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Lu S, Kakongoma N, Hu WS, Zhang YZ, Yang NN, Zhang W, Mao AF, Liang Y, Zhang ZF. Detection rates of abnormalities in over 10,000 amniotic fluid samples at a single laboratory. BMC Pregnancy Childbirth 2023; 23:102. [PMID: 36755227 PMCID: PMC9906931 DOI: 10.1186/s12884-023-05428-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 02/03/2023] [Indexed: 02/10/2023] Open
Abstract
BACKGROUND A growing number of cytogenetic techniques have been used for prenatal diagnosis. This study aimed to demonstrate the usefulness of karyotyping, BACs-on-Beads (BoBs) assay and single nucleotide polymorphism (SNP) array in prenatal diagnosis during the second trimester based on our laboratory experience. METHODS A total of 10,580 pregnant women with a variety of indications for amniocentesis were enrolled in this retrospective study between January 2015 and December 2020, of whom amniotic fluid samples were analysed in 10,320 women. The main technical indicators of participants in the three different technologies were summarized, and cases of chromosome abnormalities were further evaluated. RESULTS The overall abnormality detection rate of karyotyping among all the amniotic fluid samples was 15.4%, and trisomy 21 was the most common abnormality (20.9%). The total abnormality detection rate of the BoBs assay was 5.6%, and the diagnosis rate of microdeletion/microduplication syndromes that were not identified by karyotyping was 0.2%. The detection results of the BoBs assay were 100.0% concordant with karyotyping analysis in common aneuploidies. Seventy (87.5%) cases of structural abnormalities were missed by BoBs assay. The total abnormality detection rate of the SNP array was 21.6%. The detection results of common aneuploidies were exactly the same between SNP array and karyotyping. Overall, 60.1% of structural abnormalities were missed by SNP array. The further detection rate of pathogenic significant copy number variations (CNVs) by SNP was 1.4%. CONCLUSIONS Karyotyping analysis combined with BoBs assay or SNP array for prenatal diagnosis could provide quick and accurate results. Combined use of the technologies, especially with SNP array, improved the diagnostic yield and interpretation of the results, which contributes to genetic counselling. BoBs assay or SNP array could be a useful supplement to karyotyping.
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Affiliation(s)
- Sha Lu
- grid.268505.c0000 0000 8744 8924Zhejiang Chinese Medical University, Hangzhou, Zhejiang People’s Republic of China ,grid.508049.00000 0004 4911 1465Prenatal Screening and Prenatal Diagnosis Center, Hangzhou Women’s Hospital (Hangzhou Maternity and Child Health Care Hospital), No. 369 Kunpeng Rd., Hangzhou, Zhejiang 310008 People’s Republic of China
| | - Nisile Kakongoma
- grid.268505.c0000 0000 8744 8924Zhejiang Chinese Medical University, Hangzhou, Zhejiang People’s Republic of China
| | - Wen-sheng Hu
- grid.268505.c0000 0000 8744 8924Zhejiang Chinese Medical University, Hangzhou, Zhejiang People’s Republic of China ,grid.508049.00000 0004 4911 1465Prenatal Screening and Prenatal Diagnosis Center, Hangzhou Women’s Hospital (Hangzhou Maternity and Child Health Care Hospital), No. 369 Kunpeng Rd., Hangzhou, Zhejiang 310008 People’s Republic of China
| | - Yan-zhen Zhang
- grid.508049.00000 0004 4911 1465Prenatal Screening and Prenatal Diagnosis Center, Hangzhou Women’s Hospital (Hangzhou Maternity and Child Health Care Hospital), No. 369 Kunpeng Rd., Hangzhou, Zhejiang 310008 People’s Republic of China
| | - Nan-nan Yang
- grid.508049.00000 0004 4911 1465Prenatal Screening and Prenatal Diagnosis Center, Hangzhou Women’s Hospital (Hangzhou Maternity and Child Health Care Hospital), No. 369 Kunpeng Rd., Hangzhou, Zhejiang 310008 People’s Republic of China
| | - Wen Zhang
- grid.508049.00000 0004 4911 1465Prenatal Screening and Prenatal Diagnosis Center, Hangzhou Women’s Hospital (Hangzhou Maternity and Child Health Care Hospital), No. 369 Kunpeng Rd., Hangzhou, Zhejiang 310008 People’s Republic of China
| | - Ai-fen Mao
- grid.508049.00000 0004 4911 1465Prenatal Screening and Prenatal Diagnosis Center, Hangzhou Women’s Hospital (Hangzhou Maternity and Child Health Care Hospital), No. 369 Kunpeng Rd., Hangzhou, Zhejiang 310008 People’s Republic of China
| | - Yi Liang
- Department of Neurobiology and Acupuncture Research, The Third School of Clinical Medicine, Zhejiang Chinese Medical University, Key Laboratory of Acupuncture and Neurology of Zhejiang Province, 548 Binwen Road, Binjiang District, Hangzhou, 310053, Zhejiang, People's Republic of China.
| | - Zhi-fen Zhang
- grid.268505.c0000 0000 8744 8924Zhejiang Chinese Medical University, Hangzhou, Zhejiang People’s Republic of China ,grid.508049.00000 0004 4911 1465Prenatal Screening and Prenatal Diagnosis Center, Hangzhou Women’s Hospital (Hangzhou Maternity and Child Health Care Hospital), No. 369 Kunpeng Rd., Hangzhou, Zhejiang 310008 People’s Republic of 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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Lan L, Wu H, She L, Zhang B, He Y, Luo D, Wang H, Zheng Z. Analysis of copy number variation by sequencing in fetuses with nuchal translucency thickening. J Clin Lab Anal 2020; 34:e23347. [PMID: 32342531 PMCID: PMC7439336 DOI: 10.1002/jcla.23347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/30/2020] [Accepted: 04/03/2020] [Indexed: 12/20/2022] Open
Abstract
Objective Copy number variation sequencing (CNV‐seq) technique was used to analyze the genetic etiology of fetuses with increased nuchal translucency (NT). Methods A total of 139 women with gestational 11‐14 weeks whose fetuses were detected with increased NT (NT ≥ 2.5 mm) in our hospital from July 2016 to December 2018 were selected. Fetal specimens were performed for karyotyping analysis and CNV sequencing. Results According to the nuchal translucency thickness, 2.5‐3.4, 3.5‐4.4, 4.5‐5.4, and more than 5.5 mm, the rates of chromosomal abnormalities were 22.8% (13/57), 30.8% (12/39), 42.1% (8/19), and 62.5% (15/24), respectively. There was significant difference among the incidences of chromosomal abnormalities in four groups (χ2 = 37.69, P < .01) and the incidences increased with fetal NT thickness. Among 139 cases, there were 36 cases (25.9%) with abnormal chromosome karyotypes. Meanwhile, there were 45 cases (32.3%) with abnormal CNV. In the 12 cases with abnormal CNV and normal chromosome karyotypes, there were 2 cases of pathogenic CNV, 7 cases of CNV with unknown clinical significance, and 3 cases of possibly benign CNV. There was no significant difference in CNV between pregnant women in advanced maternal age and those in normal maternal age (χ2 = 1.389, P = .239). In the fetus who showed abnormalities in NT and ultrasonography (χ2 = 5.13, P < .05) and the fetus aborted (χ2 = 113.19, P < .05), the abnormal rate of CNV was higher with statistically significant difference. Conclusion CNV‐seq combined karyotype analysis should be performed simultaneously in fetuses with increased NT, providing a basis for genetic counseling, which is of great significance for prenatal diagnosis.
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Affiliation(s)
- Liubing Lan
- Prenatal Diagnosis Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Department of Obstetrics, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China
| | - Heming Wu
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China
| | - Lingna She
- Prenatal Diagnosis Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China
| | - Bosen Zhang
- Prenatal Diagnosis Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Department of Obstetrics, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China
| | - Yanhong He
- Prenatal Diagnosis Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Department of Obstetrics, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China
| | - Dandan Luo
- Prenatal Diagnosis Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Department of Obstetrics, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China
| | - Huaxian Wang
- Prenatal Diagnosis Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China
| | - Zhiyuan Zheng
- Prenatal Diagnosis Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China
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Diagnosis of intellectual disability/global developmental delay via genetic analysis in a central region of China. Chin Med J (Engl) 2020; 132:1533-1540. [PMID: 31205075 PMCID: PMC6616229 DOI: 10.1097/cm9.0000000000000295] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Supplemental Digital Content is available in the text Background: Advanced technology has become a valuable tool in etiological studies of intellectual disability/global developmental delay (ID/GDD). The present study investigated the role of genetic analysis to confirm the etiology in ID/GDD patients where the cause of the disease was uncertain in central China. Methods: We evaluated 1051 ID/GDD children aged 6 months to 18 years from March 2009 to April 2017. Data concerning basic clinical manifestations were collected, and the method of etiology confirmation was recorded. Genome-wide copy number variations (CNVs) detection and high-throughput sequencing of exons in the targeted regions was performed to identify genetically-based etiologies. We compared the incidence of different methods used to confirm ID/GDD etiology among groups with differing degrees of ID/GDD using the Chi-square or Fisher exact probability test. Results: We recruited 1051 children with mild (367, 34.9%), moderate (301, 28.6%), severe (310, 29.5%), and profoundly severe (73, 6.9%) ID/GDD. The main causes of ID/GDD in the children assessed were perinatal factors, such as acquired brain injury, as well as single gene imbalance and chromosomal gene mutation. We identified karyotype and/or CNVs variation in 46/96 (47.9%) of cases in severe ID/GDD patients, which was significantly higher than those with mild and moderate ID/GDD of 34/96 (35.4%) and 15/96 (15.6%), respectively. A total of 331/536 (61.8%) patients with clear etiology have undergone genetic analysis while 262/515 (50.9%) patients with unclear etiology have undergone genetic analysis (χ2 = 12.645, P < 0.001). Gene structure variation via karyotype analysis and CNV detection increased the proportion of children with confirmed etiology from 51.0% to 56.3%, and second-generation high-throughput sequencing dramatically increased this to 78.9%. Ten novel mutations were detected, recessive mutations in X-linked genes (ATPase copper transporting alpha and bromodomain and WD repeat domain containing 3) and dominant de novo heterozygous mutations in X-linked genes (cyclin-dependent kinase like 5, protocadherin 19, IQ motif and Sec7 domain 2, and methyl-CpG binding protein 2) were reported in the study. Conclusions: The present study indicates that genetic analysis is an effective method to increase the proportion of confirmed etiology in ID/GDD children and is highly recommended, especially in ID/GDD children with uncertain etiology.
