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Abstract
Neurodevelopmental disorders are the most prevalent chronic medical conditions encountered in pediatric primary care. In addition to identifying appropriate descriptive diagnoses and guiding families to evidence-based treatments and supports, comprehensive care for individuals with neurodevelopmental disorders includes a search for an underlying etiologic diagnosis, primarily through a genetic evaluation. Identification of an underlying genetic etiology can inform prognosis, clarify recurrence risk, shape clinical management, and direct patients and families to condition-specific resources and supports. Here we review the utility of genetic testing in patients with neurodevelopmental disorders and describe the three major testing modalities and their yields - chromosomal microarray, exome sequencing (with/without copy number variant calling), and FMR1 CGG repeat analysis for fragile X syndrome. Given the diagnostic yield of genetic testing and the potential for clinical and personal utility, there is consensus that genetic testing should be offered to all patients with global developmental delay, intellectual disability, and/or autism spectrum disorder. Despite this recommendation, data suggest that a minority of children with autism spectrum disorder and intellectual disability have undergone genetic testing. To address this gap in care, we describe a structured but flexible approach to facilitate integration of genetic testing into clinical practice across pediatric specialties and discuss future considerations for genetic testing in neurodevelopmental disorders to prepare pediatric providers to care for patients with such diagnoses today and tomorrow.
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Affiliation(s)
- Juliann M. Savatt
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, United States
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Cappuccio G, Vitiello F, Casertano A, Fontana P, Genesio R, Bruzzese D, Ginocchio VM, Mormile A, Nitsch L, Andria G, Melis D. New insights in the interpretation of array-CGH: autism spectrum disorder and positive family history for intellectual disability predict the detection of pathogenic variants. Ital J Pediatr 2016; 42:39. [PMID: 27072107 PMCID: PMC4830019 DOI: 10.1186/s13052-016-0246-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 03/15/2016] [Indexed: 12/08/2022] Open
Abstract
BACKGROUND Array-CGH (aCGH) is presently used into routine clinical practice for diagnosis of patients with intellectual disability (ID), multiple congenital anomalies (MCA), and autism spectrum disorder (ASD). ACGH could detect small chromosomal imbalances, copy number variations (CNVs), and closely define their size and gene content. ACGH detects pathogenic imbalances in 14-20 % of patients with ID. The aims of this study were: to establish clinical clues potentially associated with pathogenic CNVs and to identify cytogenetic indicators to predict the pathogenicity of the variants of uncertain significance (VOUS) in a large cohort of paediatric patients. METHODS We enrolled 214 patients referred for either: ID, and/or ASD and/or MCA to genetic services at the Federico II University of Naples, Department of Translational Medicine. For each patient we collected clinical and imaging data. All the patients were tested with aCGH or as first-tier test or as part of a wider diagnostic work-up. RESULTS Pathologic data were detected in 65 individuals (30 %) and 46 CNVs revealed a known syndrome. The pathological CNVs were usually deletions showing the highest gene-dosage content. The positive family history for ID/ASD/MCA and ASD were good indicators for detecting pathological chromosomal rearrangements. Other clinical features as eyes anomalies, hearing loss, neurological signs, cutaneous dyscromia and endocrinological problems seem to be potential predictors of pathological CNVs. Among patients carrying VOUS we analyzed genetic features including CNVs size, presence of deletion or duplication, genic density, multiple CNVs, to clinical features. Higher gene density was found in patients affected by ID. This result suggest that higher gene content has more chances to include pathogenic gene involved and causing ID in these patients. CONCLUSION Our study suggest the use of aCGH as first-tier test in patients with neurdevelopmental phenotypes. The inferred results have been used for building a flow-chart to be applied for children with ID.
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Affiliation(s)
- Gerarda Cappuccio
- Department of Translational Medical Sciences, Section of Pediatrics, Federico II University, Via Sergio Pansini 5, 80131, Naples, Italy
| | - Francesco Vitiello
- Department of Translational Medical Sciences, Section of Pediatrics, Federico II University, Via Sergio Pansini 5, 80131, Naples, Italy
| | - Alberto Casertano
- Department of Translational Medical Sciences, Section of Pediatrics, Federico II University, Via Sergio Pansini 5, 80131, Naples, Italy
| | - Paolo Fontana
- Department of Translational Medical Sciences, Section of Pediatrics, Federico II University, Via Sergio Pansini 5, 80131, Naples, Italy
| | - Rita Genesio
- Department of Molecular Medicine and Medical Biotechnology, Federico II University, Naples, Italy
| | - Dario Bruzzese
- Preventive Medical Sciences, Federico II University, Naples, Italy
| | | | - Angela Mormile
- Department of Molecular Medicine and Medical Biotechnology, Federico II University, Naples, Italy
| | - Lucio Nitsch
- Department of Molecular Medicine and Medical Biotechnology, Federico II University, Naples, Italy
| | - Generoso Andria
- Department of Translational Medical Sciences, Section of Pediatrics, Federico II University, Via Sergio Pansini 5, 80131, Naples, Italy
| | - Daniela Melis
- Department of Translational Medical Sciences, Section of Pediatrics, Federico II University, Via Sergio Pansini 5, 80131, Naples, Italy.
