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Bui HTP, Huy Do D, Ly HTT, Tran KT, Le HTT, Nguyen KT, Pham LTD, Le HD, Le VS, Mukhopadhyay A, Nguyen LT. De novo copy number variations in candidate genomic regions in patients of severe autism spectrum disorder in Vietnam. PLoS One 2024; 19:e0290936. [PMID: 38451970 PMCID: PMC10919600 DOI: 10.1371/journal.pone.0290936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/09/2023] [Indexed: 03/09/2024] Open
Abstract
Autism spectrum disorder (ASD) is a developmental disorder with a prevalence of around 1% children worldwide and characterized by patient behaviour (communication, social interaction, and personal development). Data on the efficacy of diagnostic tests using copy number variations (CNVs) in candidate genes in ASD is currently around 10% but it is overrepresented by patients of Caucasian background. We report here that the diagnostic success of de novo candidate CNVs in Vietnamese ASD patients is around 6%. We recruited one hundred trios (both parents and a child) where the child was clinically diagnosed with ASD while the parents were not affected. We performed genetic screening to exclude RETT syndrome and Fragile X syndrome and performed genome-wide DNA microarray (aCGH) on all probands and their parents to analyse for de novo CNVs. We detected 1708 non-redundant CNVs in 100 patients and 118 (7%) of them were de novo. Using the filter for known CNVs from the Simons Foundation Autism Research Initiative (SFARI) database, we identified six CNVs (one gain and five loss CNVs) in six patients (3 males and 3 females). Notably, 3 of our patients had a deletion involving the SHANK3 gene-which is the highest compared to previous reports. This is the first report of candidate CNVs in ASD patients from Vietnam and provides the framework for building a CNV based test as the first tier screening for clinical management.
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Affiliation(s)
- Hoa Thi Phuong Bui
- High Technology Center, Vinmec Health Care System, Hai Ba Trung, Ha Noi, Vietnam
- Translational Medicine Laboratory, Biomedical Research Centre, University of Salford, Salford, United Kingdom
| | - Duong Huy Do
- High Technology Center, Vinmec Health Care System, Hai Ba Trung, Ha Noi, Vietnam
| | - Ha Thi Thanh Ly
- High Technology Center, Vinmec Health Care System, Hai Ba Trung, Ha Noi, Vietnam
| | - Kien Trung Tran
- Vinmec Research Institute of Stem Cell and Gene Technology, Vinmec Health Care System, Hai Ba Trung, Ha Noi, Vietnam
| | - Huong Thi Thanh Le
- Vinmec Research Institute of Stem Cell and Gene Technology, Vinmec Health Care System, Hai Ba Trung, Ha Noi, Vietnam
| | - Kien Trung Nguyen
- Vinmec Research Institute of Stem Cell and Gene Technology, Vinmec Health Care System, Hai Ba Trung, Ha Noi, Vietnam
| | - Linh Thi Dieu Pham
- Vinmec Research Institute of Stem Cell and Gene Technology, Vinmec Health Care System, Hai Ba Trung, Ha Noi, Vietnam
| | - Hau Duc Le
- Big Data Institute, Vinmec Health Care System, Hai Ba Trung, Ha Noi, Vietnam
| | - Vinh Sy Le
- Vinmec Research Institute of Stem Cell and Gene Technology, Vinmec Health Care System, Hai Ba Trung, Ha Noi, Vietnam
- University of Engineering and Technology, Vietnam National University Hanoi, Cau Giay, Hanoi, Vietnam
| | - Arijit Mukhopadhyay
- Translational Medicine Laboratory, Biomedical Research Centre, University of Salford, Salford, United Kingdom
| | - Liem Thanh Nguyen
- Vinmec Research Institute of Stem Cell and Gene Technology, Vinmec Health Care System, Hai Ba Trung, Ha Noi, Vietnam
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Kim B, Park Y, Cho SI, Kim MJ, Chae JH, Kim JY, Seong MW, Park SS. Clinical Utility of Methylation-Specific Multiplex Ligation-Dependent Probe Amplification for the Diagnosis of Prader-Willi Syndrome and Angelman Syndrome. Ann Lab Med 2022; 42:79-88. [PMID: 34374352 PMCID: PMC8368237 DOI: 10.3343/alm.2022.42.1.79] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 11/17/2020] [Accepted: 07/06/2021] [Indexed: 12/17/2022] Open