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Misra S, Peters G, Barnes E, Ardern-Holmes S, Webster R, Troedson C, Mohammad SS, Gill D, Menezes M, Gupta S, Procopis P, Antony J, Kurian MA, Dale RC. Yield of comparative genomic hybridization microarray in pediatric neurology practice. NEUROLOGY-GENETICS 2019; 5:e367. [PMID: 31872051 PMCID: PMC6878849 DOI: 10.1212/nxg.0000000000000367] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 08/28/2019] [Indexed: 12/14/2022]
Abstract
Objective The present study investigated the diagnostic yield of array comparative genomic hybridization (aCGH) in a large cohort of children with diverse neurologic disorders as seen in child neurology practice to test whether pathogenic copy number variants (CNVs) were more likely to be detected in specific neurologic phenotypes. Methods A retrospective cross-sectional analysis was performed on 555 children in whom a genetic etiology was suspected and who underwent whole-genome aCGH testing between 2006 and 2012. Neurologic phenotyping was performed using hospital medical records. An assessment of pathogenicity was made for each CNV, based on recent developments in the literature. Results Forty-seven patients were found to carry a pathogenic CNV, giving an overall diagnostic yield of 8.59%. Certain phenotypes predicted for the presence of a pathogenic CNV, including developmental delay (odds ratio [OR] 3.69 [1.30-10.51]), cortical visual impairment (OR 2.73 [1.18-6.28]), dysmorphism (OR 2.75 [1.38-5.50]), and microcephaly (OR 2.16 [1.01-4.61]). The combination of developmental delay/intellectual disability with dysmorphism and abnormal head circumference was also predictive for a pathogenic CNV (OR 2.86 [1.02-8.00]). For every additional clinical feature, there was an increased likelihood of detecting a pathogenic CNV (OR 1.18 [1.01-1.38]). Conclusions The use of aCGH led to a pathogenic finding in 8.59% of patients. The results support the use of aCGH as a first tier investigation in children with diverse neurologic disorders, although whole-genome sequencing may replace aCGH as the detection method in the future. In particular, the yield was increased in children with developmental delay, dysmorphism, cortical visual impairment, and microcephaly.
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Affiliation(s)
- Shibalik Misra
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Greg Peters
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Elizabeth Barnes
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Simone Ardern-Holmes
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Richard Webster
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Christopher Troedson
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Shekeeb S Mohammad
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Deepak Gill
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Manoj Menezes
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Sachin Gupta
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Peter Procopis
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Jayne Antony
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Manju A Kurian
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Russell C Dale
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
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Traeger‐Synodinos J, Bosch CAJ, Vrettou C, Maragoudaki L, Apostolidis J, Kanavakis E, Kattamis C, Arkesteijn SGJ, Hoffer MJV, Ruivenkamp CAL, Harteveld CL. Adult‐onset beta‐thalassaemia intermedia caused by a 5‐Mb somatic clonal segmental deletion in haemopoietic stem cells involving the β‐globin locus. Br J Haematol 2019; 186:e165-e170. [DOI: 10.1111/bjh.16043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Joanne Traeger‐Synodinos
- Department of Medical Genetics National & Kapodistrian University of Athens, St. Sophia’s Children’s Hospital Athens Greece
| | - Cathy A. J. Bosch
- Department of Clinical Genetics/LDGA Leiden University Medical Centre Leiden the Netherlands
| | - Christina Vrettou
- Department of Medical Genetics National & Kapodistrian University of Athens, St. Sophia’s Children’s Hospital Athens Greece
| | - Lena Maragoudaki
- Department of Medical Genetics National & Kapodistrian University of Athens, St. Sophia’s Children’s Hospital Athens Greece
| | - Janos Apostolidis
- Department of Haematology and Bone Marrow Transplantation Evangelismos Hospital Athens Greece
| | | | - Christos Kattamis
- National & Kapodistrian University of Athens, St. Sophia’s Children’s Hospital Athens Greece
| | - Sandra G. J. Arkesteijn
- Department of Clinical Genetics/LDGA Leiden University Medical Centre Leiden the Netherlands
| | - Mariëtte J. V. Hoffer
- Department of Clinical Genetics/LDGA Leiden University Medical Centre Leiden the Netherlands
| | | | - Cornelis L. Harteveld
- Department of Clinical Genetics/LDGA Leiden University Medical Centre Leiden the Netherlands
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7
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Chen X, Li H, Chen C, Zhou L, Xu X, Xiang Y, Tang S. Genome-Wide Array Analysis Reveals Novel Genomic Regions and Candidate Gene for Intellectual Disability. Mol Diagn Ther 2019; 22:749-757. [PMID: 30259421 DOI: 10.1007/s40291-018-0358-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Intellectual disability (ID) is often sporadic, and its complex etiology makes clinical diagnosis extremely difficult. OBJECTIVE The aims of this study were to detect copy number variations (CNVs) in patients with ID and to analyze the correlation between pathogenic CNVs and clinical phenotype. METHODS After cases of ID caused by metabolic dysfunction or environmental factors were excluded, 64 patients with moderate to severe ID were enrolled. Karyotype and single nucleotide polymorphism (SNP) array analyses were performed for all patients. The relationship between CNVs and phenotype was identified with genotype-phenotype comparisons and by searching CNV databases. RESULTS Karyotype analysis showed four patients with chromosomal aneuploidy and seven with chromosomal structural abnormality. After excluding the four cases with chromosomal aneuploidy, the remaining 60 cases were analyzed using SNP array. The results revealed 87 CNVs in 45 cases, including 16 pathogenic CNVs in 12 individuals, with a diagnostic yield of 20.0% (12/60). We found large deletions at 16q22.2q23.1 and 3q24q25.32 in two patients, respectively, in whom specific syndromes had not been defined. Our array analysis showed one case carried a 210 kb deletion at 1p21.2p21.3, which included only one coding gene LPPR4, which might be a candidate gene for ID phenotype. CONCLUSIONS Use of the genome-wide array method can improve the detection rate of CNVs, reveal chromosomal abnormalities that have not been well-characterized by cytology, and provide a new way to locate genes for patients with the ID phenotype. Interpretation of CNVs remains a major challenge. Sharing of CNVs and phenotype information from different laboratories in public databases is important.
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Affiliation(s)
- Xiangnan Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Huanzheng Li
- The Center of Wenzhou Prenatal Diagnostics, Key Laboratory of Birth Defects, Wenzhou Central Hospital, Wenzhou, Zhejiang, China
| | - Chong Chen
- The Center of Wenzhou Prenatal Diagnostics, Key Laboratory of Birth Defects, Wenzhou Central Hospital, Wenzhou, Zhejiang, China
| | - Lili Zhou
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
- The Center of Wenzhou Prenatal Diagnostics, Key Laboratory of Birth Defects, Wenzhou Central Hospital, Wenzhou, Zhejiang, China
| | - Xueqin Xu
- The Center of Wenzhou Prenatal Diagnostics, Key Laboratory of Birth Defects, Wenzhou Central Hospital, Wenzhou, Zhejiang, China
| | - Yanbao Xiang
- The Center of Wenzhou Prenatal Diagnostics, Key Laboratory of Birth Defects, Wenzhou Central Hospital, Wenzhou, Zhejiang, China
| | - Shaohua Tang
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
- The Center of Wenzhou Prenatal Diagnostics, Key Laboratory of Birth Defects, Wenzhou Central Hospital, Wenzhou, Zhejiang, China.
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8
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Zhou B, Ho SS, Zhang X, Pattni R, Haraksingh RR, Urban AE. Whole-genome sequencing analysis of CNV using low-coverage and paired-end strategies is efficient and outperforms array-based CNV analysis. J Med Genet 2018; 55:735-743. [PMID: 30061371 DOI: 10.1136/jmedgenet-2018-105272] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 05/16/2018] [Accepted: 06/26/2018] [Indexed: 11/03/2022]
Abstract
BACKGROUND Copy number variation (CNV) analysis is an integral component of the study of human genomes in both research and clinical settings. Array-based CNV analysis is the current first-tier approach in clinical cytogenetics. Decreasing costs in high-throughput sequencing and cloud computing have opened doors for the development of sequencing-based CNV analysis pipelines with fast turnaround times. We carry out a systematic and quantitative comparative analysis for several low-coverage whole-genome sequencing (WGS) strategies to detect CNV in the human genome. METHODS We compared the CNV detection capabilities of WGS strategies (short insert, 3 kb insert mate pair and 5 kb insert mate pair) each at 1×, 3× and 5× coverages relative to each other and to 17 currently used high-density oligonucleotide arrays. For benchmarking, we used a set of gold standard (GS) CNVs generated for the 1000 Genomes Project CEU subject NA12878. RESULTS Overall, low-coverage WGS strategies detect drastically more GS CNVs compared with arrays and are accompanied with smaller percentages of CNV calls without validation. Furthermore, we show that WGS (at ≥1× coverage) is able to detect all seven GS deletion CNVs >100 kb in NA12878, whereas only one is detected by most arrays. Lastly, we show that the much larger 15 Mbp Cri du chat deletion can be readily detected with short-insert paired-end WGS at even just 1× coverage. CONCLUSIONS CNV analysis using low-coverage WGS is efficient and outperforms the array-based analysis that is currently used for clinical cytogenetics.
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Affiliation(s)
- Bo Zhou
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Steve S Ho
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Xianglong Zhang
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Reenal Pattni
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Rajini R Haraksingh
- Department of Life Sciences, The University of the West Indies, Saint Augustine, Trinidad and Tobago
| | - Alexander E Urban
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.,Program on Genetics of Brain Function, Stanford Center for Genomics and Personalized Medicine, Tasha and John Morgridge Faculty Scholar, Stanford Child Health Research Institute, Stanford University, Stanford, California, USA
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9
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Zanardo ÉA, Dutra RL, Piazzon FB, Dias AT, Novo-Filho GM, Nascimento AM, Montenegro MM, Damasceno JG, Madia FAR, da Costa TVMM, Melaragno MI, Kim CA, Kulikowski LD. Cytogenomic assessment of the diagnosis of 93 patients with developmental delay and multiple congenital abnormalities: The Brazilian experience. Clinics (Sao Paulo) 2017; 72:526-537. [PMID: 29069255 PMCID: PMC5629705 DOI: 10.6061/clinics/2017(09)02] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 05/04/2017] [Indexed: 01/04/2023] Open
Abstract
OBJECTIVE The human genome contains several types of variations, such as copy number variations, that can generate specific clinical abnormalities. Different techniques are used to detect these changes, and obtaining an unequivocal diagnosis is important to understand the physiopathology of the diseases. The objective of this study was to assess the diagnostic capacity of multiplex ligation-dependent probe amplification and array techniques for etiologic diagnosis of syndromic patients. METHODS We analyzed 93 patients with developmental delay and multiple congenital abnormalities using multiplex ligation-dependent probe amplifications and arrays. RESULTS Multiplex ligation-dependent probe amplification using different kits revealed several changes in approximately 33.3% of patients. The use of arrays with different platforms showed an approximately 53.75% detection rate for at least one pathogenic change and a 46.25% detection rate for patients with benign changes. A concomitant assessment of the two techniques showed an approximately 97.8% rate of concordance, although the results were not the same in all cases. In contrast with the array results, the MLPA technique detected ∼70.6% of pathogenic changes. CONCLUSION The obtained results corroborated data reported in the literature, but the overall detection rate was higher than the rates previously reported, due in part to the criteria used to select patients. Although arrays are the most efficient tool for diagnosis, they are not always suitable as a first-line diagnostic approach because of their high cost for large-scale use in developing countries. Thus, clinical and laboratory interactions with skilled technicians are required to target patients for the most effective and beneficial molecular diagnosis.
