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Fu W, Cui Q, Bu Z, Shi H, Yang Q, Hu L. Elevated sperm DNA fragmentation is correlated with an increased chromosomal aneuploidy rate of miscarried conceptus in women of advanced age undergoing fresh embryo transfer cycle. Front Endocrinol (Lausanne) 2024; 15:1289763. [PMID: 38650716 PMCID: PMC11033384 DOI: 10.3389/fendo.2024.1289763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 02/20/2024] [Indexed: 04/25/2024] Open
Abstract
Background Male sperm DNA fragmentation (SDF) may be associated with assisted reproductive technology (ART) outcomes, but the impact of SDF on the occurrence of aneuploid-related miscarriage remains controversial. Methods Genome-wide single-nucleotide polymorphism-based chromosomal microarray analysis was performed on 495 miscarried chorionic villus samples undergone IVF/ICSI treatment from the Reproductive Medicine Center of the First Affiliated Hospital of Zhengzhou University. SDF was assessed using sperm chromatin structure assay. Patients were divided into four groups according to embryo transfer cycle type and maternal age, and the correlation between SDF and chromosome aberration was analyzed. A receiver operating characteristic (ROC) curve was utilized to find the optimal threshold. Results Total chromosomal aneuploidy rate was 54.95%, and trisomy was the most common abnormality (71.32%). The chromosomally abnormal group had higher SDF than the normal group (11.42% [6.82%, 16.54%] vs. 12.95% [9.61%, 20.58%], P = 0.032). After grouping, elevated SDF was significantly correlated with an increasing chromosome aneuploidy rate only in women of advanced age who underwent fresh embryo transfer (adjusted odds ratio:1.14 [1.00-1.29], adjusted-P = 0.045). The receiver operating characteristic curve showed that SDF can predict the occurrence of chromosomal abnormality of miscarried conceptus in this group ((area under the curve = 0.76 [0.60-0.91], P = 0.005), and 8.5% was the optimum threshold. When SDF was ≥ 8.5%, the risk of such patients increased by 5.76 times (adjusted odds ratio: 6.76 [1.20-37.99], adjusted-P = 0.030). Conclusion For women of advanced maternal age undergoing fresh embryo transfer, older oocytes fertilized using sperm with high SDF in IVF/ICSI treatment might increase the risk of chromosomal abnormality in miscarried conceptus.
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Affiliation(s)
- Wanting Fu
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qiuying Cui
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhiqin Bu
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hao Shi
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qingling Yang
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Linli Hu
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Margiotti K, Fabiani M, Cima A, Libotte F, Mesoraca A, Giorlandino C. Prenatal Diagnosis by Trio Clinical Exome Sequencing: Single Center Experience. Curr Issues Mol Biol 2024; 46:3209-3217. [PMID: 38666931 PMCID: PMC11048976 DOI: 10.3390/cimb46040201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
Fetal anomalies, characterized by structural or functional abnormalities occurring during intrauterine life, pose a significant medical challenge, with a notable prevalence, affecting approximately 2-3% of live births and 20% of spontaneous miscarriages. This study aims to identify the genetic cause of ultrasound anomalies through clinical exome sequencing (CES) analysis. The focus is on utilizing CES analysis in a trio setting, involving the fetuses and both parents. To achieve this objective, prenatal trio clinical exome sequencing was conducted in 51 fetuseses exhibiting ultrasound anomalies with previously negative results from chromosomal microarray (CMA) analysis. The study revealed pathogenic variants in 24% of the analyzed cases (12 out of 51). It is worth noting that the findings include de novo variants in 50% of cases and the transmission of causative variants from asymptomatic parents in 50% of cases. Trio clinical exome sequencing stands out as a crucial tool in advancing prenatal diagnostics, surpassing the effectiveness of relying solely on chromosomal microarray analysis. This underscores its potential to become a routine diagnostic standard in prenatal care, particularly for cases involving ultrasound anomalies.
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Affiliation(s)
- Katia Margiotti
- Human Genetics Lab, Altamedica Main Centre, Viale Liegi 45, 00198 Rome, Italy; (M.F.); (A.C.); (F.L.); (A.M.); (C.G.)
| | - Marco Fabiani
- Human Genetics Lab, Altamedica Main Centre, Viale Liegi 45, 00198 Rome, Italy; (M.F.); (A.C.); (F.L.); (A.M.); (C.G.)
| | - Antonella Cima
- Human Genetics Lab, Altamedica Main Centre, Viale Liegi 45, 00198 Rome, Italy; (M.F.); (A.C.); (F.L.); (A.M.); (C.G.)
| | - Francesco Libotte
- Human Genetics Lab, Altamedica Main Centre, Viale Liegi 45, 00198 Rome, Italy; (M.F.); (A.C.); (F.L.); (A.M.); (C.G.)
| | - Alvaro Mesoraca
- Human Genetics Lab, Altamedica Main Centre, Viale Liegi 45, 00198 Rome, Italy; (M.F.); (A.C.); (F.L.); (A.M.); (C.G.)
| | - Claudio Giorlandino
- Human Genetics Lab, Altamedica Main Centre, Viale Liegi 45, 00198 Rome, Italy; (M.F.); (A.C.); (F.L.); (A.M.); (C.G.)
- Fetal-Maternal Medical Centre, Altamedica Viale Liegi 45, 00198 Rome, Italy
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Choi H, Kim JA, Cho KO, Kim HJ, Park MH. Case Report: Intellectual disability and borderline intellectual functioning in two sisters with a 12p11.22 loss. Front Genet 2024; 15:1355823. [PMID: 38628577 PMCID: PMC11018894 DOI: 10.3389/fgene.2024.1355823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/19/2024] [Indexed: 04/19/2024] Open
Abstract
Multiple genome sequencing studies have identified genetic abnormalities as major causes of severe intellectual disability (ID). However, many children affected by mild ID and borderline intellectual functioning (BIF) lack a genetic diagnosis because known causative ID genetic mutations have not been identified or the role of genetic variants in mild cases is less understood. Genetic variant testing in mild cases is necessary to provide information on prognosis and risk of occurrence. In this study, we report two sibling patients who were 5 years 9 months old and 3 years 3 months old and presented to the hospital due to developmental delay. Clinical assessment and chromosomal microarray analysis were performed. The patients were diagnosed with mild intellectual disability (ID) and borderline intellectual functioning (BIF). Genetic analysis identified a loss of 12p11.22, including the OVCH1-AS1, OVCH1, and TMTC1 genes, which was the only variant that occurred in both sisters. Identical variants were found in their father with probable BIF. Neither patient presented any brain structural abnormalities or dysmorphism, and no exogenous factors or parenting problems were reported. Thus, loss of 12p11.22 may be associated with our patients' cognitive impairment. The OVCH1, OVCH1-AS1 and TMTC1 variants identified in this study are the most likely disease-causing genes in the sisters. Our findings may expand as yet limited knowledge on mild ID and BIF causative variants, which would further support the diagnosis even if the severity is mild.
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Affiliation(s)
- Haemi Choi
- Department of Psychiatry, Eunpyeong St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jeong-A. Kim
- Department of Psychiatry, Eunpyeong St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Kyung-Ok Cho
- Department of Pharmacology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Biomedicine & Health Sciences, The Catholic University of Korea, Seoul, Republic of Korea
- Catholic Neuroscience Institute, The Catholic University of Korea, Seoul, Republic of Korea
- Institute for Aging and Metabolic Diseases, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hyun Jung Kim
- Department of Psychiatry, Harvard Medical School, Boston, MA, United States
- Division of Psychotic Disorders, McLean Hospital, Belmont, MA, United States
| | - Min-Hyeon Park
- Department of Psychiatry, Eunpyeong St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Biomedicine & Health Sciences, The Catholic University of Korea, Seoul, Republic of Korea
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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5
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Bensaid S, Bendahmane M, Loddo S, Poke G, Januel L, Nicolle R, Malan V, Chatron N, Ottombrino S, Dentici ML, Novelli A, Digilio MC, Sanlaville D. Clinical and molecular cytogenetic studies of five new patients with 20q11q12 deletion and review of the literature: Proposition of two critical regions. Am J Med Genet A 2024:e63580. [PMID: 38511524 DOI: 10.1002/ajmg.a.63580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 12/30/2023] [Accepted: 02/21/2024] [Indexed: 03/22/2024]
Abstract
Deletions of the long arm of chromosome 20 (20q) are rare, with only 16 reported patients displaying a proximal interstitial 20q deletion. A 1.62 Mb minimal critical region at 20q11.2, encompassing three genes GDF5, EPB41L1, and SAMHD1, is proposed to be responsible for this syndrome. The leading clinical features include growth retardation, intractable feeding difficulties with gastroesophageal reflux, hypotonia and psychomotor developmental delay. Common facial dysmorphisms including triangular face, hypertelorism, and hypoplastic alae nasi were additionally reported. Here, we present the clinical and molecular findings of five new patients with proximal interstitial 20q deletions. We analyzed the phenotype and molecular data of all previously reported patients with 20q11.2q12 microdeletions, along with our five new cases. Copy number variation analysis of patients in our cohort has enabled us to identify the second critical region in the 20q11.2q12 region and redefine the first region that is initially identified. The first critical region spans 359 kb at 20q11.2, containing six MIM genes, including two disease-causing genes, GDF5 and CEP250. The second critical region spans 706 kb at 20q12, encompassing four MIM genes, including two disease-causing genes, MAFB and TOP1. We propose GDF5 to be the primary candidate gene generating the phenotype of patients with 20q11.2 deletions. Moreover, we hypothesize TOP1 as a potential candidate gene for the second critical region at 20q12. Of note, we cannot exclude the possibility of a synergistic role of other genes involved in the deletion, including a contiguous gene deletion syndrome or position effect affecting both critical regions. Further studies focusing on patients with proximal 20q deletions are required to support our hypothesis.
