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Meerschaut I, Vergult S, Dheedene A, Menten B, De Groote K, De Wilde H, Muiño Mosquera L, Panzer J, Vandekerckhove K, Coucke PJ, De Wolf D, Callewaert B. A Reassessment of Copy Number Variations in Congenital Heart Defects: Picturing the Whole Genome. Genes (Basel) 2021; 12:genes12071048. [PMID: 34356064 PMCID: PMC8304049 DOI: 10.3390/genes12071048] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/03/2021] [Accepted: 07/05/2021] [Indexed: 11/17/2022] Open
Abstract
Copy number variations (CNVs) can modulate phenotypes by affecting protein-coding sequences directly or through interference of gene expression. Recent studies in cancer and limb defects pinpointed the relevance of non-coding gene regulatory elements such as long non-coding RNAs (lncRNAs) and topologically associated domain (TAD)-related gene-enhancer interactions. The contribution of such non-coding elements is largely unexplored in congenital heart defects (CHD). We performed a retrospective analysis of CNVs reported in a cohort of 270 CHD patients. We reviewed the diagnostic yield of pathogenic CNVs, and performed a comprehensive reassessment of 138 CNVs of unknown significance (CNV-US), evaluating protein-coding genes, lncRNA genes, and potential interferences with TAD-related gene-enhancer interactions. Fifty-two of the 138 CNV-US may relate to CHD, revealing three candidate CHD regions, 19 candidate CHD genes, 80 lncRNA genes of interest, and six potentially CHD-related TAD interferences. Our study thus indicates a potential relevance of non-coding gene regulatory elements in CNV-related CHD pathogenesis. Shortcomings in our current knowledge on genomic variation call for continuous reporting of CNV-US in international databases, careful patient counseling, and additional functional studies to confirm these preliminary findings.
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Affiliation(s)
- Ilse Meerschaut
- Center for Medical Genetics, Ghent University Hospital, Belgium and Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium; (I.M.); (S.V.); (A.D.); (B.M.); (L.M.M.); (P.J.C.)
- Department of Pediatric Cardiology, Ghent University Hospital, 9000 Ghent, Belgium; (K.D.G.); (H.D.W.); (J.P.); (K.V.); (D.D.W.)
| | - Sarah Vergult
- Center for Medical Genetics, Ghent University Hospital, Belgium and Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium; (I.M.); (S.V.); (A.D.); (B.M.); (L.M.M.); (P.J.C.)
| | - Annelies Dheedene
- Center for Medical Genetics, Ghent University Hospital, Belgium and Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium; (I.M.); (S.V.); (A.D.); (B.M.); (L.M.M.); (P.J.C.)
| | - Björn Menten
- Center for Medical Genetics, Ghent University Hospital, Belgium and Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium; (I.M.); (S.V.); (A.D.); (B.M.); (L.M.M.); (P.J.C.)
| | - Katya De Groote
- Department of Pediatric Cardiology, Ghent University Hospital, 9000 Ghent, Belgium; (K.D.G.); (H.D.W.); (J.P.); (K.V.); (D.D.W.)
| | - Hans De Wilde
- Department of Pediatric Cardiology, Ghent University Hospital, 9000 Ghent, Belgium; (K.D.G.); (H.D.W.); (J.P.); (K.V.); (D.D.W.)
| | - Laura Muiño Mosquera
- Center for Medical Genetics, Ghent University Hospital, Belgium and Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium; (I.M.); (S.V.); (A.D.); (B.M.); (L.M.M.); (P.J.C.)
- Department of Pediatric Cardiology, Ghent University Hospital, 9000 Ghent, Belgium; (K.D.G.); (H.D.W.); (J.P.); (K.V.); (D.D.W.)
| | - Joseph Panzer
- Department of Pediatric Cardiology, Ghent University Hospital, 9000 Ghent, Belgium; (K.D.G.); (H.D.W.); (J.P.); (K.V.); (D.D.W.)
| | - Kristof Vandekerckhove
- Department of Pediatric Cardiology, Ghent University Hospital, 9000 Ghent, Belgium; (K.D.G.); (H.D.W.); (J.P.); (K.V.); (D.D.W.)
| | - Paul J. Coucke
- Center for Medical Genetics, Ghent University Hospital, Belgium and Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium; (I.M.); (S.V.); (A.D.); (B.M.); (L.M.M.); (P.J.C.)
| | - Daniël De Wolf
- Department of Pediatric Cardiology, Ghent University Hospital, 9000 Ghent, Belgium; (K.D.G.); (H.D.W.); (J.P.); (K.V.); (D.D.W.)
- Department of Pediatric Cardiology, Brussels University Hospital, 1090 Brussels, Belgium
| | - Bert Callewaert
- Center for Medical Genetics, Ghent University Hospital, Belgium and Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium; (I.M.); (S.V.); (A.D.); (B.M.); (L.M.M.); (P.J.C.)
- Correspondence: ; Tel.: +32-9-332-3603
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Comparison of the diagnostic yield of aCGH and genome-wide sequencing across different neurodevelopmental disorders. NPJ Genom Med 2021; 6:25. [PMID: 33767182 PMCID: PMC7994713 DOI: 10.1038/s41525-021-00188-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 02/26/2021] [Indexed: 02/07/2023] Open
Abstract
Most consensus recommendations for the genetic diagnosis of neurodevelopmental disorders (NDDs) do not include the use of next generation sequencing (NGS) and are still based on chromosomal microarrays, such as comparative genomic hybridization array (aCGH). This study compares the diagnostic yield obtained by aCGH and clinical exome sequencing in NDD globally and its spectrum of disorders. To that end, 1412 patients clinically diagnosed with NDDs and studied with aCGH were classified into phenotype categories: global developmental delay/intellectual disability (GDD/ID); autism spectrum disorder (ASD); and other NDDs. These categories were further subclassified based on the most frequent accompanying signs and symptoms into isolated forms, forms with epilepsy; forms with micro/macrocephaly and syndromic forms. Two hundred and forty-five patients of the 1412 were subjected to clinical exome sequencing. Diagnostic yield of aCGH and clinical exome sequencing, expressed as the number of solved cases, was compared for each phenotype category and subcategory. Clinical exome sequencing was superior than aCGH for all cases except for isolated ASD, with no additional cases solved by NGS. Globally, clinical exome sequencing solved 20% of cases (versus 5.7% by aCGH) and the diagnostic yield was highest for all forms of GDD/ID and lowest for Other NDDs (7.1% versus 1.4% by aCGH) and ASD (6.1% versus 3% by aCGH). In the majority of cases, diagnostic yield was higher in the phenotype subcategories than in the mother category. These results suggest that NGS could be used as a first-tier test in the diagnostic algorithm of all NDDs followed by aCGH when necessary.