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Affiliation(s)
- Évelin Aline Zanardo
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
- *Corresponding author. E-mail:
| | - Roberta Lelis Dutra
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Flavia Balbo Piazzon
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Alexandre Torchio Dias
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Gil Monteiro Novo-Filho
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Amom Mendes Nascimento
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Marília Moreira Montenegro
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Jullian Gabriel Damasceno
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Fabrícia Andreia Rosa Madia
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | | | - Maria Isabel Melaragno
- Departamento de Morfologia e Genetica, Universidade Federal de Sao Paulo, Sao Paulo, SP, BR
| | - Chong Ae Kim
- Unidade de Genetica, Departamento de Pediatria, Instituto da Crianca, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Leslie Domenici Kulikowski
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
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10
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Reiner J, Karger L, Cohen N, Mehta L, Edelmann L, Scott SA. Chromosomal Microarray Detection of Constitutional Copy Number Variation Using Saliva DNA. J Mol Diagn 2017; 19:397-403. [PMID: 28315673 PMCID: PMC5417105 DOI: 10.1016/j.jmoldx.2016.11.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 10/27/2016] [Accepted: 11/16/2016] [Indexed: 01/10/2023] Open
Abstract
Chromosomal microarray (CMA) testing to detect copy number aberrations among individuals with multiple congenital anomalies and/or developmental delay is typically performed on peripheral blood DNA. However, the use of saliva DNA may be preferred for some patients, which prompted our validation study using six saliva DNA samples with a range of bacterial content (approximately 3% to 21%) and 20 paired blood and saliva specimens on the Agilent Technologies, Illumina, and Affymetrix CMA platforms. Ten of the 20 paired specimens were previously determined to carry clinically significant copy number aberrations by clinical CMA testing on blood DNA (100 kb to 2.56 Mb; five deletions, eight duplications). Notably, the quality of saliva DNA (DNA Genotek) was equivalent to blood DNA regardless of bacterial content, as was CMA quality and single-nucleotide polymorphism genotyping quality with all CMA platforms. The number of copy number variants and absence of heterozygosity regions detected by CMA were comparable between paired blood and saliva DNA and, more important, all 13 clinically significant copy number aberrations were detected in saliva DNA by all CMA platforms. These data confirm that the quality of saliva DNA is comparable to blood DNA regardless of bacterial content, including important CMA and single-nucleotide polymorphism quality metrics, and that saliva DNA is a reliable alternative for the detection of clinically significant copy number aberrations by clinical CMA testing.
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Affiliation(s)
- Jennifer Reiner
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Lisa Karger
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ninette Cohen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Lakshmi Mehta
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Lisa Edelmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.
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11
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Ben Khelifa H, Soyah N, Labalme A, Guilbert H, Sanlaville D, Saad A, Mougou-Zerelli S. Genomic Microarray in Intellectual Disability: The Usefulness of Existing Systems in the Interpretation of Copy Number Variation. J Pediatr Genet 2016; 6:84-91. [PMID: 28496995 DOI: 10.1055/s-0036-1588027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 07/19/2016] [Indexed: 10/21/2022]
Abstract
Whole genome array technology is an essential tool for the detection of a large number of copy number variants (CNVs) in patients with ID and/or multiple congenital anomalies. However, the clinical significance of some microimbalances is not known. In this article, we succeeded to detect seven new variations of unknown significance (dup12p13.33, dup2p16.3, dupXq13.2, del12q24.33, dup16p13.11, trip4q22.1, and dup9p21.3), one CNV classified as known pathogenic syndrome (del22q13.31-q33), and one CNV classified as potentially pathogenic (del11q24.3). We emphasize the role of comparative genomic hybridization arrays in the investigation of intellectual disability and evaluate the usefulness of existing systems in the interpretation of CNVs.
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Affiliation(s)
- Hela Ben Khelifa
- Department of Cytogenetic and Reproductive Biology, Farhat Hached University Teaching Hospital, Sousse, Tunisia
| | - Najla Soyah
- Department of Pediatric, Farhat Hached University Teaching Hospital, Sousse, Tunisia
| | - Audrey Labalme
- Hospices Civils de Lyon, Service de Cytogénétique Constitutionnelle, Lyon, France
| | - Helene Guilbert
- Hospices Civils de Lyon, Service de Cytogénétique Constitutionnelle, Lyon, France
| | - Damien Sanlaville
- Hospices Civils de Lyon, Service de Cytogénétique Constitutionnelle, Lyon, France
| | - Ali Saad
- Department of Cytogenetic and Reproductive Biology, Farhat Hached University Teaching Hospital, Sousse, Tunisia
| | - Soumaya Mougou-Zerelli
- Department of Cytogenetic and Reproductive Biology, Farhat Hached University Teaching Hospital, Sousse, Tunisia
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12
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Wilkins EJ, Archibald AD, Sahhar MA, White SM. “It wasn't a disaster or anything”: Parents’ experiences of their child's uncertain chromosomal microarray result. Am J Med Genet A 2016; 170:2895-2904. [DOI: 10.1002/ajmg.a.37838] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Accepted: 06/23/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Ella J. Wilkins
- Department of Paediatrics; University of Melbourne; Melbourne Victoria Australia
- Victorian Clinical Genetics Services; Melbourne; Victoria Australia
- Murdoch Childrens Research Institute; Melbourne; Victoria Australia
| | - Alison D. Archibald
- Department of Paediatrics; University of Melbourne; Melbourne Victoria Australia
- Victorian Clinical Genetics Services; Melbourne; Victoria Australia
- Murdoch Childrens Research Institute; Melbourne; Victoria Australia
| | - Margaret A. Sahhar
- Department of Paediatrics; University of Melbourne; Melbourne Victoria Australia
- Victorian Clinical Genetics Services; Melbourne; Victoria Australia
- Murdoch Childrens Research Institute; Melbourne; Victoria Australia
| | - Susan M. White
- Department of Paediatrics; University of Melbourne; Melbourne Victoria Australia
- Victorian Clinical Genetics Services; Melbourne; Victoria Australia
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13
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Malbin J, Fallah MS, Sharifi Z, Shafaei M, Bagherian H, Mostafaei TP, Aliev R, Zainal S. Cryptic de novo deletion at 2q23.3-q24.1 in a patient with intellectual disability. J Genet 2016; 95:441-5. [PMID: 27350689 DOI: 10.1007/s12041-016-0630-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jamileh Malbin
- Azerbaijan National Academy of Science (ANAS), Genetic Resources Institute, Baku AZ1005, Azerbaijan.
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14
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Giorgio E, Ciolfi A, Biamino E, Caputo V, Di Gregorio E, Belligni EF, Calcia A, Gaidolfi E, Bruselles A, Mancini C, Cavalieri S, Molinatto C, Cirillo Silengo M, Ferrero GB, Tartaglia M, Brusco A. Whole exome sequencing is necessary to clarify ID/DD cases with de novo copy number variants of uncertain significance: Two proof-of-concept examples. Am J Med Genet A 2016; 170:1772-9. [PMID: 27108886 DOI: 10.1002/ajmg.a.37649] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 03/20/2016] [Indexed: 01/09/2023]
Abstract
Whole exome sequencing (WES) is a powerful tool to identify clinically undefined forms of intellectual disability/developmental delay (ID/DD), especially in consanguineous families. Here we report the genetic definition of two sporadic cases, with syndromic ID/DD for whom array-Comparative Genomic Hybridization (aCGH) identified a de novo copy number variant (CNV) of uncertain significance. The phenotypes included microcephaly with brachycephaly and a distinctive facies in one proband, and hypotonia in the legs and mild ataxia in the other. WES allowed identification of a functionally relevant homozygous variant affecting a known disease gene for rare syndromic ID/DD in each proband, that is, c.1423C>T (p.Arg377*) in the Trafficking Protein Particle Complex 9 (TRAPPC9), and c.154T>C (p.Cys52Arg) in the Very Low Density Lipoprotein Receptor (VLDLR). Four mutations affecting TRAPPC9 have been previously reported, and the present finding further depicts this syndromic form of ID, which includes microcephaly with brachycephaly, corpus callosum hypoplasia, facial dysmorphism, and overweight. VLDLR-associated cerebellar hypoplasia (VLDLR-CH) is characterized by non-progressive congenital ataxia and moderate-to-profound intellectual disability. The c.154T>C (p.Cys52Arg) mutation was associated with a very mild form of ataxia, mild intellectual disability, and cerebellar hypoplasia without cortical gyri simplification. In conclusion, we report two novel cases with rare causes of autosomal recessive ID, which document how interpreting de novo array-CGH variants represents a challenge in consanguineous families; as such, clinical WES should be considered in diagnostic testing. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Elisa Giorgio
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCSS, Rome, Italy.,Centro di Ricerca per gli alimenti e la nutrizione, CREA, Rome, Italy
| | - Elisa Biamino
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | - Viviana Caputo
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Eleonora Di Gregorio
- Città della Salute e della Scienza University Hospital, Medical Genetics Unit, Turin, Italy
| | - Elga Fabia Belligni
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | | | - Elena Gaidolfi
- Centro Diagnostico Cernaia, Magnetic Resonance Unit, Turin, Italy
| | - Alessandro Bruselles
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Cecilia Mancini
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Simona Cavalieri
- Città della Salute e della Scienza University Hospital, Medical Genetics Unit, Turin, Italy
| | - Cristina Molinatto
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | | | | | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCSS, Rome, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Turin, Italy.,Città della Salute e della Scienza University Hospital, Medical Genetics Unit, Turin, Italy
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15
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D'Amours G, Langlois M, Mathonnet G, Fetni R, Nizard S, Srour M, Tihy F, Phillips MS, Michaud JL, Lemyre E. SNP arrays: comparing diagnostic yields for four platforms in children with developmental delay. BMC Med Genomics 2014; 7:70. [PMID: 25539807 PMCID: PMC4299176 DOI: 10.1186/s12920-014-0070-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 12/11/2014] [Indexed: 11/28/2022] Open
Abstract
Background Molecular karyotyping is now the first-tier genetic test for patients affected with unexplained intellectual disability (ID) and/or multiple congenital anomalies (MCA), since it identifies a pathogenic copy number variation (CNV) in 10-14% of them. High-resolution microarrays combining molecular karyotyping and single nucleotide polymorphism (SNP) genotyping were recently introduced to the market. In addition to identifying CNVs, these platforms detect loss of heterozygosity (LOH), which can indicate the presence of a homozygous mutation or uniparental disomy. Since these abnormalities can be associated with ID and/or MCA, their detection is of particular interest for patients whose phenotype remains unexplained. However, the diagnostic yield obtained with these platforms is not confirmed, and the real clinical value of LOH detection has not been established. Methods We selected 21 children affected with ID, with or without congenital malformations, for whom standard genetic analyses failed to provide a diagnosis. We performed high-resolution SNP array analysis with four platforms (Affymetrix Genome-Wide Human SNP Array 6.0, Affymetrix Cytogenetics Whole-Genome 2.7 M array, Illumina HumanOmni1-Quad BeadChip, and Illumina HumanCytoSNP-12 DNA Analysis BeadChip) on whole-blood samples obtained from children and their parents to detect pathogenic CNVs and LOHs, and compared the results with those obtained on a moderate resolution array-based comparative genomic hybridization platform (NimbleGen CGX-12 Cytogenetics Array), already used in the clinical setting. Results We identified a total of four pathogenic CNVs in three patients, and all arrays successfully detected them. With the SNP arrays, we also identified a LOH containing a gene associated with a recessive disorder consistent with the patient’s phenotype (i.e., an informative LOH) in four children (including two siblings). A homozygous mutation within the informative LOH was found in three of these patients. Therefore, we were able to increase the diagnostic yield from 14.3% to 28.6% as a result of the information provided by LOHs. Conclusions This study shows the clinical usefulness of SNP arrays in children with ID, since they successfully detect pathogenic CNVs, identify informative LOHs that can lead to the diagnosis of a recessive disorder. It also highlights some challenges associated with the use of SNP arrays in a clinical laboratory. Electronic supplementary material The online version of this article (doi:10.1186/s12920-014-0070-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guylaine D'Amours
- Service de génétique médicale, CHU Sainte-Justine, Montréal, QC, Canada. .,Centre de recherche, CHU Sainte-Justine, Montréal, QC, Canada. .,Faculté de médecine, Université de Montréal, Montréal, QC, Canada.
