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Carrillo YD, Rueda-Gaitán P, Gualdrón O, Estrada-Serrato C, Castro-Cuesta TA, Londoño O, Rodríguez-Salazar L, Isaza-Ruget M, Arcos-Burgos M, López Rivera JJ. Diagnostic yield of chromosomal microarray in the largest Latino clinical cohort. Am J Med Genet A 2024; 194:218-225. [PMID: 37795898 DOI: 10.1002/ajmg.a.63427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 08/30/2023] [Accepted: 09/19/2023] [Indexed: 10/06/2023]
Abstract
Copy number variants (CNVs) remain a major etiological cause of neurodevelopmental delay and congenital malformations. Chromosomal microarray analysis (CMA) represents the gold standard for CNVs molecular characterization. We applied CMA throughout the patient's clinical diagnostic workup, as the patient's medical provider requested. We collected CMA results of 3380 patients enrolled for 5 years (2016-2021). We found 830 CNVs in 719 patients with potential clinical significance, that is, (i) pathogenic, (ii) likely pathogenic, and (iii) variants of uncertain significance (VUS), from which 10.6% (predominantly involving chromosomes 15 and 22) were most likely the final cause underpinning the patients' clinical phenotype. For those associated with neurodevelopmental phenotypes, the rate of pathogenic or likely pathogenic findings among the patients with CNVs was 60.75%. When considering epileptic phenotypes, it was 59%. Interestingly, our protocol identified two gains harbored in 17q21.31 and 9q34.3, internationally classified initially as VUS. However, because of their high frequency, we propose that these two VUS be reclassified as likely benign in this widely heterogeneous phenotypic population. These results support the diagnostic yield efficiency of CMA in characterizing CNVs to define the final molecular cause of genetic diseases in this cohort of Colombian patients, the most significant sample of patients from a Latino population, and define new benign polymorphic CNVs.
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Affiliation(s)
- Yina D Carrillo
- Laboratorio Clínico Especializado, Clinica Universitaria Colombia, Clínica Colsanitas, Bogotá, Colombia
| | - Paula Rueda-Gaitán
- Laboratorio Clínico Especializado, Clinica Universitaria Colombia, Clínica Colsanitas, Bogotá, Colombia
| | - Orlando Gualdrón
- Laboratorio Clínico Especializado, Clinica Universitaria Colombia, Clínica Colsanitas, Bogotá, Colombia
- Grupo de investigación INPAC, Grupo Keralty, Bogotá, Colombia
| | - Carlos Estrada-Serrato
- Grupo de Genética Médica, Clínica Universitaria Colombia y Clínica Pediátrica Colsanitas, Clínica Colsanitas, Bogotá, Colombia
| | - Taryn A Castro-Cuesta
- Grupo de Genética Médica, Clínica Universitaria Colombia y Clínica Pediátrica Colsanitas, Clínica Colsanitas, Bogotá, Colombia
| | - Olga Londoño
- Grupo de Genética Médica, Clínica Universitaria Colombia y Clínica Pediátrica Colsanitas, Clínica Colsanitas, Bogotá, Colombia
| | - Luna Rodríguez-Salazar
- Laboratorio Clínico Especializado, Clinica Universitaria Colombia, Clínica Colsanitas, Bogotá, Colombia
| | - Mario Isaza-Ruget
- Grupo de investigación INPAC, Grupo Keralty, Bogotá, Colombia
- Fundación Universitaria Sanitas, Grupo de investigación INPAC, Bogotá, Colombia
- Laboratorio Clínico y de Patología, Clínica Colsanitas, Grupo Keralty, Bogotá, Colombia
| | - Mauricio Arcos-Burgos
- Instituto de Investigaciones Médicas, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Juan Javier López Rivera
- Laboratorio Clínico Especializado, Clinica Universitaria Colombia, Clínica Colsanitas, Bogotá, Colombia
- Grupo de investigación INPAC, Grupo Keralty, Bogotá, Colombia
- Grupo de Genética Médica, Clínica Universitaria Colombia y Clínica Pediátrica Colsanitas, Clínica Colsanitas, Bogotá, Colombia
- Clínica Pediátrica, Clínica Colsanitas, Bogotá, Colombia
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Vorstman JAS, Scherer SW. Contemplating syndromic autism. Genet Med 2023; 25:100919. [PMID: 37330697 DOI: 10.1016/j.gim.2023.100919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/19/2023] Open
Affiliation(s)
- Jacob A S Vorstman
- Department of Psychiatry, Hospital for Sick Children University of Toronto, Toronto, ON, Canada; Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada; The Centre for Applied Genomics, Hospital for Sick Children, Toronto, ON, Canada.
| | - Stephen W Scherer
- Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada; The Centre for Applied Genomics, Hospital for Sick Children, Toronto, ON, Canada; McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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Li Y, Chau MHK, Zhang YX, Zhao Y, Xue S, Li TC, Cao Y, Dong Z, Choy KW, Chung JPW. A pilot investigation of low-pass genome sequencing identifying site-specific variation in chromosomal mosaicisms by a multiple site sampling approach in first-trimester miscarriages. Hum Reprod 2023; 38:1628-1642. [PMID: 37218343 DOI: 10.1093/humrep/dead090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/06/2023] [Indexed: 05/24/2023] Open
Abstract
STUDY QUESTION Can multiple-site low-pass genome sequencing (GS) of products of conception (POCs) improve the detection of genetic abnormalities, especially heterogeneously distributed mosaicism and homogeneously distributed mosaicism in first-trimester miscarriage? SUMMARY ANSWER Multiple-site sampling combined with low-pass GS significantly increased genetic diagnostic yield (77.0%, 127/165) of first-trimester miscarriages, with mosaicisms accounting for 17.0% (28/165), especially heterogeneously distributed mosaicisms (75%, 21/28) that are currently underappreciated. WHAT IS KNOWN ALREADY Aneuploidies are well known to cause first-trimester miscarriage, which are detectable by conventional karyotyping and next-generation sequencing (NGS) on a single-site sampling basis. However, there are limited studies demonstrating the implications of mosaic genetic abnormalities in first-trimester miscarriages, especially when genetic heterogeneity is present in POCs. STUDY DESIGN, SIZE, DURATION This is a cross-sectional cohort study carried out at a university-affiliated public hospital. One hundred seventy-four patients diagnosed with first-trimester miscarriage from December 2018 to November 2021 were offered ultrasound-guided manual vacuum aspiration (USG-MVA) treatment. Products of conception were subjected to multiple-site low-pass GS for the detection of chromosomal imbalances. PARTICIPANTS/MATERIALS, SETTING, METHODS For each POC, multiple sites of villi (three sites on average) were biopsied for low-pass GS. Samples with maternal cell contamination (MCC) and polyploidy were excluded based on the quantitative fluorescence polymerase chain reaction (QF-PCR) results. The spectrum of chromosomal abnormalities, including mosaicism (heterogeneously distributed and homogeneously distributed) and constitutional abnormalities was investigated. Chromosomal microarray analysis and additional DNA fingerprinting were used for validation and MCC exclusion. A cross-platform comparison between conventional karyotyping and our multiple-site approach was also performed. MAIN RESULTS AND THE ROLE OF CHANCE One hundred sixty-five POCs (corresponding to 490 DNA samples) were subjected to low-pass GS. Genetic abnormalities were detected in 77.0% (127/165) of POCs by our novel approach. Specifically, 17.0% (28/165) of cases had either heterogeneously distributed mosaicism (12.7%, 21/165) or homogeneously distributed mosaicism (6.1%, 10/165) (three cases had both types of mosaicism). The remaining 60.0% (99/165) of cases had constitutional abnormalities. In addition, in the 71 cases with karyotyping performed in parallel, 26.8% (19/71) of the results could be revised by our approach. LIMITATIONS, REASONS FOR CAUTION Lack of a normal gestational week-matched cohort might hinder the establishment of a causative link between mosaicisms and first-trimester miscarriage. WIDER IMPLICATIONS OF THE FINDINGS Low-pass GS with multiple-site sampling increased the detection of chromosomal mosaicisms in first-trimester miscarriage POCs. This innovative multiple-site low-pass GS approach enabled the novel discovery of heterogeneously distributed mosaicism, which was prevalent in first-trimester miscarriage POCs and frequently observed in preimplantation embryos, but is currently unappreciated by conventional single-site cytogenetic investigations. STUDY FUNDING/COMPETING INTEREST(S) This work was supported partly by Research Grant Council Collaborative Research Fund (C4062-21GF to K.W.C), Science and Technology Projects in Guangzhou (202102010005 to K.W.C), Guangdong-Hong Kong Technology Cooperation Funding Scheme (TCFS), Innovation and Technology Fund (GHP/117/19GD to K.W.C), HKOG Direct Grant (2019.050 to J.P.W.C), and Hong Kong Health and Medical Research Fund (05160406 to J.P.W.C). The authors have no competing interests to declare. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- Ying Li
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- Fertility Preservation Research Centre, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Matthew Hoi Kin Chau