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Affiliation(s)
- Souad Bensaid
- Hospices Civils de Lyon, GHE, Service de Génétique, Lyon, France
- Laboratoire d'Environnement et de Santé, Université de Sidi Bel Abbés, UDL, Sidi Bel Abbés, Algeria
| | - Malika Bendahmane
- Laboratoire d'Environnement et de Santé, Université de Sidi Bel Abbés, UDL, Sidi Bel Abbés, Algeria
| | - Sara Loddo
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Gemma Poke
- Genetic Health Service New Zealand, Wellington Hospital, Wellington, New Zealand
| | - Louis Januel
- Hospices Civils de Lyon, GHE, Service de Génétique, Lyon, France
| | - Romain Nicolle
- AP-HP, Hôpital Necker-Enfants Malades, Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, Paris, France
| | - Valérie Malan
- AP-HP, Hôpital Necker-Enfants Malades, Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, Paris, France
| | - Nicolas Chatron
- Hospices Civils de Lyon, GHE, Service de Génétique, Lyon, France
- Université Claude Bernard Lyon 1, CNRS, INSERM, Physiopathologie et Génétique du Neurone et du Muscle, UMR5261, U1315, Institut NeuroMyoGène, Lyon, France
| | - Silvia Ottombrino
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Maria Lisa Dentici
- Medical Genetics Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Antonio Novelli
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Damien Sanlaville
- Hospices Civils de Lyon, GHE, Service de Génétique, Lyon, France
- Université Claude Bernard Lyon 1, CNRS, INSERM, Physiopathologie et Génétique du Neurone et du Muscle, UMR5261, U1315, Institut NeuroMyoGène, Lyon, France
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6
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Massier M, Doco-Fenzy M, Egloff M, Le Guillou X, Le Guyader G, Redon S, Benech C, Le Millier K, Uguen K, Ropars J, Sacaze E, Audebert-Bellanger S, Apetrei A, Molin A, Gruchy N, Vincent-Devulder A, Spodenkiewicz M, Jacquin C, Loron G, Thibaud M, Delplancq G, Brisset S, Lesieur-Sebellin M, Malan V, Romana S, Rio M, Marlin S, Amiel J, Marquet V, Dauriat B, Moradkhani K, Mercier S, Isidor B, Arpin S, Pujalte M, Jedraszak G, Pebrel-Richard C, Salaun G, Laffargue F, Boudjarane J, Missirian C, Chelloug N, Toutain A, Chiesa J, Keren B, Mignot C, Gouy E, Jaillard S, Landais E, Poirsier C. 3q29 duplications: A cohort of 46 patients and a literature review. Am J Med Genet A 2024:e63531. [PMID: 38421086 DOI: 10.1002/ajmg.a.63531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/15/2023] [Accepted: 12/22/2023] [Indexed: 03/02/2024]
Abstract
Duplications of the 3q29 cytoband are rare chromosomal copy number variations (CNVs) (overlapping or recurrent ~1.6 Mb 3q29 duplications). They have been associated with highly variable neurodevelopmental disorders (NDDs) with various associated features or reported as a susceptibility factor to the development of learning disabilities and neuropsychiatric disorders. The smallest region of overlap and the phenotype of 3q29 duplications remain uncertain. We here report a French cohort of 31 families with a 3q29 duplication identified by chromosomal microarray analysis (CMA), including 14 recurrent 1.6 Mb duplications, eight overlapping duplications (>1 Mb), and nine small duplications (<1 Mb). Additional genetic findings that may be involved in the phenotype were identified in 11 patients. Focusing on apparently isolated 3q29 duplications, patients present mainly mild NDD as suggested by a high rate of learning disabilities in contrast to a low proportion of patients with intellectual disabilities. Although some are de novo, most of the 3q29 duplications are inherited from a parent with a similar mild phenotype. Besides, the study of small 3q29 duplications does not provide evidence for any critical region. Our data suggest that the overlapping and recurrent 3q29 duplications seem to lead to mild NDD and that a severe or syndromic clinical presentation should warrant further genetic analyses.
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Affiliation(s)
- Marie Massier
- Department of Genetics, Reims University Hospital, Reims, France
| | - Martine Doco-Fenzy
- Department of Genetics, Reims University Hospital, Reims, France
- Department of Genetics, Nantes University Hospital, Nantes, France
| | - Matthieu Egloff
- Department of Genetics, Poitiers University Hospital, Poitiers, France
- University of Poitiers, INSERM, LNEC, Department of Genetics, Poitiers University Hospital, Poitiers, France
| | - Xavier Le Guillou
- Department of Genetics, Poitiers University Hospital, Poitiers, France
- University of Poitiers, CNRS, LMA, Department of Genetics, Poitiers University Hospital, Poitiers, France
| | | | - Sylvia Redon
- Department of Genetics, Brest University Hospital, Brest, France
- Intellectual Disability Reference Center, Department of Pediatrics, Brest University Hospital, Brest, France
- University of Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | - Caroline Benech
- University of Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | | | - Kevin Uguen
- Department of Genetics, Brest University Hospital, Brest, France
- Intellectual Disability Reference Center, Department of Pediatrics, Brest University Hospital, Brest, France
- University of Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | - Juliette Ropars
- Intellectual Disability Reference Center, Department of Pediatrics, Brest University Hospital, Brest, France
| | - Elise Sacaze
- Intellectual Disability Reference Center, Department of Pediatrics, Brest University Hospital, Brest, France
| | - Séverine Audebert-Bellanger
- Department of Genetics, Brest University Hospital, Brest, France
- Intellectual Disability Reference Center, Department of Pediatrics, Brest University Hospital, Brest, France
| | - Andreea Apetrei
- University of Normandy, UNICAEN, RU7450 BioTARGen, Caen University Hospital, Department of Genetics, Reference Center for Developmental Disorders and Malformative Syndromes, Anddi-Rares Network, Caen, France
| | - Arnaud Molin
- University of Normandy, UNICAEN, RU7450 BioTARGen, Caen University Hospital, Department of Genetics, Reference Center for Developmental Disorders and Malformative Syndromes, Anddi-Rares Network, Caen, France
| | - Nicolas Gruchy
- University of Normandy, UNICAEN, RU7450 BioTARGen, Caen University Hospital, Department of Genetics, Reference Center for Developmental Disorders and Malformative Syndromes, Anddi-Rares Network, Caen, France
| | - Aline Vincent-Devulder
- University of Normandy, UNICAEN, RU7450 BioTARGen, Caen University Hospital, Department of Genetics, Reference Center for Developmental Disorders and Malformative Syndromes, Anddi-Rares Network, Caen, France
| | | | - Clémence Jacquin
- Department of Genetics, Reims University Hospital, Reims, France
| | - Gauthier Loron
- Department of Neonatal Medicine and Pediatric Intensive Care, University of Reims Champagne-Ardenne, CReSTIC, Reims University Hospital, Reims, France
| | - Marie Thibaud
- Department of Pediatrics, American Memorial Hospital, Reims, France
| | | | - Sophie Brisset
- Constitutional Genetics Unit, Versailles Hospital, Le Chesnay, France
| | - Marion Lesieur-Sebellin
- Department of Genomic Medicine of Rare Disorders, Necker Hospital, APHP Center, University Paris Cité, Paris, France
| | - Valérie Malan
- Department of Genomic Medicine of Rare Disorders, Necker Hospital, APHP Center, University Paris Cité, Paris, France
| | - Serge Romana
- Department of Genomic Medicine of Rare Disorders, Necker Hospital, APHP Center, University Paris Cité, Paris, France
| | - Marlène Rio
- Department of Genomic Medicine of Rare Disorders, Necker Hospital, APHP Center, University Paris Cité, Paris, France
| | - Sandrine Marlin
- Department of Genomic Medicine of Rare Disorders, Necker Hospital, APHP Center, University Paris Cité, Paris, France
| | - Jeanne Amiel
- Department of Genomic Medicine of Rare Disorders, Necker Hospital, APHP Center, University Paris Cité, Paris, France
| | - Valentine Marquet
- Department of Cytogenetics, Clinical Genetics and Reproductive Biology, Limoges University Hospital, Limoges, France
| | - Benjamin Dauriat
- Department of Cytogenetics, Clinical Genetics and Reproductive Biology, Limoges University Hospital, Limoges, France
| | | | - Sandra Mercier
- Department of Genetics, Nantes University Hospital, Nantes, France
| | - Bertrand Isidor
- Department of Genetics, Nantes University Hospital, Nantes, France
| | - Stéphanie Arpin
- Department of Genetics, Tours University Hospital, UMR 1253, iBrain, University of Tours, Inserm, Tours, France
| | | | - Guillaume Jedraszak
- Constitutional Genetic Laboratory, University Hospital of Amiens & UR4666 HEMATIM, University of Picardie Jules Verne, Amiens, France
| | - Céline Pebrel-Richard
- Cytogenetic Medical Department; UIC Cytogenetics of Rare Diseases and Reproduction (GRUIC ADERGEN), Rare Diseases Reference Center (CRMR): Developmental Anomalies and Malformative Syndromes in the Auvergne Region, Clermont-Ferrand University Hospital, Clermont-Ferrand, France
| | - Gaëlle Salaun
- Cytogenetic Medical Department; UIC Cytogenetics of Rare Diseases and Reproduction (GRUIC ADERGEN), Rare Diseases Reference Center (CRMR): Developmental Anomalies and Malformative Syndromes in the Auvergne Region, Clermont-Ferrand University Hospital, Clermont-Ferrand, France
| | - Fanny Laffargue
- Department of Medical Genetics, UIC ADDIR (GRIUC ADERGEN), Constitutive Reference Center CLAD South-East: Developmental anomalies and malformative syndromes, Clermont-Ferrand University Hospital, Clermont-Ferrand, France
| | - John Boudjarane
- Medical Genetics Department, Timone Enfants University Hospital, Assistance Publique des Hôpitaux de Marseille, Marseille, France
| | - Chantal Missirian
- Medical Genetics Department, Timone Enfants University Hospital, Assistance Publique des Hôpitaux de Marseille, Marseille, France
| | - Nora Chelloug
- Department of Medical Genetics, Toulouse University Hospital, Toulouse, France
| | - Annick Toutain
- Department of Genetics, Tours University Hospital, UMR 1253, iBrain, University of Tours, Inserm, Tours, France
| | - Jean Chiesa
- Department of Genetics, Nimes, University Hospital, Nimes University Hospital, Nimes, France
| | - Boris Keren
- Department of Genetics, APHP Sorbonne University, Paris, France
| | - Cyril Mignot
- Department of Genetics, APHP Sorbonne University, Paris, France
| | - Evan Gouy
- Department of Genetics, Hospices Civils de Lyon, Lyon, France
| | - Sylvie Jaillard
- Department of Cytogenetics and Cell Biology, Rennes university hospital, Rennes, France
| | - Emilie Landais
- Department of Genetics, Reims University Hospital, Reims, France
| | - Céline Poirsier
- Department of Genetics, Reims University Hospital, Reims, France
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Minotti C, Graziani L, Sallicandro E, Digilio MC, Falasca R, Alesi V, Novelli G, Dentici ML, Loddo S, Novelli A. Case report: A new de novo 6q21q22.1 interstitial deletion case in a girl with cerebellar vermis hypoplasia and developmental delay and literature review. Front Genet 2024; 14:1315291. [PMID: 38380230 PMCID: PMC10877002 DOI: 10.3389/fgene.2023.1315291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/04/2023] [Indexed: 02/22/2024] Open
Abstract
Interstitial deletions involving 6q chromosomal region are rare. Less than 30 patients have been described to date, and fewer have been characterized by high-resolution techniques, such as chromosomal microarray. Deletions involving 6q21q22.1 region are associated with an extremely wide and heterogeneous clinical spectrum, thus genotype-phenotype correlation based on the size of the rearranged region and on the involved genes is complex, even among individuals with overlapping deletions. Here we describe the phenotypic and molecular characterization of a new 6q interstitial deletion in a girl with developmental delay, intellectual disability, cerebellar vermis hypoplasia, facial peculiar characteristics, ataxia and ocular abnormalities. Microarray analysis of the proposita revealed a 7.9 Mb interstitial de novo deletion at 6q21q22.1 chromosomal region, which spanned from nucleotides 108,337,770 to 116,279,453 (GRCh38/hg38). The present case, alongside with a systematic review of the literature, provides further evidence that could aid to the definition of the Smallest Region of Overlap and of the genomic traits that are associated with particular phenotypes, focusing on neurological findings and especially on cerebellar anomalies.