| | - Mathieu Langlois
- Centre de pharmacogénomique, Institut de cardiologie de Montréal, Montréal, QC, Canada.
| | | | - Raouf Fetni
- Centre de recherche, CHU Sainte-Justine, Montréal, QC, Canada. .,Faculté de médecine, Université de Montréal, Montréal, QC, Canada. .,Département de pathologie, CHU Sainte-Justine, Montréal, QC, Canada. .,Pathologie et biologie cellulaire, Université de Montréal, Montréal, QC, Canada.
| | - Sonia Nizard
- Service de génétique médicale, CHU Sainte-Justine, Montréal, QC, Canada. .,Faculté de médecine, Université de Montréal, Montréal, QC, Canada. .,Pédiatrie, Université de Montréal, Montréal, QC, Canada.
| | - Myriam Srour
- Centre de recherche, CHU Sainte-Justine, Montréal, QC, Canada.
| | - Frédérique Tihy
- Service de génétique médicale, CHU Sainte-Justine, Montréal, QC, Canada. .,Centre de recherche, CHU Sainte-Justine, Montréal, QC, Canada. .,Faculté de médecine, Université de Montréal, Montréal, QC, Canada. .,Pathologie et biologie cellulaire, Université de Montréal, Montréal, QC, Canada.
| | - Michael S Phillips
- Centre de pharmacogénomique, Institut de cardiologie de Montréal, Montréal, QC, Canada.
| | - Jacques L Michaud
- Service de génétique médicale, CHU Sainte-Justine, Montréal, QC, Canada. .,Centre de recherche, CHU Sainte-Justine, Montréal, QC, Canada. .,Faculté de médecine, Université de Montréal, Montréal, QC, Canada. .,Pédiatrie, Université de Montréal, Montréal, QC, Canada.
| | - Emmanuelle Lemyre
- Service de génétique médicale, CHU Sainte-Justine, Montréal, QC, Canada. .,Centre de recherche, CHU Sainte-Justine, Montréal, QC, Canada. .,Faculté de médecine, Université de Montréal, Montréal, QC, Canada. .,Pédiatrie, Université de Montréal, Montréal, QC, Canada.
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Pereira RR, Pinto IP, Minasi LB, de Melo AV, da Cruz e Cunha DM, Cruz AS, Ribeiro CL, da Silva CC, de Melo e Silva D, da Cruz AD. Screening for intellectual disability using high-resolution CMA technology in a retrospective cohort from Central Brazil. PLoS One 2014; 9:e103117. [PMID: 25061755 PMCID: PMC4111347 DOI: 10.1371/journal.pone.0103117] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 06/27/2014] [Indexed: 11/20/2022] Open
Abstract
Intellectual disability is a complex, variable, and heterogeneous disorder, representing a disabling condition diagnosed worldwide, and the etiologies are multiple and highly heterogeneous. Microscopic chromosomal abnormalities and well-characterized genetic conditions are the most common causes of intellectual disability. Chromosomal Microarray Analysis analyses have made it possible to identify putatively pathogenic copy number variation that could explain the molecular etiology of intellectual disability. The aim of the current study was to identify possible submicroscopic genomic alterations using a high-density chromosomal microarray in a retrospective cohort of patients with otherwise undiagnosable intellectual disabilities referred by doctors from the public health system in Central Brazil. The CytoScan HD technology was used to detect changes in the genome copy number variation of patients who had intellectual disability and a normal karyotype. The analysis detected 18 CNVs in 60% of patients. Pathogenic CNVs represented about 22%, so it was possible to propose the etiology of intellectual disability for these patients. Likely pathogenic and unknown clinical significance CNVs represented 28% and 50%, respectively. Inherited and de novo CNVs were equally distributed. We report the nature of CNVs in patients from Central Brazil, representing a population not yet screened by microarray technologies.
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Affiliation(s)
- Rodrigo Roncato Pereira
- Núcleo de Pesquisas Replicon, Departamento de Biologia, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Irene Plaza Pinto
- Núcleo de Pesquisas Replicon, Departamento de Biologia, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, Brazil
- Programa de Pós-Graduação (Mestrado) em Genética, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, Brazil
| | - Lysa Bernardes Minasi
- Programa de Pós-Graduação (Mestrado) em Genética, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, Brazil
| | - Aldaires Vieira de Melo
- Núcleo de Pesquisas Replicon, Departamento de Biologia, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, Brazil
- Programa de Pós-Graduação em Biotecnologia e Biodiversidade, Universidade de Brasília, Brasília, DF, Brazil
| | - Damiana Mirian da Cruz e Cunha
- Núcleo de Pesquisas Replicon, Departamento de Biologia, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, Brazil
- Programa de Pós-Graduação (Mestrado) em Genética, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, Brazil
| | - Alex Silva Cruz
- Núcleo de Pesquisas Replicon, Departamento de Biologia, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Cristiano Luiz Ribeiro
- Núcleo de Pesquisas Replicon, Departamento de Biologia, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, Brazil
| | - Cláudio Carlos da Silva
- Núcleo de Pesquisas Replicon, Departamento de Biologia, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, Brazil
- Programa de Pós-Graduação (Mestrado) em Genética, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, Brazil
- Laboratório de Citogenética Humana e Genética Molecular, Secretaria do Estado da Saúde de Goiás (LACEN/SESGO), Goiânia, GO, Brazil
| | - Daniela de Melo e Silva
- Núcleo de Pesquisas Replicon, Departamento de Biologia, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Laboratório de Genética e Biodiversidade, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Aparecido Divino da Cruz
- Núcleo de Pesquisas Replicon, Departamento de Biologia, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
- Programa de Pós-Graduação (Mestrado) em Genética, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, Brazil
- Programa de Pós-Graduação em Biotecnologia e Biodiversidade, Universidade de Brasília, Brasília, DF, Brazil
- Laboratório de Citogenética Humana e Genética Molecular, Secretaria do Estado da Saúde de Goiás (LACEN/SESGO), Goiânia, GO, Brazil
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Varvagiannis K, Papoulidis I, Koromila T, Kefalas K, Ziegler M, Liehr T, Petersen MB, Gyftodimou Y, Manolakos E. De novo 393 kb microdeletion of 7p11.2 characterized by aCGH in a boy with psychomotor retardation and dysmorphic features. Meta Gene 2014; 2:274-82. [PMID: 25606410 PMCID: PMC4287824 DOI: 10.1016/j.mgene.2014.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 03/08/2014] [Accepted: 03/17/2014] [Indexed: 01/03/2023] Open
Abstract
We report on a 27 month old boy presenting with psychomotor delay and dysmorphic features, mainly mild facial asymmetry, prominent cup-shaped ears, long eyelashes, open mouth appearance and slight abnormalities of the hands and feet. Array comparative genomic hybridization revealed a 393 kb microdeletion in 7p11.2. We discuss the possible involvement of CHCHD2, GBAS, MRPS17, SEPT14 and PSPH on our patient's phenotype. Additionally, we studied the expression of two other genes deleted in the patient, CCT6A and SUMF2, for which there is scarce data in the literature. Based on current knowledge and the de novo occurrence of this finding in our proband we presume that the aberration is likely to be pathogenic in our case. However, a single gene disorder, elsewhere in the genome or in this very region cannot be ruled out. Further elucidation of the properties of this chromosomal region, as well as of the role of the genes involved will be needed in order to draw safe conclusions regarding the association of the chromosomal deletion with the patient's features. We report in detail the clinical and cytogenetic findings of a 27-month old male. We compare our findings with current literature and online databases. We discuss the possible involvement of certain genes in our patient’s phenotype.
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Affiliation(s)
| | | | - Theodora Koromila
- Laboratory of Human Genetics, Department of Biology, University of Athens, Athens, Greece
| | | | - Monika Ziegler
- Institute of Human Genetics Anthropology, Jena University Hospital, Jena, Germany
| | - Thomas Liehr
- Institute of Human Genetics Anthropology, Jena University Hospital, Jena, Germany
| | | | | | - Emmanouil Manolakos
- Eurogenetica S.A., Laboratory of Genetics, Athens-Thessaloniki, Greece ; Cattedra di Genetica Medica, Ospedale Binaghi, Cagliari, Italy
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Yan Y, Wu Q, Zhang L, Wang X, Dan S, Deng D, Sun L, Yao L, Ma Y, Wang L. Detection of submicroscopic chromosomal aberrations by array-based comparative genomic hybridization in fetuses with congenital heart disease. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2014; 43:404-412. [PMID: 24323407 DOI: 10.1002/uog.13236] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Revised: 10/21/2013] [Accepted: 10/21/2013] [Indexed: 06/03/2023]
Abstract
OBJECTIVES To evaluate the usefulness of array-based comparative genomic hybridization (aCGH) for prenatal genetic diagnosis of congenital heart disease (CHD), with and without associated anomalies, and to explore the relationship between submicroscopic chromosomal aberrations and CHD. METHODS In this prospective study we investigated 76 consecutive singleton fetuses with abnormal cardiac ultrasound findings, normal karyotype and negative or no fluorescence in-situ hybridization results for 22q11.2 deletion syndrome. All pregnancies underwent aCGH in a comprehensive search for chromosomal aberrations. The relationship between copy number variations (CNVs) and CHD was determined by comparing clinical findings to chromosomal databases. RESULTS CNVs that were benign or had no clinical significance were detected in 18/76 (23.7%) cases. CNVs of unknown clinical significance (i.e. VOUS) were detected in 4/76 (5.3%) cases. Pathogenic CNVs were detected in 5/76 (6.6%) cases. Fetuses with CHD and additional structural abnormalities demonstrated no difference in number of pathogenic CNVs when compared with fetuses with isolated CHD (7.4% (n = 2/27) vs 6.1% (n = 3/49), P > 0.05). CONCLUSION In this study cohort, aCGH analysis significantly improved the detection of submicroscopic chromosomal aberrations in pregnancies with CHD, as compared with conventional cytogenetics. Our results suggest that aCGH can provide additional genetic information in fetuses with abnormal heart findings.