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Godoy VCSMD, Bellucco FT, Colovati M, Oliveira-Junior HRD, Moysés-Oliveira M, Melaragno MI. Copy number variation (CNV) identification, interpretation, and database from Brazilian patients. Genet Mol Biol 2020; 43:e20190218. [PMID: 33306777 PMCID: PMC7783508 DOI: 10.1590/1678-4685-gmb-2019-0218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 09/25/2020] [Indexed: 11/22/2022] Open
Abstract
Copy number variations (CNVs) constitute an important class of variation in the
human genome and the interpretation of their pathogenicity considering different
frequencies across populations is still a challenge for geneticists. Since the
CNV databases are predominantly composed of European and non-admixed
individuals, and Brazilian genetic constitution is admixed and ethnically
diverse, diagnostic screenings on Brazilian variants are greatly difficulted by
the lack of populational references. We analyzed a clinical sample of 268
Brazilian individuals, including patients with neurodevelopment disorders and/or
congenital malformations. The pathogenicity of CNVs was classified according to
their gene content and overlap with known benign and pathogenic variants. A
total of 1,504 autosomal CNVs (1,207 gains and 297 losses) were classified as
benign (92.9%), likely benign (1.6%), VUS (2.6%), likely pathogenic (0.2%) and
pathogenic (2.7%). Some of the CNVs were recurrent and with frequency increased
in our sample, when compared to populational open resources of structural
variants: 14q32.33, 22q11.22, 1q21.1, and 1p36.32 gains. Thus, these highly
recurrent CNVs classified as likely benign or VUS were considered non-pathogenic
in our Brazilian sample. This study shows the relevance of introducing CNV data
from diverse cohorts to improve on the interpretation of clinical impact of
genomic variations.
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Affiliation(s)
| | - Fernanda Teixeira Bellucco
- Universidade Federal de São Paulo, Departamento de Morfologia e Genética, Disciplina de Genética, São Paulo, SP, Brazil
| | - Mileny Colovati
- Universidade Federal de São Paulo, Departamento de Morfologia e Genética, Disciplina de Genética, São Paulo, SP, Brazil
| | | | - Mariana Moysés-Oliveira
- Universidade Federal de São Paulo, Departamento de Morfologia e Genética, Disciplina de Genética, São Paulo, SP, Brazil
| | - Maria Isabel Melaragno
- Universidade Federal de São Paulo, Departamento de Morfologia e Genética, Disciplina de Genética, São Paulo, SP, Brazil
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Suzuki H, Yamada M, Uehara T, Takenouchi T, Kosaki K. Parallel detection of single nucleotide variants and copy number variants with exome analysis: Validation in a cohort of 700 undiagnosed patients. Am J Med Genet A 2020; 182:2529-2532. [PMID: 32779332 PMCID: PMC7689761 DOI: 10.1002/ajmg.a.61822] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/22/2020] [Accepted: 07/25/2020] [Indexed: 12/23/2022]
Abstract
Copy number variants (CNVs) are significant causes of rare and undiagnosed diseases. Parallel detection of single nucleotide variants (SNVs) and CNVs with exome analysis, if feasible, would shorten the diagnostic closure in a timely manner. We validated such “parallel” approach through a cohort study of 791 undiagnosed patients. In addition to routine exome analysis, we applied an innovative algorithm EXCAVATOR2 which enhances sensitivity by paradoxically exploiting read depth data that covers nonexonic regions where baits were not originally intended to hybridize. About 48 patients had copy number variations, 42 deletions, and 6 duplications with a resolution of 0.51–14.7 mega base pairs. Importantly from a clinical standpoint, we identified three patients with “dual diagnosis” due to concurrent pathogenic CNV and SNV. We suggest “hitting two birds with one stone” approach to exome data is an efficient strategy in deciphering undiagnosed patients and may well be considered as a first‐tier genetic test.
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Affiliation(s)
- Hisato Suzuki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Mamiko Yamada
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Tomoko Uehara
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Toshiki Takenouchi
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
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de Souza LC, Dos Santos AP, Sgardioli IC, Viguetti-Campos NL, Marques Prota JR, de Oliveira-Sobrinho RP, Vieira TP, Gil-da-Silva-Lopes VL. Phenotype comparison among individuals with developmental delay/intellectual disability with or without genomic imbalances. JOURNAL OF INTELLECTUAL DISABILITY RESEARCH : JIDR 2019; 63:1379-1389. [PMID: 30900361 DOI: 10.1111/jir.12615] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 02/18/2019] [Accepted: 02/18/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND The chromosomal microarray analysis (CMA) is recommended as a first-tier test for individuals with developmental delay (DD)/intellectual disability (ID) and/or multiple congenital anomalies. However, owing to high costs, this technique is not widely performed for diagnostic purposes in several countries. The aim of this study was to identify clinical features that could favour the hypothesis of genomic imbalances (GIs) in individuals with DD/ID. METHODS The sample consisted of 63 individuals, and all of them underwent a detailed evaluation by a clinical geneticist and were investigated by the CMA. They were divided into two groups. Group A composed of 20 individuals with pathogenic copy number variants (CNVs); and group B composed of 43 individuals with normal CMA results or variants of uncertain clinical significance (VUS). RESULTS Pathogenic GIs were found in 20 cases (32%), including 11 individuals with an abnormal karyotype, VUS was found in five individuals (8%) and the results were normal in 38 individuals (60%). Major anomalies were found in 15/20 (75%) individuals in group A against 35/43 (81%) in group B. Dysmorphisms (≥5) were found in 17/20 (85%) in group A and 41/43 (95%) in group B. The most frequent major anomalies detected in group A were congenital heart disease, epilepsy and renal malformation; and in group B, they were malformations of central nervous system, congenital heart disease, microcephaly, epilepsy and hearing impairment. There was no significant statistical difference among the frequencies in groups A and B. CONCLUSIONS Evidences point that every individual with DD/ID, with no specific clinical suspicion, should have screening for GIs as a first-tier test, regardless of the presence or absence of additional major anomalies or dysmorphisms. Future studies with a similar design would be helpful, especially in countries where the access to new technologies is still limited.
