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Alagoz M, Kherad N, Gavaz M, Yuksel A. New Genetic Approaches for Early Diagnosis and Treatment of Autism Spectrum Disorders. Rev J Autism Dev Disord 2019. [DOI: 10.1007/s40489-019-00167-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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2
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Mir YR, Kuchay RAH. Advances in identification of genes involved in autosomal recessive intellectual disability: a brief review. J Med Genet 2019; 56:567-573. [PMID: 30842223 DOI: 10.1136/jmedgenet-2018-105821] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 02/01/2019] [Accepted: 02/11/2019] [Indexed: 12/28/2022]
Abstract
Intellectual disability (ID) is a clinically and genetically heterogeneous disorder, affecting 1%-3% of the general population. The number of ID-causing genes is high. Many X-linked genes have been implicated in ID. Autosomal dominant genes have recently been the focus of several large-scale studies. The total number of autosomal recessive ID (ARID) genes is estimated to be very high, and most are still unknown. Although research into the genetic causes of ID has recently gained momentum, identification of pathogenic mutations that cause ARID has lagged behind, predominantly due to non-availability of sizeable families. A commonly used approach to identify genetic loci for recessive disorders in consanguineous families is autozygosity mapping and whole-exome sequencing. Combination of these two approaches has recently led to identification of many genes involved in ID. These genes have diverse function and control various biological processes. In this review, we will present an update regarding genes that have been recently implicated in ID with focus on ARID.
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Affiliation(s)
- Yaser Rafiq Mir
- Department of Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, Jammu and Kashmir, India
| | - Raja Amir Hassan Kuchay
- Department of Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, Jammu and Kashmir, India
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3
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Ashrafi MR, Tavasoli AR. Childhood leukodystrophies: A literature review of updates on new definitions, classification, diagnostic approach and management. Brain Dev 2017; 39:369-385. [PMID: 28117190 DOI: 10.1016/j.braindev.2017.01.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 12/29/2016] [Accepted: 01/04/2017] [Indexed: 12/29/2022]
Abstract
Childhood leukodystrophies are a growing category of neurological disorders in pediatric neurology practice. With the help of new advanced genetic studies such as whole exome sequencing (WES) and whole genome sequencing (WGS), the list of childhood heritable white matter disorders has been increased to more than one hundred disorders. During the last three decades, the basic concepts and definitions, classification, diagnostic approach and medical management of these disorders much have changed. Pattern recognition based on brain magnetic resonance imaging (MRI), has played an important role in this process. We reviewed the last Global Leukodystrophy Initiative (GLIA) expert opinions in definition, new classification, diagnostic approach and medical management including emerging treatments for pediatric leukodystrophies.
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Affiliation(s)
- Mahmoud Reza Ashrafi
- Department of Child Neurology, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.
| | - Ali Reza Tavasoli
- Department of Child Neurology, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.
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4
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Lingen M, Albers L, Borchers M, Haass S, Gärtner J, Schröder S, Goldbeck L, von Kries R, Brockmann K, Zirn B. Obtaining a genetic diagnosis in a child with disability: impact on parental quality of life. Clin Genet 2015; 89:258-66. [PMID: 26084449 DOI: 10.1111/cge.12629] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 06/16/2015] [Accepted: 06/16/2015] [Indexed: 12/14/2022]
Abstract
Recent progress in genetic testing has facilitated obtaining an etiologic diagnosis in children with developmental delay/intellectual disability (DD/ID) or multiple congenital anomalies (MCA) or both. Little is known about the benefits of diagnostic elucidation for affected families. We studied the impact of a genetic diagnosis on parental quality of life (QoL) using a validated semiquantitative questionnaire in families with a disabled child investigated by array-based comparative genomic hybridization (aCGH). We received completed questionnaires from 95 mothers and 76 fathers of 99 families. We used multivariate analysis for adjustment of potential confounders. Taken all 99 families together, maternal QoL score (percentile rank scale 51.05) was significantly lower than fathers' QoL (61.83, p = 0.01). Maternal QoL score was 20.17 [95% CI (5.49; 34.82)] percentile rank scales higher in mothers of children with diagnostic (n = 34) aCGH as opposed to mothers of children with inconclusive (n = 65) aCGH (Hedges' g = 0.71). Comparison of these QoL scores with retrospectively recalled QoL before aCGH revealed an increase of maternal QoL after diagnostic clarification. Our results indicate a benefit for maternal QoL if a genetic test, here aCGH, succeeds to clarify the etiologic diagnosis in a disabled child.
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Affiliation(s)
- M Lingen
- Interdisciplinary Pediatric Center for Children with Developmental Disabilities and Severe Chronic Disorders, Department of Paediatrics and Adolescent Medicine, University of Göttingen, Göttingen, Germany
| | - L Albers
- Institute of Social Paediatrics and Adolescent Medicine, Division of Epidemiology, Ludwig Maximilians University Munich, Munich, Germany
| | - M Borchers
- Interdisciplinary Pediatric Center for Children with Developmental Disabilities and Severe Chronic Disorders, Department of Paediatrics and Adolescent Medicine, University of Göttingen, Göttingen, Germany
| | - S Haass
- Interdisciplinary Pediatric Center for Children with Developmental Disabilities and Severe Chronic Disorders, Department of Paediatrics and Adolescent Medicine, University of Göttingen, Göttingen, Germany
| | - J Gärtner
- Interdisciplinary Pediatric Center for Children with Developmental Disabilities and Severe Chronic Disorders, Department of Paediatrics and Adolescent Medicine, University of Göttingen, Göttingen, Germany
| | - S Schröder
- Interdisciplinary Pediatric Center for Children with Developmental Disabilities and Severe Chronic Disorders, Department of Paediatrics and Adolescent Medicine, University of Göttingen, Göttingen, Germany
| | - L Goldbeck
- Department of Child and Adolescent Psychiatry/Psychotherapy, University Ulm, Ulm, Germany
| | - R von Kries
- Institute of Social Paediatrics and Adolescent Medicine, Division of Epidemiology, Ludwig Maximilians University Munich, Munich, Germany
| | - K Brockmann
- Interdisciplinary Pediatric Center for Children with Developmental Disabilities and Severe Chronic Disorders, Department of Paediatrics and Adolescent Medicine, University of Göttingen, Göttingen, Germany
| | - B Zirn
- Interdisciplinary Pediatric Center for Children with Developmental Disabilities and Severe Chronic Disorders, Department of Paediatrics and Adolescent Medicine, University of Göttingen, Göttingen, Germany.,Genetikum, Genetic Counselling and Diagnostics, Stuttgart, Germany
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Bissar-Tadmouri N, Donahue WL, Al-Gazali L, Nelson SF, Bayrak-Toydemir P, Kantarci S. X chromosome exome sequencing reveals a novel ALG13 mutation in a nonsyndromic intellectual disability family with multiple affected male siblings. Am J Med Genet A 2015; 164A:164-9. [PMID: 24501762 DOI: 10.1002/ajmg.a.36233] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
X-linked intellectual disability (XLID) is a heterogeneous condition associated with mutations in >100 genes, accounting for over 10% of all cases of intellectual impairment. The majority of XLID cases show nonsyndromic forms (NSXLID), in which intellectual disability is the sole clinically consistent manifestation. Here we performed X chromosome exome (X-exome) sequencing to identify the causative mutation in an NSXLID family with four affected male siblings and five unaffected female siblings. The X-exome sequencing at 88× coverage in one affected male sibling revealed a novel missense mutation (p.Tyr1074Cys) in the asparagine-linked glycosylation 13 homolog (ALG13) gene. Segregation analysis by Sanger sequencing showed that the all affected siblings were hemizygous and the mother was heterozygous for the mutation. Recently, a de novo missense mutation in ALG13 has been reported in a patient with X-linked congenital disorders of glycosylation type I. Our study reports the first case of NSXLID caused by a mutation in ALG13 involved in protein N-glycosylation.