Abstract
Background Prader–Willi syndrome (PWS) and Angelman syndrome (AS) are genomic imprinting disorders that are mainly caused by a deletion on 15q11-q13, the uniparental disomy of chromosome 15, or an imprinting defect. We evaluated the utility of methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) as a diagnostic tool and for demonstrating the relationship between molecular mechanisms and clinical presentation. Methods We performed MS-MLPA using DNA samples from 93 subjects (45 PWS, 24 AS, and 24 non-PWS/AS controls) who had previously undergone MS-PCR for the diagnosis of PWS/AS. We compared the results of both assays, and patients’ clinical phenotypes were reviewed retrospectively. Results MS-MLPA showed a 100% concordance rate with MS-PCR. Among the 45 PWS patients, 26 (57.8%) had a deletion of 15q11-q13, and the others (42.2%) had uniparental disomy 15 or an imprinting defect. Among the 24 AS patients, 16 (66.7%) had a deletion of 15q11-q13, 7 AS patients (29.2%) had uniparental disomy 15 or an imprinting defect, and one AS patient (4.2%) showed an imprinting center deletion. Conclusions MS-MLPA has clinical utility for the diagnosis of PWS/AS, and it is superior to MS-PCR in that it can identify the molecular mechanism underlying the disease.
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Affiliation(s)
- Boram Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Yongsook Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sung Im Cho
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Man Jin Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Jong-Hee Chae
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Ji Yeon Kim
- Biomedical research Institute, Seoul National University Hospital, Seoul, Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.,Biomedical research Institute, Seoul National University Hospital, Seoul, Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.,Biomedical research Institute, Seoul National University Hospital, Seoul, Korea
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Miclea D, Szucs A, Mirea A, Stefan DM, Nazarie F, Bucerzan S, Lazea C, Grama A, Pop TL, Farcas M, Zaharie G, Matyas M, Mager M, Vintan M, Popp R, Alkhzouz C. Diagnostic Usefulness of MLPA Techniques for Recurrent Copy Number Variants Detection in Global Developmental Delay/Intellectual Disability. Int J Gen Med 2021; 14:4511-4515. [PMID: 34429637 PMCID: PMC8378908 DOI: 10.2147/ijgm.s320033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/15/2021] [Indexed: 02/05/2023] Open
Abstract
Background Genetic testing has become a standardized practice in the diagnosis of patients with global developmental delay/intellectual disability (GDD/ID). The aim of this study is to observe the frequency of recurrent copy number variations (CNVs) in patients diagnosed with GDD/ID, using MLPA technique. Methods A total of 501 paediatric patients with GDD/ID were analysed using SALSA MLPA probemix P245 Microdeletion Syndromes-1A, and the technical steps were performed according to the MRC Holland MLPA general protocol. Results Twenty-five of 501 patients (5%) were diagnosed with a microdeletion/microduplication syndrome. Amongst them, 7 of 25 (30%) with clinical suggestion have a confirmed diagnosis, for the other cases the clinical features were not evocative for a specific syndrome. Conclusion This study showed that in cases with a specific clinical diagnosis the MLPA technique could be a useful alternative, less expensive and more efficient to indicate as first intention of a targeted diagnostic test, as it is the case of Williams syndrome, Prader–Willi syndrome or DiGeorge syndrome.
