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Tapia YY, Ciaccio C, Bacınoğlu MB, D’Arrigo S, Sciacca FL. A Patient with a Small Deletion Affecting Only Exon 1-Intron 1 of the NXF5 Gene: Potential Evidence Supporting Its Role in Neurodevelopmental Disorders. Genes (Basel) 2025; 16:571. [PMID: 40428393 PMCID: PMC12111617 DOI: 10.3390/genes16050571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2025] [Revised: 05/06/2025] [Accepted: 05/09/2025] [Indexed: 05/29/2025] Open
Abstract
Genetic studies have identified numerous candidate genes for neurodevelopmental disorders associated with intellectual disability (ID) and autism spectrum disorders (ASD). Some genetic anomalies are very rare or challenging to detect, making it essential to validate the presence of gene mutations or copy number variations in additional patients with similar clinical phenotypes. Background/Objectives: Case reports play a crucial role in this process by validating rare variants in phenotypically matched patients, shedding light on novel candidate genes linked to these disorders. Methods: Patients with ID and ASD underwent neurological examinations, brain magnetic resonance imaging (MRI), sleep and wake electroencephalogram (EEG), neuropsychological evaluations, and laboratory tests including molecular analysis for fragile-X syndrome and array comparative genomic hybridization (aCGH). Results: We observed a patient with ID and ASD who carried a microdeletion in Xq22.1 that affects only exon 1 and intron 1 of the Nuclear RNA Export Factor 5 (NXF5) gene. The patient's phenotypic features overlap with those of the only four previously reported cases of variations involving the same gene. Conclusions: Our findings suggest that NXF5 may play a role in neurodevelopmental disorders and should be considered in the spectrum of X-linked ID associated with ASD.
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Affiliation(s)
- Yessica Yesenia Tapia
- Laboratory of Cytogenetic, Service of Laboratory Medicine, Department of Diagnostic and Technology, Fondazione I. R. C. C. S. Istituto Neurologico Carlo Besta, 20133 Milan, Italy;
| | - Claudia Ciaccio
- Unit of Infantile Neuropsychiatry, Fondazione I. R. C. C. S. Istituto Neurologico Carlo Besta, 20133 Milan, Italy;
| | - Merve Begüm Bacınoğlu
- Unit of Laboratory Medicine, Laboratory of Clinical Pathology, Fondazione I. R. C. C. S. Istituto Neurologico Carlo Besta, 20133 Milan, Italy;
| | - Stefano D’Arrigo
- Unit of Infantile Neuropsychiatry, Fondazione I. R. C. C. S. Istituto Neurologico Carlo Besta, 20133 Milan, Italy;
| | - Francesca Luisa Sciacca
- Laboratory of Cytogenetic, Service of Laboratory Medicine, Department of Diagnostic and Technology, Fondazione I. R. C. C. S. Istituto Neurologico Carlo Besta, 20133 Milan, Italy;
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Degeling K, Tagimacruz T, MacDonald KV, Seeger TA, Fooks K, Venkataramanan V, Boycott KM, Bernier FP, Mendoza-Londono R, Hartley T, Hayeems RZ, Marshall DA. Exome Sequencing in the Diagnostic Pathway for Suspected Rare Genetic Diseases: Does the Order of Testing Affect its Cost-Effectiveness? APPLIED HEALTH ECONOMICS AND HEALTH POLICY 2025; 23:453-466. [PMID: 39739296 DOI: 10.1007/s40258-024-00936-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/01/2024] [Indexed: 01/02/2025]
Abstract
BACKGROUND Patients with suspected rare diseases often experience lengthy and uncertain diagnostic pathways. This study aimed to estimate the cost-effectiveness of exome sequencing (ES) in different positions in the diagnostic pathway for patients suspected of having a rare genetic disease. METHODS Data collected retrospectively from 305 patients suspected of having a rare genetic disease (RGD), who received clinical-grade ES and participated in the Canadian multicentre Care4Rare-SOLVE study, informed a discrete event simulation of the diagnostic pathway. We distinguished between tests that can lead to the diagnosis of a specific RGD ('indicator tests') and more routine non-RGD diagnostic tests ('non-indicator tests'). Five strategies were considered: no-ES, and ES as 1st, 2nd, 3rd, or 4th test (Tier 1, Tier 2, Tier 3, and Tier 4, respectively), where ES was the final test in the diagnostic pathway if included. Outcomes included the diagnostic yield, time-to-diagnosis, time on the diagnostic pathway, and test costs for each strategy. The cost-effectiveness analysis from a Canadian healthcare system perspective was conducted with diagnostic yield as the primary outcome of interest. Probabilistic analyses and expert-defined scenario analyses quantified uncertainty. RESULTS Implementing ES increases the diagnostic yield by 16 percentage points from 20% with no-ES to 36%. Exome sequencing, as the first test (Tier 1), resulted in the shortest time to a diagnosis and the lowest testing cost. Mean testing costs per patient were CAD4347 (95% CI 3925, 4788) for no-ES, CAD2458 (95% CI 2406, 2512) for Tier 1, CAD3851 (95% CI 3684, 4021) for Tier 2, CAD5246 (95% CI 4956, 5551) for Tier 3 and CAD6422 (95% CI 5954, 6909) for Tier 4, with Tier 1 having the highest diagnostic yield at the lowest cost. The scenario analyses yielded results consistent with those of the base case. CONCLUSIONS Implementing ES to diagnose patients suspected of having a RGD can result in a higher diagnostic yield. Although a limitation of our study was that the yield for the non-ES indicator tests was estimated using expert opinion due to a lack of available data, the results underscore the value of ES as a first-line diagnostic test, offering reduced time to diagnosis and lower overall testing costs.
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Affiliation(s)
- Koen Degeling
- Cancer Health Services Research, Centre for Health Policy and Centre for Cancer Research, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Australia
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada
| | - Toni Tagimacruz
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada
| | - Karen V MacDonald
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada
| | - Trevor A Seeger
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada
| | - Katharine Fooks
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, ON, Canada
| | - Viji Venkataramanan
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, ON, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
- Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Francois P Bernier
- Department of Medical Genetics, University of Calgary, Calgary, AB, Canada
| | - Roberto Mendoza-Londono
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Robin Z Hayeems
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, The University of Toronto, Toronto, ON, Canada
| | - Deborah A Marshall
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada.
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada.
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Akkari Y, Conlin L, DeAvila D, Gardner JA, Halley J, Raca G, Toydemir RM, Tsuchiya K, Rehder C, CAP/ACMG Cytogenetics Committee. The CAP/ACMG CYCGH proficiency testing program: 10 years in review. Genet Med 2025; 27:101445. [PMID: 40260667 DOI: 10.1016/j.gim.2025.101445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2024] [Revised: 03/26/2025] [Accepted: 04/08/2025] [Indexed: 04/23/2025] Open
Abstract
PURPOSE The College of American Pathologists has offered proficiency testing (PT) for the detection of copy-number variations (CNV) in the constitutional setting (CYCGH) since 2008. We review and summarize data from the CYCGH PT program, including participant performance over time, changes made to the program, and ungraded challenges. METHODS The PT challenges from 2011 through 2021 (22 total mailings) and changes to the program over time were reviewed. Laboratory enrollment and performance were assessed. RESULTS Overall participation has increased over time, and laboratories have maintained a high level of proficiency. The major changes to the program have occurred twice during the time span examined. Reasons for challenges not meeting consensus were varied. The use of ungraded challenges was also discussed. CONCLUSION The CYCGH PT program is challenging because it assesses both analytical performance and interpretation as a single analyte. The program has evolved over time to address the changes in the field of CNV detection. During this time, additional technologies with the ability to detect CNVs have emerged, and the possibility of developing a platform-agnostic CNV PT program is being explored.
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Affiliation(s)
- Yassmine Akkari
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH; Department of Pathology, The Ohio State University, Columbus, OH
| | - Laura Conlin
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Juli-Anne Gardner
- Department of Pathology and Laboratory Medicine, University of Vermont Medical Center, Burlington, VT
| | | | - Gordana Raca
- Department of Pathology and Laboratory Medicine, Children's Hospital of Los Angeles, Los Angeles, CA
| | | | - Karen Tsuchiya
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH; Department of Pathology, The Ohio State University, Columbus, OH
| | - Catherine Rehder
- Department of Pathology, Duke University School of Medicine, Durham, NC.
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Elron E, Shohat M, Basel-Salmon L, Kahana S, Matar R, Klein K, Agmon-Fishman I, Gurevitch M, Berger R, Brabbing-Goldstein D, Levy M, Maya I. 2q13 Distal Microdeletion: Considering Evidence for an Emerging Syndrome Versus Susceptibility Locus: Twenty-Five New Cases and Review of the Literature. Am J Med Genet A 2025; 197:e63946. [PMID: 39587838 DOI: 10.1002/ajmg.a.63946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 10/04/2024] [Accepted: 11/11/2024] [Indexed: 11/27/2024]
Abstract
This study investigates distal 2q13 microdeletion, presenting the largest cohort to date, including prenatal cases, alongside a comprehensive literature review. A retrospective analysis was conducted on distal 2q13 microdeletions from clinical charts and laboratory reports. The cohort was divided into "clinically indicated" and "not-clinically indicated" groups based on the reason for chromosomal microarray testing. Clinical cases from medical literature were reviewed and compared with our cohort. The study included 25 cases: 17 index patients and 8 family members, with 47% males and 53% females. Of these, 2 were postnatal and 15 were prenatal. In the "clinically indicated" group, 35% had abnormalities on prenatal ultrasound, while 65% in the "not-clinically indicated" group had no major anomalies. Inheritance was 50% paternal in the "clinically indicated" group, and in the "not-clinically indicated" group, 44% paternal, 22% maternal, and 33% de novo. Symptoms varied from asymptomatic to severe developmental issues. Literature review identified 51 postnatal cases, with intellectual disability, and dysmorphism being common features. Familial cases showed 20% de novo, 20% maternal, 21.5% paternal, and 40% unknown inheritance. Distal 2q13 microdeletion is linked to cognitive impairment risk and should be reported in test results based on parental preferences, requiring special considerations for clinical classification and reporting.
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Affiliation(s)
- Eyal Elron
- The Raphael Recanati Genetics Institute, Rabin Medical Center, Petach Tikva, Israel
- Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Mordechai Shohat
- Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv, Israel
- Maccabi Genetic Institute & Bioinformatics Unit, Sheba Cancer Research Center, Ramat Gan, Israel
| | - Lina Basel-Salmon
- The Raphael Recanati Genetics Institute, Rabin Medical Center, Petach Tikva, Israel
- Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv, Israel
- Felsenstein Medical Research Center, Tel Aviv University, Tel Aviv, Israel
| | - Sarit Kahana
- The Raphael Recanati Genetics Institute, Rabin Medical Center, Petach Tikva, Israel
| | - Reut Matar
- The Raphael Recanati Genetics Institute, Rabin Medical Center, Petach Tikva, Israel
| | - Kochav Klein
- The Raphael Recanati Genetics Institute, Rabin Medical Center, Petach Tikva, Israel
| | - Ifaat Agmon-Fishman
- The Raphael Recanati Genetics Institute, Rabin Medical Center, Petach Tikva, Israel
| | - Merav Gurevitch
- The Raphael Recanati Genetics Institute, Rabin Medical Center, Petach Tikva, Israel
| | - Rachel Berger
- Maccabi Genetic Institute & Bioinformatics Unit, Sheba Cancer Research Center, Ramat Gan, Israel
| | | | - Michal Levy
- The Raphael Recanati Genetics Institute, Rabin Medical Center, Petach Tikva, Israel
- Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Idit Maya
- The Raphael Recanati Genetics Institute, Rabin Medical Center, Petach Tikva, Israel
- Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv, Israel
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Di Muro E, Petracca A, Castori M, Palumbo O. Gonadal Mosaicism for an ASH1L Intragenic Deletion Makes a Bridge Between MRD52 and 1q22 Microdeletion. Am J Med Genet A 2025; 197:e63960. [PMID: 39655631 DOI: 10.1002/ajmg.a.63960] [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: 10/18/2024] [Revised: 11/12/2024] [Accepted: 11/21/2024] [Indexed: 03/08/2025]
Abstract
ASH1L gene encodes a histone lysine methyltransferase, highly expressed in both embryonic and adult human brain. De novo loss-of-function variants in ASH1L are described in an ultrarare monogenic neurodevelopmental disorder, previously called mental retardation type 52 (MRD52). At the same time, a few cases are reported in the literature and DECIPHER with 1q22 microdeletions spanning ASH1L. We report three siblings presenting non-syndromic intellectual disability (ID) and an ASH1L intragenic deletion extending from exons 2 to 12 detected at SNP-array. Both parents resulted noncarrier suggesting gonadal/gonosomal mosaicism in one of the parents. This observation restricted the smallest region of overlap of the 1q22 microdeletion to ASH1L, and allowed to consider MRD52 and 1q22 microdeletion the same ASH1L-related neurodevelopmental disorder. We also reported the first example of gonadal/gonosomal mosaicism for an ASH1L deleterious variant, a fact that should generate the suspicion of recurrence also in sporadic cases of ASH1L-related neurodevelopmental disorder.
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Affiliation(s)
- Ester Di Muro
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, Foggia, Italy
| | - Antonio Petracca
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, Foggia, Italy
| | - Marco Castori
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, Foggia, Italy
| | - Orazio Palumbo
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, Foggia, Italy
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Han JY, Gwack J, Kim JH, Park MK, Park J. Genetic Alterations in Atypical Cerebral Palsy Identified Through Chromosomal Microarray and Exome Sequencing. Int J Mol Sci 2025; 26:2929. [PMID: 40243517 PMCID: PMC11988916 DOI: 10.3390/ijms26072929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2025] [Revised: 03/17/2025] [Accepted: 03/19/2025] [Indexed: 04/18/2025] Open
Abstract
This study investigated the genetic causes of atypical cerebral palsy (CP) through chromosomal microarray (CMA) and exome sequencing (ES) in a cohort of 10 Korean patients to identify variants and expand the spectrum of mutations associated with atypical cerebral palsy. Whole ES and/or genome sequencing (GS) after routine karyotyping and CMA was performed to identify causative variants and expand the spectrum of mutations associated with atypical CP. In cases of atypical CP, scoliosis and/or kyphosis, ranging from mild to severe, were present in all patients. Epilepsy was a comorbidity in seven patients (70%), and intellectual disability (ID) was observed in varying degrees. This study identified three copy number variations (CNVs), including 15q11.2 microdeletion (n = 1), 17p11.2 duplication (n = 1), and 12p13.33p11.23 duplication/18p11.32 microdeletion (n = 1), and six likely pathogenic variants (LPVs) or pathogenic variants (PVs) detected in the SLC2A1, PLAA, CDC42BPB, CACNA1D, ALG12, and SACS genes (n = 6). These findings emphasize the significance of incorporating genetic testing into the diagnostic process for atypical CP to improve our understanding of its molecular basis and inform personalized treatment strategies. To further advance this research, future studies should focus on exploring genotype-phenotype correlations, assessing the functional impact of identified variants, and increasing the sample size to validate the observed patterns.
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Affiliation(s)
- Ji Yoon Han
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea;
- Department of Pediatrics, Daejeon St. Mary’s Hospital, Daejeon 34943, Republic of Korea
| | - Jin Gwack
- Department of Preventive Medicine, Jeonbuk National University Medical School, Jeonju 54907, Republic of Korea;
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju 54907, Republic of Korea
| | - Jong Hun Kim
- Department of Thoracic and Cardiovascular Surgery, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Republic of Korea;
| | - Min Kyu Park
- Department of Clinical Pharmacology and Therapeutics, Chungbuk National University College of Medicine and Hospital, Cheongju 28644, Republic of Korea
- Research Institute of Cheongju-Osong Advanced Clinical Trial Center, Osong 28161, Republic of Korea
| | - Joonhong Park
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju 54907, Republic of Korea
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Republic of Korea
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Vimercati A, Tannorella P, Guzzetti S, Calzari L, Gentilini D, Manfredini E, Gori G, Gaudino R, Antona V, Piccione M, Daolio C, Auricchio R, Sirchia F, Minelli A, Rossi E, Bellini M, Biasucci G, Raucci AR, Pozzobon G, Patti G, Napoli F, Larizza L, Maghnie M, Russo S. Distinguishing Genetic Alterations Versus (Epi)Mutations in Silver-Russell Syndrome and Focus on the IGF1R Gene. J Clin Endocrinol Metab 2025; 110:e932-e944. [PMID: 39412159 PMCID: PMC11913091 DOI: 10.1210/clinem/dgae730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 10/08/2024] [Accepted: 10/14/2024] [Indexed: 01/03/2025]
Abstract
CONTEXT Silver-Russell Syndrome (SRS) is a growth retardation disorder characterized by pre- and postnatal growth failure, relative macrocephaly at birth, prominent forehead, body asymmetry, and feeding difficulties. The main molecular mechanisms are imprinting alterations at multiple loci, though a small number of pathogenic variants have been reported in the SRS genes IGF2-PLAG1-HMGA2 and CDKN1C. However, around 40% of clinically suspected SRS cases do not achieve a molecular diagnosis, highlighting the necessity to uncover the underlying mechanism in unsolved cases. OBJECTIVE Evaluate the frequency of genetic variants in undiagnosed SRS patients [Netchine-Harbison Clinical Scoring System (NH-CSS) ≥ 4], and investigate whether (epi)genetic patients may be distinguished from genetic patients. METHODS One hundred thirty-two clinically SRS patients without (epi)genetic deregulations were investigated by whole-exome (n = 15) and targeted (n = 117) Sequencing. Clinical data from our cohort and from an extensive revision of the literature were compared. RESULTS Pathogenic variants were identified in 9.1% of this cohort: 3% in IGF2, PLAG1, and HMGA2 genes and 3% in the IGF1R gene, associated with IGF-1 resistance (IGF1RES), an SRS differential diagnosis. Overall, IGF2-PLAG1-HMGA2 and IGF1R account for 3.6% of SRS with NH-CSS score ≥ 4. A clinical cross-comparison of (epi)genetic vs genetic SRS underlined (epi)genotype-phenotype correlation highlighted the prevalence of body asymmetry and relative macrocephaly in mosaic (epi)genetic SRS and recurrence of genetic familial cases. Furthermore, overlapping features were evidenced in (epi)genetic SRS and IGF1RES patients. CONCLUSION Our study explores the frequency of genetic SRS, underscores body asymmetry as a distinctive phenotype in (epi)genetic SRS and suggests IGF1R sequencing in a SRS diagnostic flowchart.
