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Chaves TF, Ocampos M, Barbato IT, de Camargo Pinto LL, de Luca GR, Barbato Filho JH, Bernardi P, Costa Netto Muniz Y, Francesca Maris A. A cohort study of neurodevelopmental disorders and/or congenital anomalies using high resolution chromosomal microarrays in southern Brazil highlighting the significance of ASD. Sci Rep 2024; 14:3762. [PMID: 38355898 PMCID: PMC10867078 DOI: 10.1038/s41598-024-54385-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/12/2024] [Indexed: 02/16/2024] Open
Abstract
Chromosomal microarray (CMA) is the reference in evaluation of copy number variations (CNVs) in individuals with neurodevelopmental disorders (NDDs), such as intellectual disability (ID) and/or autism spectrum disorder (ASD), which affect around 3-4% of the world's population. Modern platforms for CMA, also include probes for single nucleotide polymorphisms (SNPs) that detect homozygous regions in the genome, such as long contiguous stretches of homozygosity (LCSH). These regions result from complete or segmental chromosomal homozygosis and may be indicative of uniparental disomy (UPD), inbreeding, population characteristics, as well as replicative DNA repair events. In this retrospective study, we analyzed CMA reading files requested by geneticists and neurologists for diagnostic purposes along with available clinical data. Our objectives were interpreting CNVs and assess the frequencies and implications of LCSH detected by Affymetrix CytoScan HD (41%) or 750K (59%) platforms in 1012 patients from the south of Brazil. The patients were mainly children with NDDs and/or congenital anomalies (CAs). A total of 206 CNVs, comprising 132 deletions and 74 duplications, interpreted as pathogenic, were found in 17% of the patients in the cohort and across all chromosomes. Additionally, 12% presented rare variants of uncertain clinical significance, including LPCNVs, as the only clinically relevant CNV. Within the realm of NDDs, ASD carries a particular importance, owing to its escalating prevalence and its growing repercussions for individuals, families, and communities. ASD was one clinical phenotype, if not the main reason for referral to testing, for about one-third of the cohort, and these patients were further analyzed as a sub-cohort. Considering only the patients with ASD, the diagnostic rate was 10%, within the range reported in the literature (8-21%). It was higher (16%) when associated with dysmorphic features and lower (7%) for "isolated" ASD (without ID and without dysmorphic features). In 953 CMAs of the whole cohort, LCSH (≥ 3 Mbp) were analyzed not only for their potential pathogenic significance but were also explored to identify common LCSH in the South Brazilians population. CMA revealed at least one LCSH in 91% of the patients. For about 11.5% of patients, the LCSH suggested consanguinity from the first to the fifth degree, with a greater probability of clinical impact, and in 2.8%, they revealed a putative UPD. LCSH found at a frequency of 5% or more were considered common LCSH in the general population, allowing us to delineate 10 regions as potentially representing ancestral haplotypes of neglectable clinical significance. The main referrals for CMA were developmental delay (56%), ID (33%), ASD (33%) and syndromic features (56%). Some phenotypes in this population may be predictive of a higher probability of indicating a carrier of a pathogenic CNV. Here, we present the largest report of CMA data in a cohort with NDDs and/or CAs from the South of Brazil. We characterize the rare CNVs found along with the main phenotypes presented by each patient and show the importance and usefulness of LCSH interpretation in CMA results that incorporate SNPs, as well as we illustrate the value of CMA to investigate CNV in ASD.
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Affiliation(s)
- Tiago Fernando Chaves
- Laboratório de Polimorfismos Genéticos (LAPOGE), Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil.
- Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil.
| | - Maristela Ocampos
- Laboratory Neurogene (former), Florianopolis, SC, Brazil
- Mercolab Diagnóstica (actual), Florianopolis, SC, Brazil
| | | | | | | | | | - Priscila Bernardi
- University Hospital Professor Polydoro Ernani de São Thiago, Florianópolis, SC, Brazil
| | - Yara Costa Netto Muniz
- Laboratório de Polimorfismos Genéticos (LAPOGE), Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Angelica Francesca Maris
- Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil.
- Children's Hospital Joana de Gusmão, Florianópolis, SC, Brazil.
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Granocchio E, Pollina E, De Salvatore M, Scopelliti MR, Tanzi G, Sciacca FL, D'Arrigo S, Ciaccio C. 22q13.33 duplication involving SHANK3 gene: a boy and his mother with "persistent" language and speech sound disorder. Psychiatr Genet 2024; 34:19-23. [PMID: 38084626 DOI: 10.1097/ypg.0000000000000355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Patients carrying 22q13.33 duplication present variable neurodevelopmental phenotype. Among these, patients with genetic alteration disrupting SHANK3 gene are very rare and they also present neurodevelopmental disorder such as autism spectrum disorder and intellectual disability. The real incidence is unknown because mild and variable phenotype could cause reduction in diagnosed cases. We describe the first case of 22q13.33 microduplication disrupting SHANK3 gene, inherited from mother to son, that presents a "persistent" language and speech sound disorder as main symptom without intellectual disability and autism spectrum disorder. More clinical reports with accurate phenotype description are needed to better define the profile of carriers of this genetic alteration.