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Vander Pluym JH, O'Sullivan J, Andrew G, Bolduc FV. Genomic characterization of chromosome 8 pericentric trisomy. Clin Case Rep 2015; 3:570-7. [PMID: 26273445 PMCID: PMC4527799 DOI: 10.1002/ccr3.234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 01/29/2015] [Indexed: 11/10/2022] Open
Abstract
We present a patient with trisomy 8p11.21q11.21 associated with language, gross motor, fine motor, and cognitive delay. Furthermore, using array-based comparative genomic hybridization, we identify the specific genes duplicated in our patient.
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Affiliation(s)
- Juliana H Vander Pluym
- Division of Pediatric Neuroscience, Stollery Children Hospital, University of Alberta Edmonton, Alberta, Canada
| | - Julia O'Sullivan
- Division of Pediatric Neuroscience, Stollery Children Hospital, University of Alberta Edmonton, Alberta, Canada
| | - Gail Andrew
- Division of Neurodevelopmental and Neuromotor Pediatrics, University of Alberta Edmonton, Alberta, Canada
| | - Francois V Bolduc
- Division of Pediatric Neuroscience, Stollery Children Hospital, University of Alberta Edmonton, Alberta, Canada ; Neuroscience and Mental Health Institute, University of Alberta Edmonton, Alberta, Canada
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Bose D, Krishnamurthy V, Venkatesh KS, Aiyaz M, Shetty M, Rao SN, Kutty AVM. Molecular Delineation of Partial Trisomy 14q and Partial Trisomy 12p in a Patient with Dysmorphic Features, Heart Defect and Developmental Delay. Cytogenet Genome Res 2015; 145:14-8. [PMID: 25896599 DOI: 10.1159/000381294] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2015] [Indexed: 11/19/2022] Open
Abstract
This study describes a molecular analysis of partial trisomy 14q and partial trisomy 12p in a 5-year-old male child presenting with dysmorphic features, congenital heart disease and global developmental delay. Chromosomal analysis of the patient with GTG bands revealed a 47,XY,+der(14)t(12;14)(p13;q22)mat karyotype; the mother's karyotype was 46,XX,t(12;14)(p13;q22). Further, oligonucleotide array- CGH studies revealed an amplification of 32.3 Mb in the 14q11.1q22.1 region, substantiating partial trisomy 14q and additionally displaying an amplification of ∼1 Mb in the 12p13.3pter region for partial trisomy 12p. This is the first study to demonstrate a novel association of partial trisomies of 14q and 12p due to a 3:1 segregation of a maternal balanced translocation involving chromosomes 12 and 14. Gene ontology studies indicated 5 potential candidate genes in the amplified regions for the observed congenital anomalies.
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Affiliation(s)
- Divya Bose
- Division of Genomics, Department of Cell Biology and Molecular Genetics, Sri Devaraj Urs Academy of Higher Education and Research, Kolar, India
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Roselló M, Martínez F, Monfort S, Mayo S, Oltra S, Orellana C. Phenotype profiling of patients with intellectual disability and copy number variations. Eur J Paediatr Neurol 2014; 18:558-66. [PMID: 24815074 DOI: 10.1016/j.ejpn.2014.04.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Revised: 04/01/2014] [Accepted: 04/04/2014] [Indexed: 12/08/2022]
Abstract
BACKGROUND Nowadays the microarray technology allows whole-genome analysis with a high resolution and performance for the genetic diagnosis in any patient with intellectual disability or autism spectrum disorder. However in the immediate future, with the development of massive sequencing systems for application at clinical diagnosis, it will be necessary to have clinical criteria to guide studies. AIM To perform an exhaustive clinical definition of patients with pathogenic copy number variations in order to establish the clinical criteria most suggestive of this kind of genomic rearrangements. METHOD We designed and implemented a database to collect 190 different clinical variables (pregnancy, neonatal, facial dysmorphism, congenital anomalies, neurological features and family history) in a series of 246 patients, with developmental delay/intellectual disability. All cases were studied with array comparative genomic hybridization. RESULTS We have found a pathogenic genomic imbalance in 73 patients. Frequency analysis of all clinical variables showed that growth disorder, abnormalities of hands, low-set ears and hypertelorism are the more frequent features among patients with genomic rearrangements. However other clinical features, such as genital abnormalities and aggressiveness, are more specifically associated with pathogenic copy number variations in spite of their low frequencies in the overall series, yielding higher statistical significance values than other traits. CONCLUSIONS The genotype-phenotype comparison may be useful to set in the future the main clinical manifestations associated with deletions, duplications and unbalanced translocations. Theses analyses will improve the clinical indications and protocols to implement genomic arrays in the genetic study of patients with neurodevelopment disorders.