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Affiliation(s)
- Diana Miclea
- Department of Molecular Sciences, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Emergency Clinical Hospital for Children, Cluj-Napoca, Romania
| | - Adriana Szucs
- Department of Molecular Sciences, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Emergency Clinical Hospital for Children, Cluj-Napoca, Romania
| | - Andreea Mirea
- Department of Molecular Sciences, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Emergency Clinical Hospital for Children, Cluj-Napoca, Romania
| | - Delia-Maria Stefan
- Department of Molecular Sciences, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Emergency Clinical Hospital for Children, Cluj-Napoca, Romania
| | - Florina Nazarie
- Department of Molecular Sciences, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Emergency Clinical Hospital for Children, Cluj-Napoca, Romania
| | - Simona Bucerzan
- Emergency Clinical Hospital for Children, Cluj-Napoca, Romania.,Department of Mother and Child, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Cecilia Lazea
- Emergency Clinical Hospital for Children, Cluj-Napoca, Romania.,Department of Mother and Child, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Alina Grama
- Emergency Clinical Hospital for Children, Cluj-Napoca, Romania.,Department of Mother and Child, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Tudor Lucian Pop
- Emergency Clinical Hospital for Children, Cluj-Napoca, Romania.,Department of Mother and Child, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Marius Farcas
- County Emergency Clinical Hospital, Cluj-Napoca, Romania
| | - Gabriela Zaharie
- Department of Mother and Child, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania.,County Emergency Clinical Hospital, Cluj-Napoca, Romania
| | - Melinda Matyas
- Department of Mother and Child, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania.,County Emergency Clinical Hospital, Cluj-Napoca, Romania
| | - Monica Mager
- Emergency Clinical Hospital for Children, Cluj-Napoca, Romania.,Department of Mother and Child, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Mihaela Vintan
- Emergency Clinical Hospital for Children, Cluj-Napoca, Romania.,Department of Mother and Child, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Radu Popp
- Department of Molecular Sciences, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Camelia Alkhzouz
- Emergency Clinical Hospital for Children, Cluj-Napoca, Romania.,Department of Mother and Child, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
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Chromosomal Aberrations in Pediatric Patients with Developmental Delay/Intellectual Disability: A Single-Center Clinical Investigation. BIOMED RESEARCH INTERNATIONAL 2019; 2019:9352581. [PMID: 31781653 PMCID: PMC6875000 DOI: 10.1155/2019/9352581] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/03/2019] [Accepted: 09/18/2019] [Indexed: 12/12/2022]
Abstract
Introduction Chromosomal microarray analysis (CMA) has currently been considered as the first-tier genetic test for patients with developmental delay/intellectual disability (DD/ID) in many countries. In this study, we performed an extensive assessment of the value of CMA for the diagnosis of children with ID/DD in China. Methods A total of 633 patients diagnosed with DD/ID in West China Second University Hospital, Sichuan University, were recruited from January 2014 to March 2019. The patients were classified into 4 subgroups: isolated DD/ID, DD/ID with multiple congenital anomalies (MCA), isolated autism spectrum disorders (ASDs), and DD/ID with epilepsy. CMA was performed on Affymetrix 750K platform. Results Among the 633 patients, 127 cases were identified as having pathogenic copy number variations (pCNVs) with an overall positive rate of 20.06%. Of the 127 cases with abnormal results, 76 cases had 35 types of microdeletion/microduplication syndromes (59.84%) including 5 cases caused by uniparental disomy (UPD), and 18 cases had unbalanced rearrangements (14.17%) including 10 cases inherited from parental balanced translocations or pericentric inversions. The diagnostic yields of pCNVs for the subgroups of isolated DD/ID, DD/ID with MCA, isolated ASD, and DD/ID with epilepsy were 18.07% (60/332), 34.90% (52/149), 3.70% (3/81), and 16.90% (12/71), respectively. The diagnostic yield of pCNVs in DD/ID patients with MCA was significantly higher than that of the other three subgroups, and the diagnostic yield of pCNVs in isolated ASD patients was significantly lower than that of the other three subgroups (p < 0.05). Conclusion Microdeletion/microduplication syndromes and unbalanced rearrangements are probably the main genetic etiological factors for DD/ID. DD/ID patients with MCA have a higher rate of chromosomal aberrations. Parents of DD/ID children with submicroscopic unbalance rearrangements are more likely to have chromosome balanced translocations or pericentric inversions, which might have been missed by karyotyping. CMA can significantly improve the diagnostic rate for patients with DD/ID, which is of great value for medical management and clinical guidance for genetic counseling.
