: A systematic review and meta-analysis. Genet Med 2011; 13:377-84. [DOI: 10.1097/gim.0b013e3182076c0c] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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352
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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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353
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de Leeuw N, Hehir-Kwa JY, Simons A, Geurts van Kessel A, Smeets DF, Faas BHW, Pfundt R. SNP Array Analysis in Constitutional and Cancer Genome Diagnostics – Copy Number Variants, Genotyping and Quality Control. Cytogenet Genome Res 2011; 135:212-21. [PMID: 21934286 DOI: 10.1159/000331273] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- N de Leeuw
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.
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Lichtenbelt K, Knoers N, Schuring-Blom G. From Karyotyping to Array-CGH in Prenatal Diagnosis. Cytogenet Genome Res 2011; 135:241-50. [DOI: 10.1159/000334065] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
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355
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356
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Ramocki MB, Bartnik M, Szafranski P, Kołodziejska KE, Xia Z, Bravo J, Miller GS, Rodriguez DL, Williams CA, Bader PI, Szczepanik E, Mazurczak T, Antczak-Marach D, Coldwell JG, Akman CI, McAlmon K, Cohen MP, McGrath J, Roeder E, Mueller J, Kang SHL, Bacino CA, Patel A, Bocian E, Shaw CA, Cheung SW, Mazurczak T, Stankiewicz P. Recurrent distal 7q11.23 deletion including HIP1 and YWHAG identified in patients with intellectual disabilities, epilepsy, and neurobehavioral problems. Am J Hum Genet 2010; 87:857-65. [PMID: 21109226 DOI: 10.1016/j.ajhg.2010.10.019] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2010] [Revised: 10/12/2010] [Accepted: 10/22/2010] [Indexed: 11/19/2022] Open
Abstract
We report 26 individuals from ten unrelated families who exhibit variable expression and/or incomplete penetrance of epilepsy, learning difficulties, intellectual disabilities, and/or neurobehavioral abnormalities as a result of a heterozygous microdeletion distally adjacent to the Williams-Beuren syndrome region on chromosome 7q11.23. In six families with a common recurrent ∼1.2 Mb deletion that includes the Huntingtin-interacting protein 1 (HIP1) and tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein gamma (YWHAG) genes and that is flanked by large complex low-copy repeats, we identified sites for nonallelic homologous recombination in two patients. There were no cases of this ∼1.2 Mb distal 7q11.23 deletion copy number variant identified in over 20,000 control samples surveyed. Three individuals with smaller, nonrecurrent deletions (∼180-500 kb) that include HIP1 but not YWHAG suggest that deletion of HIP1 is sufficient to cause neurological disease. Mice with targeted mutation in the Hip1 gene (Hip1⁻(/)⁻) develop a neurological phenotype characterized by failure to thrive, tremor, and gait ataxia. Overall, our data characterize a neurodevelopmental and epilepsy syndrome that is likely caused by recurrent and nonrecurrent deletions, including HIP1. These data do not exclude the possibility that YWHAG loss of function is also sufficient to cause neurological phenotypes. Based on the current knowledge of Hip1 protein function and its proposed role in AMPA and NMDA ionotropic glutamate receptor trafficking, we believe that HIP1 haploinsufficiency in humans will be amenable to rational drug design for improved seizure control and cognitive and behavioral function.
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Affiliation(s)
- Melissa B Ramocki
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
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357
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Abstract
The widespread clinical utilization of array comparative genome hybridization, has led to the unraveling of many new copy number variations (CNVs). Although some of these CNVs are clearly pathogenic, the phenotypic consequences of others, such as those in 16p13.11 remain unclear. Whereas deletions of 16p13.11 have been associated with multiple congenital anomalies, the relevance of duplications of the region is still being debated. We report detailed clinical and molecular characterization of 10 patients with duplication and 4 patients with deletion of 16p13.11. We found that patients with duplication of the region have varied clinical features including behavioral abnormalities, cognitive impairment, congenital heart defects and skeletal manifestations, such as hypermobility, craniosynostosis and polydactyly. These features were incompletely penetrant. Patients with deletion of the region presented with microcephaly, developmental delay and behavioral abnormalities as previously described. The CNVs were of varying sizes and were likely mediated by non-allelic homologous recombination between low copy repeats. Our findings expand the repertoire of clinical features observed in patients with CNV in 16p13.11 and strengthen the hypothesis that this is a dosage sensitive region with clinical relevance.