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Affiliation(s)
- Alessandro Vimercati
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, 20145 Milan, Italy
| | - Pierpaola Tannorella
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, 20145 Milan, Italy
| | - Sara Guzzetti
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, 20145 Milan, Italy
| | - Luciano Calzari
- Bioinformatics and Statistical Genomic Unit, IRCCS Istituto Auxologico Italiano, 20145 Milan, Italy
| | - Davide Gentilini
- Bioinformatics and Statistical Genomic Unit, IRCCS Istituto Auxologico Italiano, 20145 Milan, Italy
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - Emanuela Manfredini
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, 20145 Milan, Italy
| | - Giulia Gori
- Medical Genetics Unit, Meyer Children's Hospital IRCCS, 50139 Florence, Italy
| | - Rossella Gaudino
- Pediatric Unit, Department of Surgical Sciences, Dentistry, Gynecology and Pediatrics, University of Verona, 37129 Verona, Italy
| | - Vincenzo Antona
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D'Alessandro,” University of Palermo, 90127 Palermo, Italy
| | - Maria Piccione
- Medical Genetics Unit Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, 90127 Palermo, Italy
| | - Cecilia Daolio
- Department of Pediatrics, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy
| | - Renata Auricchio
- European Laboratory for the Investigation of Food Induced Diseases, Department of Translational Medical Science, Section of Pediatrics, University Federico II, 80131 Naples, Italy
| | - Fabio Sirchia
- Medical Genetic Unit, Department of Diagnostic Medicine, IRCCS San Matteo Hospital Foundation, 27100 Pavia, Italy
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
| | - Antonella Minelli
- Medical Genetic Unit, Department of Diagnostic Medicine, IRCCS San Matteo Hospital Foundation, 27100 Pavia, Italy
| | - Elena Rossi
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Melissa Bellini
- Pediatrics and Neonatology Unit, Gugliemo da Saliceto Hospital, 29121 Piacenza, Italy
| | - Giacomo Biasucci
- Pediatrics and Neonatology Unit, Gugliemo da Saliceto Hospital, 29121 Piacenza, Italy
- Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy
| | - Annalisa Russo Raucci
- Division of Genetics and Cell Biology and Laboratory of Clinical Molecular Biology and Cytogenetics, Unit of Genomics for Human Disease Diagnosis, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | | | - Giuseppa Patti
- Paediatric Endocrinology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16147 Genoa, Italy
| | - Flavia Napoli
- Paediatric Endocrinology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
| | - Lidia Larizza
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, 20145 Milan, Italy
| | - Mohamad Maghnie
- Paediatric Endocrinology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16147 Genoa, Italy
| | - Silvia Russo
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, 20145 Milan, Italy
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Wang G, Zhang Y, Wu T, Qiao L, Zhao D, Shen C, Feng G. Serum Zn and Ca correlate with false positive non-invasive prenatal test results. Am J Transl Res 2025; 17:2135-2144. [PMID: 40225977 PMCID: PMC11982886 DOI: 10.62347/rbcp4815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2024] [Accepted: 02/21/2025] [Indexed: 04/15/2025]
Abstract
OBJECTIVES The precise cause of false-positive results in non-invasive prenatal testing (NIPT) associated with suspected placental chimerism - where the placenta exhibits chromosomal abnormalities absent in the fetus, is not well understood. It is also unclear whether serum minerals such as zinc (Zn) and calcium (Ca), which are essential for maternal and fetal health, influence these false positives. METHODS In this retrospective analysis, 16,270 pregnant women were evaluated for serum mineral concentrations at 14 weeks of gestation, while NIPT was conducted between 12 and 22 weeks of gestation. Positive NIPT results prompted amniotic fluid karyotyping to confirm the diagnosis. Binary logistic regression analysis and restricted cubic spline (RCS) methods were used to assess the association between individual serum mineral levels and false-positive NIPT results. RESULTS The false-positive NIPT group exhibited altered serum mineral levels compared to the normal group, with increased sodium (Na), potassium (K), and Zn and decreased Ca, phosphorus (P), and iron (Fe). Multifactor regression analysis confirmed these trends. RCS analysis revealed a non-linear relationship between Zn and Ca levels and NIPT false-positive rates. Specifically, false-positive rates decreased with increasing Zn levels up to 13.1 μmol/L but rose beyond this threshold. Conversely, false-positive rates increased with higher Ca concentrations up to 2.31 mmol/L and then declined. These associations remained significant after adjusting for confounding factors. Additionally, a strong correlation was observed between NIPT false positivity and restrictive placental chimerism, highlighting a significant link between maternal serum Zn and Ca levels and the occurrence of restrictive placental chimerism. CONCLUSION This study uncovers a non-linear relationship between maternal serum Zn and Ca levels and NIPT false positives, which are suspected to be linked to restrictive placental chimerism. Moreover, moderate Zn and Ca supplementation may contribute to the development of a more precise nutritional management program for pregnancy.
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Affiliation(s)
- Gaigai Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical UniversitySuzhou 215002, Jiangsu, China
| | - Yanqiu Zhang
- Institute of Clinical Pharmacology, Anhui Medical University, Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Anti-inflammatory Immune Drugs Collaborative Innovation CenterHefei 230032, Anhui, China
| | - Tiantian Wu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical UniversitySuzhou 215002, Jiangsu, China
| | - Longwei Qiao
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical UniversitySuzhou 215002, Jiangsu, China
| | - Dan Zhao
- Fourth Affiliated Hospital of Jiangsu UniversityZhenjiang 212008, Jiangsu, China
| | - Cong Shen
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical UniversitySuzhou 215002, Jiangsu, China
| | - Guannan Feng
- Department of Gynaecology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School of Nanjing Medical UniversitySuzhou 215002, Jiangsu, China
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Tao J, Jin ZB, Shen RJ. MFRP, PRSS56, and MYRF account for 60.5% of a Chinese cohort with nanophthalmos. Clin Exp Ophthalmol 2025; 53:194-208. [PMID: 39569896 DOI: 10.1111/ceo.14465] [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: 03/04/2024] [Revised: 10/05/2024] [Accepted: 10/30/2024] [Indexed: 11/22/2024]
Abstract
BACKGROUND This study aimed to present the genetic profile of a rare ocular disease nanophthalmos (NO) in a large Chinese cohort, to explore its genetic characteristics and genotype-phenotype correlations. METHODS A total of 43 unrelated pedigrees diagnosed with NO were recruited. Whole exome sequencing and copy number variation analysis were performed, followed by validation and pathogenicity classification of the detected variants. RESULTS The overall genetic diagnostic rate was 60.5%. Twenty-eight unique genetic variants of MFRP, PRSS56, and MYRF have been identified, of which 19 were reported for the first time. The c.1486G>A variant in MFRP and the c.1066dupC variant in PRSS56 were the two most frequent variants. Patients with variants in MFRP or PRSS56 tended to possess shorter axial lengths than those with MYRF variants. Among patients with MFRP null variants, a higher proportion developed uveal effusion syndrome (UES) than did those without null variants, whereas among patients with PRSS56 null variants, a greater number of patients developed angle-closure glaucoma (ACG). A higher proportion of MFRP-related NO patients developed both UES and ACG. CONCLUSIONS MFRP, PRSS56, and MYRF account for the majority of genetic causes of NO. MFRP-related NO patients tend to exhibit a strong predisposition to complications. Null variants in MFRP and PRSS56 may increase susceptibility to clinical complications. This study provides insights into the genetic landscape and clinical characteristics of NO. These findings will lead to a better understanding of the mechanisms underlying nanophthalmos and other diseases associated with eye development.
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Affiliation(s)
- Jing Tao
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Zi-Bing Jin
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Ren-Juan Shen
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
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10
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Krishnamurthy N, Krishna D, Sanjana, Rathinasamy J, Kumar A, Francis AM. Genetic impact of copy number variations on congenital heart defects: Current insights and future directions. Glob Med Genet 2025; 12:100008. [PMID: 39925442 PMCID: PMC11800308 DOI: 10.1016/j.gmg.2024.100008] [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: 09/20/2024] [Revised: 11/07/2024] [Accepted: 11/07/2024] [Indexed: 02/11/2025] Open
Abstract
Congenital heart defects (CHDs) are the most prevalent congenital abnormalities, and they are commonly associated with genetic alterations, namely copy number variants. CNVs, which are duplications or deletions of DNA sequences, can disrupt gene regulation, impact dosage-sensitive genes, and cause loss-of-function mutations, all of which can interfere with heart development. CNVs cause genomic instability by changing essential genes, which plays an important role in the pathophysiology of CHDs. Detecting these variants is critical for better understanding the genetic causes of these abnormalities and improving patient outcomes. Advanced genetic testing tools aid in detecting CNVs linked to CHDs. Multiplex Ligation-Dependent Probe Amplification (MLPA), High-throughput Ligation-Dependent Probe Amplification (HLPA), Whole Exome Sequencing (WES), Chromosomal Microarray Analysis (CMA), and CNV-specific sequencing (CNV-seq) have all greatly improved the detection of these variants. Furthermore, whole genome sequencing (WGS) has emerged as a potent method for detecting CNVs on a wide scale, allowing for earlier diagnosis and more effective treatment planning. Therefore, this review focuses on the rising significance of CNV research in congenital heart defects, emphasizing on how genetic differences might lead to improved diagnostic and treatment options. By combining genomic technologies, researchers and clinicians can gain a better understanding of the function of CNVs in CHDs, opening the door for personalised therapy.
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Affiliation(s)
- Nandini Krishnamurthy
- Department of Human Genetics, Sri Ramachandra Institute of Higher Education and Research, Chennai, Tamil Nadu, India
| | - Devi Krishna
- Department of Human Genetics, Sri Ramachandra Institute of Higher Education and Research, Chennai, Tamil Nadu, India
| | - Sanjana
- Department of Human Genetics, Sri Ramachandra Institute of Higher Education and Research, Chennai, Tamil Nadu, India
| | - Jebaraj Rathinasamy
- Department of Pediatric Cardiology, Sri Ramachandra Medical Centre, Chennai, Tamil Nadu, India
| | - Ashok Kumar
- Department of Biotechnology, Vels Institute of Sciences Technology and Advanced Studies (VISTAS), Chennai, Tamil Nadu, India
| | - Andrea Mary Francis
- Department of Human Genetics, Sri Ramachandra Institute of Higher Education and Research, Chennai, Tamil Nadu, India
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11
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Ćomić J, Tilch E, Riedhammer KM, Brugger M, Brunet T, Eyring K, Vill K, Redler S, Tasic V, Schmiedeke E, Schäfer FM, Abazi-Emini N, Jenetzky E, Schwarzer N, Widenmann A, Lacher M, Zech M, Grasshoff-Derr S, Geßner M, Kabs C, Seitz B, Heydweiller AC, Muensterer O, Lange-Sperandio B, Rolle U, Schumacher J, Braunisch MC, Berutti R, Reutter H, Hoefele J. Trio Exome Sequencing in VACTERL Association. Kidney Int Rep 2025; 10:877-891. [PMID: 40225364 PMCID: PMC11993224 DOI: 10.1016/j.ekir.2024.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 11/12/2024] [Accepted: 12/03/2024] [Indexed: 02/10/2025] Open
Abstract
INTRODUCTION Currently, there is only limited data on monogenic causes of vertebral defects, anorectal malformations, cardiac defects, esophageal atresia or tracheoesophageal fistula, renal malformations, and limb defects (VACTERL) association. The aim of this study was to extend the spectrum of disease-causing variants in known genes, to determine the diagnostic yield of monogenic causes, and to identify candidate genes and rare variants by applying comprehensive genetic testing or rare variant burden. METHODS The total cohort comprised 101 affected individuals and their parents. Trio exome sequencing was only performed in 96 individuals and their parents because of DNA quality reasons and case-control gene and pathway burden tests were calculated and evaluated by quantile-quantile plots, principal component analysis plots and family-based association test (FBAT). RESULTS In 5 of 96 individuals, disease-causing variants in known genes or loci were identified to be associated with the following 4 disorders: Kabuki syndrome, Sotos syndrome, MELAS syndrome, and deletion syndrome encompassing TWIST1. In 91 individuals, no disease-causing variants were found. FBAT showed 14 significant variants, 2 significant genes (LOC645752 and ZNF417), and 8 significant pathways. CONCLUSION This study shows that most individuals with VACTERL association do not have known discrete genetic syndromes, implying that pathomechanisms or variants not identifiable by exome sequencing may exist requiring further investigation.
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Affiliation(s)
- Jasmina Ćomić
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, TUM School of Medicine and Health, Munich, Germany
- Department of Nephrology, Klinikum rechts der Isar, Technical University of Munich, TUM School of Medicine and Health, Munich, Germany
| | - Erik Tilch
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, TUM School of Medicine and Health, Munich, Germany
| | - Korbinian M. Riedhammer
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, TUM School of Medicine and Health, Munich, Germany
- Department of Nephrology, Klinikum rechts der Isar, Technical University of Munich, TUM School of Medicine and Health, Munich, Germany
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Melanie Brugger
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, TUM School of Medicine and Health, Munich, Germany
| | - Theresa Brunet
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, TUM School of Medicine and Health, Munich, Germany
| | - Katharina Eyring
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, TUM School of Medicine and Health, Munich, Germany
| | - Katharina Vill
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, TUM School of Medicine and Health, Munich, Germany
- Department of Pediatric Neurology and Developmental Medicine and LMU Center for Children with Medical Complexity, Dr. von Hauner Children's Hospital, Ludwig-Maximilians University, Munich, Germany
| | - Silke Redler
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine University, Düsseldorf, Germany
| | - Velibor Tasic
- University Children’s Hospital, Medical Faculty of Skopje, North Macedonia
| | - Eberhard Schmiedeke
- Clinic for Paediatric Surgery and Paediatric Urology, Klinikum Bremen-Mitte, Bremen, Germany
| | - Frank-Mattias Schäfer
- Department of Pediatric Surgery and Urology, Cnopf'sche Kinderklinik, Nürnberg, Germany
| | - Nora Abazi-Emini
- University Children’s Hospital, Medical Faculty of Skopje, North Macedonia
| | - Ekkehart Jenetzky
- Institute of Integrative Medicine, Witten/Herdecke University, Herdecke, Germany
- Department of Pediatric and Adolescent Psychiatry and Psychotherapy, University Medical Centre, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Nicole Schwarzer
- SoMA, The German Patient Support Organization for Anorectal Malformations and Hirschsprung Disease, Munich, Germany
| | - Anke Widenmann
- Patient Organisation for Esophageal Diseases KEKS e.V., Stuttgart, Germany
| | - Martin Lacher
- Department of Pediatric Surgery, University of Leipzig, Leipzig, Germany
| | - Michael Zech
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, TUM School of Medicine and Health, Munich, Germany
- Institute of Neurogenomics, Helmholtz Munich, Neuherberg, Germany
- Institute of Advanced Study, Technical University of Munich, Garching, Germany
| | - Sabine Grasshoff-Derr
- Pediatric Surgery Unit, Buergerhospital and Clementine Kinderhospital, Frankfurt, Germany
| | - Michaela Geßner
- KfH-Board of Trustees for Dialysis and Kidney Transplantation (KfH-Kuratorium für Dialyse und Nierentransplantatione.V.), Munich, Germany
| | - Carmen Kabs
- Department of Paediatrics Surgery, Muenchen KlinikgGmbH, Munich Clinic Schwabing, Munich, Germany
| | - Barbara Seitz
- KfH-Board of Trustees for Dialysis and Kidney Transplantation (KfH-Kuratorium für Dialyse und Nierentransplantatione.V.), Munich, Germany
| | - Andreas C. Heydweiller
- Department of General, Visceral, Vascular and Thoracic Surgery, Unit of Pediatric Surgery, University Hospital Bonn, Bonn, Germany
| | - Oliver Muensterer
- Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, Ludwig-Maximilians University, Munich, Germany
| | - Bärbel Lange-Sperandio
- Division of Pediatric Nephrology, Department of Pediatrics, Dr. v. Hauner Children's Hospital, Ludwig-Maximilians University, Munich, Germany
| | - Udo Rolle
- Department of Pediatric Surgery and Pediatric Urology, University Hospital Frankfurt/M., Frankfurt am Main, Germany
| | - Johannes Schumacher
- Institute of Human Genetics, University Hospital of Marburg, Marburg, Germany
| | - Matthias C. Braunisch
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, TUM School of Medicine and Health, Munich, Germany
- Department of Nephrology, Klinikum rechts der Isar, Technical University of Munich, TUM School of Medicine and Health, Munich, Germany
| | - Riccardo Berutti
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, TUM School of Medicine and Health, Munich, Germany
| | - Heiko Reutter
- Department of Neonatology and Pediatric Intensive Care, University Erlangen-Nürnberg, Erlangen, Germany
| | - Julia Hoefele
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, TUM School of Medicine and Health, Munich, Germany
- Institute of Human Genetics, University Hospital, Ludwig-Maximilians University, Munich, Germany
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12
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Tolmacheva EN, Kashevarova AA, Fonova EA, Salyukova OA, Seitova GN, Nazarenko LP, Agafonova AA, Minaycheva LI, Ravzhaeva EG, Petrova VV, Lopatkina ME, Belyaeva EO, Vovk SL, Fedotov DA, Vasilyeva OY, Skryabin NA, Lebedev IN. Prevalence of CNVs on the X chromosome in patients with neurodevelopmental disorders. Mol Cytogenet 2025; 18:3. [PMID: 39985054 PMCID: PMC11846235 DOI: 10.1186/s13039-025-00703-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2024] [Accepted: 01/19/2025] [Indexed: 02/24/2025] Open
Abstract
BACKGROUND The X chromosome is enriched with genes related to brain development, and the hemizygous state of these genes in men causes some difficulties in the clinical interpretation of copy number variations (CNVs). In this study, we present data on the frequency and spectrum of CNVs on the X chromosome in a cohort of patients with neurodevelopmental disorders (NDDs). METHODS Chromosomal microarray analysis was performed for 1175 patients with NDDs. CNVs were confirmed by real-time quantitative PCR. X chromosome inactivation was analysed by methyl-sensitive PCR. To determine the pathogenic significance of the CNVs, several criteria, including the origin (inherited or de novo), variant type (microdeletion or microduplication), and X chromosome inactivation pattern in asymptomatic and symptomatic carriers, were considered. Additionally, the spectrum, size and molecular bases of copy number changes in genes or gene regions involved in the development of the pathological phenotype in each patient were considered. RESULTS CNVs on the X chromosome were identified in 33 patients (2.8%). Duplications and triplications (27 cases) were four times more common than deletions (6 cases). In 74% of patients, CNVs were of maternal origin; in 10% they were of paternal origin; and in 16% they arose de novo. The frequency of skewed X inactivation among family members who were healthy carriers of pathogenic and likely pathogenic CNVs and variants of uncertain significance (VUSs) on the X chromosome was 23%. For the first time, we reported several CNVs, including a pathogenic microdeletion at Xq26.1q26.2 involving the ARHGAP36 gene and a microduplication at Xp22.2 involving the OFD1 gene, CONCLUSIONS: This study expands on the frequency and spectrum of CNVs in patients with NDDs. Pathogenic variants on the X chromosome were present in 15% of cases, LP in 12%, VUS in 57%, and LB in 16% of cases. Previously unreported CNVs aid in the identification of new structural variants and genes associated with X-linked intellectual disability. We propose to consider the X-chromosome inactivation status when assessing the pathogenetic significance of CNVs using the ACMG algorithm (American College of Medical Genetics).