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Affiliation(s)
- Mónica Roselló
- Unidad de Genética y Diagnóstico Prenatal, Hospital Universitari i Politècnic "La Fe", Avenida Campanar 21, 46009 Valencia, Spain.
| | - Francisco Martínez
- Unidad de Genética y Diagnóstico Prenatal, Hospital Universitari i Politècnic "La Fe", Avenida Campanar 21, 46009 Valencia, Spain
| | - Sandra Monfort
- Unidad de Genética y Diagnóstico Prenatal, Hospital Universitari i Politècnic "La Fe", Avenida Campanar 21, 46009 Valencia, Spain
| | - Sonia Mayo
- Unidad de Genética y Diagnóstico Prenatal, Hospital Universitari i Politècnic "La Fe", Avenida Campanar 21, 46009 Valencia, Spain
| | - Silvestre Oltra
- Unidad de Genética y Diagnóstico Prenatal, Hospital Universitari i Politècnic "La Fe", Avenida Campanar 21, 46009 Valencia, Spain
| | - Carmen Orellana
- Unidad de Genética y Diagnóstico Prenatal, Hospital Universitari i Politècnic "La Fe", Avenida Campanar 21, 46009 Valencia, Spain
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Peredo J, Quintero-Rivera F, Bradley JP, Tu M, Dipple KM. Cleft Lip and Palate in a Patient with 5q35.2-q35.3 Microdeletion: The Importance of Chromosomal Microarray Testing in the Craniofacial Clinic. Cleft Palate Craniofac J 2013; 50:618-22. [DOI: 10.1597/11-071] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We report on a 3½-year-old African American female with a 1.63 Mb microdeletion in 5q35.2-q35.3. This deletion includes NSD1, the gene that causes Sotos syndrome. The patient has unilateral cleft lip and palate (CLP) status postrepair, an unrepaired alveolar cleft, speech delay, global developmental delay, macrocephaly, mild cerebral palsy, and a patent ductus arteriosus status postrepair. Dysmorphic features include a prominent forehead and midface hypoplasia. This is one of the first cases of CLP associated with Sotos syndrome and emphasizes the utility of chromosomal microarray analysis in patients with more than isolated CLP in the Craniofacial Clinic.
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Affiliation(s)
- Jane Peredo
- Department of Pediatrics, Mattel Children's Hospital of UCLA
| | - Fabiola Quintero-Rivera
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Clinical and Molecular Cytogenetics Laboratory, David Geffen School of Medicine at UCLA
| | - James P. Bradley
- Department of Pediatrics, Mattel Children's Hospital of UCLA, Department of Surgery, Division of Plastic and Reconstructive Surgery, David Geffen School of Medicine at UCLA
| | - Marinda Tu
- UCLA Craniofacial Clinic, Department of Pediatrics, Mattel Children's Hospital of UCLA
| | - Katrina M. Dipple
- UCLA Craniofacial Clinic, Departments of Human Genetics and Pediatrics, David Geffen School of Medicine at UCLA
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Sheth F, Andrieux J, Tewari S, Sheth H, Desai M, Kumari P, Nanavaty N, Sheth J. Chromosomal imbalance letter: Phenotypic consequences of combined deletion 8pter and duplication 15qter. Mol Cytogenet 2013; 6:24. [PMID: 23815819 PMCID: PMC3750467 DOI: 10.1186/1755-8166-6-24] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 05/10/2013] [Indexed: 11/10/2022] Open
Abstract
Exact breakpoint determination by oligonucleotide array-CGH has improved the analysis of genotype-phenotype correlations in cases with chromosome aberrations allowing a more accurate definition of relevant genes, particularly their isolated or combined impact on the phenotype in an unbalanced state. Chromosomal imbalances have been identified as one of the major causes of mental retardation and/or malformation syndromes and they are observed in ~2-5% of the cases. Here we report a female child born to non-consanguineous parents and having multiple congenital anomalies such as atrial septal defect and multiple ventricular septal defects, convergent strabismus, micropthalmia, seizures and mental retardation, with her head circumference and stature normal for her age. Cytogenetic study suggested 46,XX,add(8)(p23). Further analysis by array-CGH using 44K oligonucleotide probe confirmed deletion on 8p23.3p23.1 of 7.1 Mb and duplication involving 15q23q26.3 of 30 Mb size leading to 46,XX,der(8)t(8;15)(p23.3;q23)pat.arr 8p23.3p23.1(191,530-7,303,237)x1,15q23q26.3(72,338,961-102,35,195)x3. The unique phenotypic presentation in our case may have resulted from either loss or gain of a series of contiguous genes which may have resulted in a direct phenotypic effect and/or caused a genetic regulatory disturbance. Double segmental aberrations may have conferred phenotypic variability, as in our case, making it difficult to predict the characteristics that evolved as a result of the global gene imbalance, caused by the concomitant deletion and duplication.