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358
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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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359
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Ricard G, Molina J, Chrast J, Gu W, Gheldof N, Pradervand S, Schütz F, Young JI, Lupski JR, Reymond A, Walz K. Phenotypic consequences of copy number variation: insights from Smith-Magenis and Potocki-Lupski syndrome mouse models. PLoS Biol 2010; 8:e1000543. [PMID: 21124890 PMCID: PMC2990707 DOI: 10.1371/journal.pbio.1000543] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Accepted: 10/04/2010] [Indexed: 02/07/2023] Open
Abstract
The characterization of mice with different number of copies of the same genomic segment shows that structural changes influence the phenotypic outcome independently of gene dosage. A large fraction of genome variation between individuals is comprised of submicroscopic copy number variation of genomic DNA segments. We assessed the relative contribution of structural changes and gene dosage alterations on phenotypic outcomes with mouse models of Smith-Magenis and Potocki-Lupski syndromes. We phenotyped mice with 1n (Deletion/+), 2n (+/+), 3n (Duplication/+), and balanced 2n compound heterozygous (Deletion/Duplication) copies of the same region. Parallel to the observations made in humans, such variation in gene copy number was sufficient to generate phenotypic consequences: in a number of cases diametrically opposing phenotypes were associated with gain versus loss of gene content. Surprisingly, some neurobehavioral traits were not rescued by restoration of the normal gene copy number. Transcriptome profiling showed that a highly significant propensity of transcriptional changes map to the engineered interval in the five assessed tissues. A statistically significant overrepresentation of the genes mapping to the entire length of the engineered chromosome was also found in the top-ranked differentially expressed genes in the mice containing rearranged chromosomes, regardless of the nature of the rearrangement, an observation robust across different cell lineages of the central nervous system. Our data indicate that a structural change at a given position of the human genome may affect not only locus and adjacent gene expression but also “genome regulation.” Furthermore, structural change can cause the same perturbation in particular pathways regardless of gene dosage. Thus, the presence of a genomic structural change, as well as gene dosage imbalance, contributes to the ultimate phenotype. Mammalian genomes contain many forms of genetic variation. For example, some genome segments were shown to vary in their number of copies between individuals of the same species, i.e. there is a range of number of copies in the normal population instead of the usual two copies (one per chromosome). These genetic differences play an important role in determining the phenotype (the observable characteristics) of each individual. We do not know, however, if such influences are brought about solely through changes in the number of copies of the genomic segments (and of the genes that map within) or if the structural modification of the genome per se also plays a role in the outcome. We use mouse models with different number of copies of the same genomic region to show that rearrangements of the genetic materials can affect the phenotype independently of the dosage of the rearranged region.
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Affiliation(s)
- Guénola Ricard
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | | | - Jacqueline Chrast
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Wenli Gu
- Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Nele Gheldof
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Sylvain Pradervand
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Frédéric Schütz
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Juan I. Young
- Centro de Estudios Científicos (CECS), Valdivia, Chile
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States of America
- CIN (Centro de Ingeniería de la Innovación del CECS), Valdivia, Chile
| | - James R. Lupski
- Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
- Texas Children's Hospital, Houston, Texas, United States of America
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
- * E-mail: (AR); (KW)
| | - Katherina Walz
- Centro de Estudios Científicos (CECS), Valdivia, Chile
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States of America
- * E-mail: (AR); (KW)
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360
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Donev R, Thome J. Inflammation: good or bad for ADHD? ACTA ACUST UNITED AC 2010; 2:257-66. [PMID: 21432611 DOI: 10.1007/s12402-010-0038-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Accepted: 10/11/2010] [Indexed: 12/19/2022]
Abstract
Attention deficit hyperactivity disorder (ADHD) is characterised by the typical behavioural core symptoms of inattentiveness, hyperactivity and impulsiveness. ADHD is a usually chronic health conditions, mostly diagnosed in childhood, creating a significant challenge for youth, their families and professionals who treat it. This disorder requires long-term treatments, including psychotherapeutic and pharmacological interventions, which in some cases may lead to adverse effects. Understanding the mechanism by which ADHD risk factors affect the biochemical processes in the human brain and consequentially the behaviour will help to identify novel targets for the development of therapeutics with less adverse results and better efficacy including higher responder rates. Although inflammatory responses in the brain have been recognised for years as critical in neurodegeneration and behaviour in a number of neurological and psychiatric disorders, their role for the development, treatment and prevention of ADHD has been so far largely overlooked, although historically, ADHD symptoms were initially observed in patients who survived an ONJ infection, i.e. inflammation. In this review, we discuss the interrelationship between different ADHD risk factors and inflammation with respect to the triggered molecular mechanisms and the contribution they are likely to have to this disorder. This paper provides a rationale for future studies on ADHD with an intent to inspiring the development of new agents for a more efficient management of this disorder.