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Jang W, Kim Y, Han E, Park J, Chae H, Kwon A, Choi H, Kim J, Son JO, Lee SJ, Hong BY, Jang DH, Han JY, Lee JH, Kim SY, Lee IG, Sung IK, Moon Y, Kim M, Park JH. Chromosomal Microarray Analysis as a First-Tier Clinical Diagnostic Test in Patients With Developmental Delay/Intellectual Disability, Autism Spectrum Disorders, and Multiple Congenital Anomalies: A Prospective Multicenter Study in Korea. Ann Lab Med 2019; 39:299-310. [PMID: 30623622 PMCID: PMC6340852 DOI: 10.3343/alm.2019.39.3.299] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Revised: 08/06/2018] [Accepted: 11/07/2018] [Indexed: 11/20/2022] Open
Abstract
Background To validate the clinical application of chromosomal microarray analysis (CMA) as a first-tier clinical diagnostic test and to determine the impact of CMA results on patient clinical management, we conducted a multicenter prospective study in Korean patients diagnosed as having developmental delay/intellectual disability (DD/ID), autism spectrum disorders (ASD), and multiple congenital anomalies (MCA). Methods We performed both CMA and G-banding cytogenetics as the first-tier tests in 617 patients. To determine whether the CMA results directly influenced treatment recommendations, the referring clinicians were asked to complete a 39-item questionnaire for each patient separately after receiving the CMA results. Results A total of 122 patients (19.8%) had abnormal CMA results, with either pathogenic variants (N=65) or variants of possible significance (VPS, N=57). Thirty-five well-known diseases were detected: 16p11.2 microdeletion syndrome was the most common, followed by Prader-Willi syndrome, 15q11-q13 duplication, Down syndrome, and Duchenne muscular dystrophy. Variants of unknown significance (VUS) were discovered in 51 patients (8.3%). VUS of genes putatively associated with developmental disorders were found in five patients: IMMP2L deletion, PTCH1 duplication, and ATRNL1 deletion. CMA results influenced clinical management, such as imaging studies, specialist referral, and laboratory testing in 71.4% of patients overall, and in 86.0%, 83.3%, 75.0%, and 67.3% of patients with VPS, pathogenic variants, VUS, and benign variants, respectively. Conclusions Clinical application of CMA as a first-tier test improves diagnostic yields and the quality of clinical management in patients with DD/ID, ASD, and MCA.
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Affiliation(s)
- Woori Jang
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Yonggoo Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Eunhee Han
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Joonhong Park
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Hyojin Chae
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Ahlm Kwon
- Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Hayoung Choi
- Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jiyeon Kim
- Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jung Ok Son
- Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sang Jee Lee
- Department of Rehabilitation Medicine, Daejeon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Daejeon, Korea
| | - Bo Young Hong
- Department of Rehabilitation Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Suwon, Korea
| | - Dae Hyun Jang
- Department of Rehabilitation Medicine, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Incheon, Korea
| | - Ji Yoon Han
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jung Hyun Lee
- Department of Pediatrics, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Suwon, Korea
| | - So Young Kim
- Department of Pediatrics, Yeouido St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - In Goo Lee
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - In Kyung Sung
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Yeonsook Moon
- Department of Laboratory Medicine, Inha University School of Medicine, Incheon, Korea
| | - Myungshin Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea.