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Affiliation(s)
- Frenny Sheth
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, Satellite, Ahmedabad, 380 015, India
| | - Joris Andrieux
- Laboratory of Medical Genetics, Jeanne de Flandre Hospital CHRU de Lille, Lille Cedex, France
| | - Stuti Tewari
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, Satellite, Ahmedabad, 380 015, India
| | - Harsh Sheth
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle upon Tyne, NE1 4EP, UK
| | - Manisha Desai
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, Satellite, Ahmedabad, 380 015, India
| | - Pritti Kumari
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, Satellite, Ahmedabad, 380 015, India
| | - Nidhish Nanavaty
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, Satellite, Ahmedabad, 380 015, India
| | - Jayesh Sheth
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, Satellite, Ahmedabad, 380 015, India
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Shoukier M, Klein N, Auber B, Wickert J, Schröder J, Zoll B, Burfeind P, Bartels I, Alsat EA, Lingen M, Grzmil P, Schulze S, Keyser J, Weise D, Borchers M, Hobbiebrunken E, Röbl M, Gärtner J, Brockmann K, Zirn B. Array CGH in patients with developmental delay or intellectual disability: are there phenotypic clues to pathogenic copy number variants? Clin Genet 2013; 83:53-65. [DOI: 10.1111/j.1399-0004.2012.01850.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
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Filges I, Suda L, Weber P, Datta AN, Fischer D, Dill P, Glanzmann R, Benzing J, Hegi L, Wenzel F, Huber AR, Mori AC, Miny P, Röthlisberger B. High resolution array in the clinical approach to chromosomal phenotypes. Gene 2012; 495:163-9. [PMID: 22240311 DOI: 10.1016/j.gene.2011.12.042] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 12/19/2011] [Accepted: 12/23/2011] [Indexed: 12/11/2022]
Abstract
Array genomic hybridization (AGH) has recently been implemented as a diagnostic tool for the detection of submicroscopic copy number variants (CNVs) in patients with developmental disorders. However, there is no consensus regarding the choice of the platform, the minimal resolution needed and systematic interpretation of CNVs. We report our experience in the clinical diagnostic use of high resolution AGH up to 100 kb on 131 patients with chromosomal phenotypes but previously normal karyotype. We evaluated the usefulness in our clinics and laboratories by the detection rate of causal CNVs and CNVs of unknown clinical significance and to what extent their interpretation would challenge the systematic use of high-resolution arrays in clinical application. Prioritizing phenotype-genotype correlation in our interpretation strategy to criteria previously described, we identified 33 (25.2%) potentially pathogenic aberrations. 16 aberrations were confirmed pathogenic (16.4% syndromic, 8.5% non-syndromic patients); 9 were new and individual aberrations, 3 of them were pathogenic although inherited and one is as small as approx 200 kb. 13 of 16 further CNVs of unknown significance were classified likely benign, for 3 the significance remained unclear. High resolution array allows the detection of up to 12.2% of pathogenic aberrations in a diagnostic clinical setting. Although the majority of aberrations are larger, the detection of small causal aberrations may be relevant for family counseling. The number of remaining unclear CNVs is limited. Careful phenotype-genotype correlations of the individual CNVs and clinical features are challenging but remain a hallmark for CNV interpretation.