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Abstract
Diagnosing constitutional pathogenic copy number variants (CNVs) requires detecting submicroscopic segmental chromosomal imbalances. The Affymetrix GeneChip mapping array was one of the initial microarray platforms used to measure duplication and deletion of genetic material in DNA samples. Unlike oligonucleotide microarrays from NimbleGen and Agilent, developed around the same time to infer copy number status for the DNA sequence covered by the probe, the Affymetrix GeneChip system used 25-mer oligonucleotide probes designed to interrogate SNPs. Thus, it was possible to use the Affymetrix 'SNP chips' to both identify SNPs and to identify copy number status. Affymetrix now offers the CytoScan microarray platforms, which are optimized for copy-number analyses, and provides accompanying software. They also offer several other microarray platforms suitable for copy-number analyses. Here we discuss the application of the CytoScan high-density (HD) platform for the detection of genomic imbalance. We provide an overview of the sequence of computational analyses involved in identifying pathogenic CNVs and highlight important parameters for consideration in assessing the pathogenicity of a detected CNV.
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Affiliation(s)
- Farah R Zahir
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada.,University of British Columbia, Department of Medical Genetics, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada.,University of British Columbia, Department of Medical Genetics, Vancouver, British Columbia, Canada
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Cafiero C, Marangi G, Orteschi D, Ali M, Asaro A, Ponzi E, Moncada A, Ricciardi S, Murdolo M, Mancano G, Contaldo I, Leuzzi V, Battaglia D, Mercuri E, Slavotinek AM, Zollino M. Novel de novo heterozygous loss-of-function variants in MED13L and further delineation of the MED13L haploinsufficiency syndrome. Eur J Hum Genet 2015; 23:1499-504. [PMID: 25712080 DOI: 10.1038/ejhg.2015.19] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 12/09/2014] [Accepted: 12/19/2014] [Indexed: 01/16/2023] Open
Abstract
MED13L haploinsufficiency has recently been described as responsible for syndromic intellectual disability. We planned a search for causative gene variants in seven subjects with intellectual disability and overlapping dysmorphic facial features such as bulbous nasal tip, short mouth and straight eyebrows. We found two de novo frameshift variants in MED13L, consisting in single-nucleotide deletion (c.3765delC) and duplication (c.607dupT). A de novo nonsense variant (c.4420A>T) in MED13L was detected in a further subject in the course of routine whole-exome sequencing. By analyzing the clinical data of our patients along with those recently described in the literature, we confirm that there is a common, recognizable phenotype associated with MED13L haploinsufficiency, which includes intellectual disability and a distinctive facial appearance. Congenital heart diseases are found in some subjects with various degree of severity. Our observation of cleft palate, ataxia, epilepsy and childhood leukemia observed in single cases broadens the known clinical spectrum. Haploinsufficiency for MED13L should be considered in the differential diagnosis of the 1p36 microdeletion syndrome, due to overlapping dysmorphic facial features in some patients. The introduction of massive parallel-sequencing techniques into clinical practice is expected to allow for detection of other causative point variants in MED13L. Analysis of genomic data in connection with deep clinical evaluation of patients could elucidate genetic heterogeneity of the MED13L haploinsufficiency phenotype.
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Pereira RR, Pinto IP, Minasi LB, de Melo AV, da Cruz e Cunha DM, Cruz AS, Ribeiro CL, da Silva CC, de Melo e Silva D, da Cruz AD. Screening for intellectual disability using high-resolution CMA technology in a retrospective cohort from Central Brazil. PLoS One 2014; 9:e103117. [PMID: 25061755 PMCID: PMC4111347 DOI: 10.1371/journal.pone.0103117] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 06/27/2014] [Indexed: 11/20/2022] Open
Abstract
Intellectual disability is a complex, variable, and heterogeneous disorder, representing a disabling condition diagnosed worldwide, and the etiologies are multiple and highly heterogeneous. Microscopic chromosomal abnormalities and well-characterized genetic conditions are the most common causes of intellectual disability. Chromosomal Microarray Analysis analyses have made it possible to identify putatively pathogenic copy number variation that could explain the molecular etiology of intellectual disability. The aim of the current study was to identify possible submicroscopic genomic alterations using a high-density chromosomal microarray in a retrospective cohort of patients with otherwise undiagnosable intellectual disabilities referred by doctors from the public health system in Central Brazil. The CytoScan HD technology was used to detect changes in the genome copy number variation of patients who had intellectual disability and a normal karyotype. The analysis detected 18 CNVs in 60% of patients. Pathogenic CNVs represented about 22%, so it was possible to propose the etiology of intellectual disability for these patients. Likely pathogenic and unknown clinical significance CNVs represented 28% and 50%, respectively. Inherited and de novo CNVs were equally distributed. We report the nature of CNVs in patients from Central Brazil, representing a population not yet screened by microarray technologies.