| | - Joo Hyun Park
- Department of Rehabilitation Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
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Wang R, Lei T, Fu F, Li R, Jing X, Yang X, Liu J, Li D, Liao C. Application of chromosome microarray analysis in patients with unexplained developmental delay/intellectual disability in South China. Pediatr Neonatol 2019; 60:35-42. [PMID: 29631977 DOI: 10.1016/j.pedneo.2018.03.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 01/22/2018] [Accepted: 03/20/2018] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND AND METHODS Chromosome microarray analysis (CMA) is currently the first-tier diagnostic assay for the evaluation of developmental delay (DD) and intellectual disability (ID) with unknown etiology. Here, we present our clinical experience in implementing whole-genome high-resolution single nucleotide polymorphism (SNP) arrays to investigate 489 patients with unexplained DD/ID in whom standard karyotyping analyses showed normal karyotypes. This study aimed to assess the usefulness of CMA for clinical diagnostic testing in the Chinese population. RESULTS A total of 489 children were classified into three groups: isolated DD/ID (n = 358), DD/ID with epilepsy (n = 49), and DD/ID with other structural anomalies (n = 82). We identified 126 cases (25.8%, 126/489) of pathogenic copy number variants (CNVs) by CMA, including 89 (24.9%, 89/358) with isolated DD/ID, 13 (26.5%, 13/49) with DD/ID with epilepsy, and 24 (29.3%, 24/82) with DD/ID with other structural anomalies. Among the 126 cases of pathogenic CNVs, 79 cases were identified as microdeletion/microduplication syndromes, among which 76 cases were classified as common syndromes, and 3 cases were classified as rare syndromes, including 15q24 microdeletion syndrome, Xq28 microduplication syndrome and Lowe syndrome. Additionally, there were forty-seven cases of non-syndromic pathogenic CNVs. The ABAT, FTSJ1, DYNC1H1, and SETBP1 genes were identified as DD/ID candidate genes. CONCLUSION Our findings suggest the necessity of CMA as a routine diagnostic test for unexplained DD/ID in South China.
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Affiliation(s)
- Rongyue Wang
- Southern Medical University, Guangzhou, 510515, Guangdong, China; The Second Hospital affiliated to Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Tingying Lei
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Fang Fu
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Ru Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Xiangyi Jing
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Xin Yang
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Juan Liu
- Foshan Women and Children's Hospital, Foshan, 528000, Guangdong, China
| | - Dongzhi Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Can Liao
- Southern Medical University, Guangzhou, 510515, Guangdong, China; Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China.
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Han JY, Jang W, Park J, Kim M, Kim Y, Lee IG. Diagnostic approach with genetic tests for global developmental delay and/or intellectual disability: Single tertiary center experience. Ann Hum Genet 2018; 83:115-123. [PMID: 30402882 DOI: 10.1111/ahg.12294] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/17/2018] [Accepted: 10/17/2018] [Indexed: 01/24/2023]
Abstract
The child with global developmental delay (GDD)/intellectual disability (ID) is deserving of the appropriate evaluation available for improving the health and well-being of patients and their families. To better elucidate the diagnostic approach of genetic tests for patients with GDD and/or ID, we evaluated the results in a cohort of 75 patients with clinical features of GDD and/or ID who were referred for diagnostic workup. A total of 75 children were investigated for GDD or ID in the pediatric neurology department. Ten patients (13%, 10/75) with a clinically recognizable syndrome were diagnosed by single-gene analysis. Next, chromosomal microarray was performed as a first-tier test, and 25 patients (33%, 25/75) showed structural abnormalities. Then, two fragile X syndrome (3%, 2/75) were confirmed by FMR1 gene fragment analysis. Thirty-eight remaining patients received a gene panel by next-generation sequencing. Eight patients were found to have an underlying genetic etiology: CHD8, ZDHHC9, MBD5, CACNA1H, SMARCB1, FOXP1, NSD1, and PAX6. As a result, 45 patients (60%, 45/75) had been diagnosed by genetic tests. Among 30 undiagnosed patients, brain structural abnormalities related to GDD/ID were observed in eight patients (11%, 8/75). However, in 22 patients (29%, 22/75), the causes of GDD/ID remained uncertain. A genetic diagnostic approach of GDD/ID by sequential molecular analysis can help in the planning of treatment, assigning the risk of occurrence in siblings, and providing emotional relief for the family.