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Affiliation(s)
- L C de Souza
- Department of Medical Genetics, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - A P Dos Santos
- Department of Medical Genetics, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - I C Sgardioli
- Department of Medical Genetics, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - N L Viguetti-Campos
- Department of Medical Genetics, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - J R Marques Prota
- Department of Medical Genetics, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - R P de Oliveira-Sobrinho
- Department of Medical Genetics, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - T P Vieira
- Department of Medical Genetics, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - V L Gil-da-Silva-Lopes
- Department of Medical Genetics, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
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Maini I, Ivanovski I, Djuric O, Caraffi SG, Errichiello E, Marinelli M, Franchi F, Bizzarri V, Rosato S, Pollazzon M, Gelmini C, Malacarne M, Fusco C, Gargano G, Bernasconi S, Zuffardi O, Garavelli L. Prematurity, ventricular septal defect and dysmorphisms are independent predictors of pathogenic copy number variants: a retrospective study on array-CGH results and phenotypical features of 293 children with neurodevelopmental disorders and/or multiple congenital anomalies. Ital J Pediatr 2018; 44:34. [PMID: 29523172 PMCID: PMC5845186 DOI: 10.1186/s13052-018-0467-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 02/21/2018] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Since 2010, array-CGH (aCGH) has been the first-tier test in the diagnostic approach of children with neurodevelopmental disorders (NDD) or multiple congenital anomalies (MCA) of unknown origin. Its broad application led to the detection of numerous variants of uncertain clinical significance (VOUS). How to appropriately interpret aCGH results represents a challenge for the clinician. METHOD We present a retrospective study on 293 patients with age range 1 month - 29 years (median 7 years) with NDD and/or MCA and/or dysmorphisms, investigated through aCGH between 2005 and 2016. The aim of the study was to analyze clinical and molecular cytogenetic data in order to identify what elements could be useful to interpret unknown or poorly described aberrations. Comparison of phenotype and cytogenetic characteristics through univariate analysis and multivariate logistic regression was performed. RESULTS Copy number variations (CNVs) with a frequency < 1% were detected in 225 patients of the total sample, while 68 patients presented only variants with higher frequency (heterozygous deletions or amplification) and were considered to have negative aCGH. Proved pathogenic CNVs were detected in 70 patients (20.6%). Delayed psychomotor development, intellectual disability, intrauterine growth retardation (IUGR), prematurity, congenital heart disease, cerebral malformations and dysmorphisms correlated to reported pathogenic CNVs. Prematurity, ventricular septal defect and dysmorphisms remained significant predictors of pathogenic CNVs in the multivariate logistic model whereas abnormal EEG and limb dysmorphisms were mainly detected in the group with likely pathogenic VOUS. A flow-chart regarding the care for patients with NDD and/or MCA and/or dysmorphisms and the interpretation of aCGH has been made on the basis of the data inferred from this study and literature. CONCLUSION Our work contributes to make the investigative process of CNVs more informative and suggests possible directions in aCGH interpretation and phenotype correlation.
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MESH Headings
- Abnormalities, Multiple/diagnosis
- Abnormalities, Multiple/genetics
- Adolescent
- Adult
- Child
- Child, Preschool
- Comparative Genomic Hybridization/methods
- DNA Copy Number Variations
- Facies
- Female
- Genetic Testing
- Heart Septal Defects, Ventricular/diagnosis
- Heart Septal Defects, Ventricular/genetics
- Humans
- Infant
- Infant, Newborn
- Infant, Premature, Diseases/diagnosis
- Infant, Premature, Diseases/genetics
- Male
- Muscular Atrophy/diagnosis
- Muscular Atrophy/genetics
- Neurodevelopmental Disorders/diagnosis
- Neurodevelopmental Disorders/genetics
- Phenotype
- Retrospective Studies
- Young Adult
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Affiliation(s)
- I. Maini
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
- Child Neuropsychiatry Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - I. Ivanovski
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
- Department of Surgical, Medical, Dental and Morphological Sciences with Interest in Transplant, Oncology and Regenerative Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - O. Djuric
- Institute of Epidemiology, School of Medicine, University of Belgrade, Belgrade, Serbia
| | - S. G. Caraffi
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - E. Errichiello
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - M. Marinelli
- Laboratory of Genetics, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - F. Franchi
- Laboratory of Genetics, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - V. Bizzarri
- Laboratory of Genetics, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - S. Rosato
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - M. Pollazzon
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - C. Gelmini
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - M. Malacarne
- Division of Medical Genetics, Galliera Hospital, Genoa, Italy
| | - C. Fusco
- Child Neuropsychiatry Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - G. Gargano
- Neonatal Intensive Care Unit (NICU), Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - S. Bernasconi
- Former Director Pediatric Department, University of Parma, Parma, Italy
| | - O. Zuffardi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - L. Garavelli
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
- Santa Maria Nuova Hospital, viale Risorgimento 80, 42123 Reggio Emilia, Italy
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da Silva HPV, Oliveira GHDM, Ururahy MAG, Bezerra JF, de Souza KSC, Bortolin RH, Luchessi AD, Silbiger VN, Lima VMGDM, Leite GCP, Brito MEF, Ribeiro EM, Gil-da-Silva-Lopes VL, de Rezende AA. Application of high-resolution array platform for genome-wide copy number variation analysis in patients with nonsyndromic cleft lip and palate. J Clin Lab Anal 2018; 32:e22428. [PMID: 29512191 DOI: 10.1002/jcla.22428] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 02/09/2018] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Although more than 14 loci may be involved in the development of nonsyndromic cleft lip and palate (NSCLP), the etiology has not been fully elucidated due to genetic and environmental risk factor interactions. Despite advances in identifying genes associated with the NSCLP development using traditional genetic mapping strategies of candidate genes, genome-wide studies, and epidemiologic and linkage analysis, microarray techniques have become important complementary tools in the search for potential causative oral clefts genes in genetic studies. Microarray hybridization enables scanning of the whole genome and detecting copy number variants (CNVs). Although common benign CNVs are often smaller, with sizes smaller than 20 kb, here we reveal small exonic CNVs based on the importance of the encompassed genes in cleft lip and palate phenotype. METHODS Microarray hybridization analysis was performed in 15 individuals with NSCLP. RESULTS We identified 11 exonic CNVs affecting at least one exon of the candidate genes. Thirteen candidate genes (COL11A1-1p21; IRF6-1q32.3; MSX1-4p16.2; TERT-5p15.33; MIR4457-5p15.33; CLPTM1L-5p15.33; ESR1-6q25.1; GLI3-7p13; FGFR-8p11.23; TBX1-22q11.21; OFD-Xp22; PHF8-Xp11.22; and FLNA-Xq28) overlapped with the CNVs identified. CONCLUSIONS Considering the importance to NSCLP, the microdeletions that encompass MSX1, microduplications over TERT, MIR4457, CLPTM1L, and microduplication of PHF8 have been identified as small CNVs related to sequence variants associated with oral clefts susceptibility. Our findings represent a preliminary study on the clinical significance of small CNVs and their relationship with genes implicated in NSCLP.