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Affiliation(s)
- Rossen Donev
- Academic Unit of Psychiatry, The School of Medicine, University of Wales Swansea, Institute of Life Science, UK
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361
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Morrow EM. Genomic copy number variation in disorders of cognitive development. J Am Acad Child Adolesc Psychiatry 2010; 49:1091-104. [PMID: 20970697 PMCID: PMC3137887 DOI: 10.1016/j.jaac.2010.08.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Revised: 08/12/2010] [Accepted: 08/12/2010] [Indexed: 12/29/2022]
Abstract
OBJECTIVE To highlight recent discoveries in the area of genomic copy number variation in neuropsychiatric disorders including intellectual disability, autism, and schizophrenia. To emphasize new principles emerging from this area, involving the genetic architecture of disease, pathophysiology, and diagnosis. METHOD Review of studies published in PubMed including classic studies of genomic disorders and microarray and copy number studies in normal controls, intellectual disability, autism, and schizophrenia. RESULTS The advent of novel microarray technology has led to a revolution in the discovery of classic and novel copy number variants (CNVs) in various disorders affecting cognitive development. Across autism and schizophrenia, global CNV burden and de novo CNV burden are associated with disease. Also, specific recurrent CNVs may be associated with several DSM conditions. Each condition is also associated with heterogeneous and individually rare CNVs. CONCLUSIONS CNVs play an important role in the genetic architecture of the childhood neuropsychiatric disorders discussed. This discovery appears to suggest an important role for the strict regulation of gene dosage in the neurodevelopmental roots of these conditions. Microarrays have emerged as high-yield tests in the diagnosis and molecular subtyping of the childhood-onset disorders involving cognitive development. In summary, CNV studies in disorders of cognitive development have revealed interesting and important new insights and have opened an avenue of investigation that holds great promise for neuropsychiatric disease.
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Affiliation(s)
- Eric M. Morrow
- Dr. Morrow is with Brown University and the Developmental Disorders Genetics Research Program, Emma Pendleton Bradley Hospital, Providence, RI
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362
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Infantile convulsions with paroxysmal dyskinesia (ICCA syndrome) and copy number variation at human chromosome 16p11. PLoS One 2010; 5:e13750. [PMID: 21060786 PMCID: PMC2966418 DOI: 10.1371/journal.pone.0013750] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Accepted: 10/08/2010] [Indexed: 11/19/2022] Open
Abstract
Background Benign infantile convulsions and paroxysmal dyskinesia are episodic cerebral disorders that can share common genetic bases. They can be co-inherited as one single autosomal dominant trait (ICCA syndrome); the disease ICCA gene maps at chromosome 16p12-q12. Despite intensive and conventional mutation screening, the ICCA gene remains unknown to date. The critical area displays highly complicated genomic architecture and is the site of deletions and duplications associated with various diseases. The possibility that the ICCA syndrome is related to the existence of large-scale genomic alterations was addressed in the present study. Methodology/Principal Findings A combination of whole genome and dedicated oligonucleotide array comparative genomic hybridization coupled with quantitative polymerase chain reaction was used. Low copy number of a region corresponding to a genomic variant (Variation_7105) located at 16p11 nearby the centromere was detected with statistical significance at much higher frequency in patients from ICCA families than in ethnically matched controls. The genomic variant showed no apparent difference in size and copy number between patients and controls, making it very unlikely that the genomic alteration detected here is ICCA-specific. Furthermore, no other genomic alteration that would directly cause the ICCA syndrome in those nine families was detected in the ICCA critical area. Conclusions/Significance Our data excluded that inherited genomic deletion or duplication events directly cause the ICCA syndrome; rather, they help narrowing down the critical ICCA region dramatically and indicate that the disease ICCA genetic defect lies very close to or within Variation_7105 and hence should now be searched in the corresponding genomic area and its surrounding regions.