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Dutra RL, Pieri PDC, Teixeira ACD, Honjo RS, Bertola DR, Kim CA. Detection of deletions at 7q11.23 in Williams-Beuren syndrome by polymorphic markers. Clinics (Sao Paulo) 2011; 66:959-64. [PMID: 21808859 PMCID: PMC3129970 DOI: 10.1590/s1807-59322011000600007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Accepted: 02/28/2011] [Indexed: 01/05/2023] Open
Abstract
INTRODUCTION Williams-Beuren syndrome (WBS; OMIM 194050) is caused by a hemizygous contiguous gene microdeletion at 7q11.23. Supravalvular aortic stenosis, mental retardation, overfriendliness, and ocular and renal abnormalities comprise typical symptoms in WBS. Although fluorescence in situ hybridization is widely used for diagnostic confirmation, microsatellite DNA markers are considered highly informative and easily manageable. OBJECTIVES This study aimed to test the microsatellite markers for the diagnosis of Williams-Beuren syndrome, to determine the size and parental origin of microdeletion, compare the clinical characteristics between patients with different sizes of the deletion and parental origin. METHODS We studied 97 patients with clinical diagnosis of Williams-Beuren syndrome using five microsatellite markers: D7S1870, D7S489, D7S613, D7S2476 and D7S489_A. RESULTS AND DISCUSSION Using five markers together, the result was informative in all patients. The most informative marker was D7S1870 (78.4%), followed by D7S613 (75.3%), D7S489 (70.1%) and D7S2476 (62.9%). The microdeletion was present in 84 (86.6%) patients and absent in 13 (13.4%) patients. Maternal deletions were found in 52.4% of patients and paternal deletions in 47.6% of patients. The observed size of deletions was 1.55 Mb in 76/ 84 patients (90.5%) and 1.84 Mb in 8/84 patients (9.5%). SVAS as well as ocular and urinary abnormalities were more frequent in the patients with a deletion. There were no clinical differences in relation to either the size or parental origin of the deletion. CONCLUSION Using these five selected microsatellite markers was informative in all patients, thus can be considered an alternative method for molecular diagnosis in Williams-Beuren syndrome.
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Affiliation(s)
- Roberta Lelis Dutra
- Instituto da Criança, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil.
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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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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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Miller DT, Adam MP, Aradhya S, Biesecker LG, Brothman AR, Carter NP, Church DM, Crolla JA, Eichler EE, Epstein CJ, Faucett WA, Feuk L, Friedman JM, Hamosh A, Jackson L, Kaminsky EB, Kok K, Krantz ID, Kuhn RM, Lee C, Ostell JM, Rosenberg C, Scherer SW, Spinner NB, Stavropoulos DJ, Tepperberg JH, Thorland EC, Vermeesch JR, Waggoner DJ, Watson MS, Martin CL, Ledbetter DH. Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet 2010; 86:749-64. [PMID: 20466091 PMCID: PMC2869000 DOI: 10.1016/j.ajhg.2010.04.006] [Citation(s) in RCA: 1834] [Impact Index Per Article: 131.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Revised: 04/12/2010] [Accepted: 04/19/2010] [Indexed: 12/11/2022] Open
Abstract
Chromosomal microarray (CMA) is increasingly utilized for genetic testing of individuals with unexplained developmental delay/intellectual disability (DD/ID), autism spectrum disorders (ASD), or multiple congenital anomalies (MCA). Performing CMA and G-banded karyotyping on every patient substantially increases the total cost of genetic testing. The International Standard Cytogenomic Array (ISCA) Consortium held two international workshops and conducted a literature review of 33 studies, including 21,698 patients tested by CMA. We provide an evidence-based summary of clinical cytogenetic testing comparing CMA to G-banded karyotyping with respect to technical advantages and limitations, diagnostic yield for various types of chromosomal aberrations, and issues that affect test interpretation. CMA offers a much higher diagnostic yield (15%-20%) for genetic testing of individuals with unexplained DD/ID, ASD, or MCA than a G-banded karyotype ( approximately 3%, excluding Down syndrome and other recognizable chromosomal syndromes), primarily because of its higher sensitivity for submicroscopic deletions and duplications. Truly balanced rearrangements and low-level mosaicism are generally not detectable by arrays, but these are relatively infrequent causes of abnormal phenotypes in this population (<1%). Available evidence strongly supports the use of CMA in place of G-banded karyotyping as the first-tier cytogenetic diagnostic test for patients with DD/ID, ASD, or MCA. G-banded karyotype analysis should be reserved for patients with obvious chromosomal syndromes (e.g., Down syndrome), a family history of chromosomal rearrangement, or a history of multiple miscarriages.