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Affiliation(s)
- Chiara Minotti
- Medical Genetics Unit, Translational Pediatrics and Clinical Genetics Research Area, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy
- Medical Genetics Section, Depepartment of Biomedicine and Prevention, Tor Vergata University of Rome, Rome, Italy
| | - Ludovico Graziani
- Medical Genetics Unit, Translational Pediatrics and Clinical Genetics Research Area, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy
- Medical Genetics Section, Depepartment of Biomedicine and Prevention, Tor Vergata University of Rome, Rome, Italy
| | - Ester Sallicandro
- Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Maria Cristina Digilio
- Medical Genetics Unit, Translational Pediatrics and Clinical Genetics Research Area, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy
| | - Roberto Falasca
- Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Viola Alesi
- Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Giuseppe Novelli
- Medical Genetics Section, Depepartment of Biomedicine and Prevention, Tor Vergata University of Rome, Rome, Italy
- Medical Genetics Lab, Tor Vergata Hospital, Rome, Italy
| | - Maria Lisa Dentici
- Medical Genetics Unit, Translational Pediatrics and Clinical Genetics Research Area, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy
| | - Sara Loddo
- Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Antonio Novelli
- Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
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Carrillo YD, Rueda-Gaitán P, Gualdrón O, Estrada-Serrato C, Castro-Cuesta TA, Londoño O, Rodríguez-Salazar L, Isaza-Ruget M, Arcos-Burgos M, López Rivera JJ. Diagnostic yield of chromosomal microarray in the largest Latino clinical cohort. Am J Med Genet A 2024; 194:218-225. [PMID: 37795898 DOI: 10.1002/ajmg.a.63427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 08/30/2023] [Accepted: 09/19/2023] [Indexed: 10/06/2023]
Abstract
Copy number variants (CNVs) remain a major etiological cause of neurodevelopmental delay and congenital malformations. Chromosomal microarray analysis (CMA) represents the gold standard for CNVs molecular characterization. We applied CMA throughout the patient's clinical diagnostic workup, as the patient's medical provider requested. We collected CMA results of 3380 patients enrolled for 5 years (2016-2021). We found 830 CNVs in 719 patients with potential clinical significance, that is, (i) pathogenic, (ii) likely pathogenic, and (iii) variants of uncertain significance (VUS), from which 10.6% (predominantly involving chromosomes 15 and 22) were most likely the final cause underpinning the patients' clinical phenotype. For those associated with neurodevelopmental phenotypes, the rate of pathogenic or likely pathogenic findings among the patients with CNVs was 60.75%. When considering epileptic phenotypes, it was 59%. Interestingly, our protocol identified two gains harbored in 17q21.31 and 9q34.3, internationally classified initially as VUS. However, because of their high frequency, we propose that these two VUS be reclassified as likely benign in this widely heterogeneous phenotypic population. These results support the diagnostic yield efficiency of CMA in characterizing CNVs to define the final molecular cause of genetic diseases in this cohort of Colombian patients, the most significant sample of patients from a Latino population, and define new benign polymorphic CNVs.
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Affiliation(s)
- Yina D Carrillo
- Laboratorio Clínico Especializado, Clinica Universitaria Colombia, Clínica Colsanitas, Bogotá, Colombia
| | - Paula Rueda-Gaitán
- Laboratorio Clínico Especializado, Clinica Universitaria Colombia, Clínica Colsanitas, Bogotá, Colombia
| | - Orlando Gualdrón
- Laboratorio Clínico Especializado, Clinica Universitaria Colombia, Clínica Colsanitas, Bogotá, Colombia
- Grupo de investigación INPAC, Grupo Keralty, Bogotá, Colombia
| | - Carlos Estrada-Serrato
- Grupo de Genética Médica, Clínica Universitaria Colombia y Clínica Pediátrica Colsanitas, Clínica Colsanitas, Bogotá, Colombia
| | - Taryn A Castro-Cuesta
- Grupo de Genética Médica, Clínica Universitaria Colombia y Clínica Pediátrica Colsanitas, Clínica Colsanitas, Bogotá, Colombia
| | - Olga Londoño
- Grupo de Genética Médica, Clínica Universitaria Colombia y Clínica Pediátrica Colsanitas, Clínica Colsanitas, Bogotá, Colombia
| | - Luna Rodríguez-Salazar
- Laboratorio Clínico Especializado, Clinica Universitaria Colombia, Clínica Colsanitas, Bogotá, Colombia
| | - Mario Isaza-Ruget
- Grupo de investigación INPAC, Grupo Keralty, Bogotá, Colombia
- Fundación Universitaria Sanitas, Grupo de investigación INPAC, Bogotá, Colombia
- Laboratorio Clínico y de Patología, Clínica Colsanitas, Grupo Keralty, Bogotá, Colombia
| | - Mauricio Arcos-Burgos
- Instituto de Investigaciones Médicas, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Juan Javier López Rivera
- Laboratorio Clínico Especializado, Clinica Universitaria Colombia, Clínica Colsanitas, Bogotá, Colombia
- Grupo de investigación INPAC, Grupo Keralty, Bogotá, Colombia
- Grupo de Genética Médica, Clínica Universitaria Colombia y Clínica Pediátrica Colsanitas, Clínica Colsanitas, Bogotá, Colombia
- Clínica Pediátrica, Clínica Colsanitas, Bogotá, Colombia
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Ma C, Huang R, Fu F, Zhou H, Wang Y, Yan S, Guo F, Chen H, Li L, Jing X, Li F, Han J, Li D, Li R, Liao C. Prenatal diagnosis and outcomes in fetuses with duplex kidney. Int J Gynaecol Obstet 2024. [PMID: 38189110 DOI: 10.1002/ijgo.15344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/13/2023] [Accepted: 12/17/2023] [Indexed: 01/09/2024]
Abstract
OBJECTIVE Duplex kidney is a relatively frequent form of urinary system abnormality. This study aimed to elucidate the value of chromosomal microarray analysis (CMA) and whole exome sequencing (WES) for duplex kidney and the perinatal outcomes of duplex kidney fetuses. METHODS This retrospective cohort study included 63 patients with duplex kidney diagnosed using antenatal ultrasound between August 2013 and January 2023. We reviewed the clinical characteristics, genetic test results, and pregnancy outcomes of the patients. RESULTS Among the 63 cases based on the inclusion criteria, the CMA detected seven (11.1%) clinically significant variants and nine variants of uncertain significance (VUS), and the pathogenic/likely pathogenic (P/LP) copy number variations (CNVs) in the recurrent region that were associated with prenatal duplex kidney included 17q12, 17p13.3, and 22q11.2. No significant disparity was observed in the CMA detection rate between the unilateral and bilateral groups, or between the isolated and non-isolated groups. WES identified three (50%) P/LP single-gene variants in six fetuses with duplex kidney. We detected the following pathogenic genes in the duplex kidney fetuses: KMT2D, SMPD4, and FANCI. Pregnancy termination in cases where clinically significant variants were detected by genetic testing was different in statistical significance from that in cases with negative results (9/10, 90.0% vs 8/48, 16.7%, P < 0.001). CONCLUSION This study elucidated the value of CMA and WES for fetal duplex kidney, proving that CMA and WES may be useful tools in prenatal diagnosis and genetic counseling.