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Affiliation(s)
- Rodrigo Roncato Pereira
- Núcleo de Pesquisas Replicon, Departamento de Biologia, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Irene Plaza Pinto
- Núcleo de Pesquisas Replicon, Departamento de Biologia, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, Brazil
- Programa de Pós-Graduação (Mestrado) em Genética, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, Brazil
| | - Lysa Bernardes Minasi
- Programa de Pós-Graduação (Mestrado) em Genética, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, Brazil
| | - Aldaires Vieira de Melo
- Núcleo de Pesquisas Replicon, Departamento de Biologia, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, Brazil
- Programa de Pós-Graduação em Biotecnologia e Biodiversidade, Universidade de Brasília, Brasília, DF, Brazil
| | - Damiana Mirian da Cruz e Cunha
- Núcleo de Pesquisas Replicon, Departamento de Biologia, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, Brazil
- Programa de Pós-Graduação (Mestrado) em Genética, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, Brazil
| | - Alex Silva Cruz
- Núcleo de Pesquisas Replicon, Departamento de Biologia, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Cristiano Luiz Ribeiro
- Núcleo de Pesquisas Replicon, Departamento de Biologia, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, Brazil
| | - Cláudio Carlos da Silva
- Núcleo de Pesquisas Replicon, Departamento de Biologia, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, Brazil
- Programa de Pós-Graduação (Mestrado) em Genética, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, Brazil
- Laboratório de Citogenética Humana e Genética Molecular, Secretaria do Estado da Saúde de Goiás (LACEN/SESGO), Goiânia, GO, Brazil
| | - Daniela de Melo e Silva
- Núcleo de Pesquisas Replicon, Departamento de Biologia, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Laboratório de Genética e Biodiversidade, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Aparecido Divino da Cruz
- Núcleo de Pesquisas Replicon, Departamento de Biologia, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
- Programa de Pós-Graduação (Mestrado) em Genética, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, Brazil
- Programa de Pós-Graduação em Biotecnologia e Biodiversidade, Universidade de Brasília, Brasília, DF, Brazil
- Laboratório de Citogenética Humana e Genética Molecular, Secretaria do Estado da Saúde de Goiás (LACEN/SESGO), Goiânia, GO, Brazil
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Chung BHY, Tao VQ, Tso WWY. Copy number variation and autism: New insights and clinical implications. J Formos Med Assoc 2014; 113:400-8. [DOI: 10.1016/j.jfma.2013.01.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 12/03/2012] [Accepted: 01/22/2013] [Indexed: 12/11/2022] Open
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Athanasakis E, Licastro D, Faletra F, Fabretto A, Dipresa S, Vozzi D, Morgan A, d'Adamo AP, Pecile V, Biarnés X, Gasparini P. Next generation sequencing in nonsyndromic intellectual disability: from a negative molecular karyotype to a possible causative mutation detection. Am J Med Genet A 2013; 164A:170-6. [PMID: 24307393 DOI: 10.1002/ajmg.a.36274] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 08/29/2013] [Indexed: 12/12/2022]
Abstract
The identification of causes underlying intellectual disability (ID) is one of the most demanding challenges for clinical Geneticists and Researchers. Despite molecular diagnostics improvements, the vast majority of patients still remain without genetic diagnosis. Here, we report the results obtained using Whole Exome and Target Sequencing on nine patients affected by isolated ID without pathological copy number variations, which were accurately selected from an initial cohort of 236 patients. Three patterns of inheritance were used to search for: (1) de novo, (2) X-linked, and (3) autosomal recessive variants. In three of the nine proband-parent trios analyzed, we identified and validated two de novo and one X-linked potentially causative mutations located in three ID-related genes. We proposed three genes as ID candidate, carrying one de novo and three X-linked mutations. Overall, this systematic proband-parent trio approach using next generation sequencing could explain a consistent percentage of patients with isolated ID, thus increasing our knowledge on the molecular bases of this disease and opening new perspectives for a better diagnosis, counseling, and treatment.
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11
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Lee CG, Park SJ, Yun JN, Ko JM, Kim HJ, Yim SY, Sohn YB. Array-based comparative genomic hybridization in 190 Korean patients with developmental delay and/or intellectual disability: a single tertiary care university center study. Yonsei Med J 2013; 54:1463-70. [PMID: 24142652 PMCID: PMC3809862 DOI: 10.3349/ymj.2013.54.6.1463] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
PURPOSE This study analyzed and evaluated the demographic, clinical, and cytogenetic data [G-banded karyotyping and array-based comparative genomic hybridization (array CGH)] of patients with unexplained developmental delay or intellectual disability at a single Korean institution. MATERIALS AND METHODS We collected clinical and cytogenetic data based on retrospective charts at Ajou University Medical Center, Suwon, Korea from April 2008 to March 2012. RESULTS A total of 190 patients were identified. Mean age was 5.1±1.87 years. Array CGH yielded abnormal results in 26 of 190 patients (13.7%). Copy number losses were about two-fold more frequent than gains. A total of 61.5% of all patients had copy number losses. The most common deletion disorders included 22q11.2 deletion syndrome, 15q11.2q12 deletion and 18q deletion syndrome. Copy number gains were identified in 34.6% of patients, and common diseases among these included Potocki-Lupski syndrome, 15q11-13 duplication syndrome and duplication 22q. Abnormal karyotype with normal array CGH results was exhibited in 2.6% of patients; theses included balanced translocation (n=2), inversion (n=2) and low-level mosaicism (n=1). Facial abnormalities (p<0.001) and failure to thrive were (p<0.001) also more frequent in the group of patients with abnormal CGH findings. CONCLUSION Array CGH is a useful diagnostic tool in clinical settings in patients with developmental delay or intellectual disability combined with facial abnormalities or failure to thrive.
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Affiliation(s)
- Cha Gon Lee
- Department of Medical Genetics, Ajou University School of Medicine, 164 World cup-ro, Yeongtong-gu, Suwon 443-380, Korea.