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Affiliation(s)
- Ekaterina N Tolmacheva
- Laboratory of Cytogenetics, Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Ushaika Street 10, Tomsk, 634050, Russia.
| | - Anna A Kashevarova
- Laboratory of Cytogenetics, Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Ushaika Street 10, Tomsk, 634050, Russia
| | - Elizaveta A Fonova
- Laboratory of Genomics of Orphan Diseases, Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, 634050, Russia
| | - Olga A Salyukova
- Medical Genetic Center (Genetic Clinic), Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, 634050, Russia
| | - Gulnara N Seitova
- Medical Genetic Center (Genetic Clinic), Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, 634050, Russia
| | - Lyudmila P Nazarenko
- Medical Genetic Center (Genetic Clinic), Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, 634050, Russia
| | - Anna A Agafonova
- Medical Genetic Center (Genetic Clinic), Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, 634050, Russia
| | - Larisa I Minaycheva
- Medical Genetic Center (Genetic Clinic), Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, 634050, Russia
| | - Ekaterina G Ravzhaeva
- Medical Genetic Center (Genetic Clinic), Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, 634050, Russia
| | - Valeria V Petrova
- Medical Genetic Center (Genetic Clinic), Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, 634050, Russia
| | - Maria E Lopatkina
- Laboratory of Ontogenetics, Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, 634050, Russia
| | - Elena O Belyaeva
- Laboratory of Ontogenetics, Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, 634050, Russia
| | - Svetlana L Vovk
- Medical Genetic Center (Genetic Clinic), Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, 634050, Russia
| | - Dmitry A Fedotov
- Laboratory of Ontogenetics, Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, 634050, Russia
| | - Oksana Y Vasilyeva
- Laboratory of Cytogenetics, Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Ushaika Street 10, Tomsk, 634050, Russia
| | - Nikolay A Skryabin
- Laboratory of Genomics of Orphan Diseases, Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, 634050, Russia
| | - Igor N Lebedev
- Laboratory of Ontogenetics, Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, 634050, Russia
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13
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Jimoh IJ, Balicza P, Szlepak T, Csaban D, Gal A, Geresi A, Grosz Z, Palasti A, Boczan J, Klivenyi P, Molnar MJ. Expanding the Phenotypic Spectrum of SPG7 Rare Damaging Variants: Insights From a Hungarian Cohort. Clin Genet 2025. [PMID: 39978794 DOI: 10.1111/cge.14719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2024] [Revised: 01/08/2025] [Accepted: 01/27/2025] [Indexed: 02/22/2025]
Abstract
Mitochondria-associated paraplegin dysfunction is primarily linked to spastic paraplegia; however, genetic alterations in SPG7 have been associated with a broader spectrum of clinical symptoms. To identify disease-causing variants in the SPG7 gene, 437 patients with spastic ataxia, mitochondrial dysfunction-associated symptoms, or motoneuron lesions detected by EMG have been tested. We aimed to assess the clinical spectrum and determine the frequency of damaging variants within patient groups, particularly those less studied. Using ACMG criteria, we identified 10 pathogenic or likely pathogenic variants, 5 variants of uncertain significance with predicted damaging effects, and a probable risk factor variant in 58 patients. We identified 25 biallelic and 33 monoallelic cases. The most common variant was p. Leu78Ter (N = 23), followed by p. Ala510Val (N = 21). The point prevalence of SPG7-associated conditions in Hungary in 2024 is 0.46 per 100 000. In addition to well-characterized cohorts, SPG7 alterations were frequently identified in cohorts with multisystemic mitochondrial disease and lower motoneuron lesions. Multiple mtDNA deletions and histological abnormalities were consistently observed across all groups. In monoallelic cases, no evidence of a digenic effect involving AFG3L2 was found. Both autosomal dominant and recessive inheritance patterns were documented, with monoallelic cases typically presenting with a milder phenotype.
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Affiliation(s)
- Idris Janos Jimoh
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, Budapest, Hungary
- Doctoral School of Interdisciplinary Medicine, University of Szeged, Szeged, Hungary
| | - Peter Balicza
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, Budapest, Hungary
- HUN-REN Multiomics Neurodegeneration Research Group, Hungarian Research Network, Budapest, Hungary
| | - Tamas Szlepak
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, Budapest, Hungary
- HUN-REN Multiomics Neurodegeneration Research Group, Hungarian Research Network, Budapest, Hungary
| | - Dora Csaban
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, Budapest, Hungary
| | - Aniko Gal
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, Budapest, Hungary
| | - Adrienn Geresi
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, Budapest, Hungary
| | - Zoltan Grosz
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, Budapest, Hungary
| | - Agnes Palasti
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, Budapest, Hungary
| | - Judit Boczan
- Department of Neurology, University of Debrecen, Debrecen, Hungary
| | - Peter Klivenyi
- Department of Neurology, University of Szeged, Szeged, Hungary
- HUN-REN-SZTE Neuroscience Research Group, Hungarian Research Network, Danube Neuroscience Research Laboratory, University of Szeged, Szeged, Hungary
| | - Maria Judit Molnar
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, Budapest, Hungary
- HUN-REN Multiomics Neurodegeneration Research Group, Hungarian Research Network, Budapest, Hungary
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14
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Wu D, Chen R, Zhang J, Yan W, Chen M, Xia D, Li X, Dai Y, Chen Y, Li R. DNA copy number variations and craniofacial abnormalities in 1,457 children with neurodevelopmental disorders. Ital J Pediatr 2025; 51:9. [PMID: 39849549 PMCID: PMC11756179 DOI: 10.1186/s13052-025-01839-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 01/02/2025] [Indexed: 01/25/2025] Open
Abstract
BACKGROUND This study aimed to investigate deoxyribonucleic acid (DNA) copy number variations (CNVs) in children with neurodevelopmental disorders and their association with craniofacial abnormalities. METHODS A total of 1,457 children who visited the Child Health Department of our hospital for unexplained Neurodevelopmental disorders (NDDs) between November 2019 and December 2022 were enrolled. Peripheral venous blood samples (2 mL) were collected from the children and their parents for whole-exome sequencing. Positive results were verified through Sanger sequencing for locus and pedigree validation. Simultaneously, a specific sign-scoring scale was created to evaluate characteristics related to the developments of eyes, nose, ears, eyebrows, head, mouth, face, trunk, limbs, and reproductive, urinary, and cardiovascular systems. RESULTS A total of 536 children (36.78%, 536/1,457) were found to have genetic variations, with 379 (70.71%, 379/536) exhibiting pathogenic monogenic mutations. Furthermore, 157 children (29.29%, 157/536) harbored DNA copy number variants, encompassing microdeletions (68.15%, 107/157) and microduplications (31.85%, 50/157). Regarding the pathogenicity of CNVs, 91 (57.96%, 91/157) were identified as pathogenic, 28 (17.83%, 28/157) as variants of uncertain clinical significance (VOUS), and 38 (24.20%, 38/157) as benign according to the American College of Medical Genetics and Genomics (ACMG).Using a specific sign-scoring scale, the proportion of pathogenic CNVs in children graded 1 point or higher (64%, 58/91) was significantly higher than that of non-pathogenic CNVs (43%, 29/66) (P < 0.05). Furthermore, the proportion of microdeletions in children graded 1 point or higher (60.75%, 65/107) was significantly higher than those carrying microduplications (44%, 22/50) (P < 0.05). The proportion of pathogenic microdeletions in children graded 1 point or higher (73.43%,47/64) was significantly higher than those carrying pathogenic microduplications (40.74%, 11/27) (P < 0.05). CONCLUSION The positive rate of whole-exome sequencing for children with combined craniofacial abnormalities and NDDs exceeds the international average in our study cohort. Thus, whole-exome sequencing may be recommended for precise diagnosis of neurogenetic diseases in such cases.
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Affiliation(s)
- Dandan Wu
- Child Mental Health Deparment, Children's Hospital of Nanjing Medical University, NanjingJiangsu, 210008, China
| | - Ran Chen
- Child Healthcare Department, Children's Hospital of Nanjing Medical University, Jiangdong South No.8 Road, Nanjing, Jiangsu, 210008, China
| | - Jerry Zhang
- Basis International School Nanjing, Nanjing, Jiangsu, 210008, China
| | - Wu Yan
- Child Healthcare Department, Children's Hospital of Nanjing Medical University, Jiangdong South No.8 Road, Nanjing, Jiangsu, 210008, China
| | - Mengyin Chen
- Child Healthcare Department, Children's Hospital of Nanjing Medical University, Jiangdong South No.8 Road, Nanjing, Jiangsu, 210008, China
| | - Dongqing Xia
- Child Healthcare Department, Children's Hospital of Nanjing Medical University, Jiangdong South No.8 Road, Nanjing, Jiangsu, 210008, China
| | - Xiaonan Li
- Child Healthcare Department, Children's Hospital of Nanjing Medical University, Jiangdong South No.8 Road, Nanjing, Jiangsu, 210008, China
| | - Yanyan Dai
- Child Healthcare Department, Children's Hospital of Nanjing Medical University, Jiangdong South No.8 Road, Nanjing, Jiangsu, 210008, China
| | - Yinhua Chen
- Child Healthcare Department, Children's Hospital of Nanjing Medical University, Jiangdong South No.8 Road, Nanjing, Jiangsu, 210008, China.
| | - Rong Li
- Child Healthcare Department, Children's Hospital of Nanjing Medical University, Jiangdong South No.8 Road, Nanjing, Jiangsu, 210008, China.
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15
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da Silva Assis IS, Salum KCR, Felício RDFM, Palhinha L, de Medeiros Abreu G, Silva T, Mattos FCC, Rosado EL, Zembrzuski VM, Campos Junior M, Maya-Monteiro CM, Cabello PH, Carneiro JRI, Bozza PT, da Fonseca ACP. Genomic deletions on 16p11.2 associated with severe obesity in Brazil. Front Endocrinol (Lausanne) 2025; 15:1495534. [PMID: 39897959 PMCID: PMC11781945 DOI: 10.3389/fendo.2024.1495534] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2024] [Accepted: 11/25/2024] [Indexed: 02/04/2025] Open
Abstract
Introduction Genetic obesity is considered a rare disease, affecting up to 10% of patients with severe early-onset obesity. Over the past years, significant advances have been made; however, the majority of patients are misdiagnosed with polygenic obesity. Thus, this study aimed to identify deleterious copy number variations (CNVs) linked to obesity and explore the clinical phenotypes. Method The sample comprised 195 adults with severe obesity (BMI≥35kg/m2) who developed this phenotype during childhood or adolescence. We investigated the CNV using Multiplex Ligation-dependent Probe Amplification [MLPA] and real-time PCR. Chromosomal microarray analysis was used to assess the extent of genomic alterations. Results One patient showed a ~206 kb deletion in the distal of the 16p11.2 region, encompassing twelve genes. The gene linked to the development of severe obesity was SH2B1. This alteration was found in a male patient with metabolic syndrome (MS), and hypertension. Two patients exhibited a large deletion in the proximal of the 16p11.2 region. One patient showed a ~534 kb deletion without twenty-nine genes. This female patient had hypertension and bronchitis. The other patient presented a ~598 kb deletion of the proximal 16p11.2 region, including thirty-two genes. This female patient exhibited MS, and moderate binge-eating disorder. Conclusion Our study showed three genomic deletions at the 16p11.2 region in patients with severe obesity from Brazil. These results support the clinical utility of genetic testing to identify patients with the genetic form of obesity who may benefit from specific medical treatment, family genetic counseling, and targeted therapeutic intervention.
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Affiliation(s)
- Izadora Sthephanie da Silva Assis
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
- Human Genetics Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Kaio Cezar Rodrigues Salum
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
- Human Genetics Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
- Clementino Fraga Filho University Hospital, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Lohanna Palhinha
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Gabriella de Medeiros Abreu
- Human Genetics Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
- Josué de Castro Nutrition Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tamara Silva
- Genetics Laboratory, Grande Rio University/AFYA, Rio de Janeiro, Brazil
| | | | - Eliane Lopes Rosado
- Josué de Castro Nutrition Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Mario Campos Junior
- Human Genetics Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | | | - Pedro Hernán Cabello
- Human Genetics Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - João Regis Ivar Carneiro
- Clementino Fraga Filho University Hospital, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Patrícia Torres Bozza
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Ana Carolina Proença da Fonseca
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
- Human Genetics Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
- Genetics Laboratory, Grande Rio University/AFYA, Rio de Janeiro, Brazil
- Postgraduate Program in Translational Biomedicine, Grande Rio University/AFYA, Rio de Janeiro, Brazil
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16
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Akter H, Rahaman MA, Eshaque TB, Mohamed N, Islam A, Morshed M, Shahin Z, Muhaimin A, Foyzullah AM, Mim RA, Omar FB, Hasan MN, Satsangi D, Ahmed N, Al Saba A, Jahan N, Hossen MA, Mondol MA, Sakib AS, Kabir R, Jahan Chowdhury MS, Shams N, Afroz S, Kanta SI, Bhuiyan SJ, Biswas R, Hanif S, Tambi R, Nassir N, Rahman MM, Duan J, D Børglum A, Amin R, Basiruzzaman M, Kamruzzaman M, Sarker S, Woodbury-Smith M, Uddin KMF, Nabi AHMN, Uddin M. Genomic insights from a deeply phenotyped highly consanguineous neurodevelopmental disorders cohort. Genet Med 2025; 27:101282. [PMID: 39342494 DOI: 10.1016/j.gim.2024.101282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 09/19/2024] [Accepted: 09/19/2024] [Indexed: 10/01/2024] Open
Abstract
PURPOSE The genetic underpinning of neurodevelopmental disorders (NDDs) in diverse ethnic populations, especially those with high rates of consanguinity, remains largely unexplored. Here, we aim to elucidate genomic insight from 576 well-phenotyped and highly consanguineous (16%) NDD cohort. METHODS We used chromosomal microarray (CMA; N:247), exome sequencing (ES; N:127), combined CMA and ES (N:202), and long-read genome sequencing to identify genetic etiology. Deep clinical multivariate data were coupled with genomic variants for stratification analysis. RESULTS Genetic diagnosis rates were 17% with CMA, 29.92% with ES, and 37.13% with combined CMA and ES. Notably, children of consanguineous parents showed a significantly higher diagnostic yield (P < .01) compared to those from nonconsanguineous parents. Among the ES-identified pathogenic variants, 36.19% (38/105) were novel, implicating 35 unique genes. Long-read sequencing of seizure participants unresolved by combined test identified expanded FMR1 trinucleotide repeats. Additionally, we identified 2 recurrent X-linked variants in the G6PD in 3.65% (12/329) of NDD participants. These variants were absent in large-population control cohorts and cohort comprising neurodevelopmental and neuropsychiatric populations of European descendants, indicating a possible associated risk factor potentially resulting from ancient genetic drift. CONCLUSION This study unveils unique clinical and genomic insights from a consanguinity rich Bangladeshi NDD cohort.
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Affiliation(s)
- Hosneara Akter
- Genetics and Genomic Medicine Centre (GGMC), NeuroGen Healthcare, Dhaka, Bangladesh; Laboratory of Population Genetics, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Md Atikur Rahaman
- Genetics and Genomic Medicine Centre (GGMC), NeuroGen Healthcare, Dhaka, Bangladesh
| | | | - Nesrin Mohamed
- Center for Applied and Translational Genomics, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE
| | - Amirul Islam
- Genetics and Genomic Medicine Centre (GGMC), NeuroGen Healthcare, Dhaka, Bangladesh; GenomeArc Inc., Mississauga, ON, Canada
| | - Mehzabin Morshed
- Genetics and Genomic Medicine Centre (GGMC), NeuroGen Healthcare, Dhaka, Bangladesh
| | - Zaha Shahin
- Imperial College London, London, United Kingdom
| | - Al Muhaimin
- Genetics and Genomic Medicine Centre (GGMC), NeuroGen Healthcare, Dhaka, Bangladesh
| | - Arif Md Foyzullah
- Genetics and Genomic Medicine Centre (GGMC), NeuroGen Healthcare, Dhaka, Bangladesh
| | - Rabeya Akter Mim
- Genetics and Genomic Medicine Centre (GGMC), NeuroGen Healthcare, Dhaka, Bangladesh
| | - Farjana Binta Omar
- Genetics and Genomic Medicine Centre (GGMC), NeuroGen Healthcare, Dhaka, Bangladesh
| | - Md Nahid Hasan
- Genetics and Genomic Medicine Centre (GGMC), NeuroGen Healthcare, Dhaka, Bangladesh; GenomeArc Inc., Mississauga, ON, Canada
| | - Dharana Satsangi
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Nahid Ahmed
- Genetics and Genomic Medicine Centre (GGMC), NeuroGen Healthcare, Dhaka, Bangladesh
| | - Abdullah Al Saba
- Laboratory of Population Genetics, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Nargis Jahan
- Centre for Precision Therapeutics (NPT), NeuroGen Healthcare, Dhaka, Bangladesh
| | - Md Arif Hossen
- Centre for Precision Therapeutics (NPT), NeuroGen Healthcare, Dhaka, Bangladesh
| | | | | | - Rezwana Kabir
- Centre for Precision Therapeutics (NPT), NeuroGen Healthcare, Dhaka, Bangladesh
| | | | - Nusrat Shams
- Centre for Precision Therapeutics (NPT), NeuroGen Healthcare, Dhaka, Bangladesh
| | - Shireen Afroz
- Bangladesh Shishu Hospital and Institute, Dhaka, Bangladesh
| | | | | | - Rabi Biswas
- Bangladesh Shishu Hospital and Institute, Dhaka, Bangladesh
| | - Shehzad Hanif
- Center for Applied and Translational Genomics, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE
| | - Richa Tambi
- Center for Applied and Translational Genomics, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE
| | - Nasna Nassir
- Center for Applied and Translational Genomics, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE; College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Muhammad Mizanur Rahman
- Department of Paediatric Neurology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Jinjie Duan
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark; Department of Biomedicine and the iSEQ Centre, Aarhus University, Aarhus, Denmark; Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Anders D Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark; Department of Biomedicine and the iSEQ Centre, Aarhus University, Aarhus, Denmark; Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Robed Amin
- Ministry of Health and Family Welfare, Government of People Republic of Bangladesh, Dhaka, Bangaldesh
| | | | - Md Kamruzzaman
- Bangladesh Shishu Hospital and Institute, Dhaka, Bangladesh
| | - Shaoli Sarker
- Centre for Precision Therapeutics (NPT), NeuroGen Healthcare, Dhaka, Bangladesh; Bangladesh Shishu Hospital and Institute, Dhaka, Bangladesh
| | - Marc Woodbury-Smith
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - K M Furkan Uddin
- Genetics and Genomic Medicine Centre (GGMC), NeuroGen Healthcare, Dhaka, Bangladesh; Department of Biochemistry, Holy Family Red Crescent Medical College, Dhaka, Bangladesh
| | - A H M Nurun Nabi
- Laboratory of Population Genetics, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Mohammed Uddin
- Center for Applied and Translational Genomics, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE; GenomeArc Inc., Mississauga, ON, Canada; College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE.
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17
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Granata P, Zito A, Cocciadiferro D, Novelli A, Pessina C, Mazza T, Ferri M, Piccinelli P, Luoni C, Termine C, Fasano M, Casalone R. Unveiling genetic insights: Array-CGH and WES discoveries in a cohort of 122 children with essential autism spectrum disorder. BMC Genomics 2024; 25:1186. [PMID: 39654053 PMCID: PMC11629504 DOI: 10.1186/s12864-024-11077-5] [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: 07/08/2024] [Accepted: 11/21/2024] [Indexed: 12/12/2024] Open
Abstract
BACKGROUND Autistic Spectrum Disorder (ASD) is a neurodevelopmental disorder with a strong genetic component and high heterogeneity. Essential ASD refers to patients who do not have other comorbidities. This study aimed to investigate the genetic basis of essential ASD using whole exome sequencing (WES) and array-comparative genomic hybridization (array-CGH). RESULTS In a cohort of 122 children with essential ASD, WES detected 382 variants across 223 genes, while array-CGH identified 46 copy number variants (CNVs). The combined use of WES and array-CGH revealed pathogenic variants in four patients (3.1% detection rate) and likely pathogenic variants in 34 patients (27.8% detection rate). Only one patient had a pathogenic CNV (0.8% detection rate). Including likely pathogenic variants, the overall detection rate was 31.2%. Additionally, 33 de novo heterozygous sequence variants were identified by WES, with three classified as pathogenic and 13 as likely pathogenic. Sequence variants were found in 85 genes already associated with ASD, and 138 genes not previously included in the SFARI dataset were identified as potential new candidate genes. CONCLUSIONS The study enhances genetic understanding of essential ASD and identifies new candidate genes of interest. The findings suggest that using both array-CGH and WES in patients with essential ASD can improve the detection of pathogenic and likely pathogenic genetic variants, contributing to better diagnosis and potentially guiding future research and treatment strategies.