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Affiliation(s)
- Ji Yoon Han
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Woori Jang
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Joonhong Park
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Myungshin Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yonggoo Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - In Goo Lee
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
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Lee JS, Hwang H, Kim SY, Kim KJ, Choi JS, Woo MJ, Choi YM, Jun JK, Lim BC, Chae JH. Chromosomal Microarray With Clinical Diagnostic Utility in Children With Developmental Delay or Intellectual Disability. Ann Lab Med 2018; 38:473-480. [PMID: 29797819 PMCID: PMC5973923 DOI: 10.3343/alm.2018.38.5.473] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 12/01/2017] [Accepted: 05/10/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Chromosomal microarray (CMA) testing is a first-tier test for patients with developmental delay, autism, or congenital anomalies. It increases diagnostic yield for patients with developmental delay or intellectual disability. In some countries, including Korea, CMA testing is not yet implemented in clinical practice. We assessed the diagnostic utility of CMA testing in a large cohort of patients with developmental delay or intellectual disability in Korea. METHODS We conducted a genome-wide microarray analysis of 649 consecutive patients with developmental delay or intellectual disability at the Seoul National University Children's Hospital. Medical records were reviewed retrospectively. Pathogenicity of detected copy number variations (CNVs) was evaluated by referencing previous reports or parental testing using FISH or quantitative PCR. RESULTS We found 110 patients to have pathogenic CNVs, which included 100 deletions and 31 duplications of 270 kb to 30 Mb. The diagnostic yield was 16.9%, demonstrating the diagnostic utility of CMA testing in clinic. Parental testing was performed in 66 patients, 86.4% of which carried de novo CNVs. In eight patients, pathogenic CNVs were inherited from healthy parents with a balanced translocation, and genetic counseling was provided to these families. We verified five rarely reported deletions on 2p21p16.3, 3p21.31, 10p11.22, 14q24.2, and 21q22.13. CONCLUSIONS This study demonstrated the clinical utility of CMA testing in the genetic diagnosis of patients with developmental delay or intellectual disability. CMA testing should be included as a clinical diagnostic test for all children with developmental delay or intellectual disability.
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Affiliation(s)
- Jin Sook Lee
- Department of Pediatrics, Department of Genome Medicine and Science, Gil Medical Center, Gachon University College of Medicine, Incheon, Korea
| | - Hee Hwang
- Department of Pediatrics, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Soo Yeon Kim
- Department of Pediatrics, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Ki Joong Kim
- Department of Pediatrics, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Jin Sun Choi
- The Institute of Reproductive Medicine and Population, Medical Research Center, Seoul National University College of Medicine, Seoul, Korea
| | - Mi Jung Woo
- The Institute of Reproductive Medicine and Population, Medical Research Center, Seoul National University College of Medicine, Seoul, Korea
| | - Young Min Choi
- The Institute of Reproductive Medicine and Population, Medical Research Center, Seoul National University College of Medicine, Seoul, Korea
- Department of Obstetrics and Gynecology, Seoul National University Hospital, Seoul, Korea
| | - Jong Kwan Jun
- The Institute of Reproductive Medicine and Population, Medical Research Center, Seoul National University College of Medicine, Seoul, Korea
- Department of Obstetrics and Gynecology, Seoul National University Hospital, Seoul, Korea
| | - Byung Chan Lim
- Department of Pediatrics, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea
- The Institute of Reproductive Medicine and Population, Medical Research Center, Seoul National University College of Medicine, Seoul, Korea.