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- Fertility Preservation Research Centre, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Ying Xin Zhang
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China
- Center of Prenatal Diagnosis, Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Yilin Zhao
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Shuwen Xue
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Tin Chiu Li
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Ye Cao
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- Fertility Preservation Research Centre, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Zirui Dong
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- Fertility Preservation Research Centre, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Kwong Wai Choy
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- Fertility Preservation Research Centre, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China
| | - Jacqueline Pui Wah Chung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- Fertility Preservation Research Centre, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
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de Carvalho AFL, Alves ES, Pitanga PML, Ribeiro EM, Doriqui MJR, Toralles MBP, Topázio BA, dos Santos JF, de Lima RLLF, Kulikowski LD, Acosta AX. Identifying Genetic Etiology in Patients with Intellectual Disability: An Experience in Public Health Services in Northeastern Brazil. J Pediatr Genet 2022. [DOI: 10.1055/s-0042-1757888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
AbstractIntellectual disability (ID) is considered a common neuropsychiatric disorder that affects up to 3% of the population. The etiologic origin of ID may be genetic, environmental, and multifactorial. Chromosomopathies are relatively common among the genetic causes of ID, especially in the most severe cases and those associated with dysmorphic features. Currently, the application of new molecular cytogenetics technologies has increasingly allowed the identification of microdeletions, microduplications, and unbalanced translocations as causes of ID. The objective of this study was to investigate the etiology of ID in patients admitted to a public hospital in Northeastern Brazil. In total, 119 patients with ID who had normal karyotypes and fragile X exams participated in this study. The patients were initially physically examined for microdeletion syndromes and then tested using fluorescence in situ hybridization (FISH), multiplex ligation-dependent probe amplification (MLPA), methylation-sensitive polymerase chain reaction (MS-PCR), and chromosome microarray analysis (CMA), according to clinical suspicion. Patients with no diagnoses after FISH, MLPA, and/or MS-PCR evaluations were subsequently tested by CMA. The rate of etiologic diagnoses of ID in the current study was 28%. FISH diagnosed 25 out of 79 tested (31%), MLPA diagnosed 26 out of 79 tested (32%), MS-PCR diagnosed 7 out of 20 tested (35%), and the single nucleotide polymorphism array diagnosed 6 out of 27 tested (22%). Although the CMA is the most complete and recommended tool for the diagnosis of microdeletions, microduplications, and unbalance translocations in patients with ID, FISH, MLPA, and MS-PCR testing can be used as the first tests for specific syndromes, as long as the patients are first physically screened clinically, especially in the public health networks system in Brazil, where resources are scarce.
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Affiliation(s)
| | - Esmeralda Santos Alves
- Laboratory of Human Genetics and Mutagenesis, Institute of Biology, Federal University Bahia (UFBA), Salvador, Bahia, Brazil
| | - Paula Monique Leite Pitanga
- Laboratory of Human Genetics and Mutagenesis, Institute of Biology, Federal University Bahia (UFBA), Salvador, Bahia, Brazil
| | - Erlane Marques Ribeiro
- Faculty of Medicine Estacio of Juazeiro Norte, Estacio-FMJ, Hospital Infantil Albert Sabin, Fortaleza, Ceará, Brazil
| | | | - Maria Betânia Pereira Toralles
- Medical School of Medicine, Medical Genetic Service – Edgard Santos Teaching Hospital/Federal University of Bahia, Salvador, Bahia, Brazil
| | - Bianca Arcaro Topázio
- Laboratory of Human Genetics and Mutagenesis, Institute of Biology, Federal University Bahia (UFBA), Salvador, Bahia, Brazil
| | - Jéssica Fernandes dos Santos
- Laboratory of Human Genetics and Mutagenesis, Institute of Biology, Federal University Bahia (UFBA), Salvador, Bahia, Brazil
| | | | | | - Angelina Xavier Acosta
- Medical School of Medicine, Medical Genetic Service – Edgard Santos Teaching Hospital/Federal University of Bahia, Salvador, Bahia, Brazil
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Drackley A, Brew C, Wlodaver A, Spencer S, Leuer K, Rathbun P, Charrow J, Wieneke X, Lee Yap K, Ing A. Utility and Outcomes of the 2019 American College of Medical Genetics and Genomics-Clinical Genome Resource Guidelines for Interpretation of Copy Number Variants with Borderline Classifications at an Academic Clinical Diagnostic Laboratory. J Mol Diagn 2022; 24:1100-1111. [PMID: 35868509 DOI: 10.1016/j.jmoldx.2022.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/06/2022] [Accepted: 06/27/2022] [Indexed: 11/26/2022] Open
Abstract
In 2019, American College of Medical Genetics and Genomics and the Clinical Genome Resource published updated technical standards for the interpretation and reporting of copy number variants (CNVs), introducing a semiquantitative classification system that aims to foster greater standardization and consistency between laboratories. Evaluation of these guidelines' performance will inform laboratories about the impact of their implementation into clinical practice. A total of 145 difficult-to-classify CNVs, originally assessed by an academic molecular diagnostic laboratory, were re-interpreted/classified according to the American College of Medical Genetics and Genomics-Clinical Genome Resource guidelines. Classifications between interpretation systems were then compared. The concordance rate was 60.7%, and significantly more variants of uncertain significance were obtained when using the guidelines (n = 98) versus the laboratory's classification system (n = 49; P < 0.001). The concordance rate was presumably impacted by the intentionally unclear nature of the selected variants. The difference in variant of uncertain significance rate was largely due to laboratory-specific practices for variant interpretation and reporting, as well as differences in utilization of general population data. Laboratory-specific policies and practices may need to be addressed for true standardization to be achieved. Challenges to consistent guideline utilization are centered around the general lack of high-quality curated data available for CNV interpretations and the inherent subjectivity in the selection of evidence criteria and application of evidence points. Multiple aspects of the guidelines were highlighted as potential opportunities for subsequent refinements to further improve classification standardization.
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Affiliation(s)
- Andy Drackley
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Center for Genomics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Division of Genetics, Birth Defects and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Casey Brew
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Center for Genomics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Division of Genetics, Birth Defects and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Alissa Wlodaver
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Center for Genomics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | - Sara Spencer
- Department of Obstetrics and Gynecology, Northwestern Medicine, Chicago, Illinois; Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Katrin Leuer
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Center for Genomics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Pamela Rathbun
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Center for Genomics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Joel Charrow
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Division of Genetics, Birth Defects and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Xuwen Wieneke
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Center for Genomics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | - Kai Lee Yap
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Center for Genomics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Northwestern University Feinberg School of Medicine, Chicago, Illinois.
| | - Alexander Ing
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Center for Genomics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Division of Genetics, Birth Defects and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Northwestern University Feinberg School of Medicine, Chicago, Illinois.