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Affiliation(s)
- Elisa Granocchio
- Department of Pediatric Neuroscience, Foundation I.R.C.C.S. Istituto Neurologico Carlo Besta
| | | | - Marinella De Salvatore
- Department of Pediatric Neuroscience, Foundation I.R.C.C.S. Istituto Neurologico Carlo Besta
| | - Maria R Scopelliti
- Department of Pediatric Neuroscience, Foundation I.R.C.C.S. Istituto Neurologico Carlo Besta
| | | | - Francesca L Sciacca
- Laboratory of Cytogenetic, Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Stefano D'Arrigo
- Department of Pediatric Neuroscience, Foundation I.R.C.C.S. Istituto Neurologico Carlo Besta
| | - Claudia Ciaccio
- Department of Pediatric Neuroscience, Foundation I.R.C.C.S. Istituto Neurologico Carlo Besta
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Abreu NJ, Chiujdea M, Liu S, Zhang B, Spence SJ. Factors Associated With Underutilization of Genetic Testing in Autism Spectrum Disorders. Pediatr Neurol 2024; 150:17-23. [PMID: 37939453 DOI: 10.1016/j.pediatrneurol.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 09/08/2023] [Accepted: 10/04/2023] [Indexed: 11/10/2023]
Abstract
BACKGROUND We sought to identify patient and provider factors associated with low completion of genetic testing, specifically chromosomal microarray (CMA), for autism spectrum disorder (ASD). METHODS Medical record review was conducted of children newly diagnosed with ASD without prior genetic testing at a single academic medical center from February 2015 through January 2016. RESULTS Only 41.9% of individuals with ASD completed CMA testing over at least 18 months from diagnosis (n = 140 of 334). Time to CMA completion varied, with a median of 86.5 days (interquartile range 2 to 214.5 days). Provider recommendation of genetic testing at the diagnostic visit and greater number of follow-up visits were associated with CMA completion. On multivariate regression, CMA completion was inversely associated with age (odds ratio [OR] = 0.8 for each year older, 95% confidence interval [CI] 0.7, 0.9; P = 0.001) and directly associated with intellectual disability or global developmental delay (OR = 2.2, 95% CI 1.3, 3.8; P = 0.004), first-degree relative with ASD (OR = 2.5, 95% CI 1.0, 6.0; P = 0.044), and public insurance (OR = 1.7, 95% CI 1.0, 2.9; P = 0.037). Parental concern and cost/insurance coverage were the most frequently documented barriers. CONCLUSIONS Workflows to support early genetic testing recommendation and ordering soon after diagnosis may increase utilization, incorporating both family and provider perspectives. Genetic counseling highlighting the utility of genetic testing across the life span, phenotypic variability of genetic disorders, and possibility of de novo variants in ASD may also improve utilization.
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Affiliation(s)
- Nicolas J Abreu
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts.
| | - Madeline Chiujdea
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Shanshan Liu
- Biostatistics and Research Design Center, Institutional Centers for Clinical and Translational Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Bo Zhang
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts; Biostatistics and Research Design Center, Institutional Centers for Clinical and Translational Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Sarah J Spence
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
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Cai M, Que Y, Chen M, Zhang M, Huang H, Xu L, Lin N. Pathogenic copy number variations are associated with foetal short femur length in a tertiary referral centre study. J Cell Mol Med 2023; 27:2354-2361. [PMID: 37401003 PMCID: PMC10424293 DOI: 10.1111/jcmm.17821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 06/09/2023] [Accepted: 06/14/2023] [Indexed: 07/05/2023] Open
Abstract
Shortened foetal femur length (FL) is a common abnormal phenotype that often causes anxiety in pregnant women, and standard clinical treatments remain unavailable. We investigated the clinical characteristics, genetic aetiology and obstetric pregnancy outcomes of foetuses with short FL and provided a reference for perinatal management of such cases. Chromosomal microarray analysis was used to analyse the copy number variations (CNV) in short FL foetuses. Of the 218 foetuses with short FL, 33 foetuses exhibited abnormal CNVs, including 19 with pathogenic CNVs and 14 with variations of uncertain clinical significance. Of the 19 foetuses with pathogenic CNVs, four had aneuploidy, 14 had deletions/duplications, and one had pathogenic uniparental diploidy. The 7q11.23 microdeletion was detected in three foetuses. The severity of short FL was not associated with the rate of pathogenic CNVs. The duration of short FL for the intrauterine ultrasound phenotype in foetuses carrying a pathogenic CNV was independent of the gestational age. Further, maternal age was not associated with the incidence of foetal pathogenic CNVs. Adverse pregnancy outcomes occurred in 77 cases, including termination of pregnancy in 63 cases, postnatal dwarfed foetuses with intellectual disability in 11 cases, and three deaths within 3 months of birth. Pathogenic CNVs closely related to foetal short FL were identified, among which the 7q11.23 microdeletion was highly associated with short FL development. This study provides a reference for the perinatal management of foetuses with short FL.
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Affiliation(s)
- Meiying Cai
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth DefectFuzhouChina
| | - Yanting Que
- College of Clinical Medicine for Obstetrics and Gynecology and PediatricsFujian Medical UniversityFuzhouChina
| | - Meihuan Chen
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth DefectFuzhouChina
| | - Min Zhang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth DefectFuzhouChina
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth DefectFuzhouChina
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth DefectFuzhouChina
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth DefectFuzhouChina
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DiCriscio AS, Wain KE, Smith J, Beiler D, Walsh LK, Holdren K, Troiani V. Higher scores on autonomic symptom scales in pediatric patients with neurodevelopmental disorders of known genetic etiology. Brain Behav 2022; 12:e2813. [PMID: 36423250 PMCID: PMC9759134 DOI: 10.1002/brb3.2813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 10/03/2022] [Accepted: 10/18/2022] [Indexed: 11/26/2022] Open
Abstract
INTRODUCTION Features of underlying autonomic dysfunction, including sleep disturbances, gastrointestinal problems, and atypical heart rate, have been reported in neurodevelopmental conditions, including autism spectrum disorder (ASD). The current cross-sectional, between-groups study aimed to quantify symptoms of autonomic dysfunction in a neurodevelopmental pediatric cohort characterized by clinical diagnoses as well as genetic etiology. METHOD The Pediatric Autonomic Symptom Scales (PASS) questionnaire was used to assess autonomic features across a group of patients with clinical neurodevelopmental diagnoses (NPD; N = 90) and genetic etiologies. Patients were subdivided based on either having a clinical ASD diagnosis (NPD-ASD; n = 37) or other non-ASD neurodevelopmental diagnoses, such as intellectual disability without ASD, speech and language disorders, and/or attention deficit hyperactivity disorder (NPD-OTHER; n = 53). Analyses focused on characterizing differences between the NPD group compared to previously published reference samples, as well as differences between the two NPD subgroups (NPD-ASD and NPD-OTHER). RESULTS Our results indicate higher PASS scores in our NPD cohort relative to children with and without ASD from a previously published cohort. However, we did not identify significant group differences between our NPD-ASD and NPD-OTHER subgroups. Furthermore, we find a significant relationship between quantitative ASD traits and symptoms of autonomic function. CONCLUSION This work demonstrates the utility of capturing quantitative estimates of autonomic trait dimensions that may be significantly linked with psychosocial impairments and other core clinical features of ASD.