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Affiliation(s)
- Chunling Ma
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Ruibin Huang
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Fang Fu
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Hang Zhou
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - You Wang
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Shujuan Yan
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Fei Guo
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Huanyi Chen
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Lushan Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Xiangyi Jing
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Fucheng Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Jin Han
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Dongzhi Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Ru Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Can Liao
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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11
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Shreeve N, Sproule C, Choy KW, Dong Z, Gajewska-Knapik K, Kilby MD, Mone F. Incremental yield of whole-genome sequencing over chromosomal microarray analysis and exome sequencing for congenital anomalies in prenatal period and infancy: systematic review and meta-analysis. Ultrasound Obstet Gynecol 2024; 63:15-23. [PMID: 37725747 DOI: 10.1002/uog.27491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/08/2023] [Accepted: 09/08/2023] [Indexed: 09/21/2023]
Abstract
OBJECTIVES First, to determine the incremental yield of whole-genome sequencing (WGS) over quantitative fluorescence polymerase chain reaction (QF-PCR)/chromosomal microarray analysis (CMA) with and without exome sequencing (ES) in fetuses, neonates and infants with a congenital anomaly that was or could have been detected on prenatal ultrasound. Second, to evaluate the turnaround time (TAT) and quantity of DNA required for testing using these pathways. METHODS This review was registered prospectively in December 2022. Ovid MEDLINE, EMBASE, MEDLINE (Web of Science), The Cochrane Library and ClinicalTrials.gov databases were searched electronically (January 2010 to December 2022). Inclusion criteria were cohort studies including three or more fetuses, neonates or infants with (i) one or more congenital anomalies; (ii) an anomaly which was or would have been detectable on prenatal ultrasound; and (iii) negative QF-PCR and CMA. In instances in which the CMA result was unavailable, all cases of causative pathogenic copy number variants > 50 kb were excluded, as these would have been detectable on standard prenatal CMA. Pooled incremental yield was determined using a random-effects model and heterogeneity was assessed using Higgins' I2 test. Subanalyses were performed based on pre- or postnatal cohorts, cases with multisystem anomalies and those meeting the NHS England prenatal ES inclusion criteria. RESULTS A total of 18 studies incorporating 902 eligible cases were included, of which eight (44.4%) studies focused on prenatal cohorts, incorporating 755 cases, and the remaining studies focused on fetuses undergoing postmortem testing or neonates/infants with congenital structural anomalies, constituting the postnatal cohort. The incremental yield of WGS over QF-PCR/CMA was 26% (95% CI, 18-36%) (I2 = 86%), 16% (95% CI, 9-24%) (I2 = 85%) and 39% (95% CI, 27-51%) (I2 = 53%) for all, prenatal and postnatal cases, respectively. The incremental yield increased in cases in which sequencing was performed in line with the NHS England prenatal ES criteria (32% (95% CI, 22-42%); I2 = 70%) and in those with multisystem anomalies (30% (95% CI, 19-43%); I2 = 65%). The incremental yield of WGS for variants of uncertain significance (VUS) was 18% (95% CI, 7-33%) (I2 = 74%). The incremental yield of WGS over QF-PCR/CMA and ES was 1% (95% CI, 0-4%) (I2 = 47%). The pooled median TAT of WGS was 18 (range, 1-912) days, and the quantity of DNA required was 100 ± 0 ng for WGS and 350 ± 50 ng for QF-PCR/CMA and ES (P = 0.03). CONCLUSION While WGS in cases with congenital anomaly holds great promise, its incremental yield over ES is yet to be demonstrated. However, the laboratory pathway for WGS requires less DNA with a potentially faster TAT compared with sequential QF-PCR/CMA and ES. There was a relatively high rate of VUS using WGS. © 2023 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- N Shreeve
- Department of Obstetrics & Gynaecology, University of Cambridge, Cambridge, UK
| | - C Sproule
- Department of Obstetrics & Gynaecology, South Eastern Health and Social Care Trust, Belfast, UK
| | - K W Choy
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Z Dong
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - K Gajewska-Knapik
- Department of Obstetrics & Gynaecology, Cambridge University Hospitals, Cambridge, UK
| | - M D Kilby
- Fetal Medicine Centre, Birmingham Women's and Children's Foundation Trust, Birmingham, UK
- College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Medical Genomics Research Group, Illumina, Cambridge, UK
| | - F Mone
- Centre for Public Health, Queen's University Belfast, Belfast, UK
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12
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Huang R, Fu F, Guo F, Zhou H, Yu Q, Yan S, Liu L, Lu J, Ma C, Wang Y, Chen H, Wang D, Zhang Y, Jing X, Li F, Han J, Li D, Li R, Liao C. Prenatal diagnosis of polycystic renal diseases: diagnostic yield, novel disease-causing variants, and genotype-phenotype correlations. Am J Obstet Gynecol MFM 2024; 6:101228. [PMID: 37984685 DOI: 10.1016/j.ajogmf.2023.101228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 11/04/2023] [Accepted: 11/15/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND Polycystic renal disease is a frequent congenital anomaly of the kidneys, but research using chromosomal microarray analysis and exome sequencing in fetuses with polycystic renal disease remains sparse, with most studies focusing on the multisystem or genitourinary system. OBJECTIVE This study aimed to assess the detection rate of detectable genetic causes of fetal polycystic renal disease at different levels, novel disease-causing variants, and genotype-phenotype correlations. STUDY DESIGN This study included 220 fetal polycystic renal disease cases from January 2014 to June 2022. Cases were divided into the following 3 groups: isolated multicystic dysplastic kidneys, nonisolated multicystic dysplastic kidneys, and suspected polycystic kidney disease group. We reviewed data on maternal demographics, ultrasonographic results, chromosomal microarray analysis/exome sequencing results, and pregnancy outcomes. RESULTS In our cohort, chromosomal microarray analysis identified 19 (8.6%) fetuses carrying chromosomal abnormalities, and the most common copy number variation was 17q12 microdeletion (7/220; 3.2%). Furthermore, 94 families chose to perform trio-exome sequencing testing, and 21 fetuses (22.3%) were found to harbor pathogenic/likely pathogenic variants. There was a significant difference in the live birth rate among the 3 groups (91/130 vs 46/80 vs 1/10; P<.001). Among 138 live birth cases, 106 (78.5%) underwent postnatal ultrasound review, of which 95 (89.6%) had a consistent prenatal-postnatal ultrasound diagnosis. CONCLUSION For both isolated and nonisolated polycystic renal disease, our data showed high detection efficiency with both testing tools. The detection of novel pathogenic variants expands the known disease spectrum of polycystic renal disease-associated genes while enriching our understanding of the genotype-phenotype correlation. Therefore, we consider it feasible to perform chromosomal microarray analysis+exome sequencing testing in fetal polycystic renal disease. Moreover, prenatal-postnatal ultrasound concordance was greater, the live birth rate was higher, and prognosis was better when known genetic disorders were excluded, indicating that genetic testing results significantly influenced pregnancy decisions.
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Affiliation(s)
- Ruibin Huang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao)
| | - Fang Fu
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao)
| | - Fei Guo
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao)
| | - Hang Zhou
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao)
| | - Qiuxia Yu
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao)
| | - Shujuan Yan
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao)
| | - Liyuan Liu
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao); The First Clinical Medical College, Southern Medical University, Guangzhou, China (Ms Liu and Ms Ma)
| | - Jianqin Lu
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao)
| | - Chunling Ma
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao); The First Clinical Medical College, Southern Medical University, Guangzhou, China (Ms Liu and Ms Ma)
| | - You Wang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao)
| | - Huanyi Chen
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao)
| | - Dan Wang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao)
| | - Yongling Zhang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao)
| | - Xiangyi Jing
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao)
| | - Fucheng Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao)
| | - Jin Han
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao)
| | - Dongzhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao)
| | - Ru Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao)
| | - Can Liao
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao).
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Borrell A, Ordoñez E, Pauta M, Otaño J, Paz-y-Miño F, de Almeida M, León M, Cirigliano V. Prenatal Exome Sequencing Analysis in Fetuses with Various Ultrasound Findings. J Clin Med 2023; 13:181. [PMID: 38202188 PMCID: PMC10780147 DOI: 10.3390/jcm13010181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/02/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
OBJECTIVES To evaluate the use of Exome Sequencing (ES) for the detection of genome-wide Copy Number Variants (CNVs) and the frequency of SNVs-InDels in selected genes related to developmental disorders in a cohort of consecutive pregnancies undergoing invasive diagnostic procedures for minor or simple ultrasound findings with no indication of ES. METHODS Women undergoing invasive diagnostic testing (chorionic villus sampling or amniocentesis) for QF-PCR and chromosomal microarray analysis (CMA) due to prenatal ultrasound findings without an indication for ES were selected over a five-month period (May-September 2021). ES was performed to compare the efficiency of genome-wide CNV detection against CMA analysis and to detect monogenic disorders. Virtual gene panels were selected to target genes related to ultrasound findings and bioinformatic analysis was performed, prioritizing variants based on the corresponding HPO terms. The broad Fetal Gene panel for developmental disorders developed by the PAGE group was also included in the analysis. RESULTS A total of 59 out of 61 women consented to participate in this study. There were 36 isolated major fetal anomalies, 11 aneuploidy markers, 6 minor fetal anomalies, 4 multiple anomalies, and 2 other ultrasound signs. Following QF-PCR analysis, two uncultured samples were excluded from this study, and six (10%) common chromosome aneuploidies were detected. In the remaining 51 cases, no pathogenic CNVs were detected at CMA, nor were any pathogenic variants observed in gene panels only targeting the ultrasound indications. Two (3.9%) monogenic diseases, apparently unrelated to the fetal phenotype, were detected: blepharo-cheilo-odontic syndrome (spina bifida) and Duchenne muscular dystrophy (pyelocaliceal dilation). CONCLUSIONS In our series of pregnancies with ultrasound findings, common aneuploidies were the only chromosomal abnormalities present, which were detected in 10% of cases. ES CNV analysis was concordant with CMA results in all cases. No additional findings were provided by only targeting selected genes based on ultrasound findings. Broadening the analysis to a larger number of genes involved in fetal developmental disorders revealed monogenic diseases in 3.9% of cases, which, although apparently not directly related to the indications, were clinically relevant.