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Affiliation(s)
| | | | | | - João Felipe Bezerra
- Department of Clinical and Toxicological Analyses, Federal University of Rio Grande do Norte, Natal, Brazil
| | | | - Raul Hernandes Bortolin
- Department of Clinical and Toxicological Analyses, Federal University of Rio Grande do Norte, Natal, Brazil
| | - André Ducati Luchessi
- Department of Clinical and Toxicological Analyses, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Vivian Nogueira Silbiger
- Department of Clinical and Toxicological Analyses, Federal University of Rio Grande do Norte, Natal, Brazil
| | | | | | | | | | | | - Adriana Augusto de Rezende
- Department of Clinical and Toxicological Analyses, Federal University of Rio Grande do Norte, Natal, Brazil
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Nowakowska B. Clinical interpretation of copy number variants in the human genome. J Appl Genet 2017; 58:449-457. [PMID: 28963714 PMCID: PMC5655614 DOI: 10.1007/s13353-017-0407-4] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 08/31/2017] [Accepted: 09/05/2017] [Indexed: 12/15/2022]
Abstract
Molecular methods, by which copy number variants (CNVs) detection is available, have been gradually introduced into routine diagnostics over the last 15 years. Despite this, some CNVs continue to be a huge challenge when it comes to clinical interpretation. CNVs are an important source of normal and pathogenic variants, but, in many cases, their impact on human health depends on factors that are not yet known. Therefore, perception of their clinical consequences can change over time, as our knowledge grows. This review summarises guidelines that facilitate correct classification of identified changes and discusses difficulties with the interpretation of rare, small CNVs.
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Affiliation(s)
- Beata Nowakowska
- Department of Medical Genetics, Institute of Mother and Child, Kasprzaka 17a, 01-211, Warsaw, Poland.
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Wu XL, Li R, Fu F, Pan M, Han J, Yang X, Zhang YL, Li FT, Liao C. Chromosome microarray analysis in the investigation of children with congenital heart disease. BMC Pediatr 2017; 17:117. [PMID: 28472932 PMCID: PMC5418813 DOI: 10.1186/s12887-017-0863-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/11/2017] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Our study was aimed to explore the clinical implication of chromosome microarray analysis (CMA) in genetically etiological diagnosis of children with congenital heart disease (CHD). METHODS A total of 104 children with CHD with or without multiple congenital anomalies (MCA) or intellectual disabilities/developmental delay (ID/DD) but normal karyotype were investigated using Affymetrix CytoScan HD array. RESULT Pathogenic copy number variations (PCNVs) were identified in 29 children (27.9%). The detection rates in children with simple CHD and complex CHD were 31.1% (19/61) and 23.2% (10/43), respectively. The detection rates of PCNVs were 17.9% (7/39), 20% (5/25), 63.2% (12/19) and 23.8% (5/21) in isolated CHD, CHD plus MCA, CHD plus ID/DD, CHD plus MCA and ID/DD, respectively. The PCNVs rate of CHD plus ID/DD was significantly higher than that of isolated CHD. Two genomic loci including 15q11.2 deletion and 1q43-q44 deletion were considered as CHD locus. The DVL1, SKI, STIM1, CTNNA3 and PLN were identified as candidate genes associated with CHD phenotypes. CONCLUSION CMA can increase the diagnostic rate and improve the etiological diagnosis in children with CHD. We suggest CMA as a first-tier test in children with CHD, especially in children with CHD plus ID/DD.
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Affiliation(s)
- Xiao-li Wu
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangdong, China
| | - Ru Li
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangdong, China
| | - Fang Fu
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangdong, China
| | - Min Pan
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangdong, China
| | - Jin Han
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangdong, China
| | - Xin Yang
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangdong, China
| | - Yong-ling Zhang
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangdong, China
| | - Fa-tao Li
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangdong, China
| | - Can Liao
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangdong, China
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10
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Hollenbeck D, Williams CL, Drazba K, Descartes M, Korf BR, Rutledge SL, Lose EJ, Robin NH, Carroll AJ, Mikhail FM. Clinical relevance of small copy-number variants in chromosomal microarray clinical testing. Genet Med 2016; 19:377-385. [PMID: 27632688 DOI: 10.1038/gim.2016.132] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 07/21/2016] [Indexed: 11/09/2022] Open
Abstract
PURPOSE The 2010 consensus statement on diagnostic chromosomal microarray (CMA) testing recommended an array resolution ≥400 kb throughout the genome as a balance of analytical and clinical sensitivity. In spite of the clear evidence for pathogenicity of large copy-number variants (CNVs) in neurodevelopmental disorders and/or congenital anomalies, the significance of small, nonrecurrent CNVs (<500 kb) has not been well established in a clinical setting. METHODS We investigated the clinical significance of all nonpolymorphic small, nonrecurrent CNVs (<500 kb) in patients referred for CMA clinical testing over a period of 6 years, from 2009 to 2014 (a total of 4,417 patients). We excluded from our study patients with benign or likely benign CNVs and patients with only recurrent microdeletions/microduplications <500 kb. RESULTS In total, 383 patients (8.67%) were found to carry at least one small, nonrecurrent CNV, of whom 176 patients (3.98%) had one small CNV classified as a variant of uncertain significance (VUS), 45 (1.02%) had two or more small VUS CNVs, 20 (0.45%) had one small VUS CNV and a recurrent CNV, 113 (2.56%) had one small pathogenic or likely pathogenic CNV, 17 (0.38%) had two or more small pathogenic or likely pathogenic CNVs, and 12 (0.27%) had one small pathogenic or likely pathogenic CNV and a recurrent CNV. Within the pathogenic group, 80 of 142 patients (56% of all small pathogenic CNV cases) were found to have a single whole-gene or exonic deletion. The themes that emerged from our study are presented in the Discussion section. CONCLUSIONS Our study demonstrates the diagnostic clinical relevance of small, nonrecurrent CNVs <500 kb during CMA clinical testing and underscores the need for careful clinical interpretation of these CNVs.Genet Med 19 4, 377-385.