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8p21.3 deletions are rare causes of non-syndromic autism spectrum disorder. Neurogenetics 2021; 22:207-213. [PMID: 33683518 DOI: 10.1007/s10048-021-00635-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 02/23/2021] [Indexed: 10/22/2022]
Abstract
A de novo 0.95 Mb 8p21.3 deletion had been identified in an individual with non-syndromic autism spectrum disorder (ASD) through high-resolution copy number variant analysis. Subsequent screening of in-house and publicly available databases resulted in the identification of six additional individuals with 8p21.3 deletions. Through case-based reasoning, we conclude that 8p21.3 deletions are rare causes of non-syndromic neurodevelopmental and neuropsychiatric disorders. Based on literature data, we highlight six genes within the region of minimal overlap as potential ASD genes or genes for neuropsychiatric disorders: DMTN, EGR3, FGF17, LGI3, PHYHIP, and PPP3CC.
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Factors Affecting Family Compliance with Genetic Testing of Children Diagnosed with Autism Spectrum Disorder. J Autism Dev Disord 2020; 51:1201-1209. [PMID: 32651724 DOI: 10.1007/s10803-020-04589-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
There is broad consensus about the importance of post-diagnostic genetic testing for children with ASD. However, the extent of compliance with these tests and the factors affecting compliance have rarely been examined. We surveyed a sample of 114 families with a child with ASD in Israel, where such genetic testing is funded by the government. We found that only one-third of these families completed post-diagnosis genetic testing for their child. The main factor influencing compliance was the doctor's recommendation (OR 11.6; 95% CI 3.2-42.4; p < 0.001). Furthermore, > 50% of the non-compliant families reported that genetic testing was irrelevant to them. Our findings highlight the importance of providing clear recommendations and explanations regarding the benefits and relevance of post-diagnosis genetic testing for children with ASD.
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Wang J, Wang Y, Wang L, Chen WY, Sheng M. The diagnostic yield of intellectual disability: combined whole genome low-coverage sequencing and medical exome sequencing. BMC Med Genomics 2020; 13:70. [PMID: 32429945 PMCID: PMC7236547 DOI: 10.1186/s12920-020-0726-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 04/29/2020] [Indexed: 02/06/2023] Open
Abstract
Background Intellectual disability (ID) is a heterogeneous neurodevelopmental disorder with a complex genetic underpinning in its etiology. Chromosome microarray (CMA) is recommended as the first-tier diagnostic test for ID due to high detection rate of copy number variation (CNV). Methods To identify an appropriate clinical detection scheme for ID in Han Chinese patients, whole genome low-coverage sequencing was performed as the first-tier diagnostic test, and medical exome sequencing (MES) as the second-tier diagnostic test for patients with negative results of CNVs. Results A total of 19 pathogenic CNVs in 16/95(16.84%) ID patients and 10 pathogenic single-nucleotide variations (SNVs), including 6 novel mutations in 8/95(8.42%) ID patients were identified on whom no pathogenic CNVs were discovered. The detection rate of CNVs in ID with multiple congenital anomalies (MCA) subgroup was significantly higher than ID with autism spectrum disorders and other IDs subgroups. And the single-nucleotide variations showed a higher occurrence rate in the other IDs subgroup. Conclusions There were differences in the diagnostic yields of different variation types among the three ID subgroups. Our findings provided a new perspective on appropriate clinical detection scheme in different ID subgroups based on statistically significant differences among the three ID subgroups. The application of whole genome low-coverage sequencing as the first-tier diagnostic test for ID with MCA subgroup and MES as the first-tier diagnostic test for other ID subgroup was considered as an efficient clinical detection scheme.
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Affiliation(s)
- Jun Wang
- Department of Neurology, Affiliated Children's Hospital of Capital Institute of Pediatrics, Beijing, 100020, China.
| | - Yan Wang
- Department of Neurology, Affiliated Children's Hospital of Capital Institute of Pediatrics, Beijing, 100020, China
| | - Liwen Wang
- Department of Neurology, Affiliated Children's Hospital of Capital Institute of Pediatrics, Beijing, 100020, China
| | - Wang Yang Chen
- Kaiumph Medical Diagnostics Co,Ltd, Beijing, 100102, China
| | - Min Sheng
- Kaiumph Medical Diagnostics Co,Ltd, Beijing, 100102, China
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Yokoi T, Enomoto Y, Tsurusaki Y, Harada N, Saito T, Nagai JI, Naruto T, Kurosawa K. An efficient genetic test flow for multiple congenital anomalies and intellectual disability. Pediatr Int 2020; 62:556-561. [PMID: 31955471 DOI: 10.1111/ped.14159] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 04/10/2019] [Accepted: 01/16/2020] [Indexed: 11/29/2022]
Abstract
BACKGROUND Genetic testing has enabled the diagnosis of multiple congenital anomalies and/or intellectual disabilities. However, because of the phenotypic variability in these disorders, selection of an appropriate genetic test can be difficult and complex. For clinical examination, particularly in clinical facilities, a simple and standardized system is needed. METHODS We compared microarray comparative genomic hybridization and clinical exome sequencing with regard to diagnostic yield, cost, and time required to reach a definitive diagnosis. After first performing G-banding for 200 patients with multiple congenital anomalies and/or intellectual disability, as a subsequent genetic test, microarray and clinical exome sequencing were compared with regard to diagnostic yield, cost, and time required. RESULTS There was no obvious difference in the diagnostic rate between the two methods; however, clinical exome sequencing was superior in terms of cost and time. In addition, clinical exome sequencing could sufficiently identify copy number variants, and even smaller copy number variants could be identified. CONCLUSIONS Clinical exome sequencing should be implemented earlier as a genetic test for undiagnosed patients with multiple congenital anomalies and/or intellectual disabilities. Our results can be used to establish inspection methods in clinical facilities.
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Affiliation(s)
- Takayuki Yokoi
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan.,Clinical Research Institute, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Yumi Enomoto
- Department of Clinical Laboratory, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Yoshinori Tsurusaki
- Department of Clinical Laboratory, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Noriaki Harada
- Department of Pediatrics, Jikei University School of Medicine, Tokyo, Japan
| | - Toshiyuki Saito
- Department of Pediatrics, Jikei University School of Medicine, Tokyo, Japan
| | - Jun-Ichi Nagai
- Department of Pediatrics, Jikei University School of Medicine, Tokyo, Japan
| | - Takuya Naruto
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University Graduate School, Tokyo, Japan
| | - Kenji Kurosawa
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
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Wang H, Dong Z, Zhang R, Chau MHK, Yang Z, Tsang KYC, Wong HK, Gui B, Meng Z, Xiao K, Zhu X, Wang Y, Chen S, Leung TY, Cheung SW, Kwok YK, Morton CC, Zhu Y, Choy KW. Low-pass genome sequencing versus chromosomal microarray analysis: implementation in prenatal diagnosis. Genet Med 2020; 22:500-510. [PMID: 31447483 PMCID: PMC7042067 DOI: 10.1038/s41436-019-0634-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 07/26/2019] [Indexed: 11/12/2022] Open
Abstract
PURPOSE Emerging studies suggest that low-pass genome sequencing (GS) provides additional diagnostic yield of clinically significant copy-number variants (CNVs) compared with chromosomal microarray analysis (CMA). However, a prospective back-to-back comparison evaluating accuracy, efficacy, and incremental yield of low-pass GS compared with CMA is warranted. METHODS A total of 1023 women undergoing prenatal diagnosis were enrolled. Each sample was subjected to low-pass GS and CMA for CNV analysis in parallel. CNVs were classified according to guidelines of the American College of Medical Genetics and Genomics. RESULTS Low-pass GS not only identified all 124 numerical disorders or pathogenic or likely pathogenic (P/LP) CNVs detected by CMA in 121 cases (11.8%, 121/1023), but also defined 17 additional and clinically relevant P/LP CNVs in 17 cases (1.7%, 17/1023). In addition, low-pass GS significantly reduced the technical repeat rate from 4.6% (47/1023) for CMA to 0.5% (5/1023) and required less DNA (50 ng) as input. CONCLUSION In the context of prenatal diagnosis, low-pass GS identified additional and clinically significant information with enhanced resolution and increased sensitivity of detecting mosaicism as compared with the CMA platform used. This study provides strong evidence for applying low-pass GS as an alternative prenatal diagnostic test.