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Affiliation(s)
- Paola Granata
- Cytogenetics and Medical Genetics Unit, Department of Services, ASST dei Sette Laghi, Varese, Italy
| | - Alessandra Zito
- School of Medical Genetics, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Dario Cocciadiferro
- Translational Cytogenomics Research Unit, Ospedale Pediatrico Bambino Gesù, Roma, Italy
| | - Antonio Novelli
- Translational Cytogenomics Research Unit, Ospedale Pediatrico Bambino Gesù, Roma, Italy
| | - Chiara Pessina
- Cytogenetics and Medical Genetics Unit, Department of Services, ASST dei Sette Laghi, Varese, Italy
| | - Tommaso Mazza
- Translational Cytogenomics Research Unit, Ospedale Pediatrico Bambino Gesù, Roma, Italy
- Laboratory of Bioinformatics, IRCCS Casa Sollievo della Sofferenza, S. Giovanni, Rotondo, Italy
| | - Matteo Ferri
- Child Neuropsychiatry Unit, Department of Maternal and Child Health, ASST dei Sette Laghi, Varese, Italy
| | - Paolo Piccinelli
- Child Neuropsychiatry Unit, Department of Maternal and Child Health, ASST dei Sette Laghi, Varese, Italy
| | - Chiara Luoni
- Child Neuropsychiatry Unit, Department of Maternal and Child Health, ASST dei Sette Laghi, Varese, Italy
| | - Cristiano Termine
- Child Neuropsychiatry Unit, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Mauro Fasano
- Department of Science and High Technology, University of Insubria, via Manara 7, Busto Arsizio, Italy.
- Center of Neuroscience, University of Insubria, Busto Arsizio, Italy.
| | - Rosario Casalone
- Cytogenetics and Medical Genetics Unit, Department of Services, ASST dei Sette Laghi, Varese, Italy
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Yang Y, Jiang X. Comparison of chromosomal microarray and karyotyping in prenatal diagnosis using 491 amniotic fluid samples. Medicine (Baltimore) 2024; 103:e40822. [PMID: 39654217 PMCID: PMC11630984 DOI: 10.1097/md.0000000000040822] [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: 07/03/2024] [Revised: 11/11/2024] [Accepted: 11/15/2024] [Indexed: 12/12/2024] Open
Abstract
This study was aimed to investigate the performance of chromosomal microarray analysis (CMA) in prenatal diagnosis compared with traditional karyotyping analysis. Both CMA and karyotyping analyses were performed to detect the karyotypes in the amniotic fluid of 491 pregnant women who got prenatal diagnosis at the Center of Prenatal Diagnosis of Shangrao (China) during January 2019 to April 2021. After excluding 2 samples in the CMA analysis and 2 samples in the karyotyping analysis which were failed in detection, the remaining 487 amniotic fluid samples were detected. Both CMA and karyotyping analyses identified 22 cases of aneuploidy chromosome abnormalities, including trisomy 21 (10 cases), trisomy 18 (4 cases), sex chromosome abnormality (5 cases), and other chromosome abnormalities (3 cases). In addition, CMA and karyotyping analyses found 8 cases of fetal chromosomal imbalance. Interestingly, abnormal results were detected by CMA analysis in 10 cases whose results were normal by karyotype analysis. Furthermore, 23 cases of copy number variation (CNVs) with variation of unknown clinical significance (VOUS) were detected by CMA, which accounted for 4.68% (23/491) in all cases. However, CMA was not able to accurately identify some complex karyotypes and mixed chimeras, including 2 cases of chimeras, 4 cases of balanced translocations, 4 cases of pericentric inversions, and 8 cases of other chromosome polymorphisms, indicating karyotyping analysis was superior to detect these chromosome abnormalities compared with CMA analysis. CMA was better in detecting the fracture sites, microduplication and microdeletion with definite pathogenicity, and CNVs with VOUS compared with karyotype analysis.
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Affiliation(s)
- Ying Yang
- Shangrao City Maternal and Child Health Hospital, Shangrao, China
| | - Xiaowen Jiang
- Shangrao City Maternal and Child Health Hospital, Shangrao, China
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19
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Chen LL, Naesström M, Halvorsen M, Fytagoridis A, Crowley SB, Mataix-Cols D, Rück C, Crowley JJ, Pascal D. Genomics of severe and treatment-resistant obsessive-compulsive disorder treated with deep brain stimulation: A preliminary investigation. Am J Med Genet B Neuropsychiatr Genet 2024; 195:e32983. [PMID: 38650085 PMCID: PMC11493841 DOI: 10.1002/ajmg.b.32983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 01/25/2024] [Accepted: 03/20/2024] [Indexed: 04/25/2024]
Abstract
Individuals with severe and treatment-resistant obsessive-compulsive disorder (trOCD) represent a small but severely disabled group of patients. Since trOCD cases eligible for deep brain stimulation (DBS) probably comprise the most severe end of the OCD spectrum, we hypothesize that they may be more likely to have a strong genetic contribution to their disorder. Therefore, while the worldwide population of DBS-treated cases may be small (~300), screening these individuals with modern genomic methods may accelerate gene discovery in OCD. As such, we have begun to collect DNA from trOCD cases who qualify for DBS, and here we report results from whole exome sequencing and microarray genotyping of our first five cases. All participants had previously received DBS in the bed nucleus of stria terminalis (BNST), with two patients responding to the surgery and one showing a partial response. Our analyses focused on gene-disruptive rare variants (GDRVs; rare, predicted-deleterious single-nucleotide variants or copy number variants overlapping protein-coding genes). Three of the five cases carried a GDRV, including a missense variant in the ion transporter domain of KCNB1, a deletion at 15q11.2, and a duplication at 15q26.1. The KCNB1 variant (hg19 chr20-47991077-C-T, NM_004975.3:c.1020G>A, p.Met340Ile) causes substitution of methionine for isoleucine in the trans-membrane region of neuronal potassium voltage-gated ion channel KV2.1. This KCNB1 substitution (Met340Ile) is located in a highly constrained region of the protein where other rare missense variants have previously been associated with neurodevelopmental disorders. The patient carrying the Met340Ile variant responded to DBS, which suggests that genetic factors could potentially be predictors of treatment response in DBS for OCD. In sum, we have established a protocol for recruiting and genomically characterizing trOCD cases. Preliminary results suggest that this will be an informative strategy for finding risk genes in OCD.
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Affiliation(s)
- Long Long Chen
- Department of Clinical Neuroscience, Centre for Psychiatry Research Karolinska Institutet, & Stockholm Health Care Services, Stockholm, Sweden
| | - Matilda Naesström
- Department of Clinical Sciences/Psychiatry, Umeå University, Umeå, Sweden
| | - Matthew Halvorsen
- Department of Clinical Neuroscience, Centre for Psychiatry Research Karolinska Institutet, & Stockholm Health Care Services, Stockholm, Sweden
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Anders Fytagoridis
- Department of Neurosurgery, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | | | - David Mataix-Cols
- Department of Clinical Neuroscience, Centre for Psychiatry Research Karolinska Institutet, & Stockholm Health Care Services, Stockholm, Sweden
| | - Christian Rück
- Department of Clinical Neuroscience, Centre for Psychiatry Research Karolinska Institutet, & Stockholm Health Care Services, Stockholm, Sweden
| | - James J. Crowley
- Department of Clinical Neuroscience, Centre for Psychiatry Research Karolinska Institutet, & Stockholm Health Care Services, Stockholm, Sweden
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Diana Pascal
- Department of Clinical Neuroscience, Centre for Psychiatry Research Karolinska Institutet, & Stockholm Health Care Services, Stockholm, Sweden
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20
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Xu J, Su W, Wang Y, Luo Y, Ye F, Xu Y, Chen L, Li H. Genetic analysis of 280 children with unexplained developmental delay or intellectual disability using whole exome sequencing. BMC Pediatr 2024; 24:766. [PMID: 39587513 PMCID: PMC11587547 DOI: 10.1186/s12887-024-05245-5] [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: 08/22/2024] [Accepted: 11/13/2024] [Indexed: 11/27/2024] Open
Abstract
INTRODUCTION Developmental delay (DD) and intellectual disability (ID) are key manifestations of neurodevelopmental disorders (NDDs), characterized by considerable clinical and genetic variability, which complicates genetic diagnosis. Whole exome sequencing (WES) has become an effective method for uncovering genetic causes in patients with unexplained DD/ID. METHODS We retrospectively analyzed WES data from 280 patients diagnosed with unexplained DD/ID. Demographic information and genetic variants identified through WES were assessed, along with an evaluation of clinical factors that might influence the detection of genetic causes. RESULTS Pathogenic variants were detected in 73 cases (36.07%), including 25 cases involving pathogenic chromosomal copy number variations. Clinical factors such as age, sex, gestational age, birth weight, anoxia, jaundice, associated symptoms, family history, muscle strength, muscle tone, epilepsy, brain MRI findings, EEG results, and the severity of DD/ID did not significantly impact the WES outcomes. However, a significant correlation was observed between delivery mode and positive WES results, with a higher diagnostic yield among patients delivered via caesarean section. CONCLUSIONS WES is a valuable approach for identifying genetic causes in patients with unexplained DD/ID, providing benefits for patient management, family genetic counseling, and long-term prognosis assessment. CLINICAL TRIAL NUMBER Not applicable.
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Affiliation(s)
- Jinbo Xu
- Department of rehabilitation, Anhui Provincial Children's Hospital, No.39, Wangjiang Road, Baohe District, Hefei, 230051, China
| | - Wei Su
- Department of rehabilitation, Anhui Provincial Children's Hospital, No.39, Wangjiang Road, Baohe District, Hefei, 230051, China
| | - Yishan Wang
- Department of rehabilitation, Anhui Provincial Children's Hospital, No.39, Wangjiang Road, Baohe District, Hefei, 230051, China
| | - Yuanyuan Luo
- Department of rehabilitation, Anhui Provincial Children's Hospital, No.39, Wangjiang Road, Baohe District, Hefei, 230051, China
| | - Fuling Ye
- Department of rehabilitation, Anhui Provincial Children's Hospital, No.39, Wangjiang Road, Baohe District, Hefei, 230051, China
| | - Yanhong Xu
- Department of rehabilitation, Anhui Provincial Children's Hospital, No.39, Wangjiang Road, Baohe District, Hefei, 230051, China
| | - Lulu Chen
- Department of rehabilitation, Anhui Provincial Children's Hospital, No.39, Wangjiang Road, Baohe District, Hefei, 230051, China
| | - Hong Li
- Department of rehabilitation, Anhui Provincial Children's Hospital, No.39, Wangjiang Road, Baohe District, Hefei, 230051, China.
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21
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Xue S, Liu Y, Wang L, Zhang L, Chang B, Ding G, Dai P. Clinical application of chromosome microarray analysis and karyotyping in prenatal diagnosis in Northwest China. Front Genet 2024; 15:1347942. [PMID: 39568677 PMCID: PMC11576268 DOI: 10.3389/fgene.2024.1347942] [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: 12/01/2023] [Accepted: 10/15/2024] [Indexed: 11/22/2024] Open
Abstract
Introduction Karyotyping and chromosome microarray analysis (CMA) are the two main prenatal diagnostic techniques currently used for genetic testing. We aimed to evaluate the value of chromosomal karyotyping and CMA for different prenatal indications. Methods A total of 2084 amniocentesis samples from pregnant women who underwent prenatal diagnosis from 16 to 22 + 6 weeks of gestation between January 2021 and December 2022 were retrospectively collected. The pregnant women were classified according to different prenatal diagnostic indications and underwent CMA and karyotype analysis. Clinical data were collected, and the results of the CMA and karyotype analysis were statistically analyzed to compare the effects of the two diagnostic techniques. Results The total detection rate of abnormal chromosomes was significantly higher using CMA than karyotype analysis. The detection rate of abnormal chromosomes using CMA was significantly higher than that using karyotyping for ultrasound abnormalities, high-risk serologic screening, adverse pregnancy history, positive noninvasive prenatal test (NIPT) screening, and ultrasound abnormalities combined with adverse pregnancy history indications. Among the fetuses with inconsistent results between the two testing methods, 144 had an abnormal CMA but a normal karyotype, with the highest percentage of pregnant women with ultrasound abnormalities at 38.89% (56/144). CMA had the highest detection rate for structural abnormalities combined with soft-index abnormalities among all ultrasound abnormalities. The highest detection rate of copy number variants in the group of structural abnormalities in a single system was in the genitourinary system (3/29, 10.34%). Conclusion CMA can improve the detection rate of chromosomal abnormalities in patients with ultrasound abnormalities, high-risk serologic screening, adverse maternal history, positive NIPT screening, and ultrasound abnormalities combined with adverse maternal history and can increase the detection rate of chromosomal abnormalities in karyotypic normality by 6.91% (144/2,084), this result is higher than similar studies. However, karyotype analysis remains advantageous over CMA regarding balanced chromosomal rearrangement and detection of low-level chimeras, and the combination of the two methods is more helpful in improving the detection rate of prenatal chromosomal abnormalities.
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Affiliation(s)
- ShuYuan Xue
- The College of Life Sciences, Northwest University, Xi'an City, Shanxi, China
- Prenatal Diagnosis Center, Urumqi Maternal and Child Healthcare Hospital, Ürümqi City, Xinjiang Uygur Autonomous Region, China
| | - YuTong Liu
- College of Public Health, Xinjiang Medical University, Ürümqi, Xinjiang Uygur Autonomous Region, China
| | - LiXia Wang
- Prenatal Diagnosis Center, Urumqi Maternal and Child Healthcare Hospital, Ürümqi City, Xinjiang Uygur Autonomous Region, China
| | - Le Zhang
- Prenatal Diagnosis Center, Urumqi Maternal and Child Healthcare Hospital, Ürümqi City, Xinjiang Uygur Autonomous Region, China
| | - Bozhen Chang
- Prenatal Diagnosis Center, Urumqi Maternal and Child Healthcare Hospital, Ürümqi City, Xinjiang Uygur Autonomous Region, China
| | - GuiFeng Ding
- Department of Obstetrics, Urumqi Maternal and Child Healthcare Hospital, Ürümqi City, Xinjiang Uygur Autonomous Region, China
| | - PengGao Dai
- The College of Life Sciences, Northwest University, Xi'an City, Shanxi, China
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22
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Li K, Wang H, Chau MHK, Dong Z, Cao Y, Zheng Y, Leung TY, Choy KW, Zhu Y. Contribution of Genomic Imbalance in Prenatal Congenital Anomalies of the Kidney and Urinary Tract: A Multi-Center Cohort Study. Prenat Diagn 2024; 44:1451-1461. [PMID: 39363241 DOI: 10.1002/pd.6674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 09/11/2024] [Accepted: 09/11/2024] [Indexed: 10/05/2024]
Abstract
OBJECTIVES To investigate the diagnostic utility of copy-number variant (CNV) detection by chromosomal microarray analysis (CMA) and genotype-phenotype associations in prenatal congenital anomalies of the kidney and urinary tract (CAKUT). METHODS This is a retrospective multi-center study of CNV analysis in 457 fetuses with ultrasound-detected CAKUT and normal karyotypes. Cohorts from published studies were included for further pooled analyses (N = 2746). A literature review of single-nucleotide variant (SNV) and small insertions and deletions (Indel) analysis by whole-exome sequencing was performed to investigate monogenic causes. RESULTS In our multi-center cohort, 5.3% (24/457) of fetuses had pathogenic CNVs (pCNV); 3.9% (14/359) and 10.2% (10/98) in isolated and non-isolated CAKUT, respectively. Fetuses with isolated hyperechogenic kidneys (HEK) had the highest incidence of having pCNVs. In the literature review, 6.6% (180/2746) of fetuses carried pCNVs; 6.1% and 7.5% in isolated and non-isolated CAKUT, respectively. SNV/Indel analysis provided at least 16.5% (63/381) additional diagnostic yield beyond CNV analysis; 12.8% and 23.8% in isolated and non-isolated CAKUT, respectively. CONCLUSION pCNVs comprise a significant proportion of genetic diagnostic findings in prenatal CAKUT, most commonly detected in fetuses with isolated HEK, MCDK, renal agenesis, and non-isolated CAKUT. Monogenic causes should be considered when karyotyping and CMA are nondiagnostic.
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Affiliation(s)
- Keying Li
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Huilin Wang
- Maternal-Fetal Medicine Institute, Bao'an Maternity and Child Health Hospital Affiliated to Jinan University School of Medicine, Key Laboratory of Birth Defects Research, Birth Defects Prevention Research and Transformation Team, Shenzhen, China
| | - Matthew Hoi Kin Chau
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China
| | - Zirui Dong
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Ye Cao
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Yu Zheng
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China
| | - Tak Yeung Leung
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China
| | - Kwong Wai Choy
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China
| | - Yuanfang Zhu
- Maternal-Fetal Medicine Institute, Bao'an Maternity and Child Health Hospital Affiliated to Jinan University School of Medicine, Key Laboratory of Birth Defects Research, Birth Defects Prevention Research and Transformation Team, Shenzhen, China
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Garrido-Torres N, Marqués Rodríguez R, Alemany-Navarro M, Sánchez-García J, García-Cerro S, Ayuso MI, González-Meneses A, Martinez-Mir A, Ruiz-Veguilla M, Crespo-Facorro B. Exploring genetic testing requests, genetic alterations and clinical associations in a cohort of children with autism spectrum disorder. Eur Child Adolesc Psychiatry 2024; 33:3829-3840. [PMID: 38587680 PMCID: PMC11588872 DOI: 10.1007/s00787-024-02413-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 03/10/2024] [Indexed: 04/09/2024]
Abstract
Several studies show great heterogeneity in the type of genetic test requested and in the clinicopathological characteristics of patients with ASD. The following study aims, firstly, to explore the factors that might influence professionals' decisions about the appropriateness of requesting genetic testing for their patients with ASD and, secondly, to determine the prevalence of genetic alterations in a representative sample of children with a diagnosis of ASD. Methods: We studied the clinical factors associated with the request for genetic testing in a sample of 440 children with ASD and the clinical factors of present genetic alterations. Even though the main guidelines recommend genetic testing all children with an ASD diagnosis, only 56% of children with an ASD diagnosis were genetically tested. The prevalence of genetic alterations was 17.5%. These alterations were more often associated with intellectual disability and dysmorphic features. There are no objective data to explicitly justify the request for genetic testing, nor are there objective data to justify requesting one genetic study versus multiple studies. Remarkably, only 28% of males were genetically tested with the recommended tests (fragile X and CMA). Children with dysmorphic features and organic comorbidities were more likely to be genetic tested than those without. Previous diagnosis of ASD (family history of ASD) and attendance at specialist services were also associated with Genetically tested Autism Spectrum Disorder GTASD. Our findings emphasize the importance of establishing algorithms to facilitate targeted genetic consultation for individuals with ASD who are likely to benefit, considering clinical phenotypes, efficiency, ethics, and benefits.