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Affiliation(s)
- Antoinette S DiCriscio
- Geisinger Health System, Autism & Developmental Medicine Institute (ADMI), Lewisburg, Pennsylvania, USA
| | - K E Wain
- Geisinger Health System, Autism & Developmental Medicine Institute (ADMI), Lewisburg, Pennsylvania, USA
| | - J Smith
- Geisinger Health System, Autism & Developmental Medicine Institute (ADMI), Lewisburg, Pennsylvania, USA
| | - D Beiler
- Geisinger Health System, Autism & Developmental Medicine Institute (ADMI), Lewisburg, Pennsylvania, USA
| | - L K Walsh
- Geisinger Health System, Autism & Developmental Medicine Institute (ADMI), Lewisburg, Pennsylvania, USA
| | - K Holdren
- Geisinger Health System, Autism & Developmental Medicine Institute (ADMI), Lewisburg, Pennsylvania, USA
| | - Vanessa Troiani
- Geisinger Health System, Autism & Developmental Medicine Institute (ADMI), Lewisburg, Pennsylvania, USA.,Department of Imaging Science and Innovation, Center for Health Research, Geisinger, Danville, Pennsylvania, USA.,Neuroscience Institute, Geisinger, Danville, Pennsylvania, USA.,Department of Basic Sciences, Geisinger Commonwealth School of Medicine, Scranton, Pennsylvania, USA
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Cokyaman T, Silan F. Diagnostic Utility of Array Comparative Genomic Hybridization in Children with Neurological Diseases. Fetal Pediatr Pathol 2022; 41:68-76. [PMID: 32401632 DOI: 10.1080/15513815.2020.1764683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
INTRODUCTION We evaluated the contribution of array comparative genomic hybridization (aCGH) to the final diagnosis in children with neurocognitive disturbances or dysmorphic findings, but lacked a specific diagnosis. MATERIALS AND METHODS Medical files of pediatric patients with neurocognitive disturbances who underwent aCGH analysis were reviewed retrospectively. RESULTS Of 155 patients, 77 copy number variations were detected and 50% (39/77) were considered causative. The aCGH's final diagnostic rate was 25.1% (39/155). CONCLUSION With aCGH analysis, the diagnosis rate for patients with undiagnosed neurocognitive disturbances or dysmorphic syndrome may increase by 25-30%. If the phenotypic findings of the widely known neurocognitive disturbances cannot be identified during the initial clinical assessment, aCGH analysis may be beneficial.
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Affiliation(s)
- Turgay Cokyaman
- Pediatric Neurology, Faculty of Medicine, Çanakkale Onsekiz Mart University, Çanakkale, Turkey
| | - Fatma Silan
- Medical Genetics, Faculty of Medicine, Çanakkale Onsekiz Mart University, Canakkale, Turkey
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Increased Diagnostic Yield of Array Comparative Genomic Hybridization for Autism Spectrum Disorder in One Institution in Taiwan. Medicina (B Aires) 2021; 58:medicina58010015. [PMID: 35056323 PMCID: PMC8779646 DOI: 10.3390/medicina58010015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 12/31/2022] Open
Abstract
Background and Objectives: Chromosomal microarray offers superior sensitivity for identification of submicroscopic copy number variants (CNVs) and is recommended for the initial genetic testing of patients with autism spectrum disorder (ASD). This study aims to determine the diagnostic yield of array comparative genomic hybridization (array-CGH) in ASD patients from a cohort of Chinese patients in Taiwan. Materials and Methods: Enrolled in this study were 80 ASD children (49 males and 31 females; 2–16 years old) followed up at Taipei MacKay Memorial Hospital between January 2010 and December 2020. The genomic DNA extracted from blood samples was analyzed by array-CGH via the Affymetrix GeneChip Genome-Wide Human single nucleotide polymorphism (SNP) and NimbleGen International Standards for Cytogenomic Arrays (ISCA) Plus Cytogenetic Arrays. The CNVs were classified into five groups: pathogenic (pathologic variant), likely pathogenic (potential pathologic variant), likely benign (potential normal genomic variant), benign (normal genomic variant), and uncertain clinical significance (variance of uncertain significance), according to the American College of Medical Genetics (ACMG) guidelines. Results: We identified 47 CNVs, 31 of which in 27 patients were clinically significant. The overall diagnostic yield was 33.8%. The most frequently clinically significant CNV was 15q11.2 deletion, which was present in 4 (5.0%) patients. Conclusions: In this study, a satisfactory diagnostic yield of array-CGH was demonstrated in a Taiwanese ASD patient cohort, supporting the clinical usefulness of array-CGH as the first-line testing of ASD in Taiwan.
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Palka Bayard de Volo C, Alfonsi M, Morizio E, Guaciali-Franchi P, Mohn A, Chiarelli F. A 343 Italian cohort of patients analysed with array-comparative genomic hybridization: unsolved problems and genetic counselling difficulties. JOURNAL OF INTELLECTUAL DISABILITY RESEARCH : JIDR 2021; 65:863-869. [PMID: 34338393 DOI: 10.1111/jir.12867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 06/11/2021] [Accepted: 06/27/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The recent introduction of microarrays for genetic analyses has allowed higher etiological diagnostic rates in patient with intellectual disability (ID), autism spectrum disorders (ASD), epilepsy and multiple congenital anomalies (MCA), because of its resolution. This approach still results of high complexity and some limitations have been reported. In fact, it discloses several variants of unknown significance (VOUS) or incidental findings. In all cases, a massive amount of data is generated, because of this, the analysis and the interpretation is very difficult and often without a definitive conclusion. METHOD We analysed an Italian cohort of 343 patients with ID, MCA and ASD by array-comparative genomic hybridization. The purpose of this work was to consider the proportion of the chromosomal abnormalities in such cohort and to assess the distribution of the different type of the chromosomal abnormalities concerning their pathogenic significance, their origin and their correlation to these clinical phenotypes. RESULTS Array-comparative genomic hybridization analysis revealed 76 positive results. Abnormalities were detected in 27.8% of patients with ID, 11.1% with ASD, 10.7% with epilepsy and 19.4% with multiple congenital anomalies. The anomalies were classified in three major groups: group 1 (27 patients) with pathogenic alterations (P group); group 2 (34 patients) with VOUS potentially pathogenic (PP group); and group 3 (13 patients) with VOUS potentially benign (PB group). As expected, comparing the diagnostic groups, we observed a greater number of deletions in the P group and that all the abnormalities of the PB group were inherited. CONCLUSIONS Our retrospective study resulted in confirming the high detection rate of microarrays. CNV classification remains a complex procedure. The difficulty in CNV classification points out the importance of the patient selection, helping the interpretation of the molecular cytogenetic results.