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Affiliation(s)
- Huilin Wang
- Maternal-Fetal Medicine Institute, Bao'an Maternity and Child Health Hospital Affiliated to Jinan University School of Medicine, Key Laboratory of Birth Defects Research, Birth Defects Prevention Research and Transformation Team, Shenzhen, China
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Zirui Dong
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Rui Zhang
- Maternal-Fetal Medicine Institute, Bao'an Maternity and Child Health Hospital Affiliated to Jinan University School of Medicine, Key Laboratory of Birth Defects Research, Birth Defects Prevention Research and Transformation Team, Shenzhen, China
| | - Matthew Hoi Kin Chau
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Zhenjun Yang
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Kathy Yin Ching Tsang
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Hoi Kin Wong
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Baoheng Gui
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Zhuo Meng
- Maternal-Fetal Medicine Institute, Bao'an Maternity and Child Health Hospital Affiliated to Jinan University School of Medicine, Key Laboratory of Birth Defects Research, Birth Defects Prevention Research and Transformation Team, Shenzhen, China
| | - Kelin Xiao
- Maternal-Fetal Medicine Institute, Bao'an Maternity and Child Health Hospital Affiliated to Jinan University School of Medicine, Key Laboratory of Birth Defects Research, Birth Defects Prevention Research and Transformation Team, Shenzhen, China
| | - Xiaofan Zhu
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Yanfang Wang
- Maternal-Fetal Medicine Institute, Bao'an Maternity and Child Health Hospital Affiliated to Jinan University School of Medicine, Key Laboratory of Birth Defects Research, Birth Defects Prevention Research and Transformation Team, Shenzhen, China
| | - Shaoyun Chen
- Maternal-Fetal Medicine Institute, Bao'an Maternity and Child Health Hospital Affiliated to Jinan University School of Medicine, Key Laboratory of Birth Defects Research, Birth Defects Prevention Research and Transformation Team, Shenzhen, China
| | - Tak Yeung Leung
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- The Chinese University of Hong Kong-Baylor College of Medicine Joint Center For Medical Genetics, Hong Kong, China
| | - Sau Wai Cheung
- The Chinese University of Hong Kong-Baylor College of Medicine Joint Center For Medical Genetics, Hong Kong, China
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yvonne K Kwok
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Cynthia C Morton
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
- Manchester Center for Audiology and Deafness, University of Manchester, Manchester Academic Health Science Center, Manchester, UK.
| | - Yuanfang Zhu
- Maternal-Fetal Medicine Institute, Bao'an Maternity and Child Health Hospital Affiliated to Jinan University School of Medicine, Key Laboratory of Birth Defects Research, Birth Defects Prevention Research and Transformation Team, Shenzhen, China.
| | - Kwong Wai Choy
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.
- The Chinese University of Hong Kong-Baylor College of Medicine Joint Center For Medical Genetics, Hong Kong, China.
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11
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Uddin M, Wang Y, Woodbury-Smith M. Artificial intelligence for precision medicine in neurodevelopmental disorders. NPJ Digit Med 2019; 2:112. [PMID: 31799421 PMCID: PMC6872596 DOI: 10.1038/s41746-019-0191-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 10/29/2019] [Indexed: 12/23/2022] Open
Abstract
The ambition of precision medicine is to design and optimize the pathway for diagnosis, therapeutic intervention, and prognosis by using large multidimensional biological datasets that capture individual variability in genes, function and environment. This offers clinicians the opportunity to more carefully tailor early interventions- whether treatment or preventative in nature-to each individual patient. Taking advantage of high performance computer capabilities, artificial intelligence (AI) algorithms can now achieve reasonable success in predicting risk in certain cancers and cardiovascular disease from available multidimensional clinical and biological data. In contrast, less progress has been made with the neurodevelopmental disorders, which include intellectual disability (ID), autism spectrum disorder (ASD), epilepsy and broader neurodevelopmental disorders. Much hope is pinned on the opportunity to quantify risk from patterns of genomic variation, including the functional characterization of genes and variants, but this ambition is confounded by phenotypic and etiologic heterogeneity, along with the rare and variable penetrant nature of the underlying risk variants identified so far. Structural and functional brain imaging and neuropsychological and neurophysiological markers may provide further dimensionality, but often require more development to achieve sensitivity for diagnosis. Herein, therefore, lies a precision medicine conundrum: can artificial intelligence offer a breakthrough in predicting risks and prognosis for neurodevelopmental disorders? In this review we will examine these complexities, and consider some of the strategies whereby artificial intelligence may overcome them.
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Affiliation(s)
- Mohammed Uddin
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
- 2The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
| | - Yujiang Wang
- 3Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
- 4School of Computing, Newcastle University, Newcastle upon Tyne, UK
| | - Marc Woodbury-Smith
- 2The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
- 3Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
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12
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Cheng SSW, Chan KYK, Leung KKP, Au PKC, Tam WK, Li SKM, Luk HM, Kan ASY, Chung BHY, Lo IFM, Tang MHY. Experience of chromosomal microarray applied in prenatal and postnatal settings in Hong Kong. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 181:196-207. [PMID: 30903683 DOI: 10.1002/ajmg.c.31697] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/06/2019] [Accepted: 03/07/2019] [Indexed: 12/14/2022]
Abstract
Chromosomal microarray (CMA) is recommended as a first tier investigation for patients with developmental delay (DD), intellectual disability (ID), autistic spectrum disorder (ASD), and multiple congenital anomalies (MCA). It is widely used in the prenatal and postnatal settings for detection of chromosomal aberrations. This is a retrospective review of all array comparative genomic hybridization (aCGH/ array CGH) findings ascertained in two major prenatal and postnatal genetic diagnostic centers in Hong Kong from June 2012 to December 2017. Medical records were reviewed for cases with pathogenic and variants of uncertain clinical significance (VUS). Classification of copy number variants (CNVs) was based on current knowledge and experience by August 2018. The aims of this review are to study the diagnostic yield of array CGH application in prenatal and postnatal settings in Hong Kong and to describe the spectrum of abnormalities found. Prenatal indications included abnormal ultrasound findings, positive Down syndrome screening, abnormal noninvasive prenatal test results, advanced maternal age and family history of chromosomal or genetic abnormalities. Postnatal indications included unexplained DD, ID, ASD, and MCA. A total of 1,261 prenatal subjects and 3,096 postnatal patients were reviewed. The prenatal diagnostic yield of pathogenic CNV and VUS (excluding those detectable by karyotype) was 3.5%. The postnatal diagnostic yield of pathogenic CNV was 15.2%. The detection rates for well-defined microdeletion and microduplication syndromes were 4.6% in prenatal and 6.1% (1 in 16 index patients) in postnatal cases, respectively. Chromosomes 15, 16, and 22 accounted for over 21 and 25% of pathogenic CNVs detected in prenatal and postnatal cohorts, respectively. This review provides the first large scale overview of genomic imbalance of mostly Chinese patients in prenatal and postnatal settings.