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Xu X, Zhang L, Tong P, Xun G, Su W, Xiong Z, Zhu T, Zheng Y, Luo S, Pan Y, Xia K, Hu Z. Exome sequencing identifiesUPF3Bas the causative gene for a Chinese non-syndrome mental retardation pedigree. Clin Genet 2012; 83:560-4. [DOI: 10.1111/cge.12014] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 09/04/2012] [Accepted: 09/04/2012] [Indexed: 01/04/2023]
Affiliation(s)
| | | | | | - G Xun
- Mental Health Center; Shandong Provincial Mental Health Center; Jinan; Shandong; China
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Abstract
In the past decade, we have witnessed a flood of reports about mutations that cause or contribute to intellectual disability (ID). This rapid progress has been driven in large part by the implementation of chromosomal microarray analysis and next-generation sequencing methods. The findings have revealed extensive genetic heterogeneity for ID, as well as examples of a common genetic etiology for ID and other neurobehavioral/psychiatric phenotypes. Clinical diagnostic application of these new findings is already well under way, despite incomplete understanding of non-Mendelian transmission patterns that are sometimes observed.
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Affiliation(s)
- Jay W Ellison
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, Washington 99207, USA.
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15
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Verloes A, Héron D, Billette de Villemeur T, Afenjar A, Baumann C, Bahi-Buisson N, Charles P, Faudet A, Jacquette A, Mignot C, Moutard ML, Passemard S, Rio M, Robel L, Rougeot C, Ville D, Burglen L, des Portes V. Stratégie d’exploration d’une déficience intellectuelle inexpliquée. Arch Pediatr 2012; 19:194-207. [DOI: 10.1016/j.arcped.2011.11.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 11/22/2011] [Accepted: 11/25/2011] [Indexed: 02/07/2023]
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Abstract
Exome sequencing has greatly impacted the speed at which new disease genes are identified. In the last year alone, six studies have used exome sequencing to identify new genes involved in intellectual disability, a genetically heterogeneous condition affecting 1-3% of the population. These studies encompass the full gamut of modes of inheritance and phenotypic presentation, including syndromic and non-syndromic conditions, sporadic and familial cases, and dominant and recessive inheritance patterns. Because different disease presentations require different approaches to gene discovery, studies of intellectual disability provide a nearly comprehensive showcase of strategies for exome-driven gene discovery. Despite these successes, the etiology of ~60% of cases of intellectual disability remains unknown. The application of exome sequencing to the clinical diagnosis of intellectual disability in the near future will ultimately reduce the number of idiopathic cases and provide a rich source of sequence variation for the identification of new intellectual disability genes.
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Affiliation(s)
- S Topper
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
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Chung BHY, Stavropoulos J, Marshall CR, Weksberg R, Scherer SW, Yoon G. 2q23 de novo microdeletion involving the MBD5 gene in a patient with developmental delay, postnatal microcephaly and distinct facial features. Am J Med Genet A 2011; 155A:424-9. [PMID: 21271666 DOI: 10.1002/ajmg.a.33821] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We report on a female patient with a de novo interstitial deletion of chromosome region 2q23.1-23.3 identified by array-CGH. She had significant global delay with developmental regression at age 6 years. She developed seizures at age 3 years with progressive difficulties with balance, loss of fine motor skills and aggressive behavior. She had short stature, microcephaly, and distinct facial features. Her speech was dysarthric, and she demonstrated repetitive hand movements. In this article, we compare the clinical features of our patient with previously reported cases with a 2q23.1 deletion.
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Affiliation(s)
- Brian H Y Chung
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, Hospital for Sick Children, Toronto, Ontario, Canada
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18
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Tucker T, Montpetit A, Chai D, Chan S, Chénier S, Coe BP, Delaney A, Eydoux P, Lam WL, Langlois S, Lemyre E, Marra M, Qian H, Rouleau GA, Vincent D, Michaud JL, Friedman JM. Comparison of genome-wide array genomic hybridization platforms for the detection of copy number variants in idiopathic mental retardation. BMC Med Genomics 2011; 4:25. [PMID: 21439053 PMCID: PMC3076225 DOI: 10.1186/1755-8794-4-25] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Accepted: 03/25/2011] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Clinical laboratories are adopting array genomic hybridization as a standard clinical test. A number of whole genome array genomic hybridization platforms are available, but little is known about their comparative performance in a clinical context. METHODS We studied 30 children with idiopathic MR and both unaffected parents of each child using Affymetrix 500 K GeneChip SNP arrays, Agilent Human Genome 244 K oligonucleotide arrays and NimbleGen 385 K Whole-Genome oligonucleotide arrays. We also determined whether CNVs called on these platforms were detected by Illumina Hap550 beadchips or SMRT 32 K BAC whole genome tiling arrays and tested 15 of the 30 trios on Affymetrix 6.0 SNP arrays. RESULTS The Affymetrix 500 K, Agilent and NimbleGen platforms identified 3061 autosomal and 117 X chromosomal CNVs in the 30 trios. 147 of these CNVs appeared to be de novo, but only 34 (22%) were found on more than one platform. Performing genotype-phenotype correlations, we identified 7 most likely pathogenic and 2 possibly pathogenic CNVs for MR. All 9 of these putatively pathogenic CNVs were detected by the Affymetrix 500 K, Agilent, NimbleGen and the Illumina arrays, and 5 were found by the SMRT BAC array. Both putatively pathogenic CNVs identified in the 15 trios tested with the Affymetrix 6.0 were identified by this platform. CONCLUSIONS Our findings demonstrate that different results are obtained with different platforms and illustrate the trade-off that exists between sensitivity and specificity. The large number of apparently false positive CNV calls on each of the platforms supports the need for validating clinically important findings with a different technology.
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Affiliation(s)
- Tracy Tucker
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.
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Männik K, Parkel S, Palta P, Zilina O, Puusepp H, Esko T, Mägi R, Nõukas M, Veidenberg A, Nelis M, Metspalu A, Remm M, Ounap K, Kurg A. A parallel SNP array study of genomic aberrations associated with mental retardation in patients and general population in Estonia. Eur J Med Genet 2011; 54:136-43. [PMID: 21112420 DOI: 10.1016/j.ejmg.2010.11.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Accepted: 11/04/2010] [Indexed: 11/21/2022]
Abstract
The increasing use of whole-genome array screening has revealed the important role of DNA copy-number variations in the pathogenesis of neurodevelopmental disorders and several recurrent genomic disorders have been defined during recent years. However, some variants considered to be pathogenic have also been observed in phenotypically normal individuals. This underlines the importance of further characterization of genomic variants with potentially variable expressivity in both patient and general population cohorts to clarify their phenotypic consequence. In this study whole-genome SNP arrays were used to investigate genomic rearrangements in 77 Estonian families with idiopathic mental retardation. In addition to this family-based approach, phenotype and genotype data from a cohort of 1000 individuals in the general population were used for accurate interpretation of aberrations found in mental retardation patients. Relevant structural aberrations were detected in 18 of the families analyzed (23%). Fifteen of those were in genomic regions where clinical significance has previously been established. In 3 families, 4 novel aberrations associated with intellectual disability were detected in chromosome regions 2p25.1-p24.3, 3p12.1-p11.2, 7p21.2-p21.1 and Xq28. Carriers of imbalances in 15q13.3, 16p11.2 and Xp22.31 were identified among reference individuals, affirming the variable phenotypic consequence of rare variants in some genomic regions considered as pathogenic.