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Affiliation(s)
- Antoni Borrell
- Barcelona Centre for Maternal-Fetal and Neonatal Medicine (BCNatal), Hospital Clínic Barcelona, Universitat de Barcelona, 08007 Barcelona, Spain; (J.O.); (F.P.-y.-M.)
| | - Elena Ordoñez
- Veritas Genetics, c/Zamora 46-48, 08005 Barcelona, Spain; (E.O.); (M.d.A.); (M.L.); (V.C.)
| | - Montse Pauta
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Juan Otaño
- Barcelona Centre for Maternal-Fetal and Neonatal Medicine (BCNatal), Hospital Clínic Barcelona, Universitat de Barcelona, 08007 Barcelona, Spain; (J.O.); (F.P.-y.-M.)
| | - Fernanda Paz-y-Miño
- Barcelona Centre for Maternal-Fetal and Neonatal Medicine (BCNatal), Hospital Clínic Barcelona, Universitat de Barcelona, 08007 Barcelona, Spain; (J.O.); (F.P.-y.-M.)
| | - Mafalda de Almeida
- Veritas Genetics, c/Zamora 46-48, 08005 Barcelona, Spain; (E.O.); (M.d.A.); (M.L.); (V.C.)
| | - Miriam León
- Veritas Genetics, c/Zamora 46-48, 08005 Barcelona, Spain; (E.O.); (M.d.A.); (M.L.); (V.C.)
| | - Vincenzo Cirigliano
- Veritas Genetics, c/Zamora 46-48, 08005 Barcelona, Spain; (E.O.); (M.d.A.); (M.L.); (V.C.)
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Su L, Wu X, Liang B, Lin N, Xie X, Cai M, Zheng L, Wang M, Xu L. Fetal mosaicism, should conventional karyotype always be performed? J Obstet Gynaecol Res 2023; 49:2836-2848. [PMID: 37844871 DOI: 10.1111/jog.15804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 09/20/2023] [Indexed: 10/18/2023]
Abstract
BACKGROUND AND PURPOSE The application of classical cytogenetic and DNA-based molecular techniques to detect cell lineages of mosaicism derived from cultured or noncultured fetal cells may result in discordant results. This retrospective study aimed to assess the inconsistent diagnostic outcomes, technical availability, and limitations of chromosomal microarray analysis (CMA) and karyotyping for mosaicism. METHODOLOGY A total of 75 fetuses diagnosed with mosaicism by karyotype analysis or CMA were selected, and the results from both the methods were compared and further analyzed. RESULTS A total of 42 (56%, 42/75) CMA results were consistent with karyotypes, consisting of 22 cases of mosaic sex chromosomal abnormalities, 8 routine autosomal aneuploidy cases, 8 other autosome aneuploidy cases, 3 large cryptic genomic rearrangements, and 1 small supernumerary marker chromosome. Discrepancy between karyotype analysis and CMA was observed in 33 (44%, 33/75) mosaicisms involving 15 sex chromosomal abnormalities, 1 routine autosomal aneuploidies, 5 other autosome aneuploidy cases, 8 large cryptic genomic rearrangements, and 4 small supernumerary marker chromosomes. CONCLUSION Considering the disparities between methods as well as the cell populations analyzed, both CMA and karyotype analysis have their own advantages and disadvantages. Therefore, CMA should ideally be used in combination with karyotyping to detect more cases of mosaicism than using either test alone.
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Affiliation(s)
- Linjuan Su
- Fujian Provincial Matenity and Children's Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Xiaoqing Wu
- Fujian Provincial Matenity and Children's Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Bin Liang
- Fujian Provincial Matenity and Children's Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Na Lin
- Fujian Provincial Matenity and Children's Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Xiaorui Xie
- Fujian Provincial Matenity and Children's Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Meiying Cai
- Fujian Provincial Matenity and Children's Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Lin Zheng
- Fujian Provincial Matenity and Children's Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Meiying Wang
- Fujian Provincial Matenity and Children's Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Liangpu Xu
- Fujian Provincial Matenity and Children's Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
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Li R, Qiu X, Shi Q, Wang W, He M, Qiao J, He J, Wang Q. Isolated aberrant right subclavian artery: an underlying clue for genetic anomalies. J Matern Fetal Neonatal Med 2023; 36:2183762. [PMID: 36860092 DOI: 10.1080/14767058.2023.2183762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
OBJECTIVE Aberrant right subclavian artery (ARSA) is known to be associated with specific chromosomal abnormalities. However, there is no agreement regarding clinical decisions related to isolated ARSA. This study evaluated the association between ARSA and genetic abnormalities to provide evidence for prenatal consultation and the postpartum management of isolated ARSA. METHODS This single-center cross-sectional study involved fetuses diagnosed with ARSA between January 2014 and May 2021. A range of data was recorded for each patient, including screening ultrasound, fetal echocardiograms, genetic results, postnatal information, and follow-up records. RESULTS ARSA was detected in 151 fetuses, of which 136 were considered isolated cases. The remaining 9.9% (15/151) of cases had cardiac and/or extracardiac abnormalities or soft markers. Data from karyotype analysis and chromosomal microarray analysis (CMA) were available for 56 and 33 (out of 56) fetuses, respectively. Genetic abnormalities were detected in 10.7% of fetuses (6/56). Of these, 4.4% (2/45) and 36.4% (4/11) were associated with isolated and non-isolated ARSA, respectively, with a significant difference between these two groups regarding the frequency of genetic abnormality (p = 0.011). The analysis detected Klinefelter Syndrome (47, XXY) and 16p11.2 microdeletion in two isolated cases. One case each of trisomy 21 and 22q11.2 deletion, and another case of 47, XXY, were detected in fetuses with cardiac anomalies. Partial 5q deletion was found in a fetus with extracardiac malformations. In total, 141 of the fetuses survived after birth; termination of pregnancy was performed for 10 fetuses; only two fetuses had mild symptoms of dysphagia. CONCLUSION ARSA may be an underlying ultrasonic clue for genetic anomalies even in isolated ARSA. Fetuses with isolated ARSA cannot be ruled out for invasive antenatal diagnosis.
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Affiliation(s)
- Rui Li
- Department of Obstetrics and Gynecology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Xia Qiu
- Department of Obstetrics and Gynecology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Qi Shi
- Department of Obstetrics and Gynecology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Wan Wang
- Department of Obstetrics and Gynecology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Mei He
- Department of Obstetrics and Gynecology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Jing Qiao
- Department of Obstetrics and Gynecology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Jing He
- Department of Obstetrics and Gynecology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Qi Wang
- Department of Obstetrics and Gynecology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
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Xia Z, Zhou R, Li Y, Meng L, Huang M, Tan J, Qiao F, Zhu H, Hu P, Zhu Q, Xu Z, Wang Y. Reproductive outcomes in couples with sporadic miscarriage after embryonic chromosomal microarray analysis. Ann Med 2023; 55:837-848. [PMID: 36869707 PMCID: PMC9987763 DOI: 10.1080/07853890.2023.2183986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/05/2023] Open
Abstract
OBJECTIVES Chromosomal microarray analysis (CMA) has been widely applied to genetic diagnosis in miscarriages in clinical practice. However, the prognostic value of CMA testing of products of conception (POCs) after the first clinical miscarriage remains unknown. The aim of this study was to evaluate the reproductive outcomes after embryonic genetic testing by CMA in SM couples. METHODS In this retrospective study, a total of 1142 SM couples referred for embryonic genetic testing by CMA, and 1022 couples were successfully followed up after CMA. RESULTS Among 1130 cases without significant maternal cell contamination, pathogenic chromosomal abnormalities were detected in 680 cases (60.2%). The subsequent live birth rate did not differ significantly between couples with chromosomally abnormal and normal miscarriage (88.6% vs. 91.1%, p = .240), as well as the cumulative live birth rate (94.5% vs. 96.7%, p = .131). Couples with partial aneuploid miscarriage had a higher likelihood of spontaneous abortion both in the subsequent pregnancy (19.0% vs. 6.5%, p = .037) and cumulative pregnancies (19.0% vs. 6.8%, p = .044) when compared with couples with chromosomally normal miscarriage. CONCLUSIONS SM couples with chromosomally abnormal miscarriage manifested with a similar reproductive prognosis to couples with chromosomally normal miscarriage. Key messagesCMA testing of POCs could provide an accurate genetic diagnosis for couples with SM.The live birth rate of couples with partial aneuploid miscarriage was as high as couples with chromosomally normal miscarriage, despite a higher risk of adverse pregnancy event.Among couples with the most common single aneuploid miscarriage, the cumulative live birth rates of couples with trisomy 16, sex chromosomal abnormalities and trisomy 22 were 94.1%, 95.8% and 84.0%, respectively.
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Affiliation(s)
- Zhengyi Xia
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Ran Zhou
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Yiming Li
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Lulu Meng
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Mingtao Huang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Jianxin Tan
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Fengchang Qiao
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Hui Zhu
- Department of Premarital Care, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Ping Hu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Qiaoying Zhu
- Department of Gynecology, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Zhengfeng Xu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Yan Wang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
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Wright DC, Baluyot ML, Carmichael J, Darmanian A, Jose N, Ngo C, Heaps LS, Yendle A, Holman K, Ziso S, Khan F, Masi A, Silove N, Eapen V. Saliva DNA: An alternative biospecimen for single nucleotide polymorphism chromosomal microarray analysis in autism. Am J Med Genet A 2023; 191:2913-2920. [PMID: 37715344 DOI: 10.1002/ajmg.a.63400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 08/19/2023] [Accepted: 08/30/2023] [Indexed: 09/17/2023]
Abstract
Chromosomal microarray analysis (CMA) is typically performed for investigation of autism using blood DNA. However, blood collection poses significant challenges for autistic children with repetitive behaviors and sensory and communication issues, often necessitating physical restraint or sedation. Noninvasive saliva collection offers an alternative, however, no published studies to date have evaluated saliva DNA for CMA in autism. Furthermore, previous reports suggest that saliva is suboptimal for detecting copy number variation. We therefore aimed to evaluate saliva DNA for single nucleotide polymorphism (SNP) CMA in autistic children. Saliva DNA from 48 probands and parents (n = 133) was obtained with a mean concentration of 141.7 ng/μL. SNP CMA was successful in 131/133 (98.5%) patients from which we correlated the size and accuracy of a copy number variant(s) called between a proband and carrier parent, and for a subgroup (n = 17 probands) who had a previous CMA using blood sample. There were no discordant copy number variant results between the proband and carrier parent, or the subgroup, however, there was an acceptable mean size difference of 0.009 and 0.07 Mb, respectively. Our findings demonstrate that saliva DNA can be an alternative for SNP CMA in autism, which avoids blood collection with significant implications for clinical practice guidelines.