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Affiliation(s)
| | - Kelvin Y K Chan
- Prenatal Diagnostic Laboratory, Tsan Yuk Hospital, Hong Kong
| | | | - Patrick K C Au
- Prenatal Diagnostic Laboratory, Tsan Yuk Hospital, Hong Kong
| | - Wai-Keung Tam
- Prenatal Diagnostic Laboratory, Tsan Yuk Hospital, Hong Kong
| | - Samuel K M Li
- Prenatal Diagnostic Laboratory, Tsan Yuk Hospital, Hong Kong
| | - Ho-Ming Luk
- Department of Health, Clinical Genetic Service, Hong Kong
| | - Anita S Y Kan
- Department of Obstetrics and Gynaecology, Queen Mary Hospital, Hong Kong
| | - Brian H Y Chung
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, HKSAR.,Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, HKSAR
| | - Ivan F M Lo
- Department of Health, Clinical Genetic Service, Hong Kong
| | - Mary H Y Tang
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, HKSAR
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13
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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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14
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Lumaka A, Race V, Peeters H, Corveleyn A, Coban-Akdemir Z, Jhangiani SN, Song X, Mubungu G, Posey J, Lupski JR, Vermeesch JR, Lukusa P, Devriendt K. A comprehensive clinical and genetic study in 127 patients with ID in Kinshasa, DR Congo. Am J Med Genet A 2018; 176:1897-1909. [PMID: 30088852 DOI: 10.1002/ajmg.a.40382] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 06/06/2018] [Indexed: 12/21/2022]
Abstract
Pathogenic variants account for 4 to 41% of patients with intellectual disability (ID) or developmental delay (DD). In Sub-Saharan Africa, the prevalence of ID is thought to be higher, but data in Central Africa are limited to some case reports. In addition, clinical descriptions of some syndromes are not available for this population. This study aimed at providing an estimate for the fraction of ID/DD for which an underlying etiological genetic cause may be elucidated and provide insights into their clinical presentation in special institutions in a Central African country. A total of 127 patients (33 females and 94 males, mean age 10.03 ± 4.68 years), were recruited from six institutions across Kinshasa. A clinical diagnosis was achieved in 44 but molecular confirmation was achieved in 21 of the 22 patients with expected genetic defect (95% clinical sensitivity). Identified diseases included Down syndrome (15%), submicroscopic copy number variants (9%), aminoacylase deficiency (0.8%), Partington syndrome in one patient (0.8%) and his similarly affected brother, X-linked syndromic Mental Retardation type 33 (0.8%), and two conditions without clear underlying molecular genetic etiologies (Oculo-Auriculo-Vertebral and Amniotic Bands Sequence). We have shown that genetic etiologies, similar to those reported in Caucasian subjects, are a common etiologic cause of ID in African patients from Africa. We have confirmed the diagnostic utility of clinical characterization prior to genetic testing. Finally, our clinical descriptions provide insights into the presentation of these genetic diseases in African patients.
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Affiliation(s)
- Aimé Lumaka
- Centre for Human Genetics, Faculty of Medicine, University of Kinshasa, Kinshasa, DR, Congo.,Département des Sciences Biomédicales et Précliniques, GIGA-R, Laboratoire de Génétique Humaine, University of Liège, Liège, Belgium.,Institut National de Recherche Biomédicale, Kinshasa, DR, Congo.,Department of Pediatrics, Faculty of Medicine, University of Kinshasa, Kinshasa, DR, Congo
| | - Valerie Race
- Centre for Human Genetics, University Hospital, University of Leuven, Leuven, Belgium
| | - Hilde Peeters
- Centre for Human Genetics, University Hospital, University of Leuven, Leuven, Belgium
| | - Anniek Corveleyn
- Centre for Human Genetics, University Hospital, University of Leuven, Leuven, Belgium
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Shalini N Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Xiaofei Song
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Gerrye Mubungu
- Centre for Human Genetics, Faculty of Medicine, University of Kinshasa, Kinshasa, DR, Congo.,Institut National de Recherche Biomédicale, Kinshasa, DR, Congo.,Department of Pediatrics, Faculty of Medicine, University of Kinshasa, Kinshasa, DR, Congo.,Centre for Human Genetics, University Hospital, University of Leuven, Leuven, Belgium
| | - Jennifer Posey
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Genetics Clinic service, Texas Children's Hospital, Houston, Texas
| | - Joris R Vermeesch
- Centre for Human Genetics, University Hospital, University of Leuven, Leuven, Belgium
| | - Prosper Lukusa
- Centre for Human Genetics, Faculty of Medicine, University of Kinshasa, Kinshasa, DR, Congo.,Département des Sciences Biomédicales et Précliniques, GIGA-R, Laboratoire de Génétique Humaine, University of Liège, Liège, Belgium.,Institut National de Recherche Biomédicale, Kinshasa, DR, Congo.,Centre for Human Genetics, University Hospital, University of Leuven, Leuven, Belgium
| | - Koenraad Devriendt
- Centre for Human Genetics, University Hospital, University of Leuven, Leuven, Belgium
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15
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Xu M, Ji Y, Zhang T, Jiang X, Fan Y, Geng J, Li F. Clinical Application of Chromosome Microarray Analysis in Han Chinese Children with Neurodevelopmental Disorders. Neurosci Bull 2018; 34:981-991. [PMID: 29948840 DOI: 10.1007/s12264-018-0238-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 04/05/2018] [Indexed: 02/04/2023] Open
Abstract
Chromosome microarray analysis (CMA) is a cost-effective molecular cytogenetic technique that has been used as a first-line diagnostic test in neurodevelopmental disorders in the USA since 2011. The impact of CMA results on clinical practice in China is not yet well studied, so we aimed to better evaluate this phenomenon. We analyzed the CMA results from 434 patients in our clinic, and characterized their molecular diagnoses, clinical features, and follow-up clinical actions based on these results. The overall diagnostic yield for our patients was 13.6% (59 out of 434). This gave a detection rate of 14.7% for developmental delay/intellectual disability (DD/ID, 38/259) and 12% for autism spectrum disorders (ASDs, 21/175). Thirty-three recurrent (n ≥ 2) variants were found, distributed at six chromosomal loci involving known chromosome syndromes (such as DiGeorge, Williams Beuren, and Angelman/Prader-Willi syndromes). The spectrum of positive copy number variants in our study was comparable to that reported in Caucasian populations, but with specific characteristics. Parental origin tests indicated an effect involving a significant maternal transmission bias to sons. The majority of patients with positive results (94.9%) had benefits, allowing earlier diagnosis (36/59), prioritized full clinical management (28/59), medication changes (7/59), a changed prognosis (30/59), and prenatal genetic counseling (15/59). Our results provide information on de novo mutations in Chinese children with DD/ID and/or ASDs. Our data showed that microarray testing provides immediate clinical utility for patients. It is expected that the personalized medical care of children with developmental disabilities will lead to improved outcomes in long-term developmental potential. We advocate using the diagnostic yield of clinically actionable results to evaluate CMA as it provides information of both clinical validity and clinical utility.
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Affiliation(s)
- Mingyu Xu
- Developmental and Behavioral Pediatric & Child Primary Care Department, Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Yiting Ji
- Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Ting Zhang
- Developmental and Behavioral Pediatric & Child Primary Care Department, Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Xiaodong Jiang
- Developmental and Behavioral Pediatric & Child Primary Care Department, Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.,Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430016, China
| | - Yun Fan
- Developmental and Behavioral Pediatric & Child Primary Care Department, Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Juan Geng
- Hangzhou Joingenome Diagnostics, Hangzhou, 311188, China.
| | - Fei Li
- Developmental and Behavioral Pediatric & Child Primary Care Department, Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China. .,Shanghai Institute of Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.