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Affiliation(s)
| | - M Alfonsi
- Medical Genetics Unit, Ss Annunziata Hospital, Chieti, Italy
| | - E Morizio
- Department of Medical Genetics, G. d'Annunzio University, Chieti, Italy
| | - P Guaciali-Franchi
- Medical Genetics Unit, Ss Annunziata Hospital, Chieti, Italy
- Department of Medical Genetics, G. d'Annunzio University, Chieti, Italy
| | - A Mohn
- Department of Pediatrics, G. d'Annunzio University, Chieti, Italy
| | - F Chiarelli
- Department of Pediatrics, G. d'Annunzio University, Chieti, Italy
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Xi H, Peng Y, Xie W, Pang J, Ma N, Yang S, Peng J, Wang H. A chromosome 1q22 microdeletion including ASH1L is associated with intellectual disability in a Chinese family. Mol Cytogenet 2020; 13:20. [PMID: 32518592 PMCID: PMC7273683 DOI: 10.1186/s13039-020-00483-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/27/2020] [Indexed: 01/18/2023] Open
Abstract
Background Copy number variants (CNVs) associated with developmental delay and intellectual disability (DD/ID) continue to be identified in patients. This article reports identification of a chromosome 1q22 microdeletion as the genetic cause in a Chinese family affected by ID. Case presentation The proband was a 19-year-old pregnant woman referred for genetic counseling and prenatal diagnosis at 18 weeks of gestation. She had severe ID with basically normal stature (height 154 cm [0 SD], weight 61 kg [− 0.2 SD], and head circumference 54 cm [− 1.12 SD]). Her distinctive facial features included a prominent forehead; flat face; flat nasal bridge and a short upturned nose; thin lips; and small ears. The proband’s father was reported to have low intelligence, whereas her mother was of normal intelligence but with scoliosis. Chromosome microarray analysis (CMA) reveals that the proband, her father and the fetus all carry a 1q22 microdeletion of 936.3 Kb (arr[GRCh37] 1q22 (155016052_155952375)×1), which was not observed in her mother and paternal grandparents and uncles, suggesting a de novo mutation in the proband’s father. The microdeletion involves 24 OMIM genes including ASH1L (also known as KMT2H and encoding a histone lysine methyltransferase). Of note, haploinsufficiency of ASH1L has been shown to be associated with neurodevelopmental disorders. Based on the inheritance of the detected CNV in the pedigree and similar CNVs associated with ID in public databases (Decipher, DGV and ClinVar) and literature, the detected CNV is considered as pathogenic. The family chose to terminate the pregnancy. Conclusions The identified 1q22 microdeletion including ASH1L is pathogenic and associated with ID. This case broadens the spectrum of ID-related CNVs and may be useful as a reference for clinicians.
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Affiliation(s)
- Hui Xi
- NHC Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan Province P. R. China.,The Prenatal Diagnosis Center of Hunan Province, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan Province P. R. China
| | - Ying Peng
- NHC Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan Province P. R. China.,The Prenatal Diagnosis Center of Hunan Province, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan Province P. R. China
| | - Wanqin Xie
- NHC Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan Province P. R. China
| | - Jialun Pang
- NHC Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan Province P. R. China.,The Prenatal Diagnosis Center of Hunan Province, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan Province P. R. China
| | - Na Ma
- NHC Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan Province P. R. China.,The Prenatal Diagnosis Center of Hunan Province, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan Province P. R. China
| | - Shuting Yang
- NHC Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan Province P. R. China.,The Prenatal Diagnosis Center of Hunan Province, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan Province P. R. China
| | - Jinping Peng
- Department of Medical Genetics, Maternal and Child Health Care Hospital of Shaoyang City, Shaoyang, Hunan Province P. R. China
| | - Hua Wang
- NHC Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan Province P. R. China.,The Prenatal Diagnosis Center of Hunan Province, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan Province P. R. China
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Catusi I, Recalcati MP, Bestetti I, Garzo M, Valtorta C, Alfonsi M, Alghisi A, Cappellani S, Casalone R, Caselli R, Ceccarini C, Ceglia C, Ciaschini AM, Coviello D, Crosti F, D'Aprile A, Fabretto A, Genesio R, Giagnacovo M, Granata P, Longo I, Malacarne M, Marseglia G, Montaldi A, Nardone AM, Palka C, Pecile V, Pessina C, Postorivo D, Redaelli S, Renieri A, Rigon C, Tiberi F, Tonelli M, Villa N, Zilio A, Zuccarello D, Novelli A, Larizza L, Giardino D. Testing single/combined clinical categories on 5110 Italian patients with developmental phenotypes to improve array-based detection rate. Mol Genet Genomic Med 2019; 8:e1056. [PMID: 31851782 PMCID: PMC6978242 DOI: 10.1002/mgg3.1056] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/23/2019] [Accepted: 10/28/2019] [Indexed: 01/09/2023] Open
Abstract
Background Chromosomal microarray analysis (CMA) is nowadays widely used in the diagnostic path of patients with clinical phenotypes. However, there is no ascertained evidence to date on how to assemble single/combined clinical categories of developmental phenotypic findings to improve the array‐based detection rate. Methods The Italian Society of Human Genetics coordinated a retrospective study which included CMA results of 5,110 Italian patients referred to 17 genetics laboratories for variable combined clinical phenotypes. Results Non‐polymorphic copy number variants (CNVs) were identified in 1512 patients (30%) and 615 (32%) present in 552 patients (11%) were classified as pathogenic. CNVs were analysed according to type, size, inheritance pattern, distribution among chromosomes, and association to known syndromes. In addition, the evaluation of the detection rate of clinical subgroups of patients allowed to associate dysmorphisms and/or congenital malformations combined with any other single clinical sign to an increased detection rate, whereas non‐syndromic neurodevelopmental signs and non‐syndromic congenital malformations to a decreased detection rate. Conclusions Our retrospective study resulted in confirming the high detection rate of CMA and indicated new clinical markers useful to optimize their inclusion in the diagnostic and rehabilitative path of patients with developmental phenotypes.