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Affiliation(s)
- Dale Cameron Wright
- Cytogenetics Department, Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
- Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Maria Lourdes Baluyot
- Cytogenetics Department, Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Johanna Carmichael
- Cytogenetics Department, Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Artur Darmanian
- Cytogenetics Department, Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Ngaire Jose
- Cytogenetics Department, Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Con Ngo
- Cytogenetics Department, Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
- Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Luke St Heaps
- Cytogenetics Department, Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
- Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Amber Yendle
- Cytogenetics Department, Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Katherine Holman
- Cytogenetics Department, Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
- Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Sylvia Ziso
- Cytogenetics Department, Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Feroza Khan
- Academic Unit of Infant Child & Adolescent Psychiatry Services (AUCS), South Western Sydney Local Health District, Ingham Institute, Liverpool, Australia
- Discipline of Psychiatry & Mental Health, School of Clinical Medicine, University of New South Wales, Randwick, New South Wales, Australia
| | - Anne Masi
- Academic Unit of Infant Child & Adolescent Psychiatry Services (AUCS), South Western Sydney Local Health District, Ingham Institute, Liverpool, Australia
| | - Natalie Silove
- Child Development Unit, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Valsa Eapen
- Academic Unit of Infant Child & Adolescent Psychiatry Services (AUCS), South Western Sydney Local Health District, Ingham Institute, Liverpool, Australia
- Discipline of Psychiatry & Mental Health, School of Clinical Medicine, University of New South Wales, Randwick, New South Wales, Australia
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Shi X, Ding H, Li C, Liu L, Yu L, Zhu J, Wu J. Clinical utility of chromosomal microarray analysis and whole exome sequencing in foetuses with oligohydramnios. Ann Med 2023; 55:2215539. [PMID: 37243546 DOI: 10.1080/07853890.2023.2215539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 01/30/2023] [Accepted: 05/14/2023] [Indexed: 05/29/2023] Open
Abstract
OBJECTIVES To evaluate the clinical utility of chromosomal microarray analysis (CMA) and whole exome sequencing (WES) in foetuses with oligohydramnios. METHODS In this retrospective study, 126 fetuses with oligohydramnios at our centre from 2018 to 2021 were reviewed. The results of CMA and WES were analysed. RESULTS One hundred and twenty-four cases underwent CMA and 32 cases underwent WES. The detection rate of pathogenic/likely pathogenic (P/LP) copy number variant (CNV) by CMA was 1.6% (2/124). WES revealed P/LP variants in 21.8% (7/32) of the foetuses. Six (85.7%, 6/7) foetuses showed an autosomal recessive inheritance pattern. Three (42.9%, 3/7) variants were involved in the renin-angiotensin-aldosterone system (RAAS), which are the known genetic causes of autosomal recessive renal tubular dysgenesis (ARRTD). CONCLUSION CMA has low diagnostic utility for oligohydramnios, while WES offers obvious advantages in improving the detection rate. WES should be recommended for fetuses with oligohydramnios.
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Affiliation(s)
- Xiaomei Shi
- Genetic Medical Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Hongke Ding
- Genetic Medical Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Chen Li
- Genetic Medical Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Ling Liu
- Genetic Medical Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - LiHua Yu
- Genetic Medical Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Juan Zhu
- Genetic Medical Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Jing Wu
- Genetic Medical Center, Guangdong Women and Children Hospital, Guangzhou, China
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Qian Y, Hu T, Zhang Z, Xiao L, Wang J, Hu R, Liao N, Liu Z, Wang H, Liu S. Prenatal diagnosis with chromosome microarray analysis and pregnancy outcomes of fetuses with umbilical cord cysts. J Matern Fetal Neonatal Med 2023; 36:2203793. [PMID: 37088564 DOI: 10.1080/14767058.2023.2203793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
OBJECTIVE To investigate the prenatal diagnostic value of chromosome microarray analysis (CMA) in fetuses with isolated or non-isolated umbilical cord cysts (UCCs) of various locations and numbers. METHODS Between November 2015 and November 2021, 45 pregnant women carrying fetuses with UCCs underwent amniocentesis and CMA. Fetal prognoses were followed from 6 months to 5 years. RESULTS Five cases (11.1%, 5/45) of chromosomal aberrations were detected. No significant difference in total chromosome abnormalities was found between fetuses with isolated and non-isolated UCCs (13.3% [2/15] vs 10% [3/30]; p > .999). No common autosomal aneuploidies were found in fetuses with isolated UCCs. At follow-up, among 45 fetuses, there were 11 (24.4%) pregnancy terminations, 26 (57.8%) live healthy births, 4 (8.9%) postnatal UCC-related surgeries, and 4 (8.9%) live births of fetuses with other diseases. The frequency of postnatal surgeries of the infants with UCCs located adjacent to the anterior abdominal wall was higher than those located adjacent to the fetal surface of the placenta (30.8% [4/13] vs 0% [0/22]; p = .014). All 26 live healthy neonates and 4 neonates that underwent postnatal surgery had an overall good prognosis. CONCLUSIONS For fetuses with isolated or non-isolated UCC, CMA could be a choice for parents after providing detailed information. Even when surgery was required, pregnancy outcomes and short- and long-term prognoses for fetuses with UCCs were favorable.
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Affiliation(s)
- Yanping Qian
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Ministry of Education, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), China
| | - Ting Hu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Ministry of Education, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), China
| | - Zhu Zhang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Ministry of Education, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), China
| | - Like Xiao
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Ministry of Education, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), China
| | - Jiamin Wang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Ministry of Education, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), China
| | - Rui Hu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Ministry of Education, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), China
| | - Na Liao
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Ministry of Education, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), China
| | - Zhushu Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Ministry of Education, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), China
| | - He Wang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Ministry of Education, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), China
| | - Shanling Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Ministry of Education, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), China
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Guadagnolo D, Mastromoro G, Torres B, Marchionni E, di Palma F, Goldoni M, Cocciadiferro D, Novelli A, Bernardini L, Pizzuti A. Duplication at 19q13.32q13.33 Segregating with Neuropsychiatric Phenotype in a Three-Generation Family: Towards the Definition of a Critical Region. Genes (Basel) 2023; 14:2157. [PMID: 38136979 PMCID: PMC10742575 DOI: 10.3390/genes14122157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/16/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
Chromosomal submicroscopic imbalances represent well-known causes of neurodevelopmental disorders. In some cases, these can cause specific autosomal dominant syndromes, with high-to-complete penetrance and de novo occurrence of the variant. In other cases, they result in non-syndromic neurodevelopmental disorders, often acting as moderate-penetrance risk factors, possibly inherited from unaffected parents. We describe a three-generation family with non-syndromic neuropsychiatric features segregating with a novel 19q13.32q13.33 microduplication. The propositus was a 28-month-old male ascertained for psychomotor delay, with no dysmorphic features or malformations. His mother had Attention-Deficit/Hyperactivity Disorder and a learning disability. The maternal uncle had an intellectual disability. Chromosomal microarray analysis identified a 969 kb 19q13.32q13.33 microduplication in the proband. The variant segregated in the mother, the uncle, and the maternal grandmother of the proband, who also presented neuropsychiatric disorders. Fragile-X Syndrome testing was negative. Exome Sequencing did not identify Pathogenic/Likely Pathogenic variants. Imbalances involving 19q13.32 and 19q13.33 are associated with neurodevelopmental delay. A review of the reported microduplications allowed to propose BICRA (MIM *605690) and KPTN (MIM *615620) as candidates for the neurodevelopmental delay susceptibility in 19q13.32q13.33 copy number gains. The peculiarities of this case are the small extension of the duplication, the three-generation segregation, and the full penetrance of the phenotype.
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Affiliation(s)
- Daniele Guadagnolo
- Department of Experimental Medicine, School of Medicine and Dentistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Gioia Mastromoro
- Department of Experimental Medicine, School of Medicine and Dentistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Barbara Torres
- Medical Genetics Unit, Department of Diagnosis, Treatment and Transfusional Medicine Services, Fondazione Casa Sollievo della Sofferenza, Istituto di Ricovero e Cura a Carattere Scientifico, 71013 San Giovanni Rotondo (FG), Italy
| | - Enrica Marchionni
- Department of Experimental Medicine, School of Medicine and Dentistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Francesca di Palma
- Department of Experimental Medicine, School of Medicine and Dentistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Marina Goldoni
- Medical Genetics Unit, Department of Diagnosis, Treatment and Transfusional Medicine Services, Fondazione Casa Sollievo della Sofferenza, Istituto di Ricovero e Cura a Carattere Scientifico, 71013 San Giovanni Rotondo (FG), Italy
| | - Dario Cocciadiferro
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, 00165 Rome, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, 00165 Rome, Italy
| | - Laura Bernardini
- Medical Genetics Unit, Department of Diagnosis, Treatment and Transfusional Medicine Services, Fondazione Casa Sollievo della Sofferenza, Istituto di Ricovero e Cura a Carattere Scientifico, 71013 San Giovanni Rotondo (FG), Italy
| | - Antonio Pizzuti
- Department of Experimental Medicine, School of Medicine and Dentistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Medical Genetics Unit, Department of Diagnosis, Treatment and Transfusional Medicine Services, Fondazione Casa Sollievo della Sofferenza, Istituto di Ricovero e Cura a Carattere Scientifico, 71013 San Giovanni Rotondo (FG), Italy
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Moradi B, Ariaei A, Heidari-Foroozan M, Banihashemian M, Ghorani H, Rashidi-Nezhad A, Kazemi MA, Taheri MS. Diagnostic yield of prenatal exome sequencing in the genetic screening of fetuses with brain anomalies detected by MRI and ultrasonography: A systematic review and meta-analysis. BJOG 2023. [PMID: 37932235 DOI: 10.1111/1471-0528.17710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 10/03/2023] [Accepted: 10/22/2023] [Indexed: 11/08/2023]
Abstract
BACKGROUND Brain anomalies (BAs) have been the focus of research, as they have a high impact on fetal health but therapeutic and diagnostic approaches are limited. OBJECTIVES In this study, the application and efficiency of exome sequencing (ES) in detecting different cases of BAs in fetuses were evaluated and compared with chromosomal microarray analysis (CMA). SEARCH STRATEGY To conduct this study, three databases including PubMed, Web of Science and Embase were utilised with the keywords 'prenatal', 'diagnoses', 'brain anomalies' and 'exome sequencing'. SELECTION CRITERIA Studies were included based on the STARD checklist, for which the ES and CMA diagnostic yields were calculated. DATA COLLECTION AND ANALYSIS Meta-analysis was performed on the included studies using a random-effects model and subgroup analysis to define the risk difference between them. MAIN RESULTS We included 11 studies representing 779 fetuses that implemented ES along with imaging techniques. The pooled ES diagnostic yield in fetuses with BAs detected through magnetic resonance imaging (MRI) and ultrasonography was 26.53%, compared with 3.46% for CMA. The risk difference between ES and CMA for complex BAs was 0.36 [95% confidence interval (CI) 0.24-0.47], which was higher than for single BAs (0.22; 95% CI 0.18-0.25]. CONCLUSIONS ES is a useful method with a significantly higher diagnostic yield than CMA for genetic assessment of fetuses with complex BAs detected by imaging techniques. Moreover, ES could be applied to suspected fetuses with related family histories to predict congenital diseases with high efficiency.