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Affiliation(s)
- David T. Miller
- Division of Genetics and Department of Laboratory Medicine, Children's Hospital Boston and Harvard Medical School, Boston, MA, USA
| | - Margaret P. Adam
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Leslie G. Biesecker
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Arthur R. Brothman
- Department of Pediatrics, Human Genetics, Pathology and ARUP Laboratories, University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | - Deanna M. Church
- National Center for Biotechnology Information, Bethesda, MD, USA
| | - John A. Crolla
- National Genetics Reference Laboratory (Wessex), Salisbury UK
| | - Evan E. Eichler
- Department of Genome Sciences and Howard Hughes Medical Institute, University of Washington School of Medicine, Seattle, WA, USA
| | - Charles J. Epstein
- Institute for Human Genetics and Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - W. Andrew Faucett
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Lars Feuk
- Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Jan M. Friedman
- Department of Medical Genetics, University of British Columbia, and Child & Family Research Institute, Vancouver, British Columbia, Canada
| | - Ada Hamosh
- Department of Pediatrics and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Laird Jackson
- Department of Obstetrics and Gynecology, Drexel University College of Medicine and Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Erin B. Kaminsky
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Klaas Kok
- Department of Genetics, University Medical Centre Groningen, University of Groningen, The Netherlands
| | - Ian D. Krantz
- Department of Pediatrics/Human Genetics, The Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Robert M. Kuhn
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Charles Lee
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - James M. Ostell
- National Center for Biotechnology Information, Bethesda, MD, USA
| | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, University Sao Paulo, Brazil
| | - Stephen W. Scherer
- The Centre for Applied Genomics and Program in Genetics and Genetic Biology, The Hospital for Sick Children and Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Nancy B. Spinner
- Department of Pediatrics/Human Genetics, The Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Dimitri J. Stavropoulos
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Erik C. Thorland
- Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Darrel J. Waggoner
- Department of Human Genetics and Pediatrics, University of Chicago, Chicago, IL, USA
| | | | - Christa Lese Martin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - David H. Ledbetter
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
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14
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Ahn JW, Mann K, Walsh S, Shehab M, Hoang S, Docherty Z, Mohammed S, Mackie Ogilvie C. Validation and implementation of array comparative genomic hybridisation as a first line test in place of postnatal karyotyping for genome imbalance. Mol Cytogenet 2010; 3:9. [PMID: 20398301 PMCID: PMC2885406 DOI: 10.1186/1755-8166-3-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Accepted: 04/15/2010] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Several studies have demonstrated that array comparative genomic hybridisation (CGH) for genome-wide imbalance provides a substantial increase in diagnostic yield for patients traditionally referred for karyotyping by G-banded chromosome analysis. The purpose of this study was to demonstrate the feasibility of and strategies for, the use of array CGH in place of karyotyping for genome imbalance, and to report on the results of the implementation of this approach. RESULTS Following a validation period, an oligoarray platform was chosen. In order to minimise costs and increase efficiency, a patient/patient hybridisation strategy was used, and analysis criteria were set to optimise detection of pathogenic imbalance. A customised database application with direct links to a number of online resources was developed to allow efficient management and tracking of patient samples and facilitate interpretation of results. Following introduction into our routine diagnostic service for patients with suspected genome imbalance, array CGH as a follow-on test for patients with normal karyotypes (n = 1245) and as a first-line test (n = 1169) gave imbalance detection rates of 26% and 22% respectively (excluding common, benign variants). At least 89% of the abnormalities detected by first line testing would not have been detected by standard karyotype analysis. The average reporting time for first-line tests was 25 days from receipt of sample. CONCLUSIONS Array CGH can be used in a diagnostic service setting in place of G-banded chromosome analysis, providing a more comprehensive and objective test for patients with suspected genome imbalance. The increase in consumable costs can be minimised by employing appropriate hybridisation strategies; the use of robotics and a customised database application to process multiple samples reduces staffing costs and streamlines analysis, interpretation and reporting of results. Array CGH provides a substantially higher diagnostic yield than G-banded chromosome analysis, thereby alleviating the burden of further clinical investigations.
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Affiliation(s)
- Joo Wook Ahn
- Cytogenetics Department, Guy's & St Thomas' NHS Foundation Trust, London SE1 9RT, UK.