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Affiliation(s)
- Dana Hollenbeck
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Crescenda L Williams
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Current address: Children's Health Hospital, Dallas, Texas, USA
| | - Kathryn Drazba
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Maria Descartes
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - S Lane Rutledge
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Edward J Lose
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Nathaniel H Robin
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Andrew J Carroll
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
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11
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Giorgio E, Ciolfi A, Biamino E, Caputo V, Di Gregorio E, Belligni EF, Calcia A, Gaidolfi E, Bruselles A, Mancini C, Cavalieri S, Molinatto C, Cirillo Silengo M, Ferrero GB, Tartaglia M, Brusco A. Whole exome sequencing is necessary to clarify ID/DD cases with de novo copy number variants of uncertain significance: Two proof-of-concept examples. Am J Med Genet A 2016; 170:1772-9. [PMID: 27108886 DOI: 10.1002/ajmg.a.37649] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 03/20/2016] [Indexed: 01/09/2023]
Abstract
Whole exome sequencing (WES) is a powerful tool to identify clinically undefined forms of intellectual disability/developmental delay (ID/DD), especially in consanguineous families. Here we report the genetic definition of two sporadic cases, with syndromic ID/DD for whom array-Comparative Genomic Hybridization (aCGH) identified a de novo copy number variant (CNV) of uncertain significance. The phenotypes included microcephaly with brachycephaly and a distinctive facies in one proband, and hypotonia in the legs and mild ataxia in the other. WES allowed identification of a functionally relevant homozygous variant affecting a known disease gene for rare syndromic ID/DD in each proband, that is, c.1423C>T (p.Arg377*) in the Trafficking Protein Particle Complex 9 (TRAPPC9), and c.154T>C (p.Cys52Arg) in the Very Low Density Lipoprotein Receptor (VLDLR). Four mutations affecting TRAPPC9 have been previously reported, and the present finding further depicts this syndromic form of ID, which includes microcephaly with brachycephaly, corpus callosum hypoplasia, facial dysmorphism, and overweight. VLDLR-associated cerebellar hypoplasia (VLDLR-CH) is characterized by non-progressive congenital ataxia and moderate-to-profound intellectual disability. The c.154T>C (p.Cys52Arg) mutation was associated with a very mild form of ataxia, mild intellectual disability, and cerebellar hypoplasia without cortical gyri simplification. In conclusion, we report two novel cases with rare causes of autosomal recessive ID, which document how interpreting de novo array-CGH variants represents a challenge in consanguineous families; as such, clinical WES should be considered in diagnostic testing. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Elisa Giorgio
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCSS, Rome, Italy.,Centro di Ricerca per gli alimenti e la nutrizione, CREA, Rome, Italy
| | - Elisa Biamino
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | - Viviana Caputo
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Eleonora Di Gregorio
- Città della Salute e della Scienza University Hospital, Medical Genetics Unit, Turin, Italy
| | - Elga Fabia Belligni
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | | | - Elena Gaidolfi
- Centro Diagnostico Cernaia, Magnetic Resonance Unit, Turin, Italy
| | - Alessandro Bruselles
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Cecilia Mancini
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Simona Cavalieri
- Città della Salute e della Scienza University Hospital, Medical Genetics Unit, Turin, Italy
| | - Cristina Molinatto
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | | | | | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCSS, Rome, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Turin, Italy.,Città della Salute e della Scienza University Hospital, Medical Genetics Unit, Turin, Italy
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12
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Jansen FAR, Hoffer MJV, van Velzen CL, Plati SK, Rijlaarsdam MEB, Clur SAB, Blom NA, Pajkrt E, Bhola SL, Knegt AC, de Boer MA, Haak MC. Chromosomal abnormalities and copy number variations in fetal left-sided congenital heart defects. Prenat Diagn 2016; 36:177-85. [DOI: 10.1002/pd.4767] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 12/15/2015] [Accepted: 12/23/2015] [Indexed: 12/24/2022]
Affiliation(s)
- Fenna A. R. Jansen
- Department of Obstetrics and Fetal Medicine; Leiden University Medical Center; Leiden the Netherlands
| | - Mariette J. V. Hoffer
- Department of Clinical Genetics; Leiden University Medical Center; Leiden the Netherlands
| | | | | | - Marry E. B. Rijlaarsdam
- Department of Pediatric Cardiology of the Willem Alexander Children's Hospital; Leiden University Medical Center; Leiden the Netherlands
| | - Sally-Ann B. Clur
- Department of Pediatric Cardiology of the Emma Children's Hospital; Academic Medical Center; Amsterdam the Netherlands
| | - Nico A. Blom
- Department of Pediatric Cardiology of the Willem Alexander Children's Hospital; Leiden University Medical Center; Leiden the Netherlands
- Department of Pediatric Cardiology of the Emma Children's Hospital; Academic Medical Center; Amsterdam the Netherlands
| | - Eva Pajkrt
- Department of Obstetrics; Academic Medical Center; Amsterdam the Netherlands
| | - Shama L. Bhola
- Department of Clinical Genetics; VU University Medical Center; Amsterdam the Netherlands
| | - Alida C. Knegt
- Department of Clinical Genetics; Academic Medical Center; Amsterdam the Netherlands
| | - Marion A. de Boer
- Department of Obstetrics; VU University Medical Center; Amsterdam the Netherlands
| | - Monique C. Haak
- Department of Obstetrics and Fetal Medicine; Leiden University Medical Center; Leiden the Netherlands
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13
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Hang XY, Shang AJ, Zhao QJ, Bai SC, Cheng C, Tao BZ, Wang LK, Liang S, Yin L. Association between chromosomal aberration of COX8C and tethered spinal cord syndrome: array-based comparative genomic hybridization analysis. Neural Regen Res 2016; 11:1333-8. [PMID: 27651783 PMCID: PMC5020834 DOI: 10.4103/1673-5374.189200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Copy number variations have been found in patients with neural tube abnormalities. In this study, we performed genome-wide screening using high-resolution array-based comparative genomic hybridization in three children with tethered spinal cord syndrome and two healthy parents. Of eight copy number variations, four were non-polymorphic. These non-polymorphic copy number variations were associated with Angelman and Prader-Willi syndromes, and microcephaly. Gene function enrichment analysis revealed that COX8C, a gene associated with metabolic disorders of the nervous system, was located in the copy number variation region of Patient 1. Our results indicate that array-based comparative genomic hybridization can be used to diagnose tethered spinal cord syndrome. Our results may help determine the pathogenesis of tethered spinal cord syndrome and prevent occurrence of this disease.