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363
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Hayashi S, Imoto I, Aizu Y, Okamoto N, Mizuno S, Kurosawa K, Okamoto N, Honda S, Araki S, Mizutani S, Numabe H, Saitoh S, Kosho T, Fukushima Y, Mitsubuchi H, Endo F, Chinen Y, Kosaki R, Okuyama T, Ohki H, Yoshihashi H, Ono M, Takada F, Ono H, Yagi M, Matsumoto H, Makita Y, Hata A, Inazawa J. Clinical application of array-based comparative genomic hybridization by two-stage screening for 536 patients with mental retardation and multiple congenital anomalies. J Hum Genet 2010; 56:110-24. [DOI: 10.1038/jhg.2010.129] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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364
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Expanding the clinical spectrum of the 16p11.2 chromosomal rearrangements: three patients with syringomyelia. Eur J Hum Genet 2010; 19:152-6. [PMID: 20959866 DOI: 10.1038/ejhg.2010.168] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
16p11.2 rearrangements are associated with developmental delay, cognitive impairment, autism spectrum disorder, behavioral problems (especially attention-deficit hyperactivity disorder), seizures, obesity, dysmorphic features, and abnormal head size. In addition, congenital anomalies and abnormal brain findings were frequently observed in patients with these rearrangements. We identified and performed a detailed microarray, phenotypic, and radiological characterization of three new patients with 16p11.2 rearrangements: two deletion patients and one patient with the reciprocal duplication. All patients have a heterozygous loss (deletion) or gain (duplication) corresponding to chromosomal coordinates (chr16: 29 528 190-30 107 184) with a minimal size of 579 kb. The deletion patients had language delay and learning disabilities and one met criteria for pervasive developmental disorder not otherwise specified. The duplication patient received a diagnosis of autism and had academic deficits and behavioral problems. The patients with deletion had long cervicothoracic syringomyelia and the duplication patient had long thoracolumbar syringomyelia. The syringomyelia in one patient with deletion was associated with Chiari malformation. Our findings highlight the broad spectrum of clinical and neurological manifestations in patients with 16p11.2 rearrangements. Our observation suggests that genes (or a single gene) within the implicated interval have significant roles in the pathogenesis of syringomyelia. A more comprehensive and systematic research is warranted to study the frequency and spectrum of malformations in the central nervous system in these patients.
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365
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Girirajan S, Eichler EE. Phenotypic variability and genetic susceptibility to genomic disorders. Hum Mol Genet 2010; 19:R176-87. [PMID: 20807775 PMCID: PMC2953748 DOI: 10.1093/hmg/ddq366] [Citation(s) in RCA: 201] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Revised: 07/28/2010] [Accepted: 08/24/2010] [Indexed: 11/13/2022] Open
Abstract
The duplication architecture of the human genome predisposes our species to recurrent copy number variation and disease. Emerging data suggest that this mechanism of mutation contributes to both common and rare diseases. Two features regarding this form of mutation have emerged. First, common structural polymorphisms create susceptible and protective chromosomal architectures. These structural polymorphisms occur at varying frequencies in populations, leading to different susceptibility and ethnic predilection. Second, a subset of rearrangements shows extreme variability in expressivity. We propose that two types of genomic disorders may be distinguished: syndromic forms where the phenotypic features are largely invariant and those where the same molecular lesion associates with a diverse set of diagnoses including epilepsy, schizophrenia, autism, intellectual disability and congenital malformations. Copy number variation analyses of patient genomes reveal that disease type and severity may be explained by the occurrence of additional rare events and their inheritance within families. We propose that the overall burden of copy number variants creates differing sensitized backgrounds during development leading to different thresholds and disease outcomes. We suggest that the accumulation of multiple high-penetrant alleles of low frequency may serve as a more general model for complex genetic diseases, posing a significant challenge for diagnostics and disease management.