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Affiliation(s)
- Ilaria Catusi
- Lab. di Citogenetica Medica, Istituto Auxologico Italiano, IRCCS, Milano, Italy
| | | | - Ilaria Bestetti
- Lab. di Citogenetica Medica, Istituto Auxologico Italiano, IRCCS, Milano, Italy
| | - Maria Garzo
- Lab. di Citogenetica Medica, Istituto Auxologico Italiano, IRCCS, Milano, Italy
| | - Chiara Valtorta
- Lab. di Citogenetica Medica, Istituto Auxologico Italiano, IRCCS, Milano, Italy
| | - Melissa Alfonsi
- U.O.C. di Genetica medica, Ospedale SS Annunziata, Chieti, Italy
| | - Alberta Alghisi
- U.O.S. Genetica e Biologia Molecolare, Azienda ULSS 6, Vicenza, Italy
| | | | - Rosario Casalone
- SMeL specializzato Citogenetica e Genetica Medica, ASST Sette Laghi, Osp. di Circolo e Fond. Macchi, Varese, Italy
| | - Rossella Caselli
- U.O.C. Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | | | - Carlo Ceglia
- UOSD Genetica Medica, AORN "SG Moscati", Avellino, Italy
| | - Anna Maria Ciaschini
- A.O.U. Ospedali Riuniti Umberto I - G.M.Lancisi - G.Salesi, Lab. Genetica Medica SOS Malattie Rare, Ancona, Italy
| | - Domenico Coviello
- Lab. di Genetica Umana, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Francesca Crosti
- U.S. Genetica Medica, Ospedale San Gerardo ASST Monza, Monza, Italy
| | | | | | - Rita Genesio
- U.O.C. di Citogenetica, A.O.U. Federico II, Napoli, Italy
| | | | - Paola Granata
- SMeL specializzato Citogenetica e Genetica Medica, ASST Sette Laghi, Osp. di Circolo e Fond. Macchi, Varese, Italy
| | - Ilaria Longo
- U.O.C. Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Michela Malacarne
- Lab. di Genetica Umana, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | | | | | | | - Chiara Palka
- Dipartimento di Pediatria, Università G. D'Annunzio, Chieti-Pescara, Italy
| | - Vanna Pecile
- S.C. Genetica Medica, IRCCS Burlo Garofolo, Trieste, Italy
| | - Chiara Pessina
- SMeL specializzato Citogenetica e Genetica Medica, ASST Sette Laghi, Osp. di Circolo e Fond. Macchi, Varese, Italy
| | - Diana Postorivo
- U.O.C. Lab. di Genetica Medica, Policlinico Tor Vergata, Roma, Italy
| | - Serena Redaelli
- Dipartimento di Medicina e Chirurgia, Università di Milano-Bicocca, Monza, Italy
| | - Alessandra Renieri
- U.O.C. Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Chiara Rigon
- U.O.C. Genetica e Epidemiologia Clinica, A.O.U. di Padova, Padova, Italy
| | - Fabiola Tiberi
- A.O.U. Ospedali Riuniti Umberto I - G.M.Lancisi - G.Salesi, Lab. Genetica Medica SOS Malattie Rare, Ancona, Italy
| | - Mariella Tonelli
- LCGM Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Brescia, Italy
| | - Nicoletta Villa
- U.S. Genetica Medica, Ospedale San Gerardo ASST Monza, Monza, Italy
| | - Anna Zilio
- U.O.S. Genetica e Biologia Molecolare, Azienda ULSS 6, Vicenza, Italy
| | - Daniela Zuccarello
- U.O.C. Genetica e Epidemiologia Clinica, A.O.U. di Padova, Padova, Italy
| | - Antonio Novelli
- U.O.C. Laboratorio di Genetica Medica, Ospedale Pediatrico del Bambino Gesù, Roma, Italy
| | - Lidia Larizza
- Lab. di Citogenetica Medica, Istituto Auxologico Italiano, IRCCS, Milano, Italy
| | - Daniela Giardino
- Lab. di Citogenetica Medica, Istituto Auxologico Italiano, IRCCS, Milano, Italy
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11
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Chaves TF, Baretto N, Oliveira LFD, Ocampos M, Barbato IT, Anselmi M, De Luca GR, Barbato Filho JH, Pinto LLDC, Bernardi P, Maris AF. Copy Number Variations in a Cohort of 420 Individuals with Neurodevelopmental Disorders From the South of Brazil. Sci Rep 2019; 9:17776. [PMID: 31780800 PMCID: PMC6882836 DOI: 10.1038/s41598-019-54347-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 11/13/2019] [Indexed: 01/04/2023] Open
Abstract
Chromosomal microarray (CMA) is now recommended as first tier for the evaluation in individuals with unexplained neurodevelopmental disorders (ND). However, in developing countries such as Brazil, classical cytogenetic tests are still the most used in clinical practice, as reflected by the scarcity of publications of microarray investigation in larger cohorts. This is a retrospective study which analyses the reading files of CMA and available clinical data from 420 patients from the south of Brazil, mostly children, with neurodevelopmental disorders requested by medical geneticists and neurologists for diagnostic purpose. Previous karyotyping was reported for 138 and includes 17 with abnormal results. The platforms used for CMA were CYTOSCAN 750K (75%) and CYTOSCAN HD (25%). The sex ratio of the patients was 1.625 males :1 female and the mean age was 9.5 years. A total of 96 pathogenic copy number variations (CNVs), 58 deletions and 38 duplications, were found in 18% of the patients and in all chromosomes, except chromosome 11. For 12% of the patients only variants of uncertain clinical significance were found. No clinically relevant CNV was found in 70%. The main referrals for chromosomal microarrays (CMA) were developmental delay (DD), intellectual disability (ID), facial dysmorphism and autism spectrum disorder (ASD). DD/ID were present in 80%, facial dysmorphism in 52% and ASD in 32%. Some phenotypes in this population could be predictive of a higher probability to carry a pathogenic CNV, as follows: dysmorphic facial features (p-value = < 0.0001, OR = 0.32), obesity (p-value = 0.006, OR = 0.20), short stature (p-value = 0.032, OR = 0.44), genitourinary anomalies (p-value = 0.032, OR = 0.63) and ASD (p-value = 0.039, OR = 1.94). The diagnostic rate for CMA in this study was 18%. We present the largest report of CMA data in a cohort with ND in Brazil. We characterize the rare CNVs found together with the main phenotypes presented by each patient, list phenotypes which could predict a higher diagnostic probability by CMA in patients with a neurodevelopmental disorder and show how CMA and classical karyotyping results are complementary.