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20
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Abstract
Intellectual disability (ID), also referred to as mental retardation (MR), is frequently the result of genetic mutation. Where ID is present together with additional clinical symptoms or physical anomalies, there is often sufficient information available for the diagnosing physician to identify a known syndrome, which may then educe the identification of the causative defect. However, where co-morbid features are absent, narrowing down a specific gene can only be done by ‘brute force’ using the latest molecular genetic techniques. Here we attempt to provide a systematic review of genetic causes of cases of ID where no other symptoms or co-morbid features are present, or non-syndromic ID. We attempt to summarize commonalities between the genes and the molecular pathways of their encoded proteins. Since ID is a common feature of autism, and conversely autistic features are frequently present in individuals with ID, we also look at possible overlaps in genetic etiology with non-syndromic ID.
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21
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Regier DA, Friedman JM, Marra CA. Value for money? Array genomic hybridization for diagnostic testing for genetic causes of intellectual disability. Am J Hum Genet 2010; 86:765-72. [PMID: 20398885 DOI: 10.1016/j.ajhg.2010.03.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Revised: 03/05/2010] [Accepted: 03/16/2010] [Indexed: 01/22/2023] Open
Abstract
Array genomic hybridization (AGH) provides a higher detection rate than does conventional cytogenetic testing when searching for chromosomal imbalance causing intellectual disability (ID). AGH is more costly than conventional cytogenetic testing, and it remains unclear whether AGH provides good value for money. Decision analytic modeling was used to evaluate the trade-off between costs, clinical effectiveness, and benefit of an AGH testing strategy compared to a conventional testing strategy. The trade-off between cost and effectiveness was expressed via the incremental cost-effectiveness ratio. Probabilistic sensitivity analysis was performed via Monte Carlo simulation. The baseline AGH testing strategy led to an average cost increase of $217 (95% CI $172-$261) per patient and an additional 8.2 diagnoses in every 100 tested (0.082; 95% CI 0.044-0.119). The mean incremental cost per additional diagnosis was $2646 (95% CI $1619-$5296). Probabilistic sensitivity analysis demonstrated that there was a 95% probability that AGH would be cost effective if decision makers were willing to pay $4550 for an additional diagnosis. Our model suggests that using AGH instead of conventional karyotyping for most ID patients provides good value for money. Deterministic sensitivity analysis found that employing AGH after first-line cytogenetic testing had proven uninformative did not provide good value for money when compared to using AGH as first-line testing.
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Affiliation(s)
- Dean A Regier
- National Perinatal Epidemiology Unit, University of Oxford, Oxford, UK.
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22
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Willemsen MH, Fernandez BA, Bacino CA, Gerkes E, de Brouwer APM, Pfundt R, Sikkema-Raddatz B, Scherer SW, Marshall CR, Potocki L, van Bokhoven H, Kleefstra T. Identification of ANKRD11 and ZNF778 as candidate genes for autism and variable cognitive impairment in the novel 16q24.3 microdeletion syndrome. Eur J Hum Genet 2010; 18:429-35. [PMID: 19920853 PMCID: PMC2987261 DOI: 10.1038/ejhg.2009.192] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Revised: 09/02/2009] [Accepted: 09/22/2009] [Indexed: 11/09/2022] Open
Abstract
The clinical use of array comparative genomic hybridization in the evaluation of patients with multiple congenital anomalies and/or mental retardation has recently led to the discovery of a number of novel microdeletion and microduplication syndromes. We present four male patients with overlapping molecularly defined de novo microdeletions of 16q24.3. The clinical features observed in these patients include facial dysmorphisms comprising prominent forehead, large ears, smooth philtrum, pointed chin and wide mouth, variable cognitive impairment, autism spectrum disorder, structural anomalies of the brain, seizures and neonatal thrombocytopenia. Although deletions vary in size, the common region of overlap is only 90 kb and comprises two known genes, Ankyrin Repeat Domain 11 (ANKRD11) (MIM 611192) and Zinc Finger 778 (ZNF778), and is located approximately 10 kb distally to Cadherin 15 (CDH15) (MIM 114019). This region is not found as a copy number variation in controls. We propose that these patients represent a novel and distinctive microdeletion syndrome, characterized by autism spectrum disorder, variable cognitive impairment, facial dysmorphisms and brain abnormalities. We suggest that haploinsufficiency of ANKRD11 and/or ZNF778 contribute to this phenotype and speculate that further investigation of non-deletion patients who have features suggestive of this 16q24.3 microdeletion syndrome might uncover other mutations in one or both of these genes.
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Affiliation(s)
- Marjolein H Willemsen
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, PO Box 9101, Nijmegen 6500 HB, The Netherlands.
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23
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Schendel D, Rice C, Cunniff C. The contribution of rare diseases to understanding the epidemiology of neurodevelopmental disabilities. Adv Exp Med Biol 2010; 686:433-53. [PMID: 20824459 DOI: 10.1007/978-90-481-9485-8_24] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Our objective is to describe the contribution of rare diseases to our understanding of the epidemiology of neurodevelopmental disabilities (NDDs) by comparing and contrasting the epidemiologic features of NDDs classified according to key characteristics of developmental delay or deviance in such areas as behavior or cognition (the phenotypic approach; autism spectrum disorders and intellectual disability as examples) versus classification based on the identification of an etiologic diagnosis (the etiologic approach; 22q11.2 deletion syndrome and fragile X syndrome as examples). We suggest specific applications in which consideration of rare etiology-based NDDs might further our understanding of NDD epidemiology overall; what is needed to integrate the two classification approaches; and identify practical challenges in achieving that integration. Understanding commonalities and differences in the epidemiologic features of the phenotypically and etiologically defined NDD classifications provides a useful framework for furthering our understanding of the prevalence, distribution, and causes of NDDs, as well as delivering appropriate diagnostic resources, appropriate treatments, accurate prognostic information, and estimates of recurrence risk for these disorders.