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15
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Rosenfeld JA, Ballif BC, Martin DM, Aylsworth AS, Bejjani BA, Torchia BS, Shaffer LG. Clinical characterization of individuals with deletions of genes in holoprosencephaly pathways by aCGH refines the phenotypic spectrum of HPE. Hum Genet 2010; 127:421-40. [PMID: 20066439 DOI: 10.1007/s00439-009-0778-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Accepted: 12/14/2009] [Indexed: 12/31/2022]
Abstract
Holoprosencephaly (HPE) is the most common developmental forebrain anomaly in humans. Both environmental and genetic factors have been identified to play a role in the HPE phenotype. Previous studies of the genetic bases of HPE have taken a phenotype-first approach by examining groups of patients with HPE for specific mutations or deletions in known or candidate HPE genes. In this study, we characterized the presence or absence of HPE or a microform in 136 individuals in which microarray-based comparative genomic hybridization (aCGH) identified a deletion of one of 35 HPE loci. Frank holoprosencephaly was present in 11 individuals with deletions of one of the common HPE genes SHH, ZIC2, SIX3, and TGIF1, in one individual with a deletion of the HPE8 locus at 14q13, and in one individual with a deletion of FGF8, whereas deletions of other HPE loci and candidate genes (FOXA2 and LRP2) expressed microforms of HPE. Although individuals with deletions of other HPE candidates (DISP1, LSS, HHIP, SMO, BMP4, CDON, CDC42, ACVR2A, OTX2, and WIF1) had clinically significant features, none had frank HPE or a microform. A search for significant aCGH findings in individuals referred for testing for HPE revealed a novel association of a duplication involving GSK3B at 3q13.33 with HPE or a microform, seen in two unrelated individuals.
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16
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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] [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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17
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Array CGH in patients with learning disability (mental retardation) and congenital anomalies: updated systematic review and meta-analysis of 19 studies and 13,926 subjects. Genet Med 2009; 11:139-46. [PMID: 19367186 DOI: 10.1097/gim.0b013e318194ee8f] [Citation(s) in RCA: 145] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Array-based comparative genomic hybridization is being increasingly used in patients with learning disability (mental retardation) and congenital anomalies. In this article, we update our previous meta-analysis evaluating the diagnostic and false-positive yields of this technology. An updated systematic review and meta-analysis was conducted investigating patients with learning disability and congenital anomalies in whom conventional cytogenetic analyses have proven negative. Nineteen studies (13,926 patients) were included of which 12 studies (13,464 patients) were published since our previous analysis. The overall diagnostic yield of causal abnormalities was 10% (95% confidence interval: 8-12%). The overall number needed to test to identify an extra causal abnormality was 10 (95% confidence interval: 8-13). The overall false-positive yield of noncausal abnormalities was 7% (95% confidence interval: 5-10%). This updated meta-analysis provides new evidence to support the use of array-based comparative genomic hybridization in investigating patients with learning disability and congenital anomalies in whom conventional cytogenetic tests have proven negative. However, given that this technology also identifies false positives at a similar rate to causal variants, caution in clinical practice should be advised.
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18
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Shaffer LG, Bejjani BA. Using microarray-based molecular cytogenetic methods to identify chromosome abnormalities. Pediatr Ann 2009; 38:440-7. [PMID: 19711882 DOI: 10.3928/00904481-20090723-08] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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19
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Migliaccio G, Sanchez M, Leblanc A, Masiello F, Tirelli V, Migliaccio AR, Najfeld V, Whitsett C. Long-term storage does not alter functionality of in vitro generated human erythroblasts: implications for ex vivo generated erythroid transfusion products. Transfusion 2009; 49:2668-79. [PMID: 19659677 DOI: 10.1111/j.1537-2995.2009.02329.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND Cultured human erythroid cells derived in vitro may represent alternative transfusion products. It is unknown, however, if these ex vivo expanded erythroid cells remain functional or develop genetic abnormalities after storage. STUDY DESIGN AND METHODS Using mononuclear cells from four adult blood donors, erythroblasts were generated ex vivo in expansion cultures supplemented with stem cell factor, interleukin-3, erythropoietin (EPO), dexamethasone, and estradiol. The viability and in vitro function of freshly expanded or short (1-2 months)- and long (8 years)-term-stored erythroblasts cryopreserved in dimethyl sulfoxide were compared. Erythroblast function was defined as ability to proliferate in expansion media and mature in response to EPO. Cell number was determined manually and expressed as fold increase. Viability was assessed by trypan blue and propidium iodide exclusion. Maturation was evaluated by morphologic analyses and CD36/CD235a expression profiling. Cytogenetic evaluation included karyotype and multicolor fluorescence in situ hybridization analyses. RESULTS Equivalent numbers (>80%) of erythroblasts were viable after short- and long-term storage. Freshly expanded and short- and long-term-stored erythroblasts equally doubled in number (fold increase, 2.4) retaining an immature phenotype (23% of the cells were CD36(high)CD235a(neg)) when cultured for 4 days under expansion conditions. The numbers of freshly expanded and short-term-stored erythroblasts that matured when exposed for 4 days to EPO were also similar (approx. 22% of the cells became CD36(neg)CD235a(high)). In spite of the massive amplification, ex vivo generated erythroblasts demonstrated a normal (46,XY) karyotype with no obvious genomic rearrangements. CONCLUSION Ex vivo expanded erythroblasts remain functional and genetically normal after long-term storage.