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Affiliation(s)
- Y Yan
- Department of Ultrasound, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, P.R. China
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Duga B, Czakó M, Hadzsiev K, Komlósi K, Sümegi K, Kisfali P, Kosztolányi G, Melegh B. [Identifying rare genomic disorders with array comparative genomic hybridization in Hungary]. Orv Hetil 2014; 155:358-61. [PMID: 24566700 DOI: 10.1556/oh.2014.29825] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
INTRODUCTION In the past decade the study of genomic disorders has received more interest. Array comparative genome hybridization is a widely spread diagnostic method in the research of genomic disorders. This method was implemented in the laboratory of the authors in 2012. AIM This molecular cytogenetic method was first used to examine patients with complex developmental disorders in whom no genetic background was identified by traditional methods. METHOD The authors complemented traditional diagnostic methods with array comparative genome hybridization, which has not been used in routine diagnostics in Hungary so far. RESULTS Using this novel method the authors were able to identify genomic alterations in 7 out of 18 patients with complex developmental disorders. They found de novo alterations in 6 out of 7 patients, which were most likely causative in the development of the phenotype, while in one case they detected a familial genomic alteration. This method helped the authors to determine the breakpoint of genomic variation in their patients and delineate the affected genes contributing to the phenotype. CONCLUSIONS These results call attention to the usefulness of next generation diagnostic methods available in the laboratory of the authors.
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Affiliation(s)
- Balázs Duga
- Pécsi Tudományegyetem, Általános Orvostudományi Kar, Klinikai Központ Orvosi Genetikai Intézet Pécs Szigeti út 12. 7624 Pécsi Tudományegyetem Szentágothai János Kutatóközpont Pécs
| | - Márta Czakó
- Pécsi Tudományegyetem, Általános Orvostudományi Kar, Klinikai Központ Orvosi Genetikai Intézet Pécs Szigeti út 12. 7624 Pécsi Tudományegyetem Szentágothai János Kutatóközpont Pécs
| | - Kinga Hadzsiev
- Pécsi Tudományegyetem, Általános Orvostudományi Kar, Klinikai Központ Orvosi Genetikai Intézet Pécs Szigeti út 12. 7624 Pécsi Tudományegyetem Szentágothai János Kutatóközpont Pécs
| | - Katalin Komlósi
- Pécsi Tudományegyetem, Általános Orvostudományi Kar, Klinikai Központ Orvosi Genetikai Intézet Pécs Szigeti út 12. 7624 Pécsi Tudományegyetem Szentágothai János Kutatóközpont Pécs
| | - Katalin Sümegi
- Pécsi Tudományegyetem, Általános Orvostudományi Kar, Klinikai Központ Orvosi Genetikai Intézet Pécs Szigeti út 12. 7624 Pécsi Tudományegyetem Szentágothai János Kutatóközpont Pécs
| | - Péter Kisfali
- Pécsi Tudományegyetem, Általános Orvostudományi Kar, Klinikai Központ Orvosi Genetikai Intézet Pécs Szigeti út 12. 7624 Pécsi Tudományegyetem Szentágothai János Kutatóközpont Pécs
| | - György Kosztolányi
- Pécsi Tudományegyetem, Általános Orvostudományi Kar, Klinikai Központ Orvosi Genetikai Intézet Pécs Szigeti út 12. 7624 Pécsi Tudományegyetem Szentágothai János Kutatóközpont Pécs
| | - Béla Melegh
- Pécsi Tudományegyetem, Általános Orvostudományi Kar, Klinikai Központ Orvosi Genetikai Intézet Pécs Szigeti út 12. 7624 Pécsi Tudományegyetem Szentágothai János Kutatóközpont Pécs
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Multiplex ligation-dependent probe amplification to subtelomeric rearrangements in idiopathic intellectual disability in Colombia. Pediatr Neurol 2014; 50:250-4. [PMID: 24412240 DOI: 10.1016/j.pediatrneurol.2013.10.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 10/06/2013] [Accepted: 10/28/2013] [Indexed: 10/26/2022]
Abstract
BACKGROUND A cause cannot be determined in 30% to 50% of patients with intellectual disability. Determining the etiology of intellectual disability is important and useful for pediatric neurologists, geneticists, pediatricians, and patients' families because it allows assessment of recurrence risk, appropriate genetic counseling, and focus on treatment options and prognosis. This study aims to determine the prevalence, origin, and characterization of subtelomeric rearrangements through the Multiplex Ligation-Dependent Probe Amplification method in pediatric patients with idiopathic intellectual disability. METHODS A cross-sectional descriptive study was undertaken with patients seen in consultation at the neuropediatrics or genetic service of the Central Military Hospital, the Mercy' Hospital, or the Genetics Institute National University of Colombia. Patients were diagnosed with idiopathic intellectual disability between December 2010 and September 2011 and underwent a complete medical history, physical examination, and assessment to rule out other etiologies of intellectual disability. Then we applied the genetic test of Multiplex Ligation-Dependent Probe Amplification to each patient's sample of peripheral blood to determine subtelomeric rearrangements. RESULTS We studied a group of 119 patients with idiopathic intellectual disability; Multiplex Ligation-Dependent Probe Amplification showed subtelomeric rearrangements in five. In the group with subtelomeric rearrangements, the most frequent results were de novo rearrangements (80%), deletion type (60%), moderate and severe intellectual disability (80%), minor phenotypic abnormalities (80%), and family history of neurological disorders (80%). No dependence relationship was observed between subtelomeric rearrangements and family history of neurological disorders, family history of intellectual disability, severity of intellectual disability, phenotypic abnormalities, and consanguinity. CONCLUSIONS This study determined a prevalence of subtelomeric rearrangements of 4.2% in a group of Colombian pediatric patients with idiopathic intellectual disability using the genetic test Multiplex Ligation-Dependent Probe Amplification.
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21
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Considering specific clinical features as evidence of pathogenic copy number variants. J Appl Genet 2014; 55:189-96. [PMID: 24535828 DOI: 10.1007/s13353-014-0197-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Revised: 01/24/2014] [Accepted: 01/29/2014] [Indexed: 01/29/2023]
Abstract
Since the introduction of high-resolution microarray technologies, it has become apparent that structural chromosomal rearrangements can lead to a wide variety of clinical manifestations, including developmental delay/intellectual disability (DD/ID). It has been shown previously that the diagnostic yield of genome-wide array-based identification of submicroscopic alterations in patients with ID varies widely and depends on the patient selection criteria. More attempts have recently been made to define the phenotypic clues of pathogenic copy number variants (CNVs). The aim of this study was to investigate a well-phenotyped cohort of patients with DD/ID and determine whether certain clinical features may serve as indicators for pathogenic CNVs. A retrospective analysis was conducted for patients with DD/ID (n = 211) who were tested using genome-wide chromosomal microarray technologies and a review of the clinical data was performed. Pathogenic CNVs were detected in 29 patients. In comparison with individuals who had normal molecular karyotyping results (n = 182), malformations of the musculoskeletal system; congenital malformations of the CNS (particularly hydrocephalus and congenital malformations of the corpus callosum); minor anomalies of the eye, face, and neck subgroup (particularly downward-slanting palpebral fissures, minor anomalies of the ear, and micrognathia); brachydactyly; and umbilical hernia were more common in patients with chromosomal alterations. A multivariate logistic regression analysis allowed the identification of three independent pathogenic CNV predictors: congenital malformations of the corpus callosum, minor anomalies of the ear, and brachydactyly. Insights into the chromosomal phenotype may help to increase the diagnostic yield of microarray technologies and sharpen the distinction between chromosomal alterations and other conditions.
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Tzetis M, Kitsiou-Tzeli S, Frysira H, Xaidara A, Kanavakis E. The clinical utility of molecular karyotyping using high-resolution array-comparative genomic hybridization. Expert Rev Mol Diagn 2014; 12:449-57. [DOI: 10.1586/erm.12.40] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Maria Tzetis
- Department of Medical Genetics, Aghia Sophia Childrens Hospital, Thivon & Levadias, Medical School, University of Athens, 11527, Athens, Greece
- Department of Medical Genetics, Aghia Sophia Childrens Hospital, Thivon & Levadias, Medical School, University of Athens, 11527, Athens, Greece
| | - Sofia Kitsiou-Tzeli
- Department of Medical Genetics, Aghia Sophia Childrens Hospital, Thivon & Levadias, Medical School, University of Athens, 11527, Athens, Greece
| | - Helen Frysira
- Department of Medical Genetics, Aghia Sophia Childrens Hospital, Thivon & Levadias, Medical School, University of Athens, 11527, Athens, Greece
| | - Athena Xaidara
- First Department of Pediatrics, Aghia Sophia, Children’s Hospital, Medical School, University of Athens, Greece
| | - Emmanuel Kanavakis
- Department of Medical Genetics, Aghia Sophia Childrens Hospital, Thivon & Levadias, Medical School, University of Athens, 11527, Athens, Greece
- Research Institute for the Study of Genetic and Malignant Disorders in Childhood, Aghia Sophia, Children’s Hospital, Athens, Greece
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Peredo J, Quintero-Rivera F, Bradley JP, Tu M, Dipple KM. Cleft Lip and Palate in a Patient with 5q35.2-q35.3 Microdeletion: The Importance of Chromosomal Microarray Testing in the Craniofacial Clinic. Cleft Palate Craniofac J 2013; 50:618-22. [DOI: 10.1597/11-071] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We report on a 3½-year-old African American female with a 1.63 Mb microdeletion in 5q35.2-q35.3. This deletion includes NSD1, the gene that causes Sotos syndrome. The patient has unilateral cleft lip and palate (CLP) status postrepair, an unrepaired alveolar cleft, speech delay, global developmental delay, macrocephaly, mild cerebral palsy, and a patent ductus arteriosus status postrepair. Dysmorphic features include a prominent forehead and midface hypoplasia. This is one of the first cases of CLP associated with Sotos syndrome and emphasizes the utility of chromosomal microarray analysis in patients with more than isolated CLP in the Craniofacial Clinic.