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14
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Carreira IM, Ferreira SI, Matoso E, Pires LM, Ferrão J, Jardim A, Mascarenhas A, Pinto M, Lavoura N, Pais C, Paiva P, Simões L, Caramelo F, Ramos L, Venâncio M, Ramos F, Beleza A, Sá J, Saraiva J, de Melo JB. Copy number variants prioritization after array-CGH analysis - a cohort of 1000 patients. Mol Cytogenet 2015; 8:103. [PMID: 26719768 PMCID: PMC4696247 DOI: 10.1186/s13039-015-0202-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 12/17/2015] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Array-based comparative genomic hybridization has been assumed to be the first genetic test offered to detect genomic imbalances in patients with unexplained intellectual disability with or without dysmorphisms, multiple congenital anomalies, learning difficulties and autism spectrum disorders. Our study contributes to the genotype/phenotype correlation with the delineation of laboratory criteria which help to classify the different copy number variants (CNVs) detected. We clustered our findings into five classes ranging from an imbalance detected in a microdeletion/duplication syndrome region (class I) to imbalances that had previously been reported in normal subjects in the Database of Genomic Variants (DGV) and thus considered common variants (class IV). RESULTS All the analyzed 1000 patients had at least one CNV independently of its clinical significance. Most of them, as expected, were alterations already reported in the DGV for normal individuals (class IV) or without known coding genes (class III-B). In approximately 14 % of the patients an imbalance involving known coding genes, but with partially overlapping or low frequency of CNVs described in the DGV was identified (class IIIA). In 10.4 % of the patients a pathogenic CNV that explained the phenotype was identified consisting of: 40 class I imbalances, 44 class II de novo imbalances and 21 class II X-chromosome imbalances in male patients. In 20 % of the patients a familial pathogenic or potentially pathogenic CNV, consisting of inherited class II imbalances, was identified that implied a family evaluation by the clinical geneticists. CONCLUSIONS As this interpretation can be sometimes difficult, particularly if it is not possible to study the parents, using the proposed classification we were able to prioritize the multiple imbalances that are identified in each patient without immediately having to classify them as pathogenic or benign.
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Affiliation(s)
- Isabel Marques Carreira
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal ; CIMAGO - Centro de Investigação em Meio Ambiente, Genética e Oncobiologia, Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal ; Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal ; CNC, IBILI - Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal
| | - Susana Isabel Ferreira
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - Eunice Matoso
- CIMAGO - Centro de Investigação em Meio Ambiente, Genética e Oncobiologia, Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal ; Laboratório de Citogenética, Hospital Pediátrico de Coimbra, Coimbra, Portugal
| | - Luís Miguel Pires
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - José Ferrão
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - Ana Jardim
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - Alexandra Mascarenhas
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - Marta Pinto
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - Nuno Lavoura
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - Cláudia Pais
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - Patrícia Paiva
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - Lúcia Simões
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - Francisco Caramelo
- Laboratório de Bioestatística e Informática Médica, IBILI - Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal
| | - Lina Ramos
- Laboratório de Bioestatística e Informática Médica, IBILI - Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal
| | - Margarida Venâncio
- Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal ; Serviço de Genética Médica, Hospital Pediátrico - Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Fabiana Ramos
- Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal ; Serviço de Genética Médica, Hospital Pediátrico - Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Ana Beleza
- Serviço de Genética Médica, Hospital Pediátrico - Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Joaquim Sá
- Serviço de Genética Médica, Hospital Pediátrico - Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Jorge Saraiva
- Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal ; Serviço de Genética Médica, Hospital Pediátrico - Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Joana Barbosa de Melo
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal ; CIMAGO - Centro de Investigação em Meio Ambiente, Genética e Oncobiologia, Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal ; Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal ; CNC, IBILI - Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal
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15
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Sahlin E, Gustavsson P, Liedén A, Papadogiannakis N, Bjäreborn L, Pettersson K, Nordenskjöld M, Iwarsson E. Molecular and cytogenetic analysis in stillbirth: results from 481 consecutive cases. Fetal Diagn Ther 2014; 36:326-32. [PMID: 25059832 DOI: 10.1159/000361017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 02/28/2014] [Indexed: 11/19/2022]
Abstract
INTRODUCTION The underlying causes of stillbirth are heterogeneous and in many cases unexplained. Our aim was to conclude clinical results from karyotype and quantitative fluorescence-polymerase chain reaction (QF-PCR) analysis of all stillbirths occurring in Stockholm County between 2008 and 2012. By screening a subset of cases, we aimed to study the possible benefits of chromosomal microarray (CMA) in the analysis of the etiology of stillbirth. METHODS During 2008-2012, 481 stillbirths in Stockholm County were investigated according to a clinical protocol including karyotype or QF-PCR analysis. CMA screening was performed on a subset of 90 cases, corresponding to all stillbirths from 2010 without a genetic diagnosis. RESULTS Chromosomal aberrations were detected by karyotype or QF-PCR analysis in 7.5% of the stillbirths. CMA analysis additionally identified two known syndromes, one aberration disrupting a known disease gene, and 26 variants of unknown significance. Furthermore, CMA had a significantly higher success rate than karyotyping (100 vs. 80%, p < 0.001). DISCUSSION In the analysis of stillbirth, conventional karyotyping is prone to failure, and QF-PCR is a useful complement. We show that CMA has a higher success rate and aberration detection frequency than these methods, and conclude that CMA is a valuable tool for identification of chromosomal aberrations in stillbirth.
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Affiliation(s)
- Ellika Sahlin
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, CMM L8:02, Karolinska University Hospital, Stockholm, Sweden
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16
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Trakadis YJ, Buote C, Therriault JF, Jacques PÉ, Larochelle H, Lévesque S. PhenoVar: a phenotype-driven approach in clinical genomics for the diagnosis of polymalformative syndromes. BMC Med Genomics 2014; 7:22. [PMID: 24884844 PMCID: PMC4030287 DOI: 10.1186/1755-8794-7-22] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 04/24/2014] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND We propose a phenotype-driven analysis of encrypted exome data to facilitate the widespread implementation of exome sequencing as a clinical genetic screening test.Twenty test-patients with varied syndromes were selected from the literature. For each patient, the mutation, phenotypic data, and genetic diagnosis were available. Next, control exome-files, each modified to include one of these twenty mutations, were assigned to the corresponding test-patients. These data were used by a geneticist blinded to the diagnoses to test the efficiency of our software, PhenoVar. The score assigned by PhenoVar to any genetic diagnosis listed in OMIM (Online Mendelian Inheritance in Man) took into consideration both the patient's phenotype and all variations present in the corresponding exome. The physician did not have access to the individual mutations. PhenoVar filtered the search using a cut-off phenotypic match threshold to prevent undesired discovery of incidental findings and ranked the OMIM entries according to diagnostic score. RESULTS When assigning the same weight to all variants in the exome, PhenoVar predicted the correct diagnosis in 10/20 patients, while in 15/20 the correct diagnosis was among the 4 highest ranked diagnoses. When assigning a higher weight to variants known, or bioinformatically predicted, to cause disease, PhenoVar's yield increased to 14/20 (18/20 in top 4). No incidental findings were identified using our cut-off phenotypic threshold. CONCLUSION The phenotype-driven approach described could render widespread use of ES more practical, ethical and clinically useful. The implications about novel disease identification, advancement of complex diseases and personalized medicine are discussed.