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Affiliation(s)
- Nathalia Garrido-Torres
- Instituto de Biomedicina de Sevilla, Seville, Spain
- University of Seville, Seville, Spain
- CIBERSAM, ISCIII (Spanish Network for Research in Mental Health), Seville, Spain
- Hospital Universitario Virgen del Rocío, Seville, Spain
| | | | - María Alemany-Navarro
- Instituto de Biomedicina de Sevilla, Seville, Spain
- CIBERSAM, ISCIII (Spanish Network for Research in Mental Health), Seville, Spain
| | - Javier Sánchez-García
- Instituto de Biomedicina de Sevilla, Seville, Spain
- University of Seville, Seville, Spain
- Hospital Universitario Virgen del Rocío, Seville, Spain
- Department of Maternofetal Medicine, Genetics and Reproduction, Seville, Spain
- Spanish National Research Council (CSIC), Seville, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | - Susana García-Cerro
- Instituto de Biomedicina de Sevilla, Seville, Spain
- CIBERSAM, ISCIII (Spanish Network for Research in Mental Health), Seville, Spain
| | - María Irene Ayuso
- Instituto de Biomedicina de Sevilla, Seville, Spain
- CIBERSAM, ISCIII (Spanish Network for Research in Mental Health), Seville, Spain
| | | | - Amalia Martinez-Mir
- Instituto de Biomedicina de Sevilla, Seville, Spain
- University of Seville, Seville, Spain
- Hospital Universitario Virgen del Rocío, Seville, Spain
- Spanish National Research Council (CSIC), Seville, Spain
| | - Miguel Ruiz-Veguilla
- Instituto de Biomedicina de Sevilla, Seville, Spain
- University of Seville, Seville, Spain
- CIBERSAM, ISCIII (Spanish Network for Research in Mental Health), Seville, Spain
- Hospital Universitario Virgen del Rocío, Seville, Spain
| | - Benedicto Crespo-Facorro
- Instituto de Biomedicina de Sevilla, Seville, Spain.
- University of Seville, Seville, Spain.
- CIBERSAM, ISCIII (Spanish Network for Research in Mental Health), Seville, Spain.
- Hospital Universitario Virgen del Rocío, Seville, Spain.
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24
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Wang Y, Li Y, Zeng L, Li W, Dong X, Guo J, Meng X, Lu J, Xu J. A novel approach to detecting microduplication in split hand/foot malformation type 3 at the single-cell level: SHFM as a case study. Orphanet J Rare Dis 2024; 19:406. [PMID: 39482735 PMCID: PMC11526726 DOI: 10.1186/s13023-024-03386-5] [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: 05/24/2024] [Accepted: 09/25/2024] [Indexed: 11/03/2024] Open
Abstract
BACKGROUND Split hand/foot malformation (SHFM) is a congenital limb deficiency characterized by missing or shortened central digits. Several gene loci have been associated with SHFM. Identifying microduplications at the single-cell level is challenging in clinical practice, and traditional detection methods may lead to misdiagnoses in embryos and pregnant women. RESULTS In this research, we utilized a low cell count and whole-genome amplification products to employ single nucleotide polymorphism arrays, next-generation sequencing, and third-generation sequencing methods to detect copy number variants of microduplications in a SHFM3 case with limited DNA. Additionally, Karyomapping and combined linkage analysis were conducted to validate the results. CONCLUSIONS This study establishes a new strategy for identifying microduplications or microdeletions at the single-cell level in clinical preimplantation genetic testing, enhancing the efficiency and accuracy of diagnosing microduplication or microdeletion diseases during IVF-PGT and prenatal diagnosis.
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Affiliation(s)
- Yaqian Wang
- The First Affiliated Hospital, Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou University and Institute of Reproductive Health, Henan Academy of Innovations in Medical Science, Zhengzhou, China
- NHC Key Laboratory of Birth Defects Prevention, Zhengzhou, China
| | - Yang Li
- The First Affiliated Hospital, Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou University and Institute of Reproductive Health, Henan Academy of Innovations in Medical Science, Zhengzhou, China
- NHC Key Laboratory of Birth Defects Prevention, Zhengzhou, China
| | - Lidong Zeng
- Shenzhen GeneMind Biosciences Co., Ltd, Shenzhen, China
| | - Wenbo Li
- The First Affiliated Hospital, Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou University and Institute of Reproductive Health, Henan Academy of Innovations in Medical Science, Zhengzhou, China
- NHC Key Laboratory of Birth Defects Prevention, Zhengzhou, China
| | - Xin Dong
- The First Affiliated Hospital, Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou University and Institute of Reproductive Health, Henan Academy of Innovations in Medical Science, Zhengzhou, China
- NHC Key Laboratory of Birth Defects Prevention, Zhengzhou, China
| | - Jia Guo
- The First Affiliated Hospital, Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou University and Institute of Reproductive Health, Henan Academy of Innovations in Medical Science, Zhengzhou, China
- NHC Key Laboratory of Birth Defects Prevention, Zhengzhou, China
| | - Xiangrui Meng
- The First Affiliated Hospital, Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou University and Institute of Reproductive Health, Henan Academy of Innovations in Medical Science, Zhengzhou, China
- NHC Key Laboratory of Birth Defects Prevention, Zhengzhou, China
| | - Jiacheng Lu
- The First Affiliated Hospital, Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou University and Institute of Reproductive Health, Henan Academy of Innovations in Medical Science, Zhengzhou, China
- NHC Key Laboratory of Birth Defects Prevention, Zhengzhou, China
| | - Jiawei Xu
- The First Affiliated Hospital, Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou University and Institute of Reproductive Health, Henan Academy of Innovations in Medical Science, Zhengzhou, China.
- NHC Key Laboratory of Birth Defects Prevention, Zhengzhou, China.
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25
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Yang L, Yang J, Bu G, Han R, Rezhake J, La X. Efficiency of Non-Invasive Prenatal Testing in Detecting Fetal Copy Number Variation: A Retrospective Cohort Study. Int J Womens Health 2024; 16:1661-1669. [PMID: 39381715 PMCID: PMC11460342 DOI: 10.2147/ijwh.s479747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 09/25/2024] [Indexed: 10/10/2024] Open
Abstract
Purpose Screening of pathological copy number variations (CNVs) is important for early-diagnosis of hereditary disease. This study was designed to investigate the efficiency of non-invasive prenatal testing (NIPT) in detecting fetal CNVs. Methods This retrospective analysis included fetuses with CNVs between January 2018 and December 2020. Karyotype analysis and CNV sequencing (CNV-seq) were performed. We then analyzed the positive predictive values of the subchromosomal microdeletions and microduplications. Results Fifty-eight subjects with aberrant CNVs were screened after NIPT, among which 44 finally underwent amniocentesis. CNV-seq confirmed the presence of CNVs in 24 cases. This indicated that false positivity rate of NIPT was 45.5%. Among 24 cases with CNVs after CNV-seq, only 4 showed consistent findings with karyotype analysis, which showed that karyotyping analysis yielded a missed diagnosis rate of 83.3% for the genome CNV. Positive predictive value (PPV) was 50.0% for CNVs with a length of <5 Mb after NIPT screening. PPV for CNVs with a length of 5 Mb-10 Mb was 33.3%, while that for CNVs with a length of ≥10Mb was 60%. For CNVs duplication after NIPT, the PPV was 65.2%, while that for deletion was 36.4%. Conclusion For CNVs detected after NIPT, it should be combined with ultrasonographic findings, karyotype analysis, CNV-seq or CMA to determine the pregnancy outcome. Expanding NIPT may increase the risk of unnecessary invasive surgery and unintended selective termination of pregnancy.
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Affiliation(s)
- Li Yang
- Center of Reproductive Medicine, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, People’s Republic of China
| | - Jing Yang
- Department of Gynaecology, The Fifth Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, People’s Republic of China
| | - Guosen Bu
- Department of Neurology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, People’s Republic of China
| | - Rui Han
- Center of Reproductive Medicine, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, People’s Republic of China
| | - Jiamila Rezhake
- Center of Reproductive Medicine, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, People’s Republic of China
| | - Xiaolin La
- Center of Reproductive Medicine, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, People’s Republic of China
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Marques P, Moloney PB, Ji C, Zulfiqar Ali Q, Ramesh A, Goldstein DB, Barboza K, Chandran I, Rong M, Selvarajah A, Qaiser F, Lira VST, Valiante TA, Bazil CW, Choi H, Devinsky O, Depondt C, O'Brien T, Perucca P, Sen A, Dugan P, Sands TT, Delanty N, Andrade DM. Do germline genetic variants influence surgical outcomes in drug-resistant epilepsy? Epilepsy Res 2024; 206:107425. [PMID: 39168079 DOI: 10.1016/j.eplepsyres.2024.107425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 07/24/2024] [Accepted: 08/05/2024] [Indexed: 08/23/2024]
Abstract
OBJECTIVE We retrospectively explored patients with drug-resistant epilepsy (DRE) who previously underwent presurgical evaluation to identify correlations between surgical outcomes and pathogenic variants in epilepsy genes. METHODS Through an international collaboration, we evaluated adult DRE patients who were screened for surgical candidacy. Patients with pathogenic (P) or likely pathogenic (LP) germline variants in genes relevant to their epilepsy were included, regardless of whether the genetic diagnosis was made before or after the presurgical evaluation. Patients were divided into two groups: resective surgery (RS) and non-resective surgery candidates (NRSC), with the latter group further divided into: palliative surgery (vagus nerve stimulation, deep brain stimulation, responsive neurostimulation or corpus callosotomy) and no surgery. We compared surgical candidacy evaluations and postsurgical outcomes in patients with different genetic abnormalities. RESULTS We identified 142 patients with P/LP variants. After presurgical evaluation, 36 patients underwent RS, while 106 patients were NRSC. Patients with variants in ion channel and synaptic transmission genes were more common in the NRSC group (48 %), compared with the RS group (14 %) (p<0.001). Most patients in the RS group had tuberous sclerosis complex. Almost half (17/36, 47 %) in the RS group had Engel class I or II outcomes. Patients with channelopathies were less likely to undergo a surgical procedure than patients with mTORopathies, but when deemed suitable for resection had better surgical outcomes (71 % versus 41 % with Engel I/II). Within the NRSC group, 40 underwent palliative surgery, with 26/40 (65 %) having ≥50 % seizure reduction after mean follow-up of 11 years. Favourable palliative surgery outcomes were observed across a diverse range of genetic epilepsies. SIGNIFICANCE Genomic findings, including a channelopathy diagnosis, should not preclude presurgical evaluation or epilepsy surgery, and appropriately selected cases may have good surgical outcomes. Prospective registries of patients with monogenic epilepsies who undergo epilepsy surgery can provide additional insights on outcomes.
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Affiliation(s)
- Paula Marques
- Adult Genetic Epilepsy (AGE) Program, Krembil Brain Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada; Division of Neurology, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | | | - Caihong Ji
- Adult Genetic Epilepsy (AGE) Program, Krembil Brain Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Quratulain Zulfiqar Ali
- Adult Genetic Epilepsy (AGE) Program, Krembil Brain Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Archana Ramesh
- Oxford Epilepsy Research Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Karen Barboza
- Adult Genetic Epilepsy (AGE) Program, Krembil Brain Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada; Division of Neurology, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Ilakkiah Chandran
- Adult Genetic Epilepsy (AGE) Program, Krembil Brain Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada; Division of Neurology, University Health Network, University of Toronto, Toronto, Ontario, Canada; Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Marlene Rong
- Adult Genetic Epilepsy (AGE) Program, Krembil Brain Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada; Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Arunan Selvarajah
- Adult Genetic Epilepsy (AGE) Program, Krembil Brain Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada; Division of Neurology, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Farah Qaiser
- Adult Genetic Epilepsy (AGE) Program, Krembil Brain Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Victor S T Lira
- Adult Genetic Epilepsy (AGE) Program, Krembil Brain Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Taufik A Valiante
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada
| | - Carl W Bazil
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Hyunmi Choi
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Orrin Devinsky
- New York University Langone Health Comprehensive Epilepsy Center, New York, NY, USA
| | - Chantal Depondt
- Department of Neurology, CUB Erasme Hospital, Hôpital Universitaire de Bruxelles, Université Libre de Bruxelles, Brussels, Belgium
| | - Terence O'Brien
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Piero Perucca
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia; Department of Neurology, Alfred Health, Melbourne, Victoria, Australia; Department of Neurology, The Royal Melbourne Hospital, Melbourne, Victoria, Australia; Epilepsy Research Centre, Department of Medicine (Austin Health), The University of Melbourne, Melbourne, Victoria, Australia; Bladin-Berkovic Comprehensive Epilepsy Program, Department of Neurology, Austin Health, Melbourne, Victoria, Australia
| | - Arjune Sen
- Oxford Epilepsy Research Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Patricia Dugan
- New York University Langone Health Comprehensive Epilepsy Center, New York, NY, USA
| | - Tristan T Sands
- Department of Neurology, Columbia University Medical Center, New York, NY, USA.
| | - Norman Delanty
- Department of Neurology, Beaumont Hospital, Dublin, Ireland.
| | - Danielle M Andrade
- Adult Genetic Epilepsy (AGE) Program, Krembil Brain Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada; Division of Neurology, University Health Network, University of Toronto, Toronto, Ontario, Canada; Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada.
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27
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Peterlin A, Bertok S, Writzl K, Lovrečić L, Maver A, Peterlin B, Debeljak M, Nosan G. The Genetic Architecture of Congenital Heart Disease in Neonatal Intensive Care Unit Patients-The Experience of University Medical Centre, Ljubljana. Life (Basel) 2024; 14:1118. [PMID: 39337901 PMCID: PMC11433392 DOI: 10.3390/life14091118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2024] [Revised: 08/29/2024] [Accepted: 09/03/2024] [Indexed: 09/30/2024] Open
Abstract
Congenital heart disease (CHD) is the most commonly detected congenital anomaly and affects up to 1% of all live-born neonates. Current guidelines support the use of chromosomal microarray analysis (CMA) and next-generation sequencing (NGS) as diagnostic approaches to identify genetic causes. The aim of our study was to evaluate the diagnostic yield of CMA and NGS in a cohort of neonates with both isolated and syndromic CHD. The present study included 188 infants under 28 days of age with abnormal echocardiography findings hospitalized at the Department of Neonatology, UMC Ljubljana, between January 2014 and December 2023. Phenotypic data were obtained for each infant via retrospective medical chart review. We established the genetic diagnosis of 22 distinct syndromes in 17% (32/188) of neonates. The most frequent genetic diagnoses in diagnosed cases were 22q11.2 microdeletion and CHARGE syndromes, followed by Noonan syndrome and Williams syndrome. In addition, we detected variants of uncertain significance in 4.8% (9/188) of neonates. Timely genetic diagnosis is important for the detection of syndrome-related comorbidities, prognosis, reproductive genetic risks and, when appropriate, genetic testing of other family members.
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Affiliation(s)
- Ana Peterlin
- Institute of Histology and Embryology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Sara Bertok
- Department of Genetics, Department of Endocrinology, Diabetes, and Metabolic Diseases, University Children's Hospital, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Karin Writzl
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Luca Lovrečić
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Aleš Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Maruša Debeljak
- Clinical Institute for Special Laboratory Diagnostics, University Children's Hospital, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
- Department of Pediatrics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Gregor Nosan
- Department of Pediatrics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
- Department of Neonatology, Division of Paediatrics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
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28
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Sukenik-Halevy R, Mevorach N, Basel-Salmon L, Matar RT, Kahana S, Klein K, Agmon-Fishman I, Levy M, Maya I. Chromosomal microarray testing yield in 829 cases of microcephaly: a clinical characteristics-based analysis for prenatal and postnatal cases. Arch Gynecol Obstet 2024; 310:1547-1554. [PMID: 38494511 PMCID: PMC11366728 DOI: 10.1007/s00404-024-07388-3] [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: 11/17/2023] [Accepted: 01/14/2024] [Indexed: 03/19/2024]
Abstract
INTRODUCTION Microcephaly, characterized by abnormal head growth, can often serve as an initial indicator of congenital, genetic, or acquired disorders. In this study, we sought to evaluate the effectiveness of chromosomal microarray (CMA) testing in detecting abnormalities in both prenatal and postnatal cases of microcephaly. MATERIALS AND METHODS CMA Testing: We conducted CMA testing on 87 prenatally-detected microcephaly cases and 742 postnatal cases at a single laboratory. We evaluated the CMA yield in relation to specific clinical characteristics. RESULTS In prenatal cases, pathogenic and likely pathogenic (LP) results were identified in 4.6% of cases, a significantly higher rate compared to low-risk pregnancies. The male-to-female ratio in this cohort was 3, and the CMA yield was not influenced by gender or other clinical parameters. For postnatal cases, the CMA yield was 15.0%, with a significantly higher detection rate associated with dysmorphism, hypotonia, epilepsy, congenital heart malformations (CHM), learning disabilities (LD), and a history of Fetal growth restriction (FGR). No specific recurrent copy number variations (CNVs) were observed, and the rate of variants of unknown significance was 3.9%. CONCLUSIONS The yield of CMA testing in prenatal microcephaly is lower than in postnatal cases (4.6% vs. 15%). The presence of microcephaly, combined with dysmorphism, hypotonia, epilepsy, CHD, LD, and FGR, significantly increases the likelihood of an abnormal CMA result.
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Affiliation(s)
- Rivka Sukenik-Halevy
- Genetic Institute, Meir Medical Center, Kfar Saba, Israel.
- School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel.
| | - Nir Mevorach
- Genetic Institute, Meir Medical Center, Kfar Saba, Israel
| | - Lina Basel-Salmon
- School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
- Recanati Genetic Institute, Rabin Medical Center, Petah Tikva, Israel
- Felsenstein Medical Research Center, Rabin Medical Center, Petah Tikva, Israel
- Pediatric Genetics Unit, Schneider Children's Medical Center, Petah Tikva, Israel
| | | | - Sarit Kahana
- Recanati Genetic Institute, Rabin Medical Center, Petah Tikva, Israel
| | - Kochav Klein
- Recanati Genetic Institute, Rabin Medical Center, Petah Tikva, Israel
| | | | - Michal Levy
- School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
- Recanati Genetic Institute, Rabin Medical Center, Petah Tikva, Israel
| | - Idit Maya
- School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
- Recanati Genetic Institute, Rabin Medical Center, Petah Tikva, Israel
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29
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Pynaker C, McCoy J, Halliday J, Lewis S, Amor DJ, Walker SP, Hui L. Perinatal outcomes after a prenatal diagnosis of a fetal copy number variant: a retrospective population-based cohort study. BMC Pediatr 2024; 24:536. [PMID: 39174956 PMCID: PMC11340052 DOI: 10.1186/s12887-024-05012-6] [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: 02/07/2024] [Accepted: 08/13/2024] [Indexed: 08/24/2024] Open
Abstract
BACKGROUND There are no established guidelines for the follow up of infants born after a prenatal diagnosis of a genomic copy number variant (CNV), despite their increased risk of developmental issues. The aims of this study were (i) to determine the perinatal outcomes of fetuses diagnosed with and without a CNV, and (ii) to establish a population-based paediatric cohort for long term developmental follow up. METHODS An Australian state-wide research database was screened for pregnant individuals who had a prenatal chromosomal microarray (CMA) between 2013-2019 inclusive. Following linkage to laboratory records and clinical referrer details, hospital records were manually reviewed for study eligibility. Eligible participants were mother-child pairs where the pregnancy resulted in a livebirth, the mother was able to provide informed consent in English (did not require a translator) and the mother was the primary caregiver for the child at hospital discharge after birth. Research invitations were sent by registered post at an average of six years after the prenatal diagnostic test. Statistical analysis was performed in Stata17. RESULTS Of 1832 prenatal records examined, 1364 (74.5%) mother-child pairs were eligible for recruitment into the follow up cohort. Of the 468 ineligible, 282 (60.3%) had 'no live pregnancy outcome' (209 terminations of pregnancy (TOP) and 73 miscarriages, stillbirths, and infant deaths), 157 (33.5%) required a translator, and 29 (6.2%) were excluded for other reasons. TOP rates varied by the type of fetal CNV detected: 49.3% (109/221) for pathogenic CNVs, 18.2% (58/319) for variants of uncertain significance and 3.3% (42/1292) where no clinically significant CNV was reported on CMA. Almost 77% of invitation letters were successfully delivered (1047/1364), and the subsequent participation rate in the follow up cohort was 19.2% (201/1047). CONCLUSIONS This study provides Australia's first population-based data on perinatal outcomes following prenatal diagnostic testing with CMA. The relatively high rates of pregnancy loss for those with a prenatal diagnosis of a CNV presented a challenge for establishing a paediatric cohort to examine long term outcomes. Recruiting a mother-child cohort via prenatal ascertainment is a complex and resource-intensive process, but an important step in understanding the impact of a CNV diagnosis in pregnancy and beyond. TRIAL REGISTRATION ACTRN12620000446965p; Registered on April 6, 2020.