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Affiliation(s)
- Diana Schendel
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
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24
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Friedman J, Adam S, Arbour L, Armstrong L, Baross A, Birch P, Boerkoel C, Chan S, Chai D, Delaney AD, Flibotte S, Gibson WT, Langlois S, Lemyre E, Li HI, MacLeod P, Mathers J, Michaud JL, McGillivray BC, Patel MS, Qian H, Rouleau GA, Van Allen MI, Yong SL, Zahir FR, Eydoux P, Marra MA. Detection of pathogenic copy number variants in children with idiopathic intellectual disability using 500 K SNP array genomic hybridization. BMC Genomics 2009; 10:526. [PMID: 19917086 PMCID: PMC2781027 DOI: 10.1186/1471-2164-10-526] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2009] [Accepted: 11/16/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Array genomic hybridization is being used clinically to detect pathogenic copy number variants in children with intellectual disability and other birth defects. However, there is no agreement regarding the kind of array, the distribution of probes across the genome, or the resolution that is most appropriate for clinical use. RESULTS We performed 500 K Affymetrix GeneChip array genomic hybridization in 100 idiopathic intellectual disability trios, each comprised of a child with intellectual disability of unknown cause and both unaffected parents. We found pathogenic genomic imbalance in 16 of these 100 individuals with idiopathic intellectual disability. In comparison, we had found pathogenic genomic imbalance in 11 of 100 children with idiopathic intellectual disability in a previous cohort who had been studied by 100 K GeneChip array genomic hybridization. Among 54 intellectual disability trios selected from the previous cohort who were re-tested with 500 K GeneChip array genomic hybridization, we identified all 10 previously-detected pathogenic genomic alterations and at least one additional pathogenic copy number variant that had not been detected with 100 K GeneChip array genomic hybridization. Many benign copy number variants, including one that was de novo, were also detected with 500 K array genomic hybridization, but it was possible to distinguish the benign and pathogenic copy number variants with confidence in all but 3 (1.9%) of the 154 intellectual disability trios studied. CONCLUSION Affymetrix GeneChip 500 K array genomic hybridization detected pathogenic genomic imbalance in 10 of 10 patients with idiopathic developmental disability in whom 100 K GeneChip array genomic hybridization had found genomic imbalance, 1 of 44 patients in whom 100 K GeneChip array genomic hybridization had found no abnormality, and 16 of 100 patients who had not previously been tested. Effective clinical interpretation of these studies requires considerable skill and experience.
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Affiliation(s)
- Jm Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada.
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25
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Makela NL, Birch PH, Friedman JM, Marra CA. Parental perceived value of a diagnosis for intellectual disability (ID): A qualitative comparison of families with and without a diagnosis for their child's ID. Am J Med Genet A 2009; 149A:2393-402. [DOI: 10.1002/ajmg.a.33050] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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26
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Bernardini L, Alesi V, Loddo S, Novelli A, Bottillo I, Battaglia A, Digilio MC, Zampino G, Ertel A, Fortina P, Surrey S, Dallapiccola B. High-resolution SNP arrays in mental retardation diagnostics: how much do we gain? Eur J Hum Genet 2010; 18:178-85. [PMID: 19809473 DOI: 10.1038/ejhg.2009.154] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We used Affymetrix 6.0 GeneChip SNP arrays to characterize copy number variations (CNVs) in a cohort of 70 patients previously characterized on lower-density oligonucleotide arrays affected by idiopathic mental retardation and dysmorphic features. The SNP array platform includes approximately 900,000 SNP probes and 900,000 non-SNP oligonucleotide probes at an average distance of 0.7 Kb, which facilitates coverage of the whole genome, including coding and noncoding regions. The high density of probes is critical for detecting small CNVs, but it can lead to data interpretation problems. To reduce the number of false positives, parameters were set to consider only imbalances >75 Kb encompassing at least 80 probe sets. The higher resolution of the SNP array platform confirmed the increased ability to detect small CNVs, although more than 80% of these CNVs overlapped to copy number 'neutral' polymorphism regions and 4.4% of them did not contain known genes. In our cohort of 70 patients, of the 51 previously evaluated as 'normal' on the Agilent 44K array, the SNP array platform disclosed six additional CNV changes, including three in three patients, which may be pathogenic. This suggests that about 6% of individuals classified as 'normal' using the lower-density oligonucleotide array could be found to be affected by a genomic disorder when evaluated with the higher-density microarray platforms.
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27
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Regier DA, Friedman JM, Makela N, Ryan M, Marra CA. Valuing the benefit of diagnostic testing for genetic causes of idiopathic developmental disability: willingness to pay from families of affected children. Clin Genet 2009; 75:514-21. [PMID: 19508416 DOI: 10.1111/j.1399-0004.2009.01193.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Idiopathic developmental disability (DD) has been found to put significant psychological distress on families of children with DD. The cause of the disability, however, is unknown for up to one-half of the affected children. Chromosomal abnormalities identified by cytogenetic analysis are the most frequently recognized cause of DD, although they account for less than 10% of cases. Array genomic hybridization (AGH) is a new diagnostic tool that provides a much higher detection rate for chromosomal imbalance than conventional cytogenetic analysis. This increase in diagnostic capability comes at greater monetary costs, which provides an impetus for understanding how individuals value genetic testing for DD. This study estimated the willingness to pay (WTP) for diagnostic testing to find a genetic cause of DD from families of children with DD. A discrete choice experiment was used to obtain WTP values. When it was assumed that AGH resulted in twice as many diagnoses and a 1-week reduction in waiting time compared with conventional cytogenetic analysis, this study found that families were willing to pay up to CDN$1118 (95% confidence interval, $498-1788) for the expected benefit. These results support the conclusion that the introduction of AGH into the Canadian health care system may increase the perceived welfare of society, but future studies should examine the cost-benefit of AGH vs cytogenetic testing.
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Affiliation(s)
- D A Regier
- National Perinatal Epidemiology Unit, University of Oxford, Oxford, UK.