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Affiliation(s)
- Yannis J Trakadis
- Department of Medical Genetics, McGill University Health Centre, Montreal, Canada.
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17
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Duga B, Czakó M, Hadzsiev K, Komlósi K, Sümegi K, Kisfali P, Kosztolányi G, Melegh B. [Identifying rare genomic disorders with array comparative genomic hybridization in Hungary]. Orv Hetil 2014; 155:358-61. [PMID: 24566700 DOI: 10.1556/oh.2014.29825] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
INTRODUCTION In the past decade the study of genomic disorders has received more interest. Array comparative genome hybridization is a widely spread diagnostic method in the research of genomic disorders. This method was implemented in the laboratory of the authors in 2012. AIM This molecular cytogenetic method was first used to examine patients with complex developmental disorders in whom no genetic background was identified by traditional methods. METHOD The authors complemented traditional diagnostic methods with array comparative genome hybridization, which has not been used in routine diagnostics in Hungary so far. RESULTS Using this novel method the authors were able to identify genomic alterations in 7 out of 18 patients with complex developmental disorders. They found de novo alterations in 6 out of 7 patients, which were most likely causative in the development of the phenotype, while in one case they detected a familial genomic alteration. This method helped the authors to determine the breakpoint of genomic variation in their patients and delineate the affected genes contributing to the phenotype. CONCLUSIONS These results call attention to the usefulness of next generation diagnostic methods available in the laboratory of the authors.
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Affiliation(s)
- Balázs Duga
- Pécsi Tudományegyetem, Általános Orvostudományi Kar, Klinikai Központ Orvosi Genetikai Intézet Pécs Szigeti út 12. 7624 Pécsi Tudományegyetem Szentágothai János Kutatóközpont Pécs
| | - Márta Czakó
- Pécsi Tudományegyetem, Általános Orvostudományi Kar, Klinikai Központ Orvosi Genetikai Intézet Pécs Szigeti út 12. 7624 Pécsi Tudományegyetem Szentágothai János Kutatóközpont Pécs
| | - Kinga Hadzsiev
- Pécsi Tudományegyetem, Általános Orvostudományi Kar, Klinikai Központ Orvosi Genetikai Intézet Pécs Szigeti út 12. 7624 Pécsi Tudományegyetem Szentágothai János Kutatóközpont Pécs
| | - Katalin Komlósi
- Pécsi Tudományegyetem, Általános Orvostudományi Kar, Klinikai Központ Orvosi Genetikai Intézet Pécs Szigeti út 12. 7624 Pécsi Tudományegyetem Szentágothai János Kutatóközpont Pécs
| | - Katalin Sümegi
- Pécsi Tudományegyetem, Általános Orvostudományi Kar, Klinikai Központ Orvosi Genetikai Intézet Pécs Szigeti út 12. 7624 Pécsi Tudományegyetem Szentágothai János Kutatóközpont Pécs
| | - Péter Kisfali
- Pécsi Tudományegyetem, Általános Orvostudományi Kar, Klinikai Központ Orvosi Genetikai Intézet Pécs Szigeti út 12. 7624 Pécsi Tudományegyetem Szentágothai János Kutatóközpont Pécs
| | - György Kosztolányi
- Pécsi Tudományegyetem, Általános Orvostudományi Kar, Klinikai Központ Orvosi Genetikai Intézet Pécs Szigeti út 12. 7624 Pécsi Tudományegyetem Szentágothai János Kutatóközpont Pécs
| | - Béla Melegh
- Pécsi Tudományegyetem, Általános Orvostudományi Kar, Klinikai Központ Orvosi Genetikai Intézet Pécs Szigeti út 12. 7624 Pécsi Tudományegyetem Szentágothai János Kutatóközpont Pécs
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18
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Abstract
The field of cytogenetics has focused on studying the number, structure, function and origin of chromosomal abnormalities and the evolution of chromosomes. The development of fluorescent molecules that either directly or via an intermediate molecule bind to DNA has led to the development of fluorescent in situ hybridization (FISH), a technology linking cytogenetics to molecular genetics. This technique has a wide range of applications that increased the dimension of chromosome analysis. The field of cytogenetics is particularly important for medical diagnostics and research as well as for gene ordering and mapping. Furthermore, the increased application of molecular biology techniques, such as array-based technologies, has led to improved resolution, extending the recognized range of microdeletion/microduplication syndromes and genomic disorders. In adopting these newly expanded methods, cytogeneticists have used a range of technologies to study the association between visible chromosome rearrangements and defects at the single nucleotide level. Overall, molecular cytogenetic techniques offer a remarkable number of potential applications, ranging from physical mapping to clinical and evolutionary studies, making a powerful and informative complement to other molecular and genomic approaches. This manuscript does not present a detailed history of the development of molecular cytogenetics; however, references to historical reviews and experiments have been provided whenever possible. Herein, the basic principles of molecular cytogenetics, the technologies used to identify chromosomal rearrangements and copy number changes, and the applications for cytogenetics in biomedical diagnosis and research are presented and discussed.
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Affiliation(s)
- Mariluce Riegel
- Serviço de Genética Médica, Hospital de Clínicas, Porto Alegre, RS, Brazil . ; Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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Bug S, Schmitz F, Nevinny-Stickel-Hinzpeter C. The correct genetic diagnosis has already been determined more often than we think, let's report it to the parents! Clin Pediatr (Phila) 2014; 53:8-10. [PMID: 23613176 DOI: 10.1177/0009922813485811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Stefanie Bug
- 1synlab Medizinisches Versorgungszentrum Humane Genetik München, Munich, Germany
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Lukackova R, Gerykova Bujalkova M, Majerova L, Mladosievicova B. Molecular genetic methods in the diagnosis of myelodysplastic syndromes. A review. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2013; 158:339-45. [PMID: 24263214 DOI: 10.5507/bp.2013.084] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 11/06/2013] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Myelodysplastic syndromes (MDS) represent a heterogeneous group of premalignant hematologic disorders characterized by ineffective hematopoiesis, peripheral blood cytopenias and increased risk of progression to acute leukemia. Cytogenetic analysis still plays a central role in the diagnosis of MDS, as clonal chromosomal abnormalities are observed in 30-50% of MDS patients. Despite their technical limitations, standard karyotyping and fluorescence in situ hybridization (FISH) are routinely used for identifying recurrent chromosomal rearrangements. However, using this approach means that submicroscopic and not targeted chromosomal aberrations, as well as somatic mutations and epigenetic changes remain largely undetected. METHODS AND RESULTS Introduction of methods for the analysis of copy-number variations (CNV), including array-based technologies and Multiplex ligation-dependent probe amplification (MLPA) has provided novel insights into the molecular pathogenesis of MDS and considerably extended possibilities for genetic laboratory testing. Several novel molecular markers have been discovered and used for diagnosis and prognostic evaluation of patients with MDS. At present, mutational analysis is not routinely performed, as the clinical significance of somatic mutations in MDS has only begun to emerge. However, recently introduced Next-generation sequencing (NGS) technologies could help to elucidate the relationship between chromosomal and molecular aberrations in MDS and lead to further improvement in its diagnosis. CONCLUSION This review focuses on the advantages, limitations, clinical applications and future perspectives of three molecular methods (array-based analysis, MLPA and NGS) currently used in genetic testing and/ or translational research of MDS. In conclusion, a brief summary for clinicians from the routine diagnostic point of view is given.