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Affiliation(s)
- Cecilia Pynaker
- Reproductive Epidemiology Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Jacqui McCoy
- Reproductive Epidemiology Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Jane Halliday
- Reproductive Epidemiology Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Sharon Lewis
- Reproductive Epidemiology Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - David J Amor
- Reproductive Epidemiology Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Neurodisability and Rehabilitation Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Susan P Walker
- Department of Obstetrics, Gynaecology and Newborn Health, University of Melbourne, Parkville, VIC, Australia
- Mercy Hospital for Women, Heidelberg, VIC, Australia
| | - Lisa Hui
- Reproductive Epidemiology Group, Murdoch Children's Research Institute, Parkville, VIC, Australia.
- Department of Obstetrics, Gynaecology and Newborn Health, University of Melbourne, Parkville, VIC, Australia.
- Mercy Hospital for Women, Heidelberg, VIC, Australia.
- Northern Health, Melbourne, VIC, Australia.
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30
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Pereira SSS, Pinto IP, Santos VCDP, Silva RC, Costa EOA, da Cruz AS, da Cruz AD, da Silva CC, Minasi LB. Analysis of parental origin of de novo pathogenic CNVs in patients with intellectual disability. Genet Mol Biol 2024; 47:e20230313. [PMID: 39136576 PMCID: PMC11320663 DOI: 10.1590/1678-4685-gmb-2023-0313] [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: 11/01/2023] [Accepted: 06/25/2024] [Indexed: 08/16/2024] Open
Abstract
Chromosomal Microarray Analysis (CMA) has increased the comprehension of the mechanisms of copy number variation (CNV) formation, classification of these rearrangements, type of recurrence, and its origin, and has also been a powerful approach to identifying CNVs in individuals with intellectual disability. The aim of this study was to establish the parental origin of de novo pathogenic CNV in a cohort of patients with intellectual disability from the public health system of Goiás-Brazil. CMA was done in 76 trios and we identified 15 de novo pathogenic CNVs in 12 patients with intellectual disability. In a total of 15 de novo pathogenic CNV, 60% were derived from the maternal germline and 40% from the paternal germline. CNV flanked by low copy repeats (LCR) were identified in 46.7% and most of them were of maternal origin. No significant association was observed between paternal age and the mutation rate of de novo CNVs. The presence of high-identity LCRs increases the occurrence of CNV formation mediated by non-allelic homologous recombination and the majority of paternal CNVs are non-recurrent. The mechanism of formation of these CNV may have been by microhomology-mediated break-induced replication or non-homologous end joining.
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Affiliation(s)
- Samara Socorro Silva Pereira
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
- Universidade Federal de Goiás, Programa de Pós-Graduação em Genética e Biologia Molecular, Goiânia, GO, Brazil
| | - Irene Plaza Pinto
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
| | - Victor Cortázio do Prado Santos
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
- Universidade Federal de Goiás, Programa de Pós-Graduação em Genética e Biologia Molecular, Goiânia, GO, Brazil
| | - Rafael Carneiro Silva
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
| | - Emília Oliveira Alves Costa
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
| | - Alex Silva da Cruz
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
| | - Aparecido Divino da Cruz
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
- Secretaria Estadual de Saúde de Goiás, Centro Estadual de Reabilitação e Readaptação Dr. Henrique Santillo, Goiânia, GO, Brazil
- Universidade Federal de Goiás, Programa de Pós-Graduação em Genética e Biologia Molecular, Goiânia, GO, Brazil
| | - Cláudio Carlos da Silva
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
- Secretaria Estadual de Saúde de Goiás, Centro Estadual de Reabilitação e Readaptação Dr. Henrique Santillo, Goiânia, GO, Brazil
| | - Lysa Bernardes Minasi
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
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Rodriguez KM, Vaught J, Salz L, Foley J, Boulil Z, Van Dongen-Trimmer HM, Whalen D, Oluchukwu O, Liu KC, Burton J, Syngal P, Vargas-Shiraishi O, Kingsmore SF, Kobayashi ES, Coufal NG. Rapid Whole-Genome Sequencing and Clinical Management in the PICU: A Multicenter Cohort, 2016-2023. Pediatr Crit Care Med 2024; 25:699-709. [PMID: 38668387 PMCID: PMC11300160 DOI: 10.1097/pcc.0000000000003522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 08/06/2024]
Abstract
OBJECTIVES Analysis of the clinical utility of rapid whole-genome sequencing (rWGS) outside of the neonatal period is lacking. We describe the use of rWGS in PICU and cardiovascular ICU (CICU) patients across four institutions. DESIGN Ambidirectional multisite cohort study. SETTING Four tertiary children's hospitals. PATIENTS Children 0-18 years old in the PICU or CICU who underwent rWGS analysis, from May 2016 to June 2023. INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS A total of 133 patients underwent clinical, phenotype-driven rWGS analysis, 36 prospectively. A molecular diagnosis was identified in 79 patients (59%). Median (interquartile range [IQR]) age was 6 months (IQR 1.2 mo-4.6 yr). Median time for return of preliminary results was 3 days (IQR 2-4). In 79 patients with a molecular diagnosis, there was a change in ICU management in 19 patients (24%); and some change in clinical management in 63 patients (80%). Nondiagnosis changed management in 5 of 54 patients (9%). The clinical specialty ordering rWGS did not affect diagnostic rate. Factors associated with greater odds ratio (OR [95% CI]; OR [95% CI]) of diagnosis included dysmorphic features (OR 10.9 [95% CI, 1.8-105]) and congenital heart disease (OR 4.2 [95% CI, 1.3-16.8]). Variables associated with greater odds of changes in management included obtaining a genetic diagnosis (OR 16.6 [95% CI, 5.5-62]) and a shorter time to genetic result (OR 0.8 [95% CI, 0.76-0.9]). Surveys of pediatric intensivists indicated that rWGS-enhanced clinical prognostication ( p < 0.0001) and contributed to a decision to consult palliative care ( p < 0.02). CONCLUSIONS In this 2016-2023 multiple-PICU/CICU cohort, we have shown that timely genetic diagnosis is feasible across institutions. Application of rWGS had a 59% (95% CI, 51-67%) rate of diagnostic yield and was associated with changes in critical care management and long-term patient management.
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Affiliation(s)
- Katherine M. Rodriguez
- Rady Children’s Hospital, San Diego, CA
- Department of Pediatrics, University of California, San Diego
- Rady Children’s Institute for Genomic Medicine, San Diego, CA
| | - Jordan Vaught
- Rady Children’s Hospital, San Diego, CA
- Department of Pediatrics, University of California, San Diego
| | - Lisa Salz
- Rady Children’s Institute for Genomic Medicine, San Diego, CA
| | | | | | | | | | - Okonkwo Oluchukwu
- OSF Children’s Hospital of Illinois, Peoria, IL
- University of Illinois College of Medicine at Peoria, Peoria, IL
| | - Kuang Chuen Liu
- University of Illinois College of Medicine at Peoria, Peoria, IL
| | - Jennifer Burton
- OSF Children’s Hospital of Illinois, Peoria, IL
- University of Illinois College of Medicine at Peoria, Peoria, IL
| | - Prachi Syngal
- OSF Children’s Hospital of Illinois, Peoria, IL
- University of Illinois College of Medicine at Peoria, Peoria, IL
| | | | | | - Erica Sanford Kobayashi
- Rady Children’s Institute for Genomic Medicine, San Diego, CA
- Cedars-Sinai Medical Center, Department of Pediatrics, Los Angeles, CA
- Children’s Hospital of Orange County, Orange, CA
| | - Nicole G. Coufal
- Rady Children’s Hospital, San Diego, CA
- Department of Pediatrics, University of California, San Diego
- Rady Children’s Institute for Genomic Medicine, San Diego, CA
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Jones D, Hartung J, Lasalle E, Borquez A, Murillo V, Guidugli L, James KN, Kingsmore SF, Coufal NG. Novel variants in TECRL leading to catecholaminergic polymorphic ventricular tachycardia. Life Sci Alliance 2024; 7:e202402572. [PMID: 38777371 PMCID: PMC11111969 DOI: 10.26508/lsa.202402572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024] Open
Abstract
Pathogenic and likely pathogenic variants in the TECRL gene are known to be associated with recessive catecholaminergic polymorphic ventricular tachycardia 3, which can include prolonged QT intervals (MIM#614021). We report a case of cardiac arrest in a previously healthy adolescent male in the community. The patient was found to have a novel maternally inherited likely pathogenic variant in TECRL (c.915T>G [p.Tyr305Ter]) and an additional 19-kb duplication encompassing multiple exons of TECRL (chr4:65165944-65185287, dup [4q13.1]) not identified in the mother. Genetic results were revealed via rapid whole-genome sequencing, which allowed appropriate treatment and prognostication.
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Affiliation(s)
- Douglas Jones
- Rady Children's Hospital, San Diego, CA, USA
- Division of Pediatric Critical Care, Department of Pediatrics, University of California, San Diego, CA, USA
| | - Jacob Hartung
- Rady Children's Hospital, San Diego, CA, USA
- Division of Pediatric Critical Care, Department of Pediatrics, University of California, San Diego, CA, USA
| | - Elizabeth Lasalle
- Rady Children's Hospital, San Diego, CA, USA
- Division of Cardiology, Department of Pediatrics, University of California, San Diego, CA, USA
| | - Alejandro Borquez
- Rady Children's Hospital, San Diego, CA, USA
- Division of Cardiology, Department of Pediatrics, University of California, San Diego, CA, USA
| | | | - Lucia Guidugli
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Kiely N James
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | | | - Nicole G Coufal
- Rady Children's Hospital, San Diego, CA, USA
- Division of Pediatric Critical Care, Department of Pediatrics, University of California, San Diego, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
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Juan Z, Cuixia G, Yuanjie C, Yan L, Ling Y, Tiejuan Z, Li W, Jijing H, Guohui Z, Yousheng Y, Qingqing W, Lijuan S. Optimal prenatal genetic diagnostic approach for posterior fossa malformation: karyotyping, copy number variant testing, or whole-exome sequencing? Eur J Med Res 2024; 29:397. [PMID: 39085968 PMCID: PMC11290165 DOI: 10.1186/s40001-024-01993-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 07/21/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND Posterior fossa malformation (PFM) is a relatively uncommon prenatal brain malformation. Genetic diagnostic approaches, including chromosome karyotyping, copy number variant (CNV) testing, and whole-exome sequencing (WES), have been applied in several cases of fetal structural malformations. However, the clinical value of appropriate genetic diagnostic approaches for different types of PFMs has not been confirmed. Therefore, in this study, we aimed to analyze the value of different combined genetic diagnostic approaches for various types of fetal PFMs. METHODS This retrospective study was conducted at Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital. Fifty-one pregnant women diagnosed with fetal PFMs who underwent genetic testing in our hospital from January 1, 2017 to December 31, 2022 were enrolled; women with an isolated enlarged cisterna magna were excluded. All participants were categorized into two groups according to the presence of other abnormalities: isolated and non-isolated PFMs groups. Different combined approaches, including karyotype analysis, CNV testing, and trio-based WES, were used for genetic analysis. The detection rates of karyotype analysis, CNV testing, and WES were measured in the isolated and non-isolated groups. RESULTS In isolated PFMs, pathogenic/likely pathogenic (P/LP) CNVs were detected in four cases (36.36%, 4/11), whereas G-banding karyotyping and WES showed negative results. In non-isolated PFMs, a sequential genetic approach showed a detection rate of 47.5% (19/40); karyotyping revealed aneuploidies in five cases (16.67%, 5/30), CNV testing showed P/LP CNVs in five cases (16.13%, 5/31), and WES identified P/LP variants (in genes CEP20, TMEM67, OFD1, PTPN11, ARID1A, and SMARCA4) in nine cases (40.91%, 9/22). WES showed a detection rate of 83.33% (5/6) in fetuses with Joubert syndrome. Only six patients (five with Blake's pouch cyst and one with unilateral cerebellar hemisphere dysplasia) survived. CONCLUSIONS We recommend CNV testing for fetuses with isolated PFMs. A sequential genetic approach (karyotyping, CNV testing, and WES) may be beneficial in fetuses with non-isolated PFMs. Particularly, we recommend WES as the first-line genetic diagnostic tool for Joubert syndrome.
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Affiliation(s)
- Zhang Juan
- Department of Ultrasound, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, No. 251 Yaojiayuan Road, Chaoyang District, Beijing, 100026, China
| | - Guo Cuixia
- Department of Ultrasound, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, No. 251 Yaojiayuan Road, Chaoyang District, Beijing, 100026, China
| | - Cui Yuanjie
- Department of Ultrasound, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, No. 251 Yaojiayuan Road, Chaoyang District, Beijing, 100026, China
| | - Liu Yan
- Prenatal Diagnostic Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, No. 251 Yaojiayuan Road, Chaoyang District, Beijing, 100026, China
| | - Yao Ling
- Department of Ultrasound, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, No. 251 Yaojiayuan Road, Chaoyang District, Beijing, 100026, China
| | - Zhang Tiejuan
- Department of Ultrasound, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, No. 251 Yaojiayuan Road, Chaoyang District, Beijing, 100026, China
| | - Wang Li
- Department of Ultrasound, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, No. 251 Yaojiayuan Road, Chaoyang District, Beijing, 100026, China
| | - Han Jijing
- Department of Ultrasound, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, No. 251 Yaojiayuan Road, Chaoyang District, Beijing, 100026, China
| | - Zhang Guohui
- Department of Ultrasound, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, No. 251 Yaojiayuan Road, Chaoyang District, Beijing, 100026, China
| | - Yan Yousheng
- Prenatal Diagnostic Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, No. 251 Yaojiayuan Road, Chaoyang District, Beijing, 100026, China
| | - Wu Qingqing
- Department of Ultrasound, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, No. 251 Yaojiayuan Road, Chaoyang District, Beijing, 100026, China.
| | - Sun Lijuan
- Department of Ultrasound, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, No. 251 Yaojiayuan Road, Chaoyang District, Beijing, 100026, China.
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Xue H, Yu A, Chen L, Guo Q, Zhang L, Lin N, Chen X, Xu L, Huang H. Prenatal genetic diagnosis of fetuses with dextrocardia using whole exome sequencing in a tertiary center. Sci Rep 2024; 14:16266. [PMID: 39009665 PMCID: PMC11251054 DOI: 10.1038/s41598-024-67164-w] [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: 01/31/2024] [Accepted: 07/09/2024] [Indexed: 07/17/2024] Open
Abstract
To evaluate the genetic etiology of fetal dextrocardia, associated ultrasound anomalies, and perinatal outcomes, we investigated the utility of whole exome sequencing (WES) for prenatal diagnosis of dextrocardia. Fetuses with dextrocardia were prospectively collected between January 2016 and December 2022. Trio-WES was performed on fetuses with dextrocardia, following normal karyotyping and/or chromosomal microarray analysis (CMA) results. A total of 29 fetuses with dextrocardia were collected, including 27 (93.1%) diagnosed with situs inversus totalis and 2 (6.9%) with situs inversus partialis. Cardiac malformations were present in nine cases, extra-cardiac anomalies were found in seven cases, and both cardiac and extra-cardiac malformations were identified in one case. The fetal karyotypes and CMA results of 29 cases were normal. Of the 29 cases with dextrocardia, 15 underwent WES, and the other 14 cases refused. Of the 15 cases that underwent WES, clinically relevant variants were identified in 5/15 (33.3%) cases, including the diagnostic variants DNAH5, DNAH11, LRRC56, PEX10, and ZIC3, which were verified by Sanger sequencing. Of the 10 cases with non-diagnostic results via WES, eight (80%) chose to continue the pregnancies. Of the 29 fetuses with dextrocardia, 10 were terminated during pregnancy, and 19 were live born. Fetal dextrocardia is often accompanied by cardiac and extra-cardiac anomalies, and fetal dextrocardia accompanied by situs inversus is associated with a high risk of primary ciliary dyskinesia. Trio-WES is recommended following normal karyotyping and CMA results because it can improve the diagnostic utility of genetic variants of fetal dextrocardia, accurately predict fetal prognosis, and guide perinatal management and the reproductive decisions of affected families.
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Affiliation(s)
- Huili Xue
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China.
| | - Aili Yu
- Reproductive Medicine Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Lingji Chen
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Qun Guo
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Lin Zhang
- Fujian Medical University, No. 88 Jiaotong Road, Cangshan District, Fuzhou City, 350001, Fujian Province, China
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Xuemei Chen
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China.
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China.
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Luiza Benevides M, de Moraes HT, Granados DMM, Bonadia LC, Sauma L, Augusta Montenegro M, Guerreiro MM, Lopes-Cendes Í, Carolina Coan A. Predictors of genetic diagnosis in individuals with developmental and epileptic encephalopathies. Epilepsy Behav 2024; 155:109762. [PMID: 38636144 DOI: 10.1016/j.yebeh.2024.109762] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/29/2023] [Accepted: 03/23/2024] [Indexed: 04/20/2024]
Abstract
OBJECTIVE To evaluate the clinical predictors of positive genetic investigation in developmental and epileptic encephalopathies, beyond the influence of Dravet Syndrome. METHODS The study included 98 patients diagnosed with developmental and epileptic encephalopathies. The patients underwent Sanger sequencing of SCN1A, Chromosomal Microarray Analysis, and Whole Exome Sequencing. The association of clinical variables with a positive genetic test was investigated using univariate and multivariate analysis. RESULTS Genetic diagnosis was identified in 47 (48 %) patients with developmental and epileptic encephalopathies. Beyond Dravet Syndrome influence, first seizure in the context of fever (p < 0.01), seizures precipitated by temperature (p = 0.04), cognitive regression (p = 0.04), hypotonia (p < 0.01), and focal seizures (p = 0.03) increased the chances of a positive genetic investigation. In contrast, atonic seizures (p = 0.01) and generalized discharges on electroencephalogram (p = 0.02) decreased the chances. Dravet Syndrome was positively associated with a genetic developmental and epileptic encephalopathies etiology (p < 0.01), whereas epilepsy with myoclonic-atonic seizures (p = 0.01), developmental and epileptic encephalopathies with spike-wave activation in sleep (p = 0.04), and Lennox-Gastaut syndrome (p = 0.03) were negatively associated. In multivariate analysis, the first seizure in the context of fever (p < 0.01) and hypotonia (p = 0.02) were positively, and atonic seizures (p = 0.01) were negatively and independently associated with a genetic etiology. CONCLUSION The predictive variables of genetic investigation in developmental and epileptic encephalopathies are first seizure in the context of fever and hypotonia, whereas atonic seizures decrease the chances of finding a genetic cause for developmental and epileptic encephalopathies. Regarding epileptic syndromes, Dravet Syndrome is highly associated with a positive genetic test, whereas epilepsy with myoclonic-atonic seizures, developmental and epileptic encephalopathies with spike-wave activation in sleep, and Lennox-Gastaut syndrome are rarely associated with a positive genetic investigation.