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Affiliation(s)
- Jane Peredo
- Department of Pediatrics, Mattel Children's Hospital of UCLA
| | - Fabiola Quintero-Rivera
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Clinical and Molecular Cytogenetics Laboratory, David Geffen School of Medicine at UCLA
| | - James P. Bradley
- Department of Pediatrics, Mattel Children's Hospital of UCLA, Department of Surgery, Division of Plastic and Reconstructive Surgery, David Geffen School of Medicine at UCLA
| | - Marinda Tu
- UCLA Craniofacial Clinic, Department of Pediatrics, Mattel Children's Hospital of UCLA
| | - Katrina M. Dipple
- UCLA Craniofacial Clinic, Departments of Human Genetics and Pediatrics, David Geffen School of Medicine at UCLA
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Hehir-Kwa JY, Pfundt R, Veltman JA, de Leeuw N. Pathogenic or not? Assessing the clinical relevance of copy number variants. Clin Genet 2013; 84:415-21. [PMID: 23895381 DOI: 10.1111/cge.12242] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 07/24/2013] [Accepted: 07/24/2013] [Indexed: 02/04/2023]
Abstract
The availability of commercially produced genomic microarrays has resulted in the wide spread implementation of genomic microarrays, often as a first-tier diagnostic test for copy number variant (CNV) screening of patients who are suspected for chromosomal aberrations. Patients with intellectual disability (ID) and/or multiple congenital anomalies (MCA) were traditionally the main focus for this microarray-based CNV screening, but the application of microarrays to other (neurodevelopmental) disorders and tumor diagnostics has also been explored and implemented. The diagnostic workflow for patients with ID is now well established, relying on the identification of rare CNVs and determining their inheritance patterns. However, experience gained through screening large numbers of samples has revealed many subtleties and complexities of CNV interpretation. This has resulted in a better understanding of the contribution of CNVs to genomic disorders not only via de novo occurrence, but also via X-linked and recessive inheritance models as well as through models taking into account mosaicisms, imprinting, and digenic inheritance. In this review, we discuss CNV interpretation within the context of these different genetic disease models and common pitfalls that can occur when searching for supportive evidence that a CNV is clinically relevant.
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Affiliation(s)
- J Y Hehir-Kwa
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
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Key Informants’ Perspectives of Implementing Chromosomal Microarrays Into Clinical Practice in Australia. Twin Res Hum Genet 2013; 16:833-9. [DOI: 10.1017/thg.2013.43] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
High-resolution genomic tests have the potential to revolutionize healthcare by vastly improving mutation detection. The use of chromosomal microarray (CMA) represents one of the earliest examples of these new genomic tests being introduced and disseminated in the clinic. While CMA has clear advantages over traditional karyotyping in terms of mutation detection, little research has investigated the process by which CMA was implemented in clinical settings. Fifteen key informants, six clinicians, and nine laboratory scientists from four Australian states were interviewed about their experiences during and in the time since CMA was adopted for clinical use. Participants discussed challenges such as result interpretation and communication. Strengths were also highlighted, including the collaborative approaches of some centers. Clinical experiences and opinions can inform larger studies with a range of stakeholders, including patients. The historical perspectives from this retrospective study can be helpful in guiding the implementation of future genomic technologies such as whole exome/genome sequencing.
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Rare copy number variants are a common cause of short stature. PLoS Genet 2013; 9:e1003365. [PMID: 23516380 PMCID: PMC3597495 DOI: 10.1371/journal.pgen.1003365] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 01/19/2013] [Indexed: 02/06/2023] Open
Abstract
Human growth has an estimated heritability of about 80%-90%. Nevertheless, the underlying cause of shortness of stature remains unknown in the majority of individuals. Genome-wide association studies (GWAS) showed that both common single nucleotide polymorphisms and copy number variants (CNVs) contribute to height variation under a polygenic model, although explaining only a small fraction of overall genetic variability in the general population. Under the hypothesis that severe forms of growth retardation might also be caused by major gene effects, we searched for rare CNVs in 200 families, 92 sporadic and 108 familial, with idiopathic short stature compared to 820 control individuals. Although similar in number, patients had overall significantly larger CNVs (p-value<1×10(-7)). In a gene-based analysis of all non-polymorphic CNVs>50 kb for gene function, tissue expression, and murine knock-out phenotypes, we identified 10 duplications and 10 deletions ranging in size from 109 kb to 14 Mb, of which 7 were de novo (p<0.03) and 13 inherited from the likewise affected parent but absent in controls. Patients with these likely disease causing 20 CNVs were smaller than the remaining group (p<0.01). Eleven (55%) of these CNVs either overlapped with known microaberration syndromes associated with short stature or contained GWAS loci for height. Haploinsufficiency (HI) score and further expression profiling suggested dosage sensitivity of major growth-related genes at these loci. Overall 10% of patients carried a disease-causing CNV indicating that, like in neurodevelopmental disorders, rare CNVs are a frequent cause of severe growth retardation.
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Multiplex ligation-dependent probe amplification workflow for the detection of submicroscopic chromosomal abnormalities in patients with developmental delay/intellectual disability. Mol Cytogenet 2013; 6:7. [PMID: 23383958 PMCID: PMC3599182 DOI: 10.1186/1755-8166-6-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 12/31/2012] [Indexed: 12/12/2022] Open
Abstract
Background Array based comparative genomic hybridization (arrayCGH) has been increasingly used as the method of choice for diagnosis of patients with unexplained developmental delay/intellectual disability (DD/ID) but is not universally available for the high throughput use in routine practice. The next-generation sequencing (NGS) techniques, emerging as a new tool in clinical diagnostics, are at present quite labour-intensive and expensive. Since multiplex ligation-dependent probe amplification (MLPA) is relatively fast, easily interpreted and cost-effective, it is still a method of choice for screening large cohorts of patients with DD/ID. Results We prospectively studied a cohort of 150 patients with DD/ID with or without dysmorphic features or additional congenital abnormalities. We used two distinct MLPA kits, SALSA P036 and P070, for subtelomere screening and MLPA kit SALSA P245 for the 21 common microdeletion syndromes. Subtelomere analysis was performed by both kits in all patients. All imbalances were verified by follow-up MLPA kits. The MLPA analysis revealed chromosome aberrations in 21 (14%) cases: 11 subtelomeric rearrangements and 10 microdeletions. Conclusions We have presented the results of the investigation of patients with DD/ID obtained by using a combination of the MLPA sets for subtelomere aberrations and microdeletion syndromes followed by the confirmation of the aberrant results by the region-specific MLPA kits. The use of two subtelomeric kits per patient and investigation of all aberrations by follow-up sets has reduced the rate of false positive and negative results and improved the diagnostic yield. The relatively low cost, simplicity and reliability makes MLPA an effective first-tier cytogenetic diagnostic test for screening large cohorts of DD/ID patients.
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Abstract
Zusammenfassung
Die Ursache neurokognitiver Entwicklungsstörungen mit Intelligenzminderung stellt eine der häufigsten Fragestellungen in der genetischen Sprechstunde dar. Obwohl mehr als 400 krankheitsverursachende Einzelgendefekte bekannt sind, machen Chromosomenaberrationen derzeit den größten Anteil der bekannten Ursachen aus. Mittels hochauflösender Array-Techniken lassen sich nach Ausschluss des Down-Syndroms bei unselektionierten Patienten in 18% der Fälle relevante chromosomale Imbalancen nachweisen, wobei die Aberrationen nur in 4% der Fälle auch primär mikroskopisch sichtbar wären. Mit zunehmender Auflösung steigt jedoch auch die Rate an detektierten Kopienzahl-Normvarianten, welche die Beurteilung der Befunde erschweren können. Indikatoren für krankheitsrelevante Aberrationen sind Aberrationsgröße, Gengehalt und Segregation innerhalb der Familie. Eine Kausalität kann letztlich aber nur dann belegt werden, wenn Vergleichsfälle mit ähnlichem Genotyp und Phänotyp vorliegen.
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Otter M, Schrander-Stumpel CTRM, Didden R, Curfs LMG. The psychiatric phenotype in triple X syndrome: new hypotheses illustrated in two cases. Dev Neurorehabil 2012; 15:233-8. [PMID: 22582855 PMCID: PMC3399634 DOI: 10.3109/17518423.2012.655799] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND Triple X syndrome (47,XXX or trisomy X) is a relatively frequent cytogenetic condition with a large variety of physical and behavioural phenotypes. METHOD Two adult patients with a triple X karyotype are described. RESULTS Their karyotype was unknown until some years ago. What these patients have in common is that they were diagnosed with a broader autism phenotype, they were sexually abused, they suffer from psychotic illness and they show challenging behaviour, suicidality and a decline in occupational capacity. DISCUSSION These gene-environment interactions are discussed. Gene-environment interactions may explain the variety of behavioural and psychiatric phenotypes in triple X syndrome. Ongoing atypical development in adults is hypothesized. CONCLUSIONS Gene-environment interactions and ongoing atypical development in adults should be taken into account in research concerning the psychiatric phenotype of developmental disorders, especially those involving triple X syndrome.
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Affiliation(s)
- Maarten Otter
- Department of Child & Adolescent Psychiatry, Eleos, Ede, The Netherlands.
| | - Constance T. R. M. Schrander-Stumpel
- Department of clinical genetics, Maastricht University Medical Center UMC, Maastricht, The Netherlands,GROW School for Oncology and Developmental Biology, Maastricht University Medical Center UMC, Maastricht, The Netherlands
| | - Robert Didden
- Trajectum, Community Mental Health Team in ID, Zutphen, The Netherlands,Behavioural Science Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Leopold M. G. Curfs
- GROW School for Oncology and Developmental Biology, Maastricht University Medical Center UMC, Maastricht, The Netherlands,Department of Clinical Genetics, Maastricht University Medical Center UMC, Maastricht, The Netherlands
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Filges I, Suda L, Weber P, Datta AN, Fischer D, Dill P, Glanzmann R, Benzing J, Hegi L, Wenzel F, Huber AR, Mori AC, Miny P, Röthlisberger B. High resolution array in the clinical approach to chromosomal phenotypes. Gene 2012; 495:163-9. [PMID: 22240311 DOI: 10.1016/j.gene.2011.12.042] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 12/19/2011] [Accepted: 12/23/2011] [Indexed: 12/11/2022]
Abstract
Array genomic hybridization (AGH) has recently been implemented as a diagnostic tool for the detection of submicroscopic copy number variants (CNVs) in patients with developmental disorders. However, there is no consensus regarding the choice of the platform, the minimal resolution needed and systematic interpretation of CNVs. We report our experience in the clinical diagnostic use of high resolution AGH up to 100 kb on 131 patients with chromosomal phenotypes but previously normal karyotype. We evaluated the usefulness in our clinics and laboratories by the detection rate of causal CNVs and CNVs of unknown clinical significance and to what extent their interpretation would challenge the systematic use of high-resolution arrays in clinical application. Prioritizing phenotype-genotype correlation in our interpretation strategy to criteria previously described, we identified 33 (25.2%) potentially pathogenic aberrations. 16 aberrations were confirmed pathogenic (16.4% syndromic, 8.5% non-syndromic patients); 9 were new and individual aberrations, 3 of them were pathogenic although inherited and one is as small as approx 200 kb. 13 of 16 further CNVs of unknown significance were classified likely benign, for 3 the significance remained unclear. High resolution array allows the detection of up to 12.2% of pathogenic aberrations in a diagnostic clinical setting. Although the majority of aberrations are larger, the detection of small causal aberrations may be relevant for family counseling. The number of remaining unclear CNVs is limited. Careful phenotype-genotype correlations of the individual CNVs and clinical features are challenging but remain a hallmark for CNV interpretation.