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Affiliation(s)
| | - Nathacha Baretto
- Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | | | | | | | - Mayara Anselmi
- Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | | | | | | | - Pricila Bernardi
- University Hospital Professor Polydoro Ernani de São Thiago, Florianópolis, SC, Brazil
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12
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de Souza LC, Dos Santos AP, Sgardioli IC, Viguetti-Campos NL, Marques Prota JR, de Oliveira-Sobrinho RP, Vieira TP, Gil-da-Silva-Lopes VL. Phenotype comparison among individuals with developmental delay/intellectual disability with or without genomic imbalances. JOURNAL OF INTELLECTUAL DISABILITY RESEARCH : JIDR 2019; 63:1379-1389. [PMID: 30900361 DOI: 10.1111/jir.12615] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 02/18/2019] [Accepted: 02/18/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND The chromosomal microarray analysis (CMA) is recommended as a first-tier test for individuals with developmental delay (DD)/intellectual disability (ID) and/or multiple congenital anomalies. However, owing to high costs, this technique is not widely performed for diagnostic purposes in several countries. The aim of this study was to identify clinical features that could favour the hypothesis of genomic imbalances (GIs) in individuals with DD/ID. METHODS The sample consisted of 63 individuals, and all of them underwent a detailed evaluation by a clinical geneticist and were investigated by the CMA. They were divided into two groups. Group A composed of 20 individuals with pathogenic copy number variants (CNVs); and group B composed of 43 individuals with normal CMA results or variants of uncertain clinical significance (VUS). RESULTS Pathogenic GIs were found in 20 cases (32%), including 11 individuals with an abnormal karyotype, VUS was found in five individuals (8%) and the results were normal in 38 individuals (60%). Major anomalies were found in 15/20 (75%) individuals in group A against 35/43 (81%) in group B. Dysmorphisms (≥5) were found in 17/20 (85%) in group A and 41/43 (95%) in group B. The most frequent major anomalies detected in group A were congenital heart disease, epilepsy and renal malformation; and in group B, they were malformations of central nervous system, congenital heart disease, microcephaly, epilepsy and hearing impairment. There was no significant statistical difference among the frequencies in groups A and B. CONCLUSIONS Evidences point that every individual with DD/ID, with no specific clinical suspicion, should have screening for GIs as a first-tier test, regardless of the presence or absence of additional major anomalies or dysmorphisms. Future studies with a similar design would be helpful, especially in countries where the access to new technologies is still limited.
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Affiliation(s)
- L C de Souza
- Department of Medical Genetics, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - A P Dos Santos
- Department of Medical Genetics, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - I C Sgardioli
- Department of Medical Genetics, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - N L Viguetti-Campos
- Department of Medical Genetics, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - J R Marques Prota
- Department of Medical Genetics, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - R P de Oliveira-Sobrinho
- Department of Medical Genetics, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - T P Vieira
- Department of Medical Genetics, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - V L Gil-da-Silva-Lopes
- Department of Medical Genetics, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
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13
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Jang W, Kim Y, Han E, Park J, Chae H, Kwon A, Choi H, Kim J, Son JO, Lee SJ, Hong BY, Jang DH, Han JY, Lee JH, Kim SY, Lee IG, Sung IK, Moon Y, Kim M, Park JH. Chromosomal Microarray Analysis as a First-Tier Clinical Diagnostic Test in Patients With Developmental Delay/Intellectual Disability, Autism Spectrum Disorders, and Multiple Congenital Anomalies: A Prospective Multicenter Study in Korea. Ann Lab Med 2019; 39:299-310. [PMID: 30623622 PMCID: PMC6340852 DOI: 10.3343/alm.2019.39.3.299] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Revised: 08/06/2018] [Accepted: 11/07/2018] [Indexed: 11/20/2022] Open
Abstract
Background To validate the clinical application of chromosomal microarray analysis (CMA) as a first-tier clinical diagnostic test and to determine the impact of CMA results on patient clinical management, we conducted a multicenter prospective study in Korean patients diagnosed as having developmental delay/intellectual disability (DD/ID), autism spectrum disorders (ASD), and multiple congenital anomalies (MCA). Methods We performed both CMA and G-banding cytogenetics as the first-tier tests in 617 patients. To determine whether the CMA results directly influenced treatment recommendations, the referring clinicians were asked to complete a 39-item questionnaire for each patient separately after receiving the CMA results. Results A total of 122 patients (19.8%) had abnormal CMA results, with either pathogenic variants (N=65) or variants of possible significance (VPS, N=57). Thirty-five well-known diseases were detected: 16p11.2 microdeletion syndrome was the most common, followed by Prader-Willi syndrome, 15q11-q13 duplication, Down syndrome, and Duchenne muscular dystrophy. Variants of unknown significance (VUS) were discovered in 51 patients (8.3%). VUS of genes putatively associated with developmental disorders were found in five patients: IMMP2L deletion, PTCH1 duplication, and ATRNL1 deletion. CMA results influenced clinical management, such as imaging studies, specialist referral, and laboratory testing in 71.4% of patients overall, and in 86.0%, 83.3%, 75.0%, and 67.3% of patients with VPS, pathogenic variants, VUS, and benign variants, respectively. Conclusions Clinical application of CMA as a first-tier test improves diagnostic yields and the quality of clinical management in patients with DD/ID, ASD, and MCA.