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16
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Lacey CJ, Doudney K, Bridgman PG, George PM, Mulder RT, Zarifeh JJ, Kimber B, Cadzow MJ, Black MA, Merriman TR, Lehnert K, Bickley VM, Pearson JF, Cameron VA, Kennedy MA. Copy number variants implicate cardiac function and development pathways in earthquake-induced stress cardiomyopathy. Sci Rep 2018; 8:7548. [PMID: 29765130 PMCID: PMC5954162 DOI: 10.1038/s41598-018-25827-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 04/25/2018] [Indexed: 02/07/2023] Open
Abstract
The pathophysiology of stress cardiomyopathy (SCM), also known as takotsubo syndrome, is poorly understood. SCM usually occurs sporadically, often in association with a stressful event, but clusters of cases are reported after major natural disasters. There is some evidence that this is a familial condition. We have examined three possible models for an underlying genetic predisposition to SCM. Our primary study cohort consists of 28 women who suffered SCM as a result of two devastating earthquakes that struck the city of Christchurch, New Zealand, in 2010 and 2011. To seek possible underlying genetic factors we carried out exome analysis, genotyping array analysis, and array comparative genomic hybridization on these subjects. The most striking finding was the observation of a markedly elevated rate of rare, heterogeneous copy number variants (CNV) of uncertain clinical significance (in 12/28 subjects). Several of these CNVs impacted on genes of cardiac relevance including RBFOX1, GPC5, KCNRG, CHODL, and GPBP1L1. There is no physical overlap between the CNVs, and the genes they impact do not appear to be functionally related. The recognition that SCM predisposition may be associated with a high rate of rare CNVs offers a novel perspective on this enigmatic condition.
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Affiliation(s)
- Cameron J Lacey
- Department of Psychological Medicine, University of Otago, Christchurch, New Zealand.
| | - Kit Doudney
- Molecular Pathology Laboratory, Canterbury Health Laboratories, Canterbury District Health Board, Christchurch, New Zealand
| | - Paul G Bridgman
- Department of Cardiology, Christchurch Hospital, Christchurch, New Zealand
| | - Peter M George
- Molecular Pathology Laboratory, Canterbury Health Laboratories, Canterbury District Health Board, Christchurch, New Zealand
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Roger T Mulder
- Department of Psychological Medicine, University of Otago, Christchurch, New Zealand
| | - Julie J Zarifeh
- Psychiatric Consultation Service, Christchurch Hospital, Canterbury District Health Board, Christchurch, New Zealand
| | - Bridget Kimber
- Department of Psychological Medicine, University of Otago, Christchurch, New Zealand
| | - Murray J Cadzow
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Michael A Black
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Tony R Merriman
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Klaus Lehnert
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Vivienne M Bickley
- Molecular Pathology Laboratory, Canterbury Health Laboratories, Canterbury District Health Board, Christchurch, New Zealand
| | - John F Pearson
- Biostatistics and Computational Biology Unit, University of Otago, Christchurch, New Zealand
| | - Vicky A Cameron
- Christchurch Heart Institute, Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Martin A Kennedy
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
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17
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Kim HJ, Park CI, Lim JW, Lee GM, Cho E, Kim HJ. Phenotypic Analysis of Korean Patients with Abnormal Chromosomal Microarray in Patients with Unexplained Developmental Delay/Intellectual Disability. Yonsei Med J 2018; 59:431-437. [PMID: 29611406 PMCID: PMC5889996 DOI: 10.3349/ymj.2018.59.3.431] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 12/13/2017] [Accepted: 01/19/2018] [Indexed: 01/18/2023] Open
Abstract
PURPOSE The present study aimed to investigate chromosomal microarray (CMA) and clinical data in patients with unexplained developmental delay/intellectual disability (DD/ID) accompanying dysmorphism, congenital anomalies, or epilepsy. We also aimed to evaluate phenotypic clues in patients with pathogenic copy number variants (CNVs). MATERIALS AND METHODS We collected clinical and CMA data from patients at Konyang University Hospital between September 2013 and October 2014. We included patients who had taken the CMA test to evaluate the etiology of unexplained DD/ID. RESULTS All of the 50 patients identified had DD/ID. Thirty-nine patients had dysmorphism, 19 patients suffered from epilepsy, and 12 patients had congenital anomalies. Twenty-nine of the 50 patients (58%) showed abnormal results. Eighteen (36%) were considered to have pathogenic CNVs. Dysmorphism (p=0.028) was significantly higher in patients with pathogenic CNVs than in those with normal CMA. Two or more clinical features were presented by 61.9% (13/21) of the patients with normal CMA and by 83.3% (15/18) of the patients with pathogenic CMA. CONCLUSION Dysmorphism can be a phenotypic clue to pathogenic CNVs. Furthermore, pathogenic CNV might be more frequently found if patients have two or more clinical features in addition to DD/ID.
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Affiliation(s)
- Hyo Jeong Kim
- Department of Pediatrics, Gachon University Gil Medical Center, Incheon, Korea
| | - Chang Il Park
- Department of Rehabilitation Medicine, Konyang University College of Medicine, Daejeon, Korea
| | - Jae Woo Lim
- Department of Pediatrics, Konyang University College of Medicine, Daejeon, Korea
| | - Gyung Min Lee
- Department of Pediatrics, Konyang University College of Medicine, Daejeon, Korea
| | | | - Hyon J Kim
- Department of Medical Genetics, Konyang University College of Medicine, Daejeon, Korea.
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18
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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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19
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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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20
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Chen CH, Chen HI, Chien WH, Li LH, Wu YY, Chiu YN, Tsai WC, Gau SSF. High resolution analysis of rare copy number variants in patients with autism spectrum disorder from Taiwan. Sci Rep 2017; 7:11919. [PMID: 28931914 PMCID: PMC5607249 DOI: 10.1038/s41598-017-12081-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 09/04/2017] [Indexed: 12/27/2022] Open
Abstract
Rare genomic copy number variations (CNVs) (frequency <1%) contribute a part to the genetic underpinnings of autism spectrum disorders (ASD). The study aimed to understand the scope of rare CNV in Taiwanese patients with ASD. We conducted a genome-wide CNV screening of 335 ASD patients (299 males, 36 females) from Taiwan using Affymetrix Genome-Wide Human SNP Array 6.0 and compared the incidence of rare CNV with that of 1093 control subjects (525 males, 568 females). We found a significantly increased global burden of rare CNVs in the ASD group compared to the controls as a whole or when the rare CNVs were classified by the size and types of CNV. Further analysis confirmed the presence of several rare CNVs at regions strongly associated with ASD as reported in the literature in our sample. Additionally, we detected several new private pathogenic CNVs in our samples and five patients carrying two pathogenic CNVs. Our data indicate that rare genomic CNVs contribute a part to the genetic landscape of our ASD patients. These CNVs are highly heterogeneous, and the clinical interpretation of the pathogenic CNVs of ASD is not straightforward in consideration of the incomplete penetrance, varied expressivity, and individual genetic background.
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Affiliation(s)
- Chia-Hsiang Chen
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan, Taiwan.,Department and Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - Hsin-I Chen
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
| | - Wei-Hsien Chien
- Department of Occupational Therapy, College of Medicine, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Ling-Hui Li
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Yu-Yu Wu
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan, Taiwan
| | - Yen-Nan Chiu
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
| | - Wen-Che Tsai
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
| | - Susan Shur-Fen Gau
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan. .,Graduate Institute of Brain and Mind Sciences, National Taiwan University, Taipei, Taiwan. .,Graduate Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan.