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Affiliation(s)
- Behnaz Moradi
- Advanced Diagnostic and Interventional Radiology Research Center (ADIR), Tehran University of Medical Sciences, Tehran, Iran
- Department of Radiology, Yas Complex Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Armin Ariaei
- Advanced Diagnostic and Interventional Radiology Research Center (ADIR), Tehran University of Medical Sciences, Tehran, Iran
- Student Research Committee, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mahsa Heidari-Foroozan
- Advanced Diagnostic and Interventional Radiology Research Center (ADIR), Tehran University of Medical Sciences, Tehran, Iran
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoumeh Banihashemian
- Advanced Diagnostic and Interventional Radiology Research Center (ADIR), Tehran University of Medical Sciences, Tehran, Iran
- Department of Radiology, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamed Ghorani
- Advanced Diagnostic and Interventional Radiology Research Center (ADIR), Tehran University of Medical Sciences, Tehran, Iran
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Rashidi-Nezhad
- Maternal, Fetal and Neonatal Research Centre, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Ali Kazemi
- Advanced Diagnostic and Interventional Radiology Research Center (ADIR), Tehran University of Medical Sciences, Tehran, Iran
- Department of Radiology, Amiralam Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Morteza Sanei Taheri
- Department of Radiology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Cao C, Liu F, Yang Y, Zhang Q, Huang J, Liu X. Prenatal whole-exome sequencing in fetuses with increased nuchal translucency. Mol Genet Genomic Med 2023; 11:e2246. [PMID: 37766479 PMCID: PMC10655512 DOI: 10.1002/mgg3.2246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/19/2023] [Accepted: 07/12/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Increased nuchal translucency (NT) is associated with an increased risk for genetic disorders. The aim of this study was to investigate the value of whole-exome sequencing (WES) in detecting genetic abnormalities for fetuses with isolated first-trimester increased NT. METHODS After the exclusion of aneuploidies and pathogenic copy number variants (CNVs) by quantitative fluorescent polymerase chain reaction (QF-PCR) and chromosomal microarray analysis (CMA), WES was performed on 63 fetuses with isolated first-trimester increased NT (≥3.5 mm). RESULTS Overall, WES yielded a 4.8% (3/63) diagnostic rate for fetuses with isolated increased NT. Pathogenic variants were identified in 37.5% (3/8) fetuses that developed additional structural anomalies later in gestation, and no pathogenic variants were detected in increased NT that resolved or remained isolated throughout the pregnancy. CONCLUSION This study provides powerful evidence to offer prenatal WES for increased NT only when additional abnormalities are present. Early detailed ultrasound to detect emerging anomalies can help physicians offer prenatal WES to fetuses with a greater likelihood of diagnosis.
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Affiliation(s)
- Chunge Cao
- Prenatal Diagnosis CenterThe Second Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Fang Liu
- Prenatal Diagnosis CenterChongqing Maternal and Child Healthcare HospitalChongqingChina
| | - Yan Yang
- Prenatal Diagnosis CenterWest China Second University Hospital, Sichuan UniversityChengduChina
| | - Qing Zhang
- Prenatal Diagnosis CenterThe Second Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Junfang Huang
- Department of Obstetrics and GynecologyMaternal and Child Healthcare Hospital of Longhua DistrictShenzhenChina
| | - Xinhong Liu
- Department of Obstetrics and GynecologyMaternal and Child Healthcare Hospital of Longhua DistrictShenzhenChina
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Lv X, Yang X, Li L, Yue F, Zhang H, Wang R. Prenatal diagnosis of 7q11.23 microdeletion: Two cases report and literature review. Medicine (Baltimore) 2023; 102:e34852. [PMID: 37904428 PMCID: PMC10615468 DOI: 10.1097/md.0000000000034852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/21/2023] [Indexed: 11/01/2023] Open
Abstract
RATIONALE Chromosome microdeletions within 7q11.23 can result in Williams-Beuren syndrome which is a rare autosomal dominant disorder. Williams-Beuren syndrome is usually associated with developmental delay, cardiovascular anomalies, mental retardation, and characteristic facial appearance. PATIENT CONCERNS Two pregnant women underwent amniocentesis for cytogenetic analysis and chromosomal microarray analysis (CMA) because of abnormal ultrasound findings. Case 1 presented subependymal cyst and case 2 presented intrauterine growth restriction, persistent left superior vena cava and pericardial effusion in clinical ultrasound examination. DIAGNOSES Cytogenetic examination showed that the 2 fetuses presented normal karyotypic results. CMA detected 1.536 Mb (case 1) and 1.409 Mb (case 2) microdeletions in the region of 7q11.23 separately. INTERVENTIONS Both couples opted for the termination of pregnancies based upon genetic counseling. OUTCOMES The deleted region in both fetuses overlapped with Williams-Beuren syndrome. To our knowledge, case 1 was the first reported fetus of Williams-Beuren syndrome with subependymal cyst. LESSONS The genotype-phenotype of Williams-Beuren syndrome is complicated due to the phenotypic diversity. For prenatal cases, clinicians should consider the combination of ultrasonography, traditional cytogenetic, and molecular diagnosis technology when genetic counseling.
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Affiliation(s)
- Xin Lv
- Prenatal Diagnosis Center and Reproductive Medicine Center, The First Hospital of Jilin University, Changchun, China
| | - Xiao Yang
- Prenatal Diagnosis Center and Reproductive Medicine Center, The First Hospital of Jilin University, Changchun, China
| | - Linlin Li
- Prenatal Diagnosis Center and Reproductive Medicine Center, The First Hospital of Jilin University, Changchun, China
| | - Fagui Yue
- Prenatal Diagnosis Center and Reproductive Medicine Center, The First Hospital of Jilin University, Changchun, China
| | - Hongguo Zhang
- Prenatal Diagnosis Center and Reproductive Medicine Center, The First Hospital of Jilin University, Changchun, China
| | - Ruixue Wang
- Prenatal Diagnosis Center and Reproductive Medicine Center, The First Hospital of Jilin University, Changchun, China
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24
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Maya I, Sukenik-Halevy R, Basel-Salmon L, Sagi-Dain L. A call for public funding of invasive and non-invasive prenatal testing. J Perinat Med 2023; 51:992-996. [PMID: 37207994 DOI: 10.1515/jpm-2023-0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/03/2023] [Indexed: 05/21/2023]
Abstract
For decades, prenatal screening and genetic testing strategies were limited, requiring less complex decisions. Recently, however, several new advanced technologies were introduced, including chromosomal microarray analysis (CMA) and non-invasive prenatal screening (NIPS), bringing about the need to choose the most appropriate testing for each pregnancy. A worrisome issue is that opposed to the wide implementation and debates over public funding of NIPS, currently invasive testing is still recommended only in selected pregnancies with increased risk for chromosomal aberrations (according to screening tests or sonographic anomalies). This current decision-making regarding public funding for invasive and screening testing might compromise informed consent and patient's autonomy. In this manuscript, we compare several characteristics of CMA vs. NIPS, namely: the accuracy and the diagnostic scope, the risks for miscarriage and for clinically uncertain findings, the timing for testing, and pretest counselling. We argue that it must be recognized that one size might not fit all, and suggest that both options should be presented to all couples through early genetic counseling, with public funding for the specific selected test.
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Affiliation(s)
- Idit Maya
- Rabin Medical Center, Recanati Genetics Institute, Beilinson Hospital, Petach Tikva, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Rivka Sukenik-Halevy
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Meir Medical Center, Genetics Institute, Kfar Saba, Israel
| | - Lina Basel-Salmon
- Rabin Medical Center, Recanati Genetics Institute, Beilinson Hospital, Petach Tikva, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Lena Sagi-Dain
- Carmel Medical Center, Affiliated to the Ruth and Bruce Rappaport Faculty of Medicine, Genetics Institute, Technion - Israel Institute of Technology, Haifa, Israel
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25
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Zhuang J, Liu S, Wang J, Chen Y, Zhang H, Jiang Y, Wang G, Chen C. Prenatal whole exome sequencing identified two rare compound heterozygous variants in EVC2 causing Ellis-van Creveld syndrome. Mol Genet Genomic Med 2023; 11:e2242. [PMID: 37485807 PMCID: PMC10568384 DOI: 10.1002/mgg3.2242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/25/2023] Open
Abstract
BACKGROUND Pathogenic mutations in EVC or EVC2 gene can lead to Ellis-van Creveld (EvC) syndrome, which is a rare autosomal recessive skeletal dysplasia disorder. This study aimed to determine pathogenic gene variations associated with EvC syndrome in fetuses showing ultrasound anomalies. METHODS A 32-year-old pregnant woman from Quanzhou, China was investigated. In her pregnancy examination, the fetus exhibited multiple fetal malformations, including a narrow thorax, short limbs, postaxial polydactyly, cardiac malformations, and separation of double renal pelvis. Karyotype, chromosomal microarray analysis and whole exome sequencing were performed for prenatal genetic etiology analysis. RESULTS Chromosome abnormalities and copy number variants were not observed in the fetus using karyotype and chromosomal microarray analysis. Using whole exome sequencing, two compound heterozygous variants NM_147127.5:c.[2484G>A(p.Trp828Ter)];[871-2_894del] in EVC2 gene were identified in the fetus as pathogenic variants inherited from parents. CONCLUSIONS The study is the first to identify two rare compound variants in EVC2 gene in a Chinese family using whole exome sequencing. The application of whole-exome sequencing would be helpful in fetal etiological diagnosis with ultrasound anomalies.