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Affiliation(s)
- Woori Jang
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Yonggoo Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Eunhee Han
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Joonhong Park
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Hyojin Chae
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Ahlm Kwon
- Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Hayoung Choi
- Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jiyeon Kim
- Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jung Ok Son
- Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sang Jee Lee
- Department of Rehabilitation Medicine, Daejeon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Daejeon, Korea
| | - Bo Young Hong
- Department of Rehabilitation Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Suwon, Korea
| | - Dae Hyun Jang
- Department of Rehabilitation Medicine, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Incheon, Korea
| | - Ji Yoon Han
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jung Hyun Lee
- Department of Pediatrics, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Suwon, Korea
| | - So Young Kim
- Department of Pediatrics, Yeouido St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - In Goo Lee
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - In Kyung Sung
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Yeonsook Moon
- Department of Laboratory Medicine, Inha University School of Medicine, Incheon, Korea
| | - Myungshin Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea.
| | - Joo Hyun Park
- Department of Rehabilitation Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
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14
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Capkova P, Srovnal J, Capkova Z, Staffova K, Becvarova V, Trkova M, Adamova K, Santava A, Curtisova V, Hajduch M, Prochazka M. MLPA is a practical and complementary alternative to CMA for diagnostic testing in patients with autism spectrum disorders and identifying new candidate CNVs associated with autism. PeerJ 2019; 6:e6183. [PMID: 30647996 PMCID: PMC6330045 DOI: 10.7717/peerj.6183] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 11/28/2018] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) is a complex heterogeneous developmental disease with a significant genetic background that is frequently caused by rare copy number variants (CNVs). Microarray-based whole-genome approaches for CNV detection are widely accepted. However, the clinical significance of most CNV is poorly understood, so results obtained using such methods are sometimes ambiguous. We therefore evaluated a targeted approach based on multiplex ligation-dependent probe amplification (MLPA) using selected probemixes to detect clinically relevant variants for diagnostic testing of ASD patients. We compare the reliability and efficiency of this test to those of chromosomal microarray analysis (CMA) and other tests available to our laboratory. In addition, we identify new candidate genes for ASD identified in a cohort of ASD-diagnosed patients. METHOD We describe the use of MLPA, CMA, and karyotyping to detect CNV in 92 ASD patients and evaluate their clinical significance. RESULT Pathogenic and likely pathogenic mutations were identified by CMA in eight (8.07% of the studied cohort) and 12 (13.04%) ASD patients, respectively, and in eight (8.07%) and four (4.35%) patients, respectively, by MLPA. The detected mutations include the 22q13.3 deletion, which was attributed to ring chromosome 22 formation based on karyotyping. CMA revealed a total of 91 rare CNV in 55 patients: eight pathogenic, 15 designated variants of unknown significance (VOUS)-likely pathogenic, 10 VOUS-uncertain, and 58 VOUS-likely benign or benign. MLPA revealed 18 CNV in 18 individuals: eight pathogenic, four designated as VOUS-likely pathogenic, and six designated as VOUS-likely benign/benign. Rare CNVs were detected in 17 (58.62%) out of 29 females and 38 (60.32%) out of 63 males in the cohort. Two genes, DOCK8 and PARK2, were found to be overlapped by CNV designated pathogenic, VOUS-likely pathogenic, or VOUS-uncertain in multiple patients. Moreover, the studied ASD cohort exhibited significant (p < 0.05) enrichment of duplications encompassing DOCK8. CONCLUSION Multiplex ligation-dependent probe amplification and CMA yielded concordant results for 12 patients bearing CNV designated pathogenic or VOUS-likely pathogenic. Unambiguous diagnoses were achieved for eight patients (corresponding to 8.7% of the total studied population) by both MLPA and CMA, for one (1.09%) patient by karyotyping, and for one (1.09%) patient by FRAXA testing. MLPA and CMA thus achieved identical reliability with respect to clinically relevant findings. As such, MLPA could be useful as a fast and inexpensive test in patients with syndromic autism. The detection rate of potentially pathogenic variants (VOUS-likely pathogenic) achieved by CMA was higher than that for MLPA (13.04% vs. 4.35%). However, there was no corresponding difference in the rate of unambiguous diagnoses of ASD patients. In addition, the results obtained suggest that DOCK8 may play a role in the etiology of ASD.
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Affiliation(s)
- Pavlina Capkova
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic
| | - Josef Srovnal
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Zuzana Capkova
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic
| | - Katerina Staffova
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | | | | | - Katerina Adamova
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic
| | - Alena Santava
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic
| | - Vaclava Curtisova
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic
| | - Marian Hajduch
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Martin Prochazka
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic
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15
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Kessi M, Xiong J, Wu L, Yang L, He F, Chen C, Pang N, Duan H, Zhang W, Arafat A, Yin F, Peng J. Rare Copy Number Variations and Predictors in Children With Intellectual Disability and Epilepsy. Front Neurol 2018; 9:947. [PMID: 30510536 PMCID: PMC6252327 DOI: 10.3389/fneur.2018.00947] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 10/23/2018] [Indexed: 11/19/2022] Open
Abstract
Introduction: The concurrence of intellectual disability/global developmental delay and epilepsy (ID/GDD-EP) is very common in the pediatric population. The etiologies for both conditions are complex and largely unknown. The predictors of significant copy number variations (CNVs) are known for the cases with ID/GDD, but unknown for those with exclusive ID/GDD-EP. Importantly, the known predictors are largely from the same ethnic group; hence, they lack replication. Purpose: We aimed to determine and investigate the diagnostic yield of CNV tests, new causative CNVs, and the independent predictors of significant CNVs in Chinese children with unexplained ID/GDD-EP. Materials and methods: A total of 100 pediatric patients with unexplained ID/GDD-EP and 1,000 healthy controls were recruited. The American College of Medical Genetics guideline was used to classify the CNVs. Additionally, clinical information was collected and compared between those with significant and non-significant CNVs. Results: Twenty-eight percent of the patients had significant CNVs, 16% had variants of unknown significance, and 56% had non-significant CNVs. In total, 31 CNVs were identified in 28% (28/100) of cases: 25 pathogenic and 6 likely pathogenic. Eighteen known syndromes were diagnosed in 17 cases. Thirteen rare CNVs (8 novel and 5 reported in literature) were identified, of which three spanned dosage-sensitive genes: 19q13.2 deletion (ATP1A3), Xp11.4-p11.3 deletion (CASK), and 6q25.3-q25.3 deletion (ARID1B). By comparing clinical features in patients with significant CNVs against those with non-significant CNVs, a statistically significant association was found between the presence of significant CNVs and speech and language delay for those aged above 2 years and for those with facial malformations, microcephaly, congenital heart disease, fair skin, eye malformations, and mega cisterna magna. Multivariate logistic regression analysis allowed the identification of two independent significant CNV predictors, which are eye malformations and facial malformations. Conclusion: Our study supports the performance of CNV tests in pediatric patients with unexplained ID/GDD-EP, as there is high diagnostic yield, which informs genetic counseling. It adds 13 rare CNVs (8 novel), which can be accountable for both conditions. Moreover, congenital eye and facial malformations are clinical markers that can aid clinicians to understand which patients can benefit from the CNV testing and which will not, thus helping patients to avoid unnecessary and expensive tests.
