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Yang EH, Shin YB, Choi SH, Yoo HW, Kim HY, Kwak MJ, Park KH, Bae MH, Kong JH, Lee YJ, Nam SO, Kim YM. Chromosomal Microarray in Children With Developmental Delay: The Experience of a Tertiary Center in Korea. Front Pediatr 2021; 9:690493. [PMID: 34604135 PMCID: PMC8480257 DOI: 10.3389/fped.2021.690493] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 08/13/2021] [Indexed: 11/20/2022] Open
Abstract
Background and Objectives: Chromosomal microarray (CMA) is a first-tier genetic test for children with developmental delay (DD), intellectual disability (ID), autism spectrum disorders (ASDs), and multiple congenital anomalies (MCA). In this study, we report our experiences with the use of CMA in Korean children with unexplained DD/ID. Methods: We performed CMA in a cohort of 308 children with DD/ID between January 2010 and September 2020. We also retrospectively reviewed their medical records. The Affymetrix CytoScan 750 K array with an average resolution of 100 kb was used to perform CMA. Results: Comorbid neurodevelopmental disorders were ASD (37 patients; 12.0%), epilepsy (34 patients; 11.0%), and attention deficit hyperactivity disorders (12 patients; 3.9%). The diagnostic yield was 18.5%. Among the 221 copy number variants (CNVs) identified, 70 CNVs (57 patients; 18.5%) were pathogenic. Deletion CNVs were more common among pathogenic CNVs (PCNVs) than in non-PCNVs (P < 0.001). The size difference between PCNVs and non-PCNVs was not significant (P = 0.023). The number of included genes within CNV intervals was significantly higher in PCNVs (average 8.6; 0-347) than in non-PCNVs (average 47.5; 1-386) (P < 0.001). Short stature and hearing difficulty were also more common in the PCNV group than in the non-PCNV group (P = 0.010 and 0.070, respectively). Conclusion: This study provides additional evidence for the usefulness of CMA in genetic testing of children with DD/ID in Korea. The pathogenicity of CNVs correlated with the number of included genes within the CNV interval and deletion type of the CNVs, but not with CNV size.
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Affiliation(s)
- Eun Hye Yang
- Department of Pediatrics, Pusan National University Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Busan, South Korea
| | - Yong Beom Shin
- Department of Rehabilitation, Pusan National University Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Busan, South Korea, Busan, South Korea
| | - Soo Han Choi
- Department of Pediatrics, Pusan National University Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Busan, South Korea
| | - Hye Won Yoo
- Department of Pediatrics, Pusan National University Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Busan, South Korea
| | - Hye Young Kim
- Department of Pediatrics, Pusan National University Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Busan, South Korea
| | - Min Jung Kwak
- Department of Pediatrics, Pusan National University Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Busan, South Korea
| | - Kyung Hee Park
- Department of Pediatrics, Pusan National University Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Busan, South Korea
| | - Mi Hye Bae
- Department of Pediatrics, Pusan National University Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Busan, South Korea
| | - Ju Hyun Kong
- Department of Pediatrics, Pusan National University Children's Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Yangsan, South Korea
| | - Yun-Jin Lee
- Department of Pediatrics, Pusan National University Children's Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Yangsan, South Korea
| | - Sang Ook Nam
- Department of Pediatrics, Pusan National University Children's Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Yangsan, South Korea
| | - Young Mi Kim
- Department of Pediatrics, Pusan National University Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Busan, South Korea
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Savory K, Manivannan S, Zaben M, Uzun O, Syed YA. Impact of copy number variation on human neurocognitive deficits and congenital heart defects: A systematic review. Neurosci Biobehav Rev 2019; 108:83-93. [PMID: 31682886 DOI: 10.1016/j.neubiorev.2019.10.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 10/26/2019] [Indexed: 12/16/2022]
Abstract
Copy number variant (CNV) syndromes are often associated with both neurocognitive deficits (NCDs) and congenital heart defects (CHDs). Children and adults with cardiac developmental defects likely to have NCDs leading to increased risk of hospitalisation and reduced level of independence. To date, the association between these two phenotypes have not been explored in relation to CNV syndromes. In order to address this question, we systematically reviewed the prevalence of CHDs in a range of CNV syndromes associated with NCDs. A meta-analysis showed a relationship with the size of CNV and its association with both NCDs and CHDs, and also inheritance pattern. To our knowledge, this is the first review to establish association between NCD and CHDs in CNV patients, specifically in relation to the severity of NCD. Importantly, we also found specific types of CHDs were associated with severe neurocognitive deficits. Finally, we discuss the implications of these results for patients in the clinical setting which warrants further exploration of this association in order to lead an improvement in the quality of patient's life.