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Affiliation(s)
- Maria Luiza Benevides
- Child Neurology Service, Department of Neurology, University of Campinas (UNICAMP), Campinas - São Paulo (SP), Brazil.
| | | | | | - Luciana C Bonadia
- Department of Translational Medicine, UNICAMP, Campinas - SP, Brazil.
| | - Letícia Sauma
- Child Neurology Service, Department of Neurology, University of Campinas (UNICAMP), Campinas - São Paulo (SP), Brazil.
| | | | - Marilisa M Guerreiro
- Child Neurology Service, Department of Neurology, University of Campinas (UNICAMP), Campinas - São Paulo (SP), Brazil; Brazilian Institute of Neuroscience and Neurotechnology, BRAINN, at UNICAMP, Campinas, SP, Brazil.
| | - Íscia Lopes-Cendes
- Department of Translational Medicine, UNICAMP, Campinas - SP, Brazil; Brazilian Institute of Neuroscience and Neurotechnology, BRAINN, at UNICAMP, Campinas, SP, Brazil.
| | - Ana Carolina Coan
- Child Neurology Service, Department of Neurology, University of Campinas (UNICAMP), Campinas - São Paulo (SP), Brazil; Brazilian Institute of Neuroscience and Neurotechnology, BRAINN, at UNICAMP, Campinas, SP, Brazil; Neuroimaging Laboratory, UNICAMP, Campinas, SP, Brazil.
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Chen X, Jiang Y, Zeng S, Zhuang J, Lin N. Prenatal diagnosis of fetuses with absent/hypoplastic nasal bone in second-trimester using chromosomal microarray analysis. Birth Defects Res 2024; 116:e2351. [PMID: 38766695 DOI: 10.1002/bdr2.2351] [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: 12/06/2023] [Revised: 02/28/2024] [Accepted: 04/26/2024] [Indexed: 05/22/2024]
Abstract
BACKGROUND Pathogenic copy number variants (pCNVs) are associated with fetal ultrasound anomalies, which can be efficiently identified through chromosomal microarray analysis (CMA). The primary objective of the present study was to enhance understanding of the genotype-phenotype correlation in fetuses exhibiting absent or hypoplastic nasal bones using CMA. METHODS Enrolled in the present study were 94 cases of fetuses with absent/hypoplastic nasal bone, which were divided into an isolated absent/hypoplastic nasal bone group (n = 49) and a non-isolated group (n = 45). All pregnant women enrolled in the study underwent karyotype analysis and CMA to assess chromosomal abnormalities in the fetuses. RESULTS Karyotype analysis and CMA detection were successfully performed in all cases. The results of karyotype and CMA indicate the presence of 11 cases of chromosome aneuploidy, with trisomy 21 being the most prevalent among them. A small supernumerary marker chromosome (sSMC) detected by karyotype analysis was further interpreted as a pCNV by CMA. Additionally, CMA detection elicited three cases of pCNVs, despite normal findings in their karyotype analysis results. Among them, one case of Roche translocation was identified to be a UPD in chromosome 15 with a low proportion of trisomy 15. Further, a significant difference in the detection rate of pCNVs was observed between non-isolated and isolated absent/hypoplastic nasal bone (24.44% vs. 8.16%, p < .05). CONCLUSION The present study enhances the utility of CMA in diagnosing the etiology of absent or hypoplastic nasal bone in fetuses. Further, isolated cases of absent or hypoplastic nasal bone strongly suggest the presence of chromosomal abnormalities, necessitating genetic evaluation through CMA.
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Affiliation(s)
- Xinying Chen
- Fujian Medical University, Fuzhou, China
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, China
| | - Yuying Jiang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, China
| | - Shuhong Zeng
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, China
| | - Jianlong Zhuang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, China
| | - 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 Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
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Chen Y, Han X, Hua R, Li N, Zhang L, Hu W, Wang Y, Qian Z, Li S. Copy number variation sequencing for the products of conception: What is the optimal testing strategy. Clin Chim Acta 2024; 557:117884. [PMID: 38522821 DOI: 10.1016/j.cca.2024.117884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/01/2024] [Accepted: 03/21/2024] [Indexed: 03/26/2024]
Abstract
BACKGROUND Copy number variation sequencing (CNV-seq) is crucial in prenatal diagnosis, but its limitations in detecting polyploidy, maternal cell contamination (MCC), and uniparental disomy (UPD) restrict its application in the analysis of products of conception (POCs). This study aimed to investigate an optimal genetic testing strategy for POCs in the era of CNV-seq. METHODS CNV-seq and quantitative fluorescent polymerase chain reaction (QF-PCR) were performed in all 4,211 spontaneous miscarriage cases. Different testing strategies were compared and the optimal testing strategies were proposed. RESULTS Of the 4,211 cases, 2561 (60.82%) exhibited clinically significant chromosomal abnormalities. CNV-seq alone, without QF-PCR, might misdiagnose 311 (7.39%) cases, including 278 polyploidy, 13 UPD, and 20 MCC. In 20 MCC cases identified by QF-PCR, CNV-seq successfully pinpointed the cause of miscarriage in 13 cases. Furthermore, in cases where QF-PCR suggested polyploidy, CNV-seq improved the diagnostic accuracy in 54 (1.28%) hypo/hypertriploidy cases. After comparing four different strategies, the sequential approach (initiating with CNV-seq followed by QF-PCR if necessary) emerged as advantageous, reducing approximately 70% of the cost associated with QF-PCR while maintaining result accuracy. CONCLUSIONS We propose an initial CNV-seq followed by QF-PCR if needed-an efficient and cost-effective strategy for the genetic analysis of POCs.
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Affiliation(s)
- Yiyao Chen
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xu Han
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Renyi Hua
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Niu Li
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lanlan Zhang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wenjing Hu
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yanlin Wang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Zhida Qian
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Shuyuan Li
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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Буянова АА, Воронцова ИГ, Самитова АФ, Василиадис ЮА, Петряйкина ЕЕ, Демина ЕС, Тюльпаков АН. [A case of 46,XX testicular disorders of sex development due to an apparent synonymous variant in the WT1 gene: difficulties of differential diagnosis of intrauterine virililzation syndrome in a girl]. PROBLEMY ENDOKRINOLOGII 2024; 71:60-65. [PMID: 40089886 PMCID: PMC11931460 DOI: 10.14341/probl13436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 03/31/2024] [Accepted: 04/02/2024] [Indexed: 03/17/2025]
Abstract
Disorders of sex development (DSD) represent a group of congenital conditions in which there is a discrepancy between the chromosomal and (or) gonadal sex and the structure of the genitals. Within the DSD there is a subgroup of 46,XX testicular DSD (46,XX TDSD), which may be caused by the translocation of the SRY gene, and more rarely - due to other causes (SRY-negative forms). In this report, we present an observation of a patient with SRY-negative 46,XX TDSD, in whom the condition was initially regarded as a virile form of congenital adrenal hyperplasia, then as idiopathic intrauterine virilization in a girl. Due to the development of virilization at the age of 11, the presence of testicular tissue was suspected. Molecular genetic analysis (whole exome sequencing with Sanger validation) revealed a de novo variant in exon 9 of the WT1 gene (chr11:32413528T>C), which, according to predictions, did not lead to a change in the amino acid sequence (p.Thr479=, NM_024426.6), but disrupted splicing, resulting in a previously described in 46,XX TDSD a change in the C-terminal domain of WT1. After verification of the diagnosis, a gonadectomy was performed and estrogen replacement therapy was prescribed. Thus, we have described a patient with a rare form of 46,XX TDSD caused by a variant in the WT1 gene. The presented observation illustrates the difficulties of differential diagnosis of intrauterine virilization syndrome in female karyotype.
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Affiliation(s)
- А. А. Буянова
- Центр высокоточного редактирования и генетических технологий для биомедицины
| | | | - А. Ф. Самитова
- Центр высокоточного редактирования и генетических технологий для биомедицины
| | - Ю. А. Василиадис
- Центр высокоточного редактирования и генетических технологий для биомедицины
| | | | | | - А. Н. Тюльпаков
- Российская детская клиническая больница; Медико-генетический научный центр им. акад. Н.П. Бочкова
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Zhuang J, Zhang N, Wang J, Jiang Y, Zhang H, Chen C. Initial clinical and molecular investigation of 20q13.33 microdeletion with 17q25.3/14q32.31q32.33 microduplication in Chinese pediatric patients. Mol Genet Genomic Med 2024; 12:e2429. [PMID: 38553934 PMCID: PMC10980884 DOI: 10.1002/mgg3.2429] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 03/01/2024] [Accepted: 03/19/2024] [Indexed: 04/02/2024] Open
Abstract
BACKGROUND Limited research has been conducted regarding the elucidation of genotype-phenotype correlations within the 20q13.33 region. The genotype-phenotype association of 20q13.33 microdeletion remains inadequately understood. In the present study, two novel cases of 20q13.33 microdeletion were introduced, with the objective of enhancing understanding of the genotype-phenotype relationship. METHODS Two unrelated patients with various abnormal clinical phenotypes from Fujian province Southeast China were enrolled in the present study. Karyotype analysis and chromosomal microarray analysis (CMA) were performed to investigate chromosomal abnormalities and copy number variants. RESULTS The results of high-resolution G-banding karyotype analysis elicited a 46,XY,der(20)add(20)(q13.3) in Patient 1. This patient exhibited various clinical manifestations, such as global developmental delay, intellectual disability, seizures, and other congenital diseases. Subsequently, a 1.0-Mb deletion was identified in the 20q13.33 region alongside a 5.2-Mb duplication in the 14q32.31q32.33 region. In Patient 2, CMA results revealed a 1.8-Mb deletion in the 20q13.33 region with a 4.8-Mb duplication of 17q25.3. The patient exhibited additional abnormal clinical features, including micropenis, congenital heart disease, and a distinctive crying pattern characterized by a crooked mouth. CONCLUSION In the present study, for the first time, an investigation was conducted into two novel cases of 20q13.33 microdeletion with microduplications in the 17q25.3 and 14q32.31q32.33 regions in the Chinese population. The presence of micropenis may be attributed to the 20q13.33 microdeletion, potentially expanding the phenotypic spectrum associated with this deletion.
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Affiliation(s)
- Jianlong Zhuang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's HospitalQuanzhouChina
| | - Na Zhang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's HospitalQuanzhouChina
| | - Junyu Wang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's HospitalQuanzhouChina
| | - Yuying Jiang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's HospitalQuanzhouChina
| | - Hegan Zhang
- Department of GynecologyQuanzhou Women's and Children's HospitalQuanzhouChina
| | - Chunnuan Chen
- Department of NeurologyThe Second Affiliated Hospital of Fujian Medical UniversityQuanzhouChina
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40
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Riedhammer KM, Simmendinger H, Tasic V, Putnik J, Abazi-Emini N, Stajic N, Berutti R, Weidenbusch M, Patzer L, Lungu A, Milosevski-Lomic G, Günthner R, Braunisch MC, Ćomić J, Hoefele J. Is there a dominant-negative effect in individuals with heterozygous disease-causing variants in COL4A3/COL4A4? Clin Genet 2024; 105:406-414. [PMID: 38214412 DOI: 10.1111/cge.14471] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 01/13/2024]
Abstract
Alport syndrome (AS) shows a broad phenotypic spectrum ranging from isolated microscopic hematuria (MH) to end-stage kidney disease (ESKD). Monoallelic disease-causing variants in COL4A3/COL4A4 have been associated with autosomal dominant AS (ADAS) and biallelic variants with autosomal recessive AS (ARAS). The aim of this study was to analyze clinical and genetic data regarding a possible genotype-phenotype correlation in individuals with disease-causing variants in COL4A3/COL4A4. Eighty-nine individuals carrying at least one COL4A3/COL4A4 variant classified as (likely) pathogenic according to the American College of Medical Genetics guidelines and current amendments were recruited. Clinical data concerning the prevalence and age of first reported manifestation of MH, proteinuria, ESKD, and extrarenal manifestations were collected. Individuals with monoallelic non-truncating variants reported a significantly higher prevalence and earlier diagnosis of MH and proteinuria than individuals with monoallelic truncating variants. Individuals with biallelic variants were more severely affected than those with monoallelic variants. Those with biallelic truncating variants were more severely affected than those with compound heterozygous non-truncating/truncating variants or individuals with biallelic non-truncating variants. In this study an association of heterozygous non-truncating COL4A3/COL4A4 variants with a more severe phenotype in comparison to truncating variants could be shown indicating a potential dominant-negative effect as an explanation for this observation. The results for individuals with ARAS support the, still scarce, data in the literature.
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Affiliation(s)
- Korbinian M Riedhammer
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, TUM School of Medicine and Health, Munich, Germany
- Department of Nephrology, Klinikum rechts der Isar, Technical University of Munich, TUM School of Medicine and Health, Munich, Germany
| | - Hannes Simmendinger
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, TUM School of Medicine and Health, Munich, Germany
| | - Velibor Tasic
- Medical Faculty of Skopje, University Children's Hospital, Macedonia
| | - Jovana Putnik
- Institute for Mother and Child Health Care of Serbia "Dr Vukan Čupić", Department of Nephrology, University of Belgrade, Faculty of Medicine, Belgrade, Serbia
| | - Nora Abazi-Emini
- Medical Faculty of Skopje, University Children's Hospital, Macedonia
| | - Natasa Stajic
- Institute for Mother and Child Health Care of Serbia "Dr Vukan Čupić", Department of Nephrology, University of Belgrade, Faculty of Medicine, Belgrade, Serbia
| | - Riccardo Berutti
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, TUM School of Medicine and Health, Munich, Germany
| | - Marc Weidenbusch
- Nephrologisches Zentrum, Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, Ludwig-Maximilians University, Munich, Germany
| | - Ludwig Patzer
- Department of Pediatric Nephrology, Children's Hospital St. Elisabeth and St. Barbara, Halle/Saale, Germany
| | - Adrian Lungu
- Pediatric Nephrology Department, Fundeni Clinical Institute, Bucharest, Romania
| | - Gordana Milosevski-Lomic
- Institute for Mother and Child Health Care of Serbia "Dr Vukan Čupić", Department of Nephrology, University of Belgrade, Faculty of Medicine, Belgrade, Serbia
| | - Roman Günthner
- Department of Nephrology, Klinikum rechts der Isar, Technical University of Munich, TUM School of Medicine and Health, Munich, Germany
| | - Matthias C Braunisch
- Department of Nephrology, Klinikum rechts der Isar, Technical University of Munich, TUM School of Medicine and Health, Munich, Germany
| | - Jasmina Ćomić
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, TUM School of Medicine and Health, Munich, Germany
- Department of Nephrology, Klinikum rechts der Isar, Technical University of Munich, TUM School of Medicine and Health, Munich, Germany
| | - Julia Hoefele
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, TUM School of Medicine and Health, Munich, Germany
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Bui HTP, Huy Do D, Ly HTT, Tran KT, Le HTT, Nguyen KT, Pham LTD, Le HD, Le VS, Mukhopadhyay A, Nguyen LT. De novo copy number variations in candidate genomic regions in patients of severe autism spectrum disorder in Vietnam. PLoS One 2024; 19:e0290936. [PMID: 38451970 PMCID: PMC10919600 DOI: 10.1371/journal.pone.0290936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/09/2023] [Indexed: 03/09/2024] Open
Abstract
Autism spectrum disorder (ASD) is a developmental disorder with a prevalence of around 1% children worldwide and characterized by patient behaviour (communication, social interaction, and personal development). Data on the efficacy of diagnostic tests using copy number variations (CNVs) in candidate genes in ASD is currently around 10% but it is overrepresented by patients of Caucasian background. We report here that the diagnostic success of de novo candidate CNVs in Vietnamese ASD patients is around 6%. We recruited one hundred trios (both parents and a child) where the child was clinically diagnosed with ASD while the parents were not affected. We performed genetic screening to exclude RETT syndrome and Fragile X syndrome and performed genome-wide DNA microarray (aCGH) on all probands and their parents to analyse for de novo CNVs. We detected 1708 non-redundant CNVs in 100 patients and 118 (7%) of them were de novo. Using the filter for known CNVs from the Simons Foundation Autism Research Initiative (SFARI) database, we identified six CNVs (one gain and five loss CNVs) in six patients (3 males and 3 females). Notably, 3 of our patients had a deletion involving the SHANK3 gene-which is the highest compared to previous reports. This is the first report of candidate CNVs in ASD patients from Vietnam and provides the framework for building a CNV based test as the first tier screening for clinical management.
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Affiliation(s)
- Hoa Thi Phuong Bui
- High Technology Center, Vinmec Health Care System, Hai Ba Trung, Ha Noi, Vietnam
- Translational Medicine Laboratory, Biomedical Research Centre, University of Salford, Salford, United Kingdom
| | - Duong Huy Do
- High Technology Center, Vinmec Health Care System, Hai Ba Trung, Ha Noi, Vietnam
| | - Ha Thi Thanh Ly
- High Technology Center, Vinmec Health Care System, Hai Ba Trung, Ha Noi, Vietnam
| | - Kien Trung Tran
- Vinmec Research Institute of Stem Cell and Gene Technology, Vinmec Health Care System, Hai Ba Trung, Ha Noi, Vietnam
| | - Huong Thi Thanh Le
- Vinmec Research Institute of Stem Cell and Gene Technology, Vinmec Health Care System, Hai Ba Trung, Ha Noi, Vietnam
| | - Kien Trung Nguyen
- Vinmec Research Institute of Stem Cell and Gene Technology, Vinmec Health Care System, Hai Ba Trung, Ha Noi, Vietnam
| | - Linh Thi Dieu Pham
- Vinmec Research Institute of Stem Cell and Gene Technology, Vinmec Health Care System, Hai Ba Trung, Ha Noi, Vietnam
| | - Hau Duc Le
- Big Data Institute, Vinmec Health Care System, Hai Ba Trung, Ha Noi, Vietnam
| | - Vinh Sy Le
- Vinmec Research Institute of Stem Cell and Gene Technology, Vinmec Health Care System, Hai Ba Trung, Ha Noi, Vietnam
- University of Engineering and Technology, Vietnam National University Hanoi, Cau Giay, Hanoi, Vietnam
| | - Arijit Mukhopadhyay
- Translational Medicine Laboratory, Biomedical Research Centre, University of Salford, Salford, United Kingdom
| | - Liem Thanh Nguyen
- Vinmec Research Institute of Stem Cell and Gene Technology, Vinmec Health Care System, Hai Ba Trung, Ha Noi, Vietnam
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Tang X, Du Y, Chen M, Zhang Y, Wang Z, Zhang F, Tan J, Yin T, Wang L. Relationships among maternal monosomy X mosaicism, maternal trisomy, and discordant sex chromosome aneuploidies. Clin Chim Acta 2024; 554:117770. [PMID: 38199578 DOI: 10.1016/j.cca.2024.117770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/05/2024] [Accepted: 01/06/2024] [Indexed: 01/12/2024]
Abstract
OBJECTIVE To explore the impact of maternal factors on the false-positive fetal sex chromosome aneuploidies (SCAs) results obtained through noninvasive prenatal screening (NIPS). METHODS We retrospectively analyzed pregnant women with high-risk SCAs as revealed using NIPS between January 2017 and December 2022. Clinical data such as results of invasive prenatal diagnoses, copy number variation sequencing (CNV-seq) and pregnancy outcomes were analysed. RESULTS Overall, 177 (0.6 %) women with SCA-positive results were collected from 27,941 patients who had undergone NIPS. Among them, 110 (62.2 %) pregnant women chose prenatal diagnosis and 39 (35.5 %) cases were confirmed. For the women with monosomy X false-positive results from the NIPS, 53.1 % (17/32) were found to be maternal mosaicism monosomy X. In cases with 47, XXX false-positive results, 60 % (6/10) of them were maternal 47,XXX (5 cases) or maternal mosaicism 47,XXX (1 case). One (1/6, 16.7 %) case of maternal mosaicism monosomy X was detected in the false positive results of 47, XXY/47, XYY revealed. The incidence rate of maternal sex chromosome abnormalities was positively correlated with the Z-score of ChrX. When the Z-score of ChrX ≥ 15, more than 50 % of pregnant women were found to be maternal sex chromosome abnormalities, and when Z-score ≥ 30, the incidence rate was as high as 100 %. CONCLUSIONS Maternal monosomy X mosaicism and trisomy X respectively played an important role in the discordance of 45, X and 47, XXX revealed by NIPS. CNV-seq was recommended for the pregnant women at risk of maternal sex chromosome abnormalities, which could help clinicians to provide more accurate and efficient advice during genetic counseling and to guide appropriate prenatal diagnosis strategy for the next pregnancy.