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Affiliation(s)
| | - Evan E. Eichler
- Department of Genome Sciences, Howard Hughes Medical Institute,University of Washington School of Medicine, PO Box 355065, Foege S413C, 3720 15th Avenue NE, Seattle, WA 98195, USA
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366
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MLPA for confirmation of array CGH results and determination of inheritance. Mol Cytogenet 2010; 3:19. [PMID: 20942916 PMCID: PMC2964523 DOI: 10.1186/1755-8166-3-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Accepted: 10/13/2010] [Indexed: 12/22/2022] Open
Abstract
Background Array CGH has recently been introduced into our laboratory in place of karyotype analysis for patients with suspected genomic imbalance. Results require confirmation to check sample identity, and analysis of parental samples to determine inheritance and thus assess the clinical significance of the abnormality. Here we describe an MLPA-based strategy for the follow-up of abnormal aCGH results. Results In the first 17 months of our MLPA-based aCGH follow-up service, 317 different custom MLPA probes for novel aCGH-detected abnormalities were developed for inheritance studies in 164 families. In addition, 110 samples were tested for confirmation of aCGH-detected abnormalities in common syndromic or subtelomeric regions using commercial MLPA kits. Overall, a total of 1215 samples have been tested by MLPA. A total of 72 de novo abnormalities were confirmed. Conclusions Confirmation of aCGH-detected abnormalities and inheritance of these abnormalities are essential for accurate diagnosis and interpretation of aCGH results. The development of a new service utilising custom made MLPA probes and commercial MLPA kits for follow-up studies of array CGH results has been found to be efficient and flexible in our laboratory.
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367
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Abstract
OBJECTIVE To describe cognitive and behavioral features of patients with chromosome 16p11.2 deletion syndrome, a recently identified and common genetic cause of neurodevelopmental disability, especially autism spectrum disorder (ASD). METHOD Twenty-one patients with 16p11.2 deletion were evaluated by medical record review. A subset of 11 patients consented to detailed cognitive, behavioral, and autism diagnostic assessment. RESULTS Patients with 16p11.2 deletion had varying levels of intellectual disability, variable adaptive skills, and a high incidence of language delay. Attention issues were not as frequent as had been reported in previous clinical reports. Atypical language, reduced social skills, and maladaptive behaviors were common, as was diagnosis of ASD. Based on medical record review, 7 of 21 patients (33%) had an ASD diagnosis. Among patients receiving detailed phenotyping, 3 of 11 (27%) met full criteria (met cutoff scores on both Autism Diagnostic Observation Schedule and Autism Diagnostic Interview) for an ASD diagnosis, whereas 6 other patients (55%) met criteria for ASD on either the Autism Diagnostic Observation Schedule or the Autism Diagnostic Interview, but not both measures. CONCLUSIONS Rates of ASD were similar to previous reports that are based on medical record reviews, but formal assessment revealed that a majority of patients with 16p11.2 deletion demonstrate features of ASD beyond simple language impairment. All patients with 16p11.2 deletion should receive formal neurodevelopmental evaluation including measures to specifically assess cognitive, adaptive, language, and psychiatric/behavioral issues. Clinical evaluation of this patient population should always include assessment by Autism Diagnostic Interview and Autism Diagnostic Observation Schedule to detect behaviors related to ASD and possible ASD diagnosis.
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368
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Abstract
Intellectual disability (ID) is the leading socio-economic problem of health care, but compared to autism and schizophrenia, it has received very little public attention. Important risk factors for ID are malnutrition, cultural deprivation, poor health care, and parental consanguinity. In the Western world, fetal alcohol exposure is the most common preventable cause. Most severe forms of ID have genetic causes. Cytogenetically detectable and submicroscopic chromosomal rearrangements account for approximately 25% of all cases. X-linked gene defects are responsible in 10-12% of males with ID; to date, 91 of these defects have been identified. In contrast, autosomal gene defects have been largely disregarded, but due to coordinated efforts and the advent of next-generation DNA sequencing, this is about to change. As shown for Fra(X) syndrome, this renewed focus on autosomal gene defects will pave the way for molecular diagnosis and prevention, shed more light on the pathogenesis of ID, and reveal new opportunities for therapy.
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369
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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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