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Affiliation(s)
- Katrina Savory
- Neuroscience and Mental Health Research Institute (NMHRI), Hadyn Ellis Building, Cathays, CF24 4HQ, Cardiff, UK; School of Bioscience, The Sir Martin Evans Building, Museum Ave, Cardiff, CF10 3AX, UK
| | - Susruta Manivannan
- Neuroscience and Mental Health Research Institute (NMHRI), Hadyn Ellis Building, Cathays, CF24 4HQ, Cardiff, UK
| | - Malik Zaben
- Neuroscience and Mental Health Research Institute (NMHRI), Hadyn Ellis Building, Cathays, CF24 4HQ, Cardiff, UK
| | - Orhan Uzun
- University Hospital of Wales, Heath Park, Cardiff, CF10 3AX, UK
| | - Yasir Ahmed Syed
- Neuroscience and Mental Health Research Institute (NMHRI), Hadyn Ellis Building, Cathays, CF24 4HQ, Cardiff, UK; School of Bioscience, The Sir Martin Evans Building, Museum Ave, Cardiff, CF10 3AX, UK.
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3
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Bateman MS, Collinson MN, Bunyan DJ, Collins AL, Duncan P, Firth R, Harrison V, Homfray T, Huang S, Kirk B, Lachlan KL, Maloney VK, Barber JCK. Incomplete penetrance, variable expressivity, or dosage insensitivity in four families with directly transmitted unbalanced chromosome abnormalities. Am J Med Genet A 2017; 176:319-329. [DOI: 10.1002/ajmg.a.38564] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 09/15/2017] [Accepted: 11/13/2017] [Indexed: 12/29/2022]
Affiliation(s)
- Mark S. Bateman
- Wessex Regional Genetics LaboratorySalisbury NHS Foundation TrustSalisburyUK
| | - Morag N. Collinson
- Wessex Regional Genetics LaboratorySalisbury NHS Foundation TrustSalisburyUK
| | - David J. Bunyan
- Wessex Regional Genetics LaboratorySalisbury NHS Foundation TrustSalisburyUK
| | - Amanda L. Collins
- Wessex Clinical Genetics ServiceSouthampton University Hospitals NHS Foundation TrustPrincess Anne HospitalSouthamptonUK
| | - Philippa Duncan
- Wessex Regional Genetics LaboratorySalisbury NHS Foundation TrustSalisburyUK
| | - Rachel Firth
- Wessex Clinical Genetics ServiceSouthampton University Hospitals NHS Foundation TrustPrincess Anne HospitalSouthamptonUK
| | - Victoria Harrison
- Wessex Clinical Genetics ServiceSouthampton University Hospitals NHS Foundation TrustPrincess Anne HospitalSouthamptonUK
| | | | - Shuwen Huang
- National Genetics Reference Laboratory (Wessex)Salisbury NHS Foundation TrustSalisburyUK
| | - Beth Kirk
- Wessex Regional Genetics LaboratorySalisbury NHS Foundation TrustSalisburyUK
| | - Katherine L. Lachlan
- Wessex Clinical Genetics ServiceSouthampton University Hospitals NHS Foundation TrustPrincess Anne HospitalSouthamptonUK
| | - Viv K. Maloney
- Wessex Regional Genetics LaboratorySalisbury NHS Foundation TrustSalisburyUK
| | - John C. K. Barber
- Department of Human Genetics and Genomic MedicineUniversity of SouthamptonSouthampton General HospitalSouthamptonUK
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4
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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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5
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Prenatally detected interstitial deletion 13q12.3-q22 in a fetus with a cystic hygroma. Gene 2013; 531:90-1. [PMID: 23999188 DOI: 10.1016/j.gene.2013.08.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2013] [Revised: 07/13/2013] [Accepted: 08/07/2013] [Indexed: 11/19/2022]
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6
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Papoulidis I, Vetro A, Kefalas K, Orru S, Thomaidis L, Iliodromiti Z, Zuffardi O, Manolakos E. De novo 15.5-Mb Interstitial Deletion in 5p in a Male Ascertained by Oligospermia. Mol Syndromol 2013; 4:250-4. [PMID: 23885232 DOI: 10.1159/000351656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/15/2013] [Indexed: 11/19/2022] Open
Abstract
We describe a case of a 34-year-old male presenting with oligospermia and an otherwise normal phenotype. Investigation with array-based comparative genomic hybridization (aCGH) revealed an interstitial deletion of about 15.5 Mb in chromosome 5p13.3p14.3. We compared the phenotype of our patient with recently reported patients studied by aCGH, who show an overlapping deletion. We also analyzed the gene content of the deleted region in order to propose a possible involvement of specific genes in the clinical phenotype.