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21
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Lintas C, Picinelli C, Piras IS, Sacco R, Brogna C, Persico AM. Copy number variation in 19 Italian multiplex families with autism spectrum disorder: Importance of synaptic and neurite elongation genes. Am J Med Genet B Neuropsychiatr Genet 2017; 174:547-556. [PMID: 28304131 DOI: 10.1002/ajmg.b.32537] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 02/17/2017] [Indexed: 12/11/2022]
Abstract
Autism Spectrum Disorder (ASD) is endowed with impressive heritability estimates and high recurrence rates. Its genetic underpinnings are nonetheless very heterogeneous, with common, and rare contributing variants located in hundreds of different loci, each characterized by variable levels of penetrance. Multiplex families from single ethnic groups represent a useful means to reduce heterogeneity and enhance genetic load. We screened 19 Italian ASD multiplex families (3 triplets and 16 duplets, total N = 41 ASD subjects), using array-CGH (Agilent 180 K). Causal or ASD-relevant CNVs were detected in 36.6% (15/41) of ASD probands, corresponding to 36.8% (7/19) multiplex families with at least one affected sibling genetically positive. However, only in less than half (3/7) of positive families, affected siblings share the same causal or ASD-relevant CNV. Even in these three families, additional potentially relevant CNVs not shared by affected sib pairs were also detected. These results provide further evidence of genetic heterogeneity in ASD even within multiplex families belonging to a single ethnic group. Differences in CNV burden may likely contribute to the substantial clinical heterogeneity observed between affected siblings. In addition, Gene Ontology enrichment analysis indicates that most potentially causal or relevant ASD genes detected in our cohort belong to nervous system-specific categories, especially involved in neurite elongation and synaptic structure/function. These findings point toward the existence of genomic instability in these families, whose underlying genetic and epigenetic mechanisms deserve further scrutiny.
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Affiliation(s)
- Carla Lintas
- Service for Neurodevelopmental Disorders and Laboratory of Molecular Psychiatry and Neurogenetics, University "Campus Bio-Medico", Rome, Italy
| | - Chiara Picinelli
- Mafalda Luce Center for Pervasive Developmental Disorders, Milan, Italy
| | | | - Roberto Sacco
- Service for Neurodevelopmental Disorders and Laboratory of Molecular Psychiatry and Neurogenetics, University "Campus Bio-Medico", Rome, Italy
| | - Claudia Brogna
- Service for Neurodevelopmental Disorders and Laboratory of Molecular Psychiatry and Neurogenetics, University "Campus Bio-Medico", Rome, Italy
| | - Antonio M Persico
- Mafalda Luce Center for Pervasive Developmental Disorders, Milan, Italy.,Unit of Child and Adolescent Neuropsychiatry, "Gaetano Martino" University Hospital, University of Messina, Messina, Italy
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22
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Management of Severe Developmental Regression in an Autistic Child with a 1q21.3 Microdeletion and Self-Injurious Blindness. Case Rep Psychiatry 2017. [PMID: 28626596 PMCID: PMC5463149 DOI: 10.1155/2017/7582780] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
We report the case of a young boy with nonverbal autism and intellectual disability, with a rare de novo 1q21.3 microdeletion. The patient had early and extreme self-injurious behaviours that led to blindness, complicated by severe developmental regression. A significant reduction in the self-injurious behaviours and the recovery of developmental dynamics were attained in a multidisciplinary neurodevelopmental inpatient unit. Improvement was obtained after managing all causes of somatic pains, using opiate blockers and stabilizing the patient's mood. We offered both sensorimotor developmental approach with therapeutic body wrap and specific psychoeducation adapted to his blindness condition for improving his communication abilities.
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23
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Genome-wide copy number variation analysis in a Chinese autism spectrum disorder cohort. Sci Rep 2017; 7:44155. [PMID: 28281572 PMCID: PMC5345089 DOI: 10.1038/srep44155] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 02/03/2017] [Indexed: 12/27/2022] Open
Abstract
Autism spectrum disorder (ASD) describes a group of neurodevelopmental disorders with high heritability, although the underlying genetic determinants of ASDs remain largely unknown. Large-scale whole-genome studies of copy number variation in Han Chinese samples are still lacking. We performed a genome-wide copy number variation analysis of 343 ASD trios, 203 patients with sporadic cases and 988 controls in a Chinese population using Illumina genotyping platforms to identify CNVs and related genes that may contribute to ASD risk. We identified 32 rare CNVs larger than 1 Mb in 31 patients. ASD patients were found to carry a higher global burden of rare, large CNVs than controls. Recurrent de novo or case-private CNVs were found at 15q11-13, Xp22.3, 15q13.1–13.2, 3p26.3 and 2p12. The de novo 15q11–13 duplication was more prevalent in this Chinese population than in those with European ancestry. Several genes, including GRAMD2 and STAM, were implicated as novel ASD risk genes when integrating whole-genome CNVs and whole-exome sequencing data. We also identified several CNVs that include known ASD genes (SHANK3, CDH10, CSMD1) or genes involved in nervous system development (NYAP2, ST6GAL2, GRM6). Besides, our study also implicated Contactins-NYAPs-WAVE1 pathway in ASD pathogenesis. Our findings identify ASD-related CNVs in a Chinese population and implicate novel ASD risk genes and related pathway for further study.
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24
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Mackenzie AE, Milligan G. The emerging pharmacology and function of GPR35 in the nervous system. Neuropharmacology 2017; 113:661-671. [DOI: 10.1016/j.neuropharm.2015.07.035] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 07/20/2015] [Accepted: 07/27/2015] [Indexed: 02/07/2023]
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25
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Martin-Vilchez S, Whitmore L, Asmussen H, Zareno J, Horwitz R, Newell-Litwa K. RhoGTPase Regulators Orchestrate Distinct Stages of Synaptic Development. PLoS One 2017; 12:e0170464. [PMID: 28114311 PMCID: PMC5256999 DOI: 10.1371/journal.pone.0170464] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 01/05/2017] [Indexed: 11/19/2022] Open
Abstract
Small RhoGTPases regulate changes in post-synaptic spine morphology and density that support learning and memory. They are also major targets of synaptic disorders, including Autism. Here we sought to determine whether upstream RhoGTPase regulators, including GEFs, GAPs, and GDIs, sculpt specific stages of synaptic development. The majority of examined molecules uniquely regulate either early spine precursor formation or later maturation. Specifically, an activator of actin polymerization, the Rac1 GEF β-PIX, drives spine precursor formation, whereas both FRABIN, a Cdc42 GEF, and OLIGOPHRENIN-1, a RhoA GAP, regulate spine precursor elongation. However, in later development, a novel Rac1 GAP, ARHGAP23, and RhoGDIs inactivate actomyosin dynamics to stabilize mature synapses. Our observations demonstrate that specific combinations of RhoGTPase regulatory proteins temporally balance RhoGTPase activity during post-synaptic spine development.