| | - Jong Hee Chae
- Department of Pediatrics, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea
- The Institute of Reproductive Medicine and Population, Medical Research Center, Seoul National University College of Medicine, Seoul, Korea
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Peycheva V, Kamenarova K, Ivanova N, Stamatov D, Avdjieva-Tzavella D, Alexandrova I, Zhelyazkova S, Pacheva I, Dimova P, Ivanov I, Litvinenko I, Bozhinova V, Tournev I, Simeonov E, Mitev V, Jordanova A, Kaneva R. Chromosomal microarray analysis of Bulgarian patients with epilepsy and intellectual disability. Gene 2018; 667:45-55. [DOI: 10.1016/j.gene.2018.05.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 04/13/2018] [Accepted: 05/03/2018] [Indexed: 12/08/2022]
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10
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Cri-du-Chat Syndrome interactome network: Correlating genotypic variations to associated phenotypes. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2018.03.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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11
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Lee SH, Song WJ. Chromosomal Microarray Testing in 42 Korean Patients with Unexplained Developmental Delay, Intellectual Disability, Autism Spectrum Disorders, and Multiple Congenital Anomalies. Genomics Inform 2017; 15:82-86. [PMID: 29020723 PMCID: PMC5637341 DOI: 10.5808/gi.2017.15.3.82] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 08/28/2017] [Accepted: 09/01/2017] [Indexed: 11/20/2022] Open
Abstract
Chromosomal microarray (CMA) is a high-resolution, high-throughput method of identifying submicroscopic genomic copy number variations (CNVs). CMA has been established as the first-line diagnostic test for individuals with developmental delay (DD), intellectual disability (ID), autism spectrum disorders (ASDs), and multiple congenital anomalies (MCAs). CMA analysis was performed in 42 Korean patients who had been diagnosed with unexplained DD, ID, ASDs, and MCAs. Clinically relevant CNVs were discovered in 28 patients. Variants of unknown significance were detected in 13 patients. The diagnostic yield was high (66.7%). CMA is a superior diagnostic tool compared with conventional karyotyping and fluorescent in situ hybridization.
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Affiliation(s)
- Sun Ho Lee
- Department of Diagnostic Laboratory Medicine, Chungnam National University Graduate School of Medicine, Daejeon 35015, Korea
| | - Wung Joo Song
- Department of Genetic Counseling, Konyang University Graduate School of Public Health and Welfare, Daejeon 35365, Korea
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12
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Hnoonual A, Thammachote W, Tim-Aroon T, Rojnueangnit K, Hansakunachai T, Sombuntham T, Roongpraiwan R, Worachotekamjorn J, Chuthapisith J, Fucharoen S, Wattanasirichaigoon D, Ruangdaraganon N, Limprasert P, Jinawath N. Chromosomal microarray analysis in a cohort of underrepresented population identifies SERINC2 as a novel candidate gene for autism spectrum disorder. Sci Rep 2017; 7:12096. [PMID: 28935972 PMCID: PMC5608768 DOI: 10.1038/s41598-017-12317-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 09/07/2017] [Indexed: 01/11/2023] Open
Abstract
Chromosomal microarray (CMA) is now recognized as the first-tier genetic test for detection of copy number variations (CNVs) in patients with autism spectrum disorder (ASD). The aims of this study were to identify known and novel ASD associated-CNVs and to evaluate the diagnostic yield of CMA in Thai patients with ASD. The Infinium CytoSNP-850K BeadChip was used to detect CNVs in 114 Thai patients comprised of 68 retrospective ASD patients (group 1) with the use of CMA as a second line test and 46 prospective ASD and developmental delay patients (group 2) with the use of CMA as the first-tier test. We identified 7 (6.1%) pathogenic CNVs and 22 (19.3%) variants of uncertain clinical significance (VOUS). A total of 29 patients with pathogenic CNVs and VOUS were found in 22% (15/68) and 30.4% (14/46) of the patients in groups 1 and 2, respectively. The difference in detected CNV frequencies between the 2 groups was not statistically significant (Chi square = 1.02, df = 1, P = 0.31). In addition, we propose one novel ASD candidate gene, SERINC2, which warrants further investigation. Our findings provide supportive evidence that CMA studies using population-specific reference databases in underrepresented populations are useful for identification of novel candidate genes.