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Verloes A, Héron D, Billette de Villemeur T, Afenjar A, Baumann C, Bahi-Buisson N, Charles P, Faudet A, Jacquette A, Mignot C, Moutard ML, Passemard S, Rio M, Robel L, Rougeot C, Ville D, Burglen L, des Portes V. Stratégie d’exploration d’une déficience intellectuelle inexpliquée. Arch Pediatr 2012; 19:194-207. [DOI: 10.1016/j.arcped.2011.11.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 11/22/2011] [Accepted: 11/25/2011] [Indexed: 02/07/2023]
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Abstract
Array-based genome-wide segmental aneuploidy screening detects both de novo and inherited copy number variations (CNVs). In sporadic patients de novo CNVs are interpreted as potentially pathogenic. However, a deletion, transmitted from a healthy parent, may be pathogenic if it overlaps with a mutated second allele inherited from the other healthy parent. To detect such events, we performed multiplex enrichment and next-generation sequencing of the entire coding sequence of all genes within unique hemizygous deletion regions in 20 patients (1.53 Mb capture footprint). Out of the detected 703 non-synonymous single-nucleotide variants (SNVs), 8 represented variants being unmasked by a hemizygous deletion. Although evaluation of inheritance patterns, Grantham matrix scores, evolutionary conservation and bioinformatic predictions did not consistently indicate pathogenicity of these variants, no definitive conclusions can be drawn without functional validation. However, in one patient with severe mental retardation, lack of speech, microcephaly, cheilognathopalatoschisis and bilateral hearing loss, we discovered a second smaller deletion, inherited from the other healthy parent, resulting in loss of both alleles of the highly conserved heat shock factor binding protein 1 (HSBP1) gene. Conceivably, inherited deletions may unmask rare pathogenic variants that may exert a phenotypic impact through a recessive mode of gene action.
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Gijsbers ACJ, Schoumans J, Ruivenkamp CAL. Interpretation of array comparative genome hybridization data: a major challenge. Cytogenet Genome Res 2011; 135:222-7. [PMID: 22086107 DOI: 10.1159/000334066] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The advent and application of high-resolution array-based comparative genome hybridization (array CGH) has led to the detection of large numbers of copy number variants (CNVs) in patients with developmental delay and/or multiple congenital anomalies as well as in healthy individuals. The notion that CNVs are also abundantly present in the normal population challenges the interpretation of the clinical significance of detected CNVs in patients. In this review we will illustrate a general clinical workflow based on our own experience that can be used in routine diagnostics for the interpretation of CNVs.
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Affiliation(s)
- A C J Gijsbers
- Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
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Hochstenbach R, Buizer-Voskamp JE, Vorstman JAS, Ophoff RA. Genome arrays for the detection of copy number variations in idiopathic mental retardation, idiopathic generalized epilepsy and neuropsychiatric disorders: lessons for diagnostic workflow and research. Cytogenet Genome Res 2011; 135:174-202. [PMID: 22056632 DOI: 10.1159/000332928] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022] Open
Abstract
We review the contributions and limitations of genome-wide array-based identification of copy number variants (CNVs) in the clinical diagnostic evaluation of patients with mental retardation (MR) and other brain-related disorders. In unselected MR referrals a causative genomic gain or loss is detected in 14-18% of cases. Usually, such CNVs arise de novo, are not found in healthy subjects, and have a major impact on the phenotype by altering the dosage of multiple genes. This high diagnostic yield justifies array-based segmental aneuploidy screening as the initial genetic test in these patients. This also pertains to patients with autism (expected yield about 5-10% in nonsyndromic and 10-20% in syndromic patients) and schizophrenia (at least 5% yield). CNV studies in idiopathic generalized epilepsy, attention-deficit hyperactivity disorder, major depressive disorder and Tourette syndrome indicate that patients have, on average, a larger CNV burden as compared to controls. Collectively, the CNV studies suggest that a wide spectrum of disease-susceptibility variants exists, most of which are rare (<0.1%) and of variable and usually small effect. Notwithstanding, a rare CNV can have a major impact on the phenotype. Exome sequencing in MR and autism patients revealed de novo mutations in protein coding genes in 60 and 20% of cases, respectively. Therefore, it is likely that arrays will be supplanted by next-generation sequencing methods as the initial and perhaps ultimate diagnostic tool in patients with brain-related disorders, revealing both CNVs and mutations in a single test.
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Affiliation(s)
- R Hochstenbach
- Division of Biomedical Genetics, Department of Medical Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands.
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Practical guidelines for interpreting copy number gains detected by high-resolution array in routine diagnostics. Eur J Hum Genet 2011; 20:161-5. [PMID: 21934709 DOI: 10.1038/ejhg.2011.174] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The correct interpretation of copy number gains in patients with developmental delay and multiple congenital anomalies is hampered by the large number of copy number variations (CNVs) encountered in healthy individuals. The variable phenotype associated with copy number gains makes interpretation even more difficult. Literature shows that inheritence, size and presence in healthy individuals are commonly used to decide whether a certain copy number gain is pathogenic, but no general consensus has been established. We aimed to develop guidelines for interpreting gains detected by array analysis using array CGH data of 300 patients analysed with the 105K Agilent oligo array in a diagnostic setting. We evaluated the guidelines in a second, independent, cohort of 300 patients. In the first 300 patients 797 gains of four or more adjacent oligonucleotides were observed. Of these, 45.4% were de novo and 54.6% were familial. In total, 94.8% of all de novo gains and 87.1% of all familial gains were concluded to be benign CNVs. Clinically relevant gains ranged from 288 to 7912 kb in size, and were significantly larger than benign gains and gains of unknown clinical relevance (P < 0.001). Our study showed that a threshold of 200 kb is acceptable in a clinical setting, whereas heritability does not exclude a pathogenic nature of a gain. Evaluation of the guidelines in the second cohort of 300 patients revealed that the interpretation guidelines were clear, easy to follow and efficient.
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Hirschfeldova K, Baxova A, Kebrdlova V, Solc R, Mihalova R, Lnenicka P, Vesela K, Stekrova J. Cryptic Chromosomal Rearrangements in Children with Idiopathic Mental Retardation in the Czech Population. Genet Test Mol Biomarkers 2011; 15:607-11. [DOI: 10.1089/gtmb.2010.0218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Katerina Hirschfeldova
- Institute of Biology and Medical Genetics, 1st Faculty of Medicine and General Teaching Hospital, Charles University in Prague, Prague, Czech Republic
| | - Alice Baxova
- Institute of Biology and Medical Genetics, 1st Faculty of Medicine and General Teaching Hospital, Charles University in Prague, Prague, Czech Republic
| | - Vera Kebrdlova
- Institute of Biology and Medical Genetics, 1st Faculty of Medicine and General Teaching Hospital, Charles University in Prague, Prague, Czech Republic
| | - Roman Solc
- Institute of Biology and Medical Genetics, 1st Faculty of Medicine and General Teaching Hospital, Charles University in Prague, Prague, Czech Republic
| | - Romana Mihalova
- Institute of Biology and Medical Genetics, 1st Faculty of Medicine and General Teaching Hospital, Charles University in Prague, Prague, Czech Republic
| | - Petr Lnenicka
- Institute of Biology and Medical Genetics, 1st Faculty of Medicine and General Teaching Hospital, Charles University in Prague, Prague, Czech Republic
| | - Kamila Vesela
- Institute of Biology and Medical Genetics, 1st Faculty of Medicine and General Teaching Hospital, Charles University in Prague, Prague, Czech Republic
| | - Jitka Stekrova
- Institute of Biology and Medical Genetics, 1st Faculty of Medicine and General Teaching Hospital, Charles University in Prague, Prague, Czech Republic
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Gijsbers AC, Dauwerse JG, Bosch CA, Boon EM, van den Ende W, Kant SG, Hansson KM, Breuning MH, Bakker E, Ruivenkamp CA. Three new cases with a mosaicism involving a normal cell line and a cryptic unbalanced autosomal reciprocal translocation. Eur J Med Genet 2011; 54:e409-12. [DOI: 10.1016/j.ejmg.2011.05.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Accepted: 05/04/2011] [Indexed: 02/04/2023]
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Vermeesch JR, Balikova I, Schrander-Stumpel C, Fryns JP, Devriendt K. The causality of de novo copy number variants is overestimated. Eur J Hum Genet 2011; 19:1112-3. [PMID: 21587321 DOI: 10.1038/ejhg.2011.83] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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Using a combination of MLPA kits to detect chromosomal imbalances in patients with multiple congenital anomalies and mental retardation is a valuable choice for developing countries. Eur J Med Genet 2011; 54:e425-32. [PMID: 21457803 DOI: 10.1016/j.ejmg.2011.03.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2010] [Accepted: 03/14/2011] [Indexed: 12/26/2022]
Abstract
Conventional karyotyping detects anomalies in 3-15% of patients with multiple congenital anomalies and mental retardation (MCA/MR). Whole-genome array screening (WGAS) has been consistently suggested as the first choice diagnostic test for this group of patients, but it is very costly for large-scale use in developing countries. We evaluated the use of a combination of Multiplex Ligation-dependent Probe Amplification (MLPA) kits to increase the detection rate of chromosomal abnormalities in MCA/MR patients. We screened 261 MCA/MR patients with two subtelomeric and one microdeletion kits. This would theoretically detect up to 70% of all submicroscopic abnormalities. Additionally we scored the de Vries score for 209 patients in an effort to find a suitable cut-off for MLPA screening. Our results reveal that chromosomal abnormalities were present in 87 (33.3%) patients, but only 57 (21.8%) were considered causative. Karyotyping detected 15 abnormalities (6.9%), while MLPA identified 54 (20.7%). Our combined MLPA screening raised the total detection number of pathogenic imbalances more than three times when compared to conventional karyotyping. We also show that using the de Vries score as a cut-off for this screening would only be suitable under financial restrictions. A decision analytic model was constructed with three possible strategies: karyotype, karyotype + MLPA and karyotype + WGAS. Karyotype + MLPA strategy detected anomalies in 19.8% of cases which account for 76.45% of the expected yield for karyotype + WGAS. Incremental Cost Effectiveness Ratio (ICER) of MLPA is three times lower than that of WGAS, which means that, for the same costs, we have three additional diagnoses with MLPA but only one with WGAS. We list all causative alterations found, including rare findings, such as reciprocal duplications of regions deleted in Sotos and Williams-Beuren syndromes. We also describe imbalances that were considered polymorphisms or rare variants, such as the new SNP that confounded the analysis of the 22q13.3 deletion syndrome.