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Affiliation(s)
- Xinxin Tang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China
| | - Yunqiu Du
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China
| | - Min Chen
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China
| | - Yue Zhang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China
| | - Zhiwei Wang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China
| | - Fang Zhang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China
| | - Juan Tan
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China
| | - Ting Yin
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China
| | - Leilei Wang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China.
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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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Xue H, Yu A, Zhang L, Chen L, Guo Q, Lin M, Lin N, Chen X, Xu L, Huang H. Genetic testing for fetal loss of heterozygosity using single nucleotide polymorphism array and whole-exome sequencing. Sci Rep 2024; 14:2190. [PMID: 38273042 PMCID: PMC10810965 DOI: 10.1038/s41598-024-52812-y] [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: 07/03/2023] [Accepted: 01/23/2024] [Indexed: 01/27/2024] Open
Abstract
The study explored the clinical significance of fetal loss of heterozygosity (LOH) identified by single-nucleotide polymorphism array (SNP array). We retrospectively reviewed data from pregnant women who underwent invasive diagnostic procedures at prenatal diagnosis centers in southeastern China from December 2016 to December 2021. SNP array was performed by the Affymetrix CytoScan 750 K array platform. Fetuses with LOH were further identified by parental verification, MS-MLPA, and/or trio whole-exome sequencing (trio-WES). The genetic results, fetal clinical manifestations, and perinatal outcome were analyzed. Of 11,062 fetuses, 106 (0.96%) had LOH exhibiting a neutral copy number, 88 (83.0%) had LOH in a single chromosome, whereas 18 (17.0%) had multiple LOHs on different chromosomes. Sixty-six fetuses had ultrasound anomalies (UAs), most frequently fetal growth restriction (18/66 (27.3%)). Parental SNP array verification was performed in 21 cases and trio-WES in 21 cases. Twelve cases had clinically relevant uniparental disomy, five had pathogenic variants, four had likely pathogenic variants, six had variants of unknown significance, and eight had identity by descent. The rate of adverse pregnancy outcomes in fetuses with LOH and UAs (24/66 (36.4%)) was higher than in those without UAs (6/40 (15.0%)) (p < 0.05). LOH is not uncommon. Molecular genetic testing techniques, including parental SNP array verification, trio-WES, methylation-specific multiplex ligation-dependent probe amplification, regular and systematic ultrasonic monitoring, and placental study, can accurately assess the prognosis and guide the management of the affected pregnancy.
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Affiliation(s)
- Huili Xue
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China.
| | - Aili Yu
- Reproductive Medicine Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Lin Zhang
- Fujian Medical University, No. 88 Jiaotong Road, Cangshan District, Fuzhou City, 350001, Fujian Province, China
| | - Lingji Chen
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Qun Guo
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Min Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Xuemei Chen
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China.
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China.
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Hu X, Hu Y, Wang H, Yu C, Zheng J, Zhang H, Zheng J. Comparison of Chromosomal Microarray Analysis and Noninvasive Prenatal Testing in Pregnant Women with Fetal Ultrasonic Soft Markers. Risk Manag Healthc Policy 2024; 17:29-40. [PMID: 38196919 PMCID: PMC10775152 DOI: 10.2147/rmhp.s437441] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 12/20/2023] [Indexed: 01/11/2024] Open
Abstract
Objective This study aimed to assess the utility of chromosomal microarray analysis (CMA) and noninvasive prenatal testing (NIPT) in detecting clinically significant chromosomal abnormalities among fetuses presenting ultrasonic soft markers (USMs). Methods A retrospective observational study, spanning from January 1, 2019, to September 30, 2022, enrolled 539 singleton pregnant women with fetal USMs at our center. Of these, 418 cases (77.6%) underwent NIPT, while 121 cases (22.4%) opted for invasive prenatal diagnosis post-appropriate genetic counseling. Cases with high-risk NIPT results proceeded to invasive prenatal diagnosis, where conventional karyotyping and CMA were concurrently performed. Further stratification was done based on the number of USMs, classifying cases into single-USM and multiple-USM groups. Results Of the 24 cases (4.5%) exhibiting abnormal findings, 17 presented numerical chromosomal abnormalities, 2 featured clinically significant copy number variations (CNVs), 3 showed variants of unknown significance (VOUS), 1 displayed LOH, and 1 exhibited chromosome nine inversion. Notably, 18 cases (75%) theoretically detectable by karyotyping (eg, sizes above 10Mb) and 16 cases (66.7%) detectable by NIPT for five common aneuploidies were identified. Six submicroscopic findings (25%) were exclusively detectable by CMA. The predominant clinically relevant aberrations were observed in the thickened nuchal-translucency (TNT) group (9/35, 25.7%), followed by the multiple soft markers group (3/32, 9.3%). In the NIPT group, the false positive rate was 1.22%, and the false negative rate was 0%. Conclusion The prevalence of chromosome aneuploidy exceeded that of submicroscopic chromosomal imbalance in pregnant women with fetal USMs. NIPT demonstrated efficacy, particularly for soft markers like echogenic intracardiac focus. However, for those with TNT and multiple soft markers, invasive prenatal diagnosis, including CMA testing, is recommended as the primary investigative approach.
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Affiliation(s)
- Xianqing Hu
- Department of Obstetrics and Gynecology, The Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou People’s Hospital, Wenzhou Maternal and Child Health Care Hospital, Wenzhou, People’s Republic of China
| | - Yanjun Hu
- Department of Obstetrics and Gynecology, The Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou People’s Hospital, Wenzhou Maternal and Child Health Care Hospital, Wenzhou, People’s Republic of China
| | - Hai Wang
- Department of Fetal Medicine and Prenatal Diagnosis, The Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou People’s Hospital, Wenzhou Maternal and Child Health Care Hospital, Wenzhou, People’s Republic of China
| | - Caicha Yu
- Department of Ultrasonography, The Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou People’s Hospital, Wenzhou Maternal and Child Health Care Hospital, Wenzhou, People’s Republic of China
| | - Jiayong Zheng
- Department of Fetal Medicine and Prenatal Diagnosis, The Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou People’s Hospital, Wenzhou Maternal and Child Health Care Hospital, Wenzhou, People’s Republic of China
| | - Hongping Zhang
- Department of Obstetrics and Gynecology, The Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou People’s Hospital, Wenzhou Maternal and Child Health Care Hospital, Wenzhou, People’s Republic of China
| | - Jianqiong Zheng
- Department of Obstetrics and Gynecology, The Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou People’s Hospital, Wenzhou Maternal and Child Health Care Hospital, Wenzhou, People’s Republic of China
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Cai M, Lv A, Zhao W, Xu L, Lin N, Huang H. Intrauterine ultrasound phenotyping, molecular characteristics, and postnatal follow-up of fetuses with the 15q11.2 BP1-BP2 microdeletion syndrome: a single-center, retrospective clinical study. BMC Pregnancy Childbirth 2024; 24:23. [PMID: 38172840 PMCID: PMC10763152 DOI: 10.1186/s12884-023-06223-y] [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: 09/03/2023] [Accepted: 12/22/2023] [Indexed: 01/05/2024] Open
Abstract
OBJECTIVES The 15q11.2 BP1-BP2 microdeletion is associated with neurodevelopmental diseases. However, most studies on this microdeletion have focused on adults and children. Thus, in this study, we summarized the molecular characteristics of fetuses with the 15q11.2 BP1-BP2 microdeletion and their postnatal follow-up to guide prenatal diagnosis. METHODS Ten thousand fetuses were retrospectively subjected to karyotype analysis and chromosome microarray analysis. RESULTS Chromosome microarray analysis revealed that 37 (0.4%) of the 10,000 fetuses had 15q11.2 BP1-BP2 microdeletions. The fragment size of the 15q11.2 BP1-BP2 region was approximately 312-855 kb and encompassed TUBGCP5, CYFIP1, NIPA2, and NIPA1 genes. Twenty-five of the 37 fetuses with this microdeletion showed phenotypic abnormalities. The most common ultrasonic structural abnormality was congenital heart disease, followed by renal dysplasia and Dandy-Walker malformation. The 15q11.2 BP1-BP2 microdeletion was inherited from the father and mother in 6 and 10 cases, respectively, and de novo inherited in 4 cases. In the postnatal follow-up, 16.1% of the children had postnatal abnormalities. CONCLUSION Fetuses with the 15q11.2 BP1-BP2 microdeletion showed high proportions of phenotypic abnormalities, but the specificity of penetrance was low. Thus, fetuses with this syndrome are potentially at a higher risk of postnatal growth/behavioral problems and require continuous monitoring of growth and development.
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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 Defect, Fuzhou, China
| | - Aixiang Lv
- 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 Defect, Fuzhou, China
| | - Wantong Zhao
- 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 Defect, Fuzhou, China
| | - 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 Defect, Fuzhou, China.
| | - 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 Defect, Fuzhou, China.
| | - 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 Defect, Fuzhou, China.
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Workalemahu T, Dalton S, Son SL, Allshouse A, Carey AZ, Page JM, Blue NR, Thorsten V, Goldenberg RL, Pinar H, Reddy UM, Silver RM. Copy number variants and fetal structural abnormalities in stillborn fetuses: A secondary analysis of the Stillbirth Collaborative Research Network study. BJOG 2024; 131:157-162. [PMID: 37264725 PMCID: PMC10689565 DOI: 10.1111/1471-0528.17561] [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: 11/11/2022] [Revised: 05/07/2023] [Accepted: 05/15/2023] [Indexed: 06/03/2023]
Abstract
OBJECTIVE To examine the association of placental and fetal DNA copy number variants (CNVs) with fetal structural malformations (FSMs) in stillborn fetuses. DESIGN A secondary analysis of stillbirth cases in the Stillbirth Collaborative Research Network (SCRN) study. SETTING Multicenter, 59 hospitals in five geographic regions in the USA. POPULATION 388 stillbirth cases of the SCRN study (2006-2008). METHODS Fetal structural malformations were grouped by anatomic system and specific malformation type (e.g. central nervous system, thoracic, cardiac, gastrointestinal, skeletal, umbilical cord and craniofacial defects). Single-nucleotide polymorphism array detected CNVs of at least 500 kb. CNVs were classified into two groups: normal, defined as no CNVs >500 kb or benign CNVs, and abnormal, defined as pathogenic or variants of unknown clinical significance. MAIN OUTCOME MEASURES The proportions of abnormal CNVs and normal CNVs were compared between stillbirth cases with and without FSMs using the Wald Chi-square test. RESULTS The proportion of stillbirth cases with any FSMs was higher among those with abnormal CNVs than among those with normal CNVs (47.5 versus 19.1%; P-value <0.001). The most common organ system-specific FSMs associated with abnormal CNVs were cardiac defects, followed by hydrops, craniofacial defects and skeletal defects. A pathogenic deletion of 1q21.1 involving 46 genes (e.g. CHD1L) and a duplication of 21q22.13 involving four genes (SIM2, CLDN14, CHAF1B, HLCS) were associated with a skeletal and cardiac defect, respectively. CONCLUSION Specific CNVs involving several genes were associated with FSMs in stillborn fetuses. The findings warrant further investigation and may inform counselling and care surrounding pregnancies affected by FSMs at risk for stillbirth.
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Affiliation(s)
| | | | - Shannon L. Son
- University of Utah Health, Salt Lake City, UT
- Intermountain Healthcare, Salt Lake City, UT
| | | | | | - Jessica M. Page
- University of Utah Health, Salt Lake City, UT
- Intermountain Healthcare, Salt Lake City, UT
| | | | - Vanessa Thorsten
- Columbia University Medical Center, New York, NY
- RTI International, Research Triangle Park, NC
| | | | - Halit Pinar
- Division of Perinatal Pathology, Brown University School of Medicine, Providence, RI
| | - Uma M. Reddy
- Obstetrics, Gynecology & Reproductive Sciences, Yale University, New Haven, CT
| | - Robert M. Silver
- University of Utah Health, Salt Lake City, UT
- Intermountain Healthcare, Salt Lake City, UT
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Berkalieva A, Kelly NR, Fisher A, Hohmann SF, Sebastin M, Di Biase M, Bonini KE, Marathe P, Odgis JA, Suckiel SA, Ramos MA, Rhodes R, Abul-Husn NS, Greally JM, Horowitz CR, Wasserstein MP, Kenny EE, Gelb BD, Ferket BS. Physician services and costs after disclosure of diagnostic sequencing results in the NYCKidSeq program. Genet Med 2024; 26:101011. [PMID: 37897232 PMCID: PMC10842442 DOI: 10.1016/j.gim.2023.101011] [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: 06/30/2023] [Revised: 10/19/2023] [Accepted: 10/22/2023] [Indexed: 10/29/2023] Open
Abstract
PURPOSE To better understand the effects of returning diagnostic sequencing results on clinical actions and economic outcomes for pediatric patients with suspected genetic disorders. METHODS Longitudinal physician claims data after diagnostic sequencing were obtained for patients aged 0 to 21 years with neurologic, cardiac, and immunologic disorders with suspected genetic etiology. We assessed specialist consultation rates prompted by primary diagnostic results, as well as marginal effects on overall 18-month physician services and costs. RESULTS We included data on 857 patients (median age: 9.6 years) with a median follow-up of 17.3 months after disclosure of diagnostic sequencing results. The likelihood of having ≥1 recommendation for specialist consultation in 155 patients with positive findings was high (72%) vs 23% in 443 patients with uncertain findings and 21% in 259 patients with negative findings (P < .001). Follow-through consultation occurred in 30%. Increases in 18-month physician services and costs following a positive finding diminished after multivariable adjustment. Also, no significant differences between those with uncertain and negative findings were demonstrated. CONCLUSION Our study did not provide evidence for significant increases in downstream physician services and costs after returning positive or uncertain diagnostic sequencing findings. More large-scale longitudinal studies are needed to confirm these findings.
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Affiliation(s)
- Asem Berkalieva
- Institute for Healthcare Delivery Science, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Nicole R Kelly
- Division of Pediatric Genetic Medicine, Department of Pediatrics, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | | | | | - Monisha Sebastin
- Division of Pediatric Genetic Medicine, Department of Pediatrics, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Miranda Di Biase
- Division of Pediatric Genetic Medicine, Department of Pediatrics, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Katherine E Bonini
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Priya Marathe
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jacqueline A Odgis
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Sabrina A Suckiel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Michelle A Ramos
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Rosamond Rhodes
- Department of Education, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Noura S Abul-Husn
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY; 23andMe Inc, Sunnyvale, CA
| | - John M Greally
- Division of Genomics, Department of Genetics, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Carol R Horowitz
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY; Division of General Internal Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Melissa P Wasserstein
- Division of Pediatric Genetic Medicine, Department of Pediatrics, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Eimear E Kenny
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY; Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY; Division for Genomic Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Bruce D Gelb
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Bart S Ferket
- Institute for Healthcare Delivery Science, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY.
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James KN, Chowdhury S, Ding Y, Batalov S, Watkins K, Kwon YH, Van Der Kraan L, Ellsworth K, Kingsmore SF, Guidugli L. Genome sequencing detects a wide range of clinically relevant copy-number variants and other genomic alterations. Genet Med 2024; 26:101006. [PMID: 37869996 PMCID: PMC11542619 DOI: 10.1016/j.gim.2023.101006] [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: 04/04/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 10/24/2023] Open
Abstract
PURPOSE Copy-number variants (CNVs) and other non-single nucleotide variant/indel variant types contribute an important proportion of diagnoses in individuals with suspected genetic disease. This study describes the range of such variants detected by genome sequencing (GS). METHODS For a pediatric cohort of 1032 participants undergoing clinical GS, we characterize the CNVs and other non-single nucleotide variant/indel variant types that were reported, including aneuploidies, mobile element insertions, and uniparental disomies, and we describe the bioinformatic pipeline used to detect these variants. RESULTS Together, these genetic alterations accounted for 15.8% of reported variants. Notably, 67.9% of these were deletions, 32.9% of which overlapped a single gene, and many deletions were reported together with a second variant in the same gene in cases of recessive disease. A retrospective medical record review in a subset of this cohort revealed that up to 6 additional genetic tests were ordered in 68% (26/38) of cases, some of which failed to report the CNVs/rare variants reported on GS. CONCLUSION GS detected a broad range of reported variant types, including CNVs ranging in size from 1 Kb to 46 Mb.
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Affiliation(s)
- Kiely N James
- Rady Children's Institute for Genomic Medicine, San Diego, CA
| | | | - Yan Ding
- Rady Children's Institute for Genomic Medicine, San Diego, CA
| | - Sergey Batalov
- Rady Children's Institute for Genomic Medicine, San Diego, CA
| | - Kelly Watkins
- Rady Children's Institute for Genomic Medicine, San Diego, CA
| | - Yong Hyun Kwon
- Rady Children's Institute for Genomic Medicine, San Diego, CA
| | | | | | | | - Lucia Guidugli
- Rady Children's Institute for Genomic Medicine, San Diego, CA.
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Oketch DJA, Giulietti M, Piva F. Copy Number Variations in Pancreatic Cancer: From Biological Significance to Clinical Utility. Int J Mol Sci 2023; 25:391. [PMID: 38203561 PMCID: PMC10779192 DOI: 10.3390/ijms25010391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/20/2023] [Accepted: 12/24/2023] [Indexed: 01/12/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the most common type of pancreatic cancer, characterized by high tumor heterogeneity and a poor prognosis. Inter- and intra-tumoral heterogeneity in PDAC is a major obstacle to effective PDAC treatment; therefore, it is highly desirable to explore the tumor heterogeneity and underlying mechanisms for the improvement of PDAC prognosis. Gene copy number variations (CNVs) are increasingly recognized as a common and heritable source of inter-individual variation in genomic sequence. In this review, we outline the origin, main characteristics, and pathological aspects of CNVs. We then describe the occurrence of CNVs in PDAC, including those that have been clearly shown to have a pathogenic role, and further highlight some key examples of their involvement in tumor development and progression. The ability to efficiently identify and analyze CNVs in tumor samples is important to support translational research and foster precision oncology, as copy number variants can be utilized to guide clinical decisions. We provide insights into understanding the CNV landscapes and the role of both somatic and germline CNVs in PDAC, which could lead to significant advances in diagnosis, prognosis, and treatment. Although there has been significant progress in this field, understanding the full contribution of CNVs to the genetic basis of PDAC will require further research, with more accurate CNV assays such as single-cell techniques and larger cohorts than have been performed to date.
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Affiliation(s)
| | - Matteo Giulietti
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Francesco Piva
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
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