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Affiliation(s)
- Renata Lukackova
- Department of Clinical Genetics, Medirex a.s., Bratislava, Slovak Republic
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Spreiz A, Haberlandt E, Baumann M, Baumgartner Sigl S, Fauth C, Gautsch K, Karall D, Janetschek C, Rostasy K, Scholl-Bürgi S, Zotter S, Utermann G, Zschocke J, Kotzot D. Chromosomal microaberrations in patients with epilepsy, intellectual disability, and congenital anomalies. Clin Genet 2013; 86:361-6. [PMID: 24116836 DOI: 10.1111/cge.12288] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 09/23/2013] [Accepted: 09/23/2013] [Indexed: 01/01/2023]
Abstract
Epilepsy is a common finding in patients with chromosomal macro- and micro-rearrangements but only few aberrations show a constant pattern of seizures. DNA array-based studies have reported causative copy number variations (CNVs) in 5-30% of patients with epilepsy with or without co-morbidities. The interpretation of many of the detected CNVs remains challenging. In order to identify CNVs carrying epilepsy-related genes we investigated 43 children with various patterns of epileptic seizures, intellectual disability (ID), and minor dysmorphism, using the Illumina® Infinium Human1M-DuoV1 array. In three patients we found likely causative de novo CNVs, i.e. deletions in 1q41q42.12 (3.4 Mb) and 19p13.2 (834 kb), and a mosaic two-segment duplication in 17p13.2 (218 kb) and 17p13.1 (422 kb). In six additional patients there were aberrations (a deletion in one and duplications in five patients) with uncertain clinical consequences. In total, the finding of causative chromosomal micro-rearrangements in 3 out of 43 patients (7%) and potentially causative CNVs in 6 additional patients (14%) with epilepsy and ID but without major malformations confirms the power of DNA arrays for the detection of new disease-related genetic regions.
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Affiliation(s)
- A Spreiz
- Division of Human Genetics, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
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Helsmoortel C, Vandeweyer G, Kooy RF. On the spot: very local chromosomal rearrangements. F1000 BIOLOGY REPORTS 2012. [PMID: 23189093 PMCID: PMC3505860 DOI: 10.3410/b4-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Over the last decade, the detection of chromosomal abnormalities has shifted from conventional karyotyping under a light microscope to molecular detection using microarrays. The latter technology identified copy number variation as a major source of variation in the human genome; moreover, copy number variants were found responsible for 10-20% of cases of intellectual disability. Recent technological advances in microarray technology have also enabled the detection of very small local chromosomal rearrangements, sometimes affecting the function of only a single gene. Here, we illustrate how high resolution microarray analysis has led to increased insights into the contribution of specific genes in disease.
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Affiliation(s)
- Céline Helsmoortel
- Cognitive Genetics, Department of Medical Genetics, University of Antwerp Prins Boudewijnlaan 43, B-2650 Edegem, Belgium
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Abu-Amero KK, Kondkar AA, Salih MAM, Alorainy IA, Khan AO, Oystreck DT, Bosley TM. Partial chromosome 7 duplication with a phenotype mimicking the HOXA1 spectrum disorder. Ophthalmic Genet 2012; 34:90-6. [DOI: 10.3109/13816810.2012.718850] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Poot M. Beware of Hemizygous Deletions That May Unmask Deleterious Variants. Mol Syndromol 2012; 3:45-46. [PMID: 23112749 DOI: 10.1159/000339564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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Abstract
Zusammenfassung
Die Ursache neurokognitiver Entwicklungsstörungen mit Intelligenzminderung stellt eine der häufigsten Fragestellungen in der genetischen Sprechstunde dar. Obwohl mehr als 400 krankheitsverursachende Einzelgendefekte bekannt sind, machen Chromosomenaberrationen derzeit den größten Anteil der bekannten Ursachen aus. Mittels hochauflösender Array-Techniken lassen sich nach Ausschluss des Down-Syndroms bei unselektionierten Patienten in 18% der Fälle relevante chromosomale Imbalancen nachweisen, wobei die Aberrationen nur in 4% der Fälle auch primär mikroskopisch sichtbar wären. Mit zunehmender Auflösung steigt jedoch auch die Rate an detektierten Kopienzahl-Normvarianten, welche die Beurteilung der Befunde erschweren können. Indikatoren für krankheitsrelevante Aberrationen sind Aberrationsgröße, Gengehalt und Segregation innerhalb der Familie. Eine Kausalität kann letztlich aber nur dann belegt werden, wenn Vergleichsfälle mit ähnlichem Genotyp und Phänotyp vorliegen.
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Sporadic male patients with intellectual disability: contribution of X-chromosome copy number variants. Eur J Med Genet 2012; 55:577-85. [PMID: 22659343 DOI: 10.1016/j.ejmg.2012.05.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Revised: 05/19/2012] [Accepted: 05/20/2012] [Indexed: 12/18/2022]
Abstract
Genome-wide array comparative genome hybridization has become the first in line diagnostic tool in the clinical work-up of patients presenting with intellectual disability. As a result, chromosome X-copy number variations are frequently being detected in routine diagnostics. We retrospectively reviewed genome wide array-CGH data in order to determine the frequency and nature of chromosome X-copy number variations (X-CNV) in a cohort of 2222 sporadic male patients with intellectual disability (ID) referred to us for diagnosis. In this cohort, 68 males were found to have at least one X-CNV (3.1%). However, correct interpretation of causality remains a challenging task, and is essential for proper counseling, especially when the CNV is inherited. On the basis of these data, earlier experience and literature data we designed and propose an algorithm that can be used to evaluate the clinical relevance of X-CNVs detected in sporadic male ID patients. Applied to our cohort, 19 male ID patients (0.85%) were found to carry a (likely) pathogenic X-CNV.
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