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Gijsbers ACJ, den Hollander NS, Helderman-van de Enden ATJM, Schuurs-Hoeijmakers JHM, Vijfhuizen L, Bijlsma EK, van Haeringen A, Hansson KBM, Bakker E, Breuning MH, Ruivenkamp CAL. X-chromosome duplications in males with mental retardation: pathogenic or benign variants? Clin Genet 2011; 79:71-8. [PMID: 20486941 DOI: 10.1111/j.1399-0004.2010.01438.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Studies to identify copy number variants (CNVs) on the X-chromosome have revealed novel genes important in the causation of X-linked mental retardation (XLMR). Still, for many CNVs it is unclear whether they are associated with disease or are benign variants. We describe six different CNVs on the X-chromosome in five male patients with mental retardation that were identified by conventional karyotyping and single nucleotide polymorphism array analysis. One deletion and five duplications ranging in size from 325 kb to 12.5 Mb were observed. Five CNVs were maternally inherited and one occurred de novo. We discuss the involvement of potential candidate genes and focus on the complexity of X-chromosomal duplications in males inherited from healthy mothers with different X-inactivation patterns. Based on size and/or the presence of XLMR genes we were able to classify CNVs as pathogenic in two patients. However, it remains difficult to decide if the CNVs in the other three patients are pathogenic or benign.
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Affiliation(s)
- A C J Gijsbers
- Center for Human and Clinical Genetics, Leiden University Medical Center (LUMC), Einthovenweg 20, Leiden, The Netherlands.
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de Leeuw N, Hehir-Kwa JY, Simons A, Geurts van Kessel A, Smeets DF, Faas BHW, Pfundt R. SNP Array Analysis in Constitutional and Cancer Genome Diagnostics – Copy Number Variants, Genotyping and Quality Control. Cytogenet Genome Res 2011; 135:212-21. [PMID: 21934286 DOI: 10.1159/000331273] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- N de Leeuw
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.
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A three-step workflow procedure for the interpretation of array-based comparative genome hybridization results in patients with idiopathic mental retardation and congenital anomalies. Genet Med 2010; 12:478-85. [PMID: 20734469 DOI: 10.1097/gim.0b013e3181e3914a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
One of the aims of clinical genetics is to identify gene mutations or genomic rearrangements that may underlie complex presentations of phenotypic features, such as multiple congenital malformations and mental retardation. During the decade after publication of the first article on array-based comparative genome hybridization, this technique has supplemented karyotyping as the prime genome-wide screening method in patients with idiopathic multiple congenital malformations and mental retardation. The use of this novel, discovery-based, approach has dramatically increased the detection rate of genomic imbalances. Array-based comparative genome hybridization detects copy number changes in the genome of patients and healthy subjects, some of which may represent phenotypically neutral copy number variations. This prompts the need for properly distinguishing between those copy number changes that may contribute to the clinical phenotype amid a pool of neutral copy number variations. We briefly review the characteristics of copy number changes in relation to their clinical relevance. Second, we discuss several published workflow schemes to identify copy number changes putatively contributing to the phenotype, and third, we propose a three-step procedure aiming to rapidly evaluate copy number changes on a case-by-case basis as to their potential contribution to the phenotype of patients with idiopathic multiple congenital malformations and mental retardation. This workflow is gene-centered and should aid in identification of disease-related candidate genes and in estimating the recurrence risk for the disorder in the family.
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A parallel SNP array study of genomic aberrations associated with mental retardation in patients and general population in Estonia. Eur J Med Genet 2010; 54:136-43. [PMID: 21112420 DOI: 10.1016/j.ejmg.2010.11.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Accepted: 11/04/2010] [Indexed: 11/21/2022]
Abstract
The increasing use of whole-genome array screening has revealed the important role of DNA copy-number variations in the pathogenesis of neurodevelopmental disorders and several recurrent genomic disorders have been defined during recent years. However, some variants considered to be pathogenic have also been observed in phenotypically normal individuals. This underlines the importance of further characterization of genomic variants with potentially variable expressivity in both patient and general population cohorts to clarify their phenotypic consequence. In this study whole-genome SNP arrays were used to investigate genomic rearrangements in 77 Estonian families with idiopathic mental retardation. In addition to this family-based approach, phenotype and genotype data from a cohort of 1000 individuals in the general population were used for accurate interpretation of aberrations found in mental retardation patients. Relevant structural aberrations were detected in 18 of the families analyzed (23%). Fifteen of those were in genomic regions where clinical significance has previously been established. In 3 families, 4 novel aberrations associated with intellectual disability were detected in chromosome regions 2p25.1-p24.3, 3p12.1-p11.2, 7p21.2-p21.1 and Xq28. Carriers of imbalances in 15q13.3, 16p11.2 and Xp22.31 were identified among reference individuals, affirming the variable phenotypic consequence of rare variants in some genomic regions considered as pathogenic.
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Additional cryptic CNVs in mentally retarded patients with apparently balanced karyotypes. Eur J Med Genet 2010; 53:227-33. [PMID: 20542150 DOI: 10.1016/j.ejmg.2010.06.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Accepted: 06/01/2010] [Indexed: 01/01/2023]
Abstract
Apparently balanced chromosome abnormalities are occasionally associated with mental retardation (MR). These balanced rearrangements may disrupt genes. However, the phenotype may also be caused by small abnormalities present at the breakpoints or elsewhere in the genome. Conventional karyotyping is not instrumental for detecting small abnormalities because it only identifies genomic imbalances larger than 5-10 Mb. In contrast, high-resolution whole-genome arrays enable the detection of submicroscopic abnormalities in patients with apparently balanced rearrangements. Here, we report on the whole-genome analysis of 13 MR patients with previously detected balanced chromosomal abnormalities, five de novo, four inherited, and four of unknown inheritance, using Single Nucleotide Polymorphism (SNP) arrays. In all the cases, the patient had an abnormal phenotype. In one familial case and one unknown inheritance case, one of the parents had a phenotype which appeared identical to the patient's phenotype. Additional copy number variants (CNVs) were identified in eight patients. Three patients contained CNVs adjacent to one or either breakpoints. One of these patients showed four and two deletions near the breakpoints of a de novo pericentric inversion. In five patients we identified CNVs on chromosomes unrelated to the previously observed genomic imbalance. These data demonstrate that high-resolution array screening and conventional karyotyping is necessary to tie complex karyotypes to phenotypes of MR patients.
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Detection of low-level mosaicism and placental mosaicism by oligonucleotide array comparative genomic hybridization. Genet Med 2010; 12:85-92. [PMID: 20084009 DOI: 10.1097/gim.0b013e3181cc75d0] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
PURPOSE To determine the sensitivity of whole-genome oligonucleotide array comparative genomic hybridization for the detection of mosaic cytogenetic abnormalities. METHODS Mosaicism sensitivity was evaluated by testing artificially derived whole chromosome and segmental aneuploidies ranging from 0% to 100% abnormal and additional naturally occurring mosaic specimens. RESULTS Using combined dye-reversed replicates and an unfiltered analysis, oligonucleotide array comparative genomic hybridization detected as low as 10% and 20-30% mosaicism from whole chromosome and segmental aneuploidies, respectively. To investigate discrepancies between cultured and uncultured specimens, array comparative genomic hybridization was performed on DNA from additional direct product of conception specimens with abnormal karyotypes in culture. Interestingly, 5 of 10 product of conception specimens with double trisomies on cultured cell analysis had only a single trisomy by array comparative genomic hybridization and quantitative polymerase chain reaction on DNA from the uncultured direct specimen, and all harbored the more commonly observed trisomy. Thus, oligonucleotide array comparative genomic hybridization revealed previously unidentified placental mosaicism in half of the products of conception with double-aneuploid conventional karyotypes. CONCLUSION Oligonucleotide array comparative genomic hybridization can detect low-level mosaicism for whole chromosome ( approximately 10%) and segmental ( approximately 20-30%) aneuploidies when using specific detection criteria. In addition, careful interpretation is required when performing array comparative genomic hybridization on DNA isolated from direct specimens as the results may differ from the cultured chromosome analysis.
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van Gool SA, Kamp GA, Odink RJ, de Muinck Keizer-Schrama SMPF, Delemarre-van de Waal HA, Oostdijk W, Wit JM. High-dose GH treatment limited to the prepubertal period in young children with idiopathic short stature does not increase adult height. Eur J Endocrinol 2010; 162:653-60. [PMID: 20110402 DOI: 10.1530/eje-09-0880] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
OBJECTIVE To assess the long-term effect of prepubertal high-dose GH treatment on growth in children with idiopathic short stature (ISS). DESIGN AND METHODS Forty children with no signs of puberty, age at start 4-8 years (girls) or 4-10 years (boys), height SDS <-2.0 SDS, and birth length >-2.0 SDS, were randomly allocated to receive GH at a dose of 2 mg/m(2) per day (equivalent to 75 microg/kg per day at start and 64 microg/kg per day at stop) until the onset of puberty for at least 2 years (preceded by two 3-month periods of treatment with low or intermediate doses of GH separated by two washout periods of 3 months) or no treatment. In 28 cases, adult height (AH) was assessed at a mean (S.D.) age of 20.4 (2.3) years. RESULTS GH-treated children (mean treatment period on high-dose GH 2.3 years (range 1.2-5.0 years)) showed an increased mean height SDS at discontinuation of the treatment compared with the controls (-1.3 (0.8) SDS versus -2.6 (0.8) SDS respectively). However, bone maturation was significantly accelerated in the GH-treated group compared with the controls (1.6 (0.4) versus 1.0 (0.2) years per year, respectively), and pubertal onset tended to advance. After an untreated interval of 3-12 years, AH was -2.1 (0.7) and -1.9 (0.6) in the GH-treated and control groups respectively. Age was a positive predictor of adult height gain. CONCLUSION High-dose GH treatment restricted to the prepubertal period in young ISS children augments height gain during treatment, but accelerates bone maturation, resulting in a similar adult height compared with the untreated controls.
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Affiliation(s)
- S A van Gool
- Department of Pediatrics, Leiden University Medical Center, Postal Zone J6-S, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
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Galasso C, Lo-Castro A, El-Malhany N, Curatolo P. "Idiopathic" mental retardation and new chromosomal abnormalities. Ital J Pediatr 2010; 36:17. [PMID: 20152051 PMCID: PMC2844383 DOI: 10.1186/1824-7288-36-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Accepted: 02/14/2010] [Indexed: 02/07/2023] Open
Abstract
Mental retardation is a heterogeneous condition, affecting 1-3% of general population. In the last few years, several emerging clinical entities have been described, due to the advent of newest genetic techniques, such as array Comparative Genomic Hybridization. The detection of cryptic microdeletion/microduplication abnormalities has allowed genotype-phenotype correlations, delineating recognizable syndromic conditions that are herein reviewed. With the aim to provide to Paediatricians a combined clinical and genetic approach to the child with cognitive impairment, a practical diagnostic algorithm is also illustrated. The use of microarray platforms has further reduced the percentage of "idiopathic" forms of mental retardation, previously accounted for about half of total cases. We discussed the putative pathways at the basis of remaining "pure idiopathic" forms of mental retardation, highlighting possible environmental and epigenetic mechanisms as causes of altered cognition.
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Affiliation(s)
- Cinzia Galasso
- Department of Neuroscience, Paediatric Neurology Unit, "Tor Vergata" University of Rome, Italy
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A complex chromosome 7q rearrangement identified in a patient with mental retardation, anxiety disorder, and autistic features. Am J Med Genet A 2010; 152A:427-33. [DOI: 10.1002/ajmg.a.33203] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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