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28
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Abstract
Neural tube defects (NTDs) represent a common group of severe congenital malformations of the central nervous system. They result from failure of neural tube closure during early embryonic life. Their etiology is complex, involving environmental and genetic factors that interact to modulate the incidence and severity of the developing phenotype. Despite a long history of etiologic studies, the molecular and cellular pathogenic mechanisms underlining NTDs remain poorly understood. The major epidemiologic finding in NTDs is the protective effect of perinatal folic acid supplementation that reduces their risk by 60%-70%. Genetic studies in NTDs have focused mainly on folate-related genes and identified a few significant associations between variants in these genes and an increased risk for NTDs. The candidate gene approach investigating genes involved in neurulation and inferred from animal models has faced limited success in identifying major causative genes predisposing to NTDs. However, we are witnessing a rapid and impressive progress in understanding the genetic basis of NTDs, based mainly on the development of whole genome innovative technologies and the powerful tool of animal models.
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29
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Gécz J, Shoubridge C, Corbett M. The genetic landscape of intellectual disability arising from chromosome X. Trends Genet 2009; 25:308-16. [PMID: 19556021 DOI: 10.1016/j.tig.2009.05.002] [Citation(s) in RCA: 140] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Revised: 05/14/2009] [Accepted: 05/14/2009] [Indexed: 01/07/2023]
Abstract
X-linked mental retardation (XLMR) or intellectual disability (ID) is a common, clinically complex and genetically heterogeneous disease arising from many mutations along the X chromosome. It affects between 1/600-1/1000 males and a substantial number of females. Research during the past decade has identified >90 different XLMR genes, affecting a wide range of cellular processes. Many more genes remain uncharacterized, especially for the non-syndromic XLMR forms. Currently, approximately 11% of X-chromosome genes are implicated in XLMR; however, apart from a few notable exceptions, most contribute individually to <0.1% of the total landscape, which arguably remains only about half complete. There remain many hills to climb and valleys to cross before the ID landscape is fully triangulated.
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Affiliation(s)
- Jozef Gécz
- Molecular Pathology, SA Pathology at Women's and Children's Hospital, North Adelaide, SA 5006, Australia
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30
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Yeshaya J, Amir I, Rimon A, Freedman J, Shohat M, Avivi L. Microdeletion syndromes disclose replication timing alterations of genes unrelated to the missing DNA. Mol Cytogenet 2009; 2:11. [PMID: 19284877 PMCID: PMC2660353 DOI: 10.1186/1755-8166-2-11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2009] [Accepted: 03/14/2009] [Indexed: 11/26/2022] Open
Abstract
Background The temporal order of allelic replication is interrelated to the epigenomic profile. A significant epigenetic marker is the asynchronous replication of monoallelically-expressed genes versus the synchronous replication of biallelically-expressed genes. The present study sought to determine whether a microdeletion in the genome affects epigenetic profiles of genes unrelated to the missing segment. In order to test this hypothesis, we checked the replication patterns of two genes – SNRPN, a normally monoallelically expressed gene (assigned to 15q11.13), and the RB1, an archetypic biallelically expressed gene (assigned to 13.q14) in the genomes of patients carrying the 22q11.2 deletion (DiGeorge/Velocardiofacial syndrome) and those carrying the 7q11.23 deletion (Williams syndrome). Results The allelic replication timing was determined by fluorescence in situ hybridization (FISH) technology performed on peripheral blood cells. As expected, in the cells of normal subjects the frequency of cells showing asynchronous replication for SNRPN was significantly (P < 10-12) higher than the corresponding value for RB1. In contrast, cells of the deletion-carrying patients exhibited a reversal in this replication pattern: there was a significantly lower frequency of cells engaging in asynchronous replication for SNRPN than for RB1 (P < 10-4 and P < 10-3 for DiGeorge/Velocardiofacial and Williams syndromes, respectively). Accordingly, the significantly lower frequency of cells showing asynchronous replication for SNRPN than for RB1 is a new epigenetic marker distinguishing these deletion syndrome genotypes from normal ones. Conclusion In cell samples of each deletion-carrying individual, an aberrant, reversed pattern of replication is delineated, namely, where a monoallelic gene replicates more synchronously than a biallelic gene. This inverted pattern, which appears to be non-deletion-specific, clearly distinguishes cells of deletion-carriers from normal ones. As such, it offers a potential epigenetic marker for suspecting a hidden microdeletion that is too small to be detected by conventional karyotyping methods.
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Affiliation(s)
- Josepha Yeshaya
- Raphael Recanati Genetic Institute, Rabin Medical Center Beilinson Campus, Petah-Tikva, Israel
| | - Itay Amir
- Raphael Recanati Genetic Institute, Rabin Medical Center Beilinson Campus, Petah-Tikva, Israel.,Department of Human Molecular Genetics & Biochemistry, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Ayelet Rimon
- Raphael Recanati Genetic Institute, Rabin Medical Center Beilinson Campus, Petah-Tikva, Israel
| | - Jane Freedman
- Raphael Recanati Genetic Institute, Rabin Medical Center Beilinson Campus, Petah-Tikva, Israel
| | - Mordechai Shohat
- Raphael Recanati Genetic Institute, Rabin Medical Center Beilinson Campus, Petah-Tikva, Israel.,Department of Human Molecular Genetics & Biochemistry, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Department of Pediatrics C, Schneider Children's Medical Center of Israel, Petah Tikva, Israel
| | - Lydia Avivi
- Department of Human Molecular Genetics & Biochemistry, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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31
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Delaney AD, Qian H, Friedman JM, Marra MA. Use of Affymetrix mapping arrays in the diagnosis of gene copy number variation. ACTA ACUST UNITED AC 2008; Chapter 8:Unit 8.13. [PMID: 18972373 DOI: 10.1002/0471142905.hg0813s59] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Diagnosing constitutional pathogenic copy number variants requires measuring the submicroscopic segmental chromosomal imbalance. The Affymetrix GeneChip mapping array has been used to measure duplication and deletion of genetic material in DNA samples. This protocol describes the measurement and analysis processes, specifically the computational analyses that are involved in identifying pathogenic copy number variants.