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Affiliation(s)
- Areerat Hnoonual
- Graduate Program in Biomedical Sciences, Prince of Songkla University, Songkhla, Thailand
| | - Weerin Thammachote
- Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Thipwimol Tim-Aroon
- Division of Medical Genetics, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Kitiwan Rojnueangnit
- Division of Medical Genetics, Department of Pediatrics, Faculty of Medicine, Thammasart University, Pathumthani, Thailand
| | - Tippawan Hansakunachai
- Division of Child Development, Department of Pediatrics, Faculty of Medicine, Thammasart University, Pathumthani, Thailand
| | - Tasanawat Sombuntham
- Division of Developmental-Behavioral Pediatrics, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Rawiwan Roongpraiwan
- Division of Developmental-Behavioral Pediatrics, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Juthamas Worachotekamjorn
- Division of Child Development, Department of Pediatrics, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Jariya Chuthapisith
- Division of Developmental-Behavioral Pediatrics, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Suthat Fucharoen
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, Thailand
| | - Duangrurdee Wattanasirichaigoon
- Division of Medical Genetics, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Nichara Ruangdaraganon
- Division of Developmental-Behavioral Pediatrics, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Pornprot Limprasert
- Division of Human Genetics, Department of Pathology, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand.
| | - Natini Jinawath
- Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand. .,Integrative Computational Bioscience Center, Mahidol University, Salaya, Nakhon Pathom, Thailand.
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13
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Song Q, Chu Y, Yao Y, Peng M, Yang W, Li X, Huang S. Identify latent chromosomal aberrations relevant to myelodysplastic syndromes. Sci Rep 2017; 7:10354. [PMID: 28871208 PMCID: PMC5583229 DOI: 10.1038/s41598-017-10551-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 08/11/2017] [Indexed: 12/02/2022] Open
Abstract
Myelodysplastic syndromes (MDS) are a group of heterogeneous hematologic malignancies. This study aims to identify latent chromosomal abnormalities relevant to MDS, which may optimize the current diagnosis of MDS. Affymetrix CytoScan 750 K microarray platform was utilized to perform a genome-wide detection of chromosomal aberrations in the bone marrow cells of the patients. The findings were compared with the results from traditional karyotypic analysis and FISH to reveal latent chromosomal aberrations. Chromosomal gain, loss, and UPD, and complex karyotypes were identified in those samples. In addition to established cytogenetic aberrations detected by karyotypic analysis, CytoScan 750 K microarray also detected cryptic chromosomal lesions in MDS. Those latent defects underlying multiple gene mutations may construe the clinical variability of MDS. In Conclusion, Affymetrix CytoScan 750 K microarray is efficient in identifying latent chromosomal aberrations in MDS.
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Affiliation(s)
- Qibin Song
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China.
| | - Yuxin Chu
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yi Yao
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Min Peng
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Weihong Yang
- Molecular department, Kindstar global, Wuhan, China
| | - Xiaoqing Li
- Molecular department, Kindstar global, Wuhan, China
| | - Shiang Huang
- Molecular department, Kindstar global, Wuhan, China
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14
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The prevalence of chromosomal aberrations associated with myelodysplastic syndromes in China. Ann Hematol 2016; 95:1241-8. [DOI: 10.1007/s00277-016-2698-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 05/16/2016] [Indexed: 02/05/2023]
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