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Affiliation(s)
- Miriam Kessi
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Juan Xiong
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Liwen Wu
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Lifen Yang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Fang He
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Chen Chen
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Nan Pang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Haolin Duan
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Wen Zhang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Ahmed Arafat
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Fei Yin
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Jing Peng
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
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16
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Maini I, Ivanovski I, Djuric O, Caraffi SG, Errichiello E, Marinelli M, Franchi F, Bizzarri V, Rosato S, Pollazzon M, Gelmini C, Malacarne M, Fusco C, Gargano G, Bernasconi S, Zuffardi O, Garavelli L. Prematurity, ventricular septal defect and dysmorphisms are independent predictors of pathogenic copy number variants: a retrospective study on array-CGH results and phenotypical features of 293 children with neurodevelopmental disorders and/or multiple congenital anomalies. Ital J Pediatr 2018; 44:34. [PMID: 29523172 PMCID: PMC5845186 DOI: 10.1186/s13052-018-0467-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 02/21/2018] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Since 2010, array-CGH (aCGH) has been the first-tier test in the diagnostic approach of children with neurodevelopmental disorders (NDD) or multiple congenital anomalies (MCA) of unknown origin. Its broad application led to the detection of numerous variants of uncertain clinical significance (VOUS). How to appropriately interpret aCGH results represents a challenge for the clinician. METHOD We present a retrospective study on 293 patients with age range 1 month - 29 years (median 7 years) with NDD and/or MCA and/or dysmorphisms, investigated through aCGH between 2005 and 2016. The aim of the study was to analyze clinical and molecular cytogenetic data in order to identify what elements could be useful to interpret unknown or poorly described aberrations. Comparison of phenotype and cytogenetic characteristics through univariate analysis and multivariate logistic regression was performed. RESULTS Copy number variations (CNVs) with a frequency < 1% were detected in 225 patients of the total sample, while 68 patients presented only variants with higher frequency (heterozygous deletions or amplification) and were considered to have negative aCGH. Proved pathogenic CNVs were detected in 70 patients (20.6%). Delayed psychomotor development, intellectual disability, intrauterine growth retardation (IUGR), prematurity, congenital heart disease, cerebral malformations and dysmorphisms correlated to reported pathogenic CNVs. Prematurity, ventricular septal defect and dysmorphisms remained significant predictors of pathogenic CNVs in the multivariate logistic model whereas abnormal EEG and limb dysmorphisms were mainly detected in the group with likely pathogenic VOUS. A flow-chart regarding the care for patients with NDD and/or MCA and/or dysmorphisms and the interpretation of aCGH has been made on the basis of the data inferred from this study and literature. CONCLUSION Our work contributes to make the investigative process of CNVs more informative and suggests possible directions in aCGH interpretation and phenotype correlation.
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MESH Headings
- Abnormalities, Multiple/diagnosis
- Abnormalities, Multiple/genetics
- Adolescent
- Adult
- Child
- Child, Preschool
- Comparative Genomic Hybridization/methods
- DNA Copy Number Variations
- Facies
- Female
- Genetic Testing
- Heart Septal Defects, Ventricular/diagnosis
- Heart Septal Defects, Ventricular/genetics
- Humans
- Infant
- Infant, Newborn
- Infant, Premature, Diseases/diagnosis
- Infant, Premature, Diseases/genetics
- Male
- Muscular Atrophy/diagnosis
- Muscular Atrophy/genetics
- Neurodevelopmental Disorders/diagnosis
- Neurodevelopmental Disorders/genetics
- Phenotype
- Retrospective Studies
- Young Adult
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Affiliation(s)
- I. Maini
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
- Child Neuropsychiatry Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - I. Ivanovski
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
- Department of Surgical, Medical, Dental and Morphological Sciences with Interest in Transplant, Oncology and Regenerative Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - O. Djuric
- Institute of Epidemiology, School of Medicine, University of Belgrade, Belgrade, Serbia
| | - S. G. Caraffi
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - E. Errichiello
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - M. Marinelli
- Laboratory of Genetics, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - F. Franchi
- Laboratory of Genetics, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - V. Bizzarri
- Laboratory of Genetics, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - S. Rosato
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - M. Pollazzon
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - C. Gelmini
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - M. Malacarne
- Division of Medical Genetics, Galliera Hospital, Genoa, Italy
| | - C. Fusco
- Child Neuropsychiatry Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - G. Gargano
- Neonatal Intensive Care Unit (NICU), Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - S. Bernasconi
- Former Director Pediatric Department, University of Parma, Parma, Italy
| | - O. Zuffardi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - L. Garavelli
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
- Santa Maria Nuova Hospital, viale Risorgimento 80, 42123 Reggio Emilia, Italy
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