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Affiliation(s)
- I Papoulidis
- Laboratory of Genetics of Eurogenetica S.A., Aglaia Kyriakou Children's Hospital, Athens, Greece
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7
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Kearney HM, Thorland EC, Brown KK, Quintero-Rivera F, South ST. American College of Medical Genetics standards and guidelines for interpretation and reporting of postnatal constitutional copy number variants. Genet Med 2011; 13:680-5. [PMID: 21681106 DOI: 10.1097/gim.0b013e3182217a3a] [Citation(s) in RCA: 655] [Impact Index Per Article: 50.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Genomic microarrays used to assess DNA copy number are now recommended as first-tier tests for the postnatal evaluation of individuals with intellectual disability, autism spectrum disorders, and/or multiple congenital anomalies. Application of this technology has resulted in the discovery of widespread copy number variation in the human genome, both polymorphic variation in healthy individuals and novel pathogenic copy number imbalances. To assist clinical laboratories in the evaluation of copy number variants and to promote consistency in interpretation and reporting of genomic microarray results, the American College of Medical Genetics has developed the following professional guidelines for the interpretation and reporting of copy number variation. These guidelines apply primarily to evaluation of constitutional copy number variants detected in the postnatal setting.
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Affiliation(s)
- Hutton M Kearney
- Fullerton Genetics Center, Mission Health System, 267 McDowell St., Asheville, NC 28803, USA.
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8
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Pyatt RE, Astbury C. Interpretation of copy number alterations identified through clinical microarray-comparative genomic hybridization. Clin Lab Med 2011; 31:565-80, viii. [PMID: 22118737 DOI: 10.1016/j.cll.2011.08.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Many copy number alterations (CNA) currently interpreted as variants of unknown significance (VUS) will ultimately be determined to be benign; however, their classification requires a more extensive characterization of the human genome than currently exists. There is no definitive set of rules or level of evidence required to define a CNA as benign. The information needed to accurately assess the pathogenic impact of CNA is beginning to be assembled. Although the lack of understanding of the human genome can make clinical array-comparative genomic hybridization interpretation frustrating, it is precisely why clinical human genetics is an exciting arena in which to work.
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Affiliation(s)
- Robert E Pyatt
- Cytogenetics and Molecular Genetics Laboratory, Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA.
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9
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Tosca L, Brisset S, Petit FM, Metay C, Latour S, Lautier B, Lebas A, Druart L, Picone O, Mas AE, Prévot S, Tardieu M, Goossens M, Tachdjian G. Genotype-phenotype correlation in 13q13.3-q21.3 deletion. Eur J Med Genet 2011; 54:e489-94. [PMID: 21741501 DOI: 10.1016/j.ejmg.2011.06.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Accepted: 06/10/2011] [Indexed: 10/18/2022]
Abstract
Pure interstitial deletions of the long arm of chromosome 13 are correlated with variable phenotypes according to the size and the location of the deleted region. Deletions involving the 13q13q21 region are rare. In order to establish interstitial 13q genotype-phenotype correlation, we used high resolution 244K oligonucleotide array in addition to conventional karyotype and molecular (fluorescent in situ hybridization, microsatellite markers analysis) techniques in two independent probands carrying a deletion 13q13 to 13q21. First patient was a 3-year-old girl with mental retardation and dysmorphy carrying a 13q13.3q21.31 de novo deletion diagnosed post-natally. The second one was a fetus with de novo del(13)(q14q21.2) associated with first trimester increased nuchal translucency. We showed that specific dysmorphic features (macrocephaly, high forehead, hypertelorism, large nose, large and malformed ears and retrognathia) were correlated to the common 13q14q21 chromosomal segment. Physical examination revealed overgrowth with global measurement up to the 95th percentile in both probands. This is the second description of overgrowth in patients carrying a 13q deletion. Haploinsufficiency of common candidates genes such as CKAP2, SUGT1, LECT1, DCLK1 and SMAD9, involved in cell division and bone development, is a possible mechanism that could explain overgrowth in both patients. This study underlines also that cytogenetic analysis could be performed in patients with overgrowth.