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Affiliation(s)
- Samuel Martin-Vilchez
- Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, VA, United States of America
| | - Leanna Whitmore
- Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, VA, United States of America
| | - Hannelore Asmussen
- Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, VA, United States of America
| | - Jessica Zareno
- Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, VA, United States of America
| | - Rick Horwitz
- Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, VA, United States of America
| | - Karen Newell-Litwa
- Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, VA, United States of America
- Department of Anatomy and Cell Biology, Brody School of Medicine, East Carolina University, Greenville, NC, United States of America
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26
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AlAyadhi LY, Hashmi JA, Iqbal M, Albalawi AM, Samman MI, Elamin NE, Bashir S, Basit S. High-resolution SNP genotyping platform identified recurrent and novel CNVs in autism multiplex families. Neuroscience 2016; 339:561-570. [DOI: 10.1016/j.neuroscience.2016.10.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 10/10/2016] [Accepted: 10/11/2016] [Indexed: 12/27/2022]
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27
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Sharma P, Gupta N, Chowdhury MR, Sapra S, Ghosh M, Gulati S, Kabra M. Application of chromosomal microarrays in the evaluation of intellectual disability/global developmental delay patients – A study from a tertiary care genetic centre in India. Gene 2016; 590:109-19. [DOI: 10.1016/j.gene.2016.06.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Revised: 06/07/2016] [Accepted: 06/08/2016] [Indexed: 01/21/2023]
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28
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Low-pass whole-genome sequencing in clinical cytogenetics: a validated approach. Genet Med 2016; 18:940-8. [PMID: 26820068 DOI: 10.1038/gim.2015.199] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 11/19/2015] [Indexed: 01/12/2023] Open
Abstract
PURPOSE Chromosomal microarray analysis is the gold standard for copy-number variant (CNV) detection in prenatal and postnatal diagnosis. We aimed to determine whether next-generation sequencing (NGS) technology could be an alternative method for CNV detection in routine clinical application. METHODS Genome-wide CNV analysis (>50 kb) was performed on a multicenter group of 570 patients using a low-coverage whole-genome sequencing pipeline. These samples were referred for chromosomal analysis; CNVs (i.e., pathogenic CNVs, pCNVs) were classified according to the American College of Medical Genetics and Genomics guidelines. RESULTS Overall, a total of 198 abortuses, 37 stillbirths, 149 prenatal, and 186 postnatal samples were tested. Our approach yielded results in 549 samples (96.3%). In addition to 119 subjects with aneuploidies, 103 pCNVs (74 losses and 29 gains) were identified in 82 samples, giving diagnostic yields of 53.2% (95% confidence interval: 45.8, 60.5), 14.7% (5.0, 31.1), 28.5% (21.1, 36.6), and 30.1% (23.6, 37.3) in each group, respectively. Mosaicism was observed at a level as low as 25%. CONCLUSIONS Patients with chromosomal diseases or microdeletion/microduplication syndromes were diagnosed using a high-resolution genome-wide method. Our study revealed the potential of NGS to facilitate genetic diagnoses that were not evident in the prenatal and postnatal groups.Genet Med 18 9, 940-948.
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29
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Zhu Z, Li W, Zhan J, Hu L, Wu L, Zhao Z. Adaptive behaviour of Chinese boys with fragile X syndrome. JOURNAL OF INTELLECTUAL DISABILITY RESEARCH : JIDR 2016; 60:1-8. [PMID: 26344058 DOI: 10.1111/jir.12222] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Revised: 07/30/2015] [Accepted: 08/06/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND Adaptive behaviour is closely related to quality of life in children with intellectual disability (ID), but little is known about the adaptive behaviour of children with fragile X syndrome (FXS) in China. METHOD In boys with FXS, the adaptive behaviours in six domains, including self-dependence, locomotion, work skills, communication, socialisation and self-management, were assessed by the Infants-Junior Middle School Students Social-life Abilities Scale. In addition, we compared the adaptive skills of boys with FXS to those of three control groups of boys, including boys with Down syndrome (DS) and typically developing (TD) boys matched by chronological age (CA) or mental age (MA). The profile of the adaptive behaviour of boys with FXS is discussed in detail. RESULTS Compared to boys with DS, boys with FXS obtained lower scores in three domains in adaptive behaviour, including work skills, socialisation and self-management skills; boys with FXS had better scores in self-dependence and locomotion skills than boys matched for MA; as expected, boys with FXS had significantly poorer adaptive skills in all six domains assessed compared to CA boys. CONCLUSION The development of adaptive skills in boys with FXS was worse than that of boys with DS. The profile of the adaptive behaviour of boys with FXS establishes a basis for the development of targeted interventions to promote social development in this population.
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Affiliation(s)
- Z Zhu
- Children's Hospital, Zhejiang University School of Medicine Developmental and Behavioral Pediatrics, Hangzhou, Zhejiang, China
| | - W Li
- Children's Hospital, Zhejiang University School of Medicine Developmental and Behavioral Pediatrics, Hangzhou, Zhejiang, China
| | - J Zhan
- Children's Hospital, Zhejiang University School of Medicine Developmental and Behavioral Pediatrics, Hangzhou, Zhejiang, China
| | - L Hu
- Children's Hospital, Zhejiang University School of Medicine Developmental and Behavioral Pediatrics, Hangzhou, Zhejiang, China
| | - L Wu
- Children's Hospital, Zhejiang University School of Medicine Developmental and Behavioral Pediatrics, Hangzhou, Zhejiang, China
| | - Z Zhao
- Children's Hospital, Zhejiang University School of Medicine Developmental and Behavioral Pediatrics, Hangzhou, Zhejiang, China
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30
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Lim ECP, Brett M, Lai AHM, Lee SP, Tan ES, Jamuar SS, Ng ISL, Tan EC. Next-generation sequencing using a pre-designed gene panel for the molecular diagnosis of congenital disorders in pediatric patients. Hum Genomics 2015; 9:33. [PMID: 26666243 PMCID: PMC4678573 DOI: 10.1186/s40246-015-0055-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 11/22/2015] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) has revolutionized genetic research and offers enormous potential for clinical application. Sequencing the exome has the advantage of casting the net wide for all known coding regions while targeted gene panel sequencing provides enhanced sequencing depths and can be designed to avoid incidental findings in adult-onset conditions. A HaloPlex panel consisting of 180 genes within commonly altered chromosomal regions is available for use on both the Ion Personal Genome Machine (PGM) and MiSeq platforms to screen for causative mutations in these genes. METHODS We used this Haloplex ICCG panel for targeted sequencing of 15 patients with clinical presentations indicative of an abnormality in one of the 180 genes. Sequencing runs were done using the Ion 318 Chips on the Ion Torrent PGM. Variants were filtered for known polymorphisms and analysis was done to identify possible disease-causing variants before validation by Sanger sequencing. When possible, segregation of variants with phenotype in family members was performed to ascertain the pathogenicity of the variant. RESULTS More than 97% of the target bases were covered at >20×. There was an average of 9.6 novel variants per patient. Pathogenic mutations were identified in five genes for six patients, with two novel variants. There were another five likely pathogenic variants, some of which were unreported novel variants. CONCLUSIONS In a cohort of 15 patients, we were able to identify a likely genetic etiology in six patients (40%). Another five patients had candidate variants for which further evaluation and segregation analysis are ongoing. Our results indicate that the HaloPlex ICCG panel is useful as a rapid, high-throughput and cost-effective screening tool for 170 of the 180 genes. There is low coverage for some regions in several genes which might have to be supplemented by Sanger sequencing. However, comparing the cost, ease of analysis, and shorter turnaround time, it is a good alternative to exome sequencing for patients whose features are suggestive of a genetic etiology involving one of the genes in the panel.
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Affiliation(s)
- Eileen C P Lim
- KK Research Centre, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore, 229899, Singapore.
| | - Maggie Brett
- KK Research Centre, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore, 229899, Singapore.
| | - Angeline H M Lai
- Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital, Singapore, 229899, Singapore. .,Paediatrics Academic Clinical Programme, SingHealth Duke-NUS Graduate Medical School, Singapore, 169857, Singapore.
| | - Siew-Peng Lee
- KK Research Centre, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore, 229899, Singapore.
| | - Ee-Shien Tan
- Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital, Singapore, 229899, Singapore. .,Paediatrics Academic Clinical Programme, SingHealth Duke-NUS Graduate Medical School, Singapore, 169857, Singapore.
| | - Saumya S Jamuar
- Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital, Singapore, 229899, Singapore. .,Paediatrics Academic Clinical Programme, SingHealth Duke-NUS Graduate Medical School, Singapore, 169857, Singapore.
| | - Ivy S L Ng
- Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital, Singapore, 229899, Singapore. .,Paediatrics Academic Clinical Programme, SingHealth Duke-NUS Graduate Medical School, Singapore, 169857, Singapore.
| | - Ene-Choo Tan
- KK Research Centre, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore, 229899, Singapore. .,Paediatrics Academic Clinical Programme, SingHealth Duke-NUS Graduate Medical School, Singapore, 169857, Singapore.
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