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Affiliation(s)
- Giovanni Migliaccio
- Division of Hematology and Oncology, Tisch Cancer Institute, Mount Sinai School of Medicine, New York, New York, USA
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20
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Hochstenbach R, van Binsbergen E, Engelen J, Nieuwint A, Polstra A, Poddighe P, Ruivenkamp C, Sikkema-Raddatz B, Smeets D, Poot M. Array analysis and karyotyping: Workflow consequences based on a retrospective study of 36,325 patients with idiopathic developmental delay in the Netherlands. Eur J Med Genet 2009; 52:161-9. [DOI: 10.1016/j.ejmg.2009.03.015] [Citation(s) in RCA: 147] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2009] [Accepted: 03/27/2009] [Indexed: 12/20/2022]
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Abstract
Mental retardation--known more commonly nowadays as intellectual disability--is a severe neurological condition affecting up to 3% of the general population. As a result of the analysis of familial cases and recent advances in clinical genetic testing, great strides have been made in our understanding of the genetic etiologies of mental retardation. Nonetheless, no treatment is currently clinically available to patients suffering from intellectual disability. Several animal models have been used in the study of memory and cognition. Established paradigms in Drosophila have recently captured cognitive defects in fly mutants for orthologs of genes involved in human intellectual disability. We review here three protocols designed to understand the molecular genetic basis of learning and memory in Drosophila and the genes identified so far with relation to mental retardation. In addition, we explore the mental retardation genes for which evidence of neuronal dysfunction other than memory has been established in Drosophila. Finally, we summarize the findings in Drosophila for mental retardation genes for which no neuronal information is yet available. All in all, this review illustrates the impressive overlap between genes identified in human mental retardation and genes involved in physiological learning and memory.
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Affiliation(s)
- François V Bolduc
- Watson School of Biological Sciences, Cold Spring Harbor, New York, USA
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22
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Shao L, Shaw CA, Lu XY, Sahoo T, Bacino CA, Lalani SR, Stankiewicz P, Yatsenko SA, Li Y, Neill S, Pursley AN, Chinault AC, Patel A, Beaudet AL, Lupski JR, Cheung SW. Identification of chromosome abnormalities in subtelomeric regions by microarray analysis: a study of 5,380 cases. Am J Med Genet A 2008; 146A:2242-51. [PMID: 18663743 DOI: 10.1002/ajmg.a.32399] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Subtelomeric imbalances are a significant cause of congenital disorders. Screening for these abnormalities has traditionally utilized GTG-banding analysis, fluorescence in situ hybridization (FISH) assays, and multiplex ligation-dependent probe amplification. Microarray-based comparative genomic hybridization (array-CGH) is a relatively new technology that can identify microscopic and submicroscopic chromosomal imbalances. It has been proposed that an array with extended coverage at subtelomeric regions could characterize subtelomeric aberrations more efficiently in a single experiment. The targeted arrays for chromosome microarray analysis (CMA), developed by Baylor College of Medicine, have on average 12 BAC/PAC clones covering 10 Mb of each of the 41 subtelomeric regions. We screened 5,380 consecutive clinical patients using CMA. The most common reasons for referral included developmental delay (DD), and/or mental retardation (MR), dysmorphic features (DF), multiple congenital anomalies (MCA), seizure disorders (SD), and autistic, or other behavioral abnormalities. We found pathogenic rearrangements at subtelomeric regions in 236 patients (4.4%). Among these patients, 103 had a deletion, 58 had a duplication, 44 had an unbalanced translocation, and 31 had a complex rearrangement. The detection rates varied among patients with a normal karyotype analysis (2.98%), with an abnormal karyotype analysis (43.4%), and with an unavailable or no karyotype analysis (3.16%). Six patients out of 278 with a prior normal subtelomere-FISH analysis showed an abnormality including an interstitial deletion, two terminal deletions, two interstitial duplications, and a terminal duplication. In conclusion, genomic imbalances at subtelomeric regions contribute significantly to congenital disorders. Targeted array-CGH with extended coverage (up to 10 Mb) of subtelomeric regions will enhance the detection of subtelomeric imbalances, especially for submicroscopic imbalances.
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Affiliation(s)
- Lina Shao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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23
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Ropers HH. Genetics of intellectual disability. Curr Opin Genet Dev 2008; 18:241-50. [DOI: 10.1016/j.gde.2008.07.008] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2008] [Accepted: 07/15/2008] [Indexed: 11/16/2022]
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