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Affiliation(s)
- Lucie Tosca
- AP-HP, Histologie-Embryologie-Cytogénétique, Hôpital Antoine Béclère, France.
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10
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Li P, Pomianowski P, DiMaio MS, Florio JR, Rossi MR, Xiang B, Xu F, Yang H, Geng Q, Xie J, Mahoney MJ. Genomic characterization of prenatally detected chromosomal structural abnormalities using oligonucleotide array comparative genomic hybridization. Am J Med Genet A 2011; 155A:1605-15. [PMID: 21671377 DOI: 10.1002/ajmg.a.34043] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2010] [Accepted: 03/18/2011] [Indexed: 12/17/2022]
Abstract
Detection of chromosomal structural abnormalities using conventional cytogenetic methods poses a challenge for prenatal genetic counseling due to unpredictable clinical outcomes and risk of recurrence. Of the 1,726 prenatal cases in a 3-year period, we performed oligonucleotide array comparative genomic hybridization (aCGH) analysis on 11 cases detected with various structural chromosomal abnormalities. In nine cases, genomic aberrations and gene contents involving a 3p distal deletion, a marker chromosome from chromosome 4, a derivative chromosome 5 from a 5p/7q translocation, a de novo distal 6q deletion, a recombinant chromosome 8 comprised of an 8p duplication and an 8q deletion, an extra derivative chromosome 9 from an 8p/9q translocation, mosaicism for chromosome 12q with added material of initially unknown origin, an unbalanced 13q/15q rearrangement, and a distal 18q duplication and deletion were delineated. An absence of pathogenic copy number changes was noted in one case with a de novo 11q/14q translocation and in another with a familial insertion of 21q into a 19q. Genomic characterization of the structural abnormalities aided in the prediction of clinical outcomes. These results demonstrated the value of aCGH analysis in prenatal cases with subtle or complex chromosomal rearrangements. Furthermore, a retrospective analysis of clinical indications of our prenatal cases showed that approximately 20% of them had abnormal ultrasound findings and should be considered as high risk pregnancies for a combined chromosome and aCGH analysis.
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Affiliation(s)
- Peining Li
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.
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11
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Vogler C, Gschwind L, Röthlisberger B, Huber A, Filges I, Miny P, Auschra B, Stetak A, Demougin P, Vukojevic V, Kolassa IT, Elbert T, de Quervain DJF, Papassotiropoulos A. Microarray-based maps of copy-number variant regions in European and sub-Saharan populations. PLoS One 2010; 5:e15246. [PMID: 21179565 PMCID: PMC3002949 DOI: 10.1371/journal.pone.0015246] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Accepted: 11/16/2010] [Indexed: 02/03/2023] Open
Abstract
The genetic basis of phenotypic variation can be partially explained by the presence of copy-number variations (CNVs). Currently available methods for CNV assessment include high-density single-nucleotide polymorphism (SNP) microarrays that have become an indispensable tool in genome-wide association studies (GWAS). However, insufficient concordance rates between different CNV assessment methods call for cautious interpretation of results from CNV-based genetic association studies. Here we provide a cross-population, microarray-based map of copy-number variant regions (CNVRs) to enable reliable interpretation of CNV association findings. We used the Affymetrix Genome-Wide Human SNP Array 6.0 to scan the genomes of 1167 individuals from two ethnically distinct populations (Europe, N = 717; Rwanda, N = 450). Three different CNV-finding algorithms were tested and compared for sensitivity, specificity, and feasibility. Two algorithms were subsequently used to construct CNVR maps, which were also validated by processing subsamples with additional microarray platforms (Illumina 1M-Duo BeadChip, Nimblegen 385K aCGH array) and by comparing our data with publicly available information. Both algorithms detected a total of 42669 CNVs, 74% of which clustered in 385 CNVRs of a cross-population map. These CNVRs overlap with 862 annotated genes and account for approximately 3.3% of the haploid human genome. We created comprehensive cross-populational CNVR-maps. They represent an extendable framework that can leverage the detection of common CNVs and additionally assist in interpreting CNV-based association studies.
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Affiliation(s)
- Christian Vogler
- Department of Psychology, University of Basel, and Department of Biomedicine, University Children's Hospital, Basel, Switzerland.
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