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Affiliation(s)
- Allen D Delaney
- Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
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32
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Dufke A, Riess O, Bonin M. Molekulare Karyotypisierung in der klinischen Anwendung. MED GENET-BERLIN 2008; 20:419-31. [DOI: 10.1007/s11825-008-0112-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Zusammenfassung
In den vergangenen Jahren hat sich die Anwendung der Mikroarraytechnologie für die Detektion von putativ pathologischen submikroskopischen Copy-Number-Variationen (CNV) einen festen Platz in der molekularen Zytogenetik erobert. Neben der Identifikation somatischer CNV in der onkologischen Diagnostik wird diese Technologie nunmehr für die Analyse von konstitutionellen CNV bei Patienten mit mentaler Retardierung genutzt. Arraybasierte genomische Hybridisierungen zeigen eine deutliche Verbesserung zu der bereits seit Jahren angewendeten komparativen genomischen Hybridisierung (CGH). Insbesondere weisen die dazugehörigen Technologien eine verbesserte Auflösung von weniger als 100 kb für Deletionen und Duplikationen auf und haben damit eine deutlich bessere Aufklärungsrate von Krankheiten mit Behinderungen ungeklärter Ursache. In einigen Zentren gehört die Arraytechnologie daher bereits zur Routinetechnologie der Syndromabklärung. Im vorliegenden Beitrag soll deshalb auch auf die Gemeinsamkeiten bzw. Unterschiede der verschiedenen Basistechnologien der Arraytechnik eingegangen werden.
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33
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Mizuguchi T, Hashimoto R, Itokawa M, Sano A, Shimokawa O, Yoshimura Y, Harada N, Miyake N, Nishimura A, Saitsu H, Sosonkina N, Niikawa N, Kunugi H, Matsumoto N. Microarray comparative genomic hybridization analysis of 59 patients with schizophrenia. J Hum Genet 2008; 53:914-919. [PMID: 18685808 DOI: 10.1007/s10038-008-0327-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Accepted: 07/08/2008] [Indexed: 10/21/2022]
Abstract
Schizophrenia is a common psychiatric disorder with a strong genetic contribution. Disease-associated chromosomal abnormalities in this condition may provide important clues, such as DISC1. In this study, 59 schizophrenia patients were analyzed by microarray comparative genomic hybridization (CGH) using custom bacterial artificial chromosome (BAC) microarray (4,219 BACs with 0.7-Mb resolution). Chromosomal abnormalities were found in six patients (10%): 46,XY,der(13)t(12;13)(p12.1; p11).ish del(5)(p11p12); 46,XY, ish del(17)(p12p12); 46,XX.ish dup(11)(p13p13); and 46,X,idic(Y)(q11.2); and in two cases, mos 45,X/46XX. Autosomal abnormalities in three cases are likely to be pathogenic, and sex chromosome abnormalities in three follow previous findings. It is noteworthy that 10% of patients with schizophrenia have (sub)microscopic chromosomal abnormalities, indicating that genome-wide copy number survey should be considered in genetic studies of schizophrenia.
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Affiliation(s)
- Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura 3-9, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Ryota Hashimoto
- Department of Mental Disorder Research, National Center of Neurology and Psychiatry, Kodaira, Japan.,Department of Psychiatry, Osaka University Graduate School of Medicine, Suita, Japan
| | - Masanari Itokawa
- Schizophrenia Research Team, Schizophrenia Project, Tokyo Institute of Psychiatry, Tokyo, Japan
| | - Akira Sano
- Department of Psychiatry, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Osamu Shimokawa
- Department of Molecular Cytogenetics, Kyushu Medical Science, Inc., Nagasaki, Japan
| | - Yukiko Yoshimura
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura 3-9, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Naoki Harada
- Department of Molecular Cytogenetics, Kyushu Medical Science, Inc., Nagasaki, Japan
| | - Noriko Miyake
- Department of Medicine (Genetics), Children's Hospital Boston, Boston, MA, USA.,Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Akira Nishimura
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura 3-9, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Hirotomo Saitsu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura 3-9, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Nadiya Sosonkina
- The Research Institute of Personalized Health Sciences, Health Sciences University of Hokkaido, Tobetsu-cho, Ishikari-gun, Japan
| | - Norio Niikawa
- The Research Institute of Personalized Health Sciences, Health Sciences University of Hokkaido, Tobetsu-cho, Ishikari-gun, Japan
| | - Hiroshi Kunugi
- Department of Mental Disorder Research, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura 3-9, Kanazawa-ku, Yokohama, 236-0004, Japan.
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Ou Z, Kang SHL, Shaw CA, Carmack CE, White LD, Patel A, Beaudet AL, Cheung SW, Chinault AC. Bacterial artificial chromosome-emulation oligonucleotide arrays for targeted clinical array-comparative genomic hybridization analyses. Genet Med 2008; 10:278-89. [PMID: 18414211 DOI: 10.1097/gim.0b013e31816b4420] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
PURPOSE The goal of this work was to test the ability of oligonucleotide-based arrays to reproduce the results of focused bacterial artificial chromosome (BAC)-based arrays used clinically in comparative genomic hybridization experiments to detect constitutional copy number changes in genomic DNA. METHODS Custom oligonucleotide (oligo) arrays were designed using the Agilent Technologies platform to give high-resolution coverage of regions within the genome sequence coordinates of BAC/P1 artificial chromosome (PAC) clones that had already been validated for use in previous versions of clone arrays used in clinical practice. Standard array-comparative genomic hybridization experiments, including a simultaneous blind analysis of a set of clinical samples, were conducted on both array platforms to identify copy number differences between patient samples and normal reference controls. RESULTS Initial experiments successfully demonstrated the capacity of oligo arrays to emulate BAC data without the need for dye-reversal comparisons. Empirical data and computational analyses of oligo response and distribution from a pilot array were used to design an optimized array of 44,000 oligos (44K). This custom 44K oligo array consists of probes localized to the genomic positions of >1400 fluorescence in situ hybridization-verified BAC/PAC clones covering more than 140 regions implicated in genetic diseases, as well as all clinically relevant subtelomeric and pericentromeric regions. CONCLUSIONS Our data demonstrate that oligo-based arrays offer a valid alternative for focused BAC arrays. Furthermore, they have significant advantages, including better design flexibility, avoidance of repetitive sequences, manufacturing processes amenable to good manufacturing practice standards in the future, increased robustness because of an enhanced dynamic range (signal to background), and increased resolution that allows for detection of smaller regions of change.
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Affiliation(s)
- Zhishuo Ou
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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