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Affiliation(s)
- Jianlong Zhuang
- Prenatal Diagnosis CenterQuanzhou Women's and Children's HospitalQuanzhouChina
| | - Shufen Liu
- Department of NeurologyThe Second Affiliated Hospital of Fujian Medical UniversityQuanzhouChina
| | - Junyu Wang
- Prenatal Diagnosis CenterQuanzhou Women's and Children's HospitalQuanzhouChina
| | - Yu'e Chen
- Department of UltrasoundQuanzhou Women's and Children's HospitalQuanzhouChina
| | - Hegan Zhang
- Department of GynecologyQuanzhou Women's and Children's HospitalQuanzhouChina
| | - Yuying Jiang
- Prenatal Diagnosis CenterQuanzhou Women's and Children's HospitalQuanzhouChina
| | - Gaoxiong Wang
- Quanzhou Women's and Children's HospitalQuanzhouChina
| | - Chunnuan Chen
- Department of NeurologyThe Second Affiliated Hospital of Fujian Medical UniversityQuanzhouChina
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Hu P, Zhang Q, Cheng Q, Luo C, Zhang C, Zhou R, Meng L, Huang M, Wang Y, Wang Y, Qiao F, Xu Z. Whole genome sequencing vs chromosomal microarray analysis in prenatal diagnosis. Am J Obstet Gynecol 2023; 229:302.e1-302.e18. [PMID: 36907537 DOI: 10.1016/j.ajog.2023.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 02/27/2023] [Accepted: 03/03/2023] [Indexed: 03/12/2023]
Abstract
BACKGROUND Emerging studies suggest that whole genome sequencing provides additional diagnostic yield of genomic variants when compared with chromosomal microarray analysis in the etiologic diagnosis of infants and children with suspected genetic diseases. However, the application and evaluation of whole genome sequencing in prenatal diagnosis remain limited. OBJECTIVE This study aimed to evaluate the accuracy, efficacy, and incremental yield of whole genome sequencing in comparison with chromosomal microarray analysis for routine prenatal diagnosis. STUDY DESIGN In this prospective study, a total of 185 unselected singleton fetuses with ultrasound-detected structural anomalies were enrolled. In parallel, each sample was subjected to whole genome sequencing and chromosomal microarray analysis. Aneuploidies and copy number variations were detected and analyzed in a blinded fashion. Single nucleotide variations and insertions and deletions were confirmed by Sanger sequencing, and trinucleotide repeats expansion variants were verified using polymerase chain reaction plus fragment-length analysis. RESULTS Overall, genetic diagnoses using whole genome sequencing were obtained for 28 (15.1%) cases. Whole genome sequencing not only detected all these aneuploidies and copy number variations in the 20 (10.8%) diagnosed cases identified by chromosomal microarray analysis, but also detected 1 case with an exonic deletion of COL4A2 and 7 (3.8%) cases with single nucleotide variations or insertions and deletions. In addition, 3 incidental findings were detected including an expansion of the trinucleotide repeat in ATXN3, a splice-sites variant in ATRX, and an ANXA11 missense mutation in a case of trisomy 21. CONCLUSION Compared with chromosomal microarray analysis, whole genome sequencing increased the additional detection rate by 5.9% (11/185). Using whole genome sequencing, we detected not only aneuploidies and copy number variations, but also single nucleotide variations and insertions and deletions, trinucleotide repeat expansions, and exonic copy number variations with high accuracy in an acceptable turnaround time (3-4 weeks). Our results suggest that whole genome sequencing has the potential to be a new promising prenatal diagnostic test for fetal structural anomalies.
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Affiliation(s)
- Ping Hu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Qinxin Zhang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Qing Cheng
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Chunyu Luo
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Cuiping Zhang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Ran Zhou
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Lulu Meng
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Mingtao Huang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Yuguo Wang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Yan Wang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China.
| | - Fengchang Qiao
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China.
| | - Zhengfeng Xu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China.
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Yue F, Yang X, Jiang Y, Li S, Liu R, Zhang H. Prenatal phenotypes and pregnancy outcomes of fetuses with recurrent 1q21.1 microdeletions and microduplications. Front Med (Lausanne) 2023; 10:1207891. [PMID: 37692779 PMCID: PMC10484100 DOI: 10.3389/fmed.2023.1207891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/19/2023] [Indexed: 09/12/2023] Open
Abstract
Objective Chromosomal 1q21.1 deletions and duplications are genomic disorders that are usually diagnosed postnatally. However, the genotype-phenotype correlations of 1q21.1 copy number variants (CNVs) during the prenatal period are still not clear. This study aimed to provide a systematic summary of prenatal phenotypes for such genomic disorders. Methods In total, 26 prenatal amniotic fluid samples diagnosed with 1q21.1 microdeletions/microduplications were obtained from pregnant women who opted for invasive prenatal testing. Karyotypic analysis and chromosomal microarray analysis (CMA) were performed for all cases simultaneously. The pregnancy outcomes and health conditions after birth in all cases were followed up. Meanwhile, prenatal cases with 1q21.1 microdeletions or microduplications in the literature were retrospectively collected. Results In total, 11 pregnancies (11/8,252, 0.13%) with 1q21.1 microdeletions and 15 (15/8,252, 0.18%) with 1q21.1 microduplications were identified. Among these 1q21.1 CNVs, 4 cases covered the thrombocytopenia-absent radius (TAR) region, 16 cases covered the 1q21.1 recurrent microdeletion/microduplication region, and 6 cases covered all regions mentioned above. The prenatal abnormal ultrasound findings were recorded in four participants with 1q21.1 deletions and seven participants with 1q21.1 duplications. Finally, three cases with 1q21.1 deletions and five with 1q21.1 duplications terminated their pregnancies. Conclusion In the prenatal setting, 1q21.1 microdeletions were associated with increased nuchal translucency (NT), anomalies of the urinary system, and cardiovascular abnormalities, while 1q21.1 microduplications were correlated with cardiovascular malformations, nasal bone dysplasia, and increased NT. In addition, cerebral ventriculomegaly might be correlated with 1q21.1 microduplications. Considering the variable expressivity and incomplete penetrance of 1q21.1 CNVs, long-term follow-up after birth should be carried out in these cases.
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Affiliation(s)
- Fagui Yue
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Xiao Yang
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Yuting Jiang
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Shibo Li
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Ruizhi Liu
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Hongguo Zhang
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
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Cai M, Que Y, Chen M, Zhang M, Huang H, Xu L, Lin N. Pathogenic copy number variations are associated with foetal short femur length in a tertiary referral centre study. J Cell Mol Med 2023; 27:2354-2361. [PMID: 37401003 PMCID: PMC10424293 DOI: 10.1111/jcmm.17821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 06/09/2023] [Accepted: 06/14/2023] [Indexed: 07/05/2023] Open
Abstract
Shortened foetal femur length (FL) is a common abnormal phenotype that often causes anxiety in pregnant women, and standard clinical treatments remain unavailable. We investigated the clinical characteristics, genetic aetiology and obstetric pregnancy outcomes of foetuses with short FL and provided a reference for perinatal management of such cases. Chromosomal microarray analysis was used to analyse the copy number variations (CNV) in short FL foetuses. Of the 218 foetuses with short FL, 33 foetuses exhibited abnormal CNVs, including 19 with pathogenic CNVs and 14 with variations of uncertain clinical significance. Of the 19 foetuses with pathogenic CNVs, four had aneuploidy, 14 had deletions/duplications, and one had pathogenic uniparental diploidy. The 7q11.23 microdeletion was detected in three foetuses. The severity of short FL was not associated with the rate of pathogenic CNVs. The duration of short FL for the intrauterine ultrasound phenotype in foetuses carrying a pathogenic CNV was independent of the gestational age. Further, maternal age was not associated with the incidence of foetal pathogenic CNVs. Adverse pregnancy outcomes occurred in 77 cases, including termination of pregnancy in 63 cases, postnatal dwarfed foetuses with intellectual disability in 11 cases, and three deaths within 3 months of birth. Pathogenic CNVs closely related to foetal short FL were identified, among which the 7q11.23 microdeletion was highly associated with short FL development. This study provides a reference for the perinatal management of foetuses with short FL.
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Affiliation(s)
- Meiying Cai
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth DefectFuzhouChina
| | - Yanting Que
- College of Clinical Medicine for Obstetrics and Gynecology and PediatricsFujian Medical UniversityFuzhouChina
| | - Meihuan Chen
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth DefectFuzhouChina
| | - Min Zhang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth DefectFuzhouChina
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth DefectFuzhouChina
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth DefectFuzhouChina
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth DefectFuzhouChina
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Liao N, Zhang Z, Liu X, Wang J, Hu R, Xiao L, Yang Y, Lai Y, Zhu H, Li L, Liu S, Wang H, Hu T. A chromosomal microarray analysis-based laboratory algorithm for the detection of genetic etiology of early pregnancy loss. Front Genet 2023; 14:1203891. [PMID: 37470043 PMCID: PMC10352453 DOI: 10.3389/fgene.2023.1203891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/20/2023] [Indexed: 07/21/2023] Open
Abstract
Background: Chromosomal abnormalities are a major cause of early pregnancy loss. However, models synthesizing existing genetic technologies to improve pregnancy outcomes are lacking. We aim to provide an integrated laboratory algorithm for the genetic etiology of couples who experienced pregnancy loss. Methods: Over a 6-year period, 3,634 products of conception (POCs) following early pregnancy loss were collected. The clinical outcomes from a laboratory algorithm based on single nucleotide polymorphism (SNP) array, fluorescence in situ hybridization (FISH), and parental chromosomal karyotyping assays were comprehensively evaluated. Results: In total, 3,445 of 3,634 (94.8%) POCs had no maternal-cell contamination. Of those POCs, the detection rate of abnormal results was 65.2% (2,247/3,445), of which 91.2% (2,050/2,247) had numerical chromosomal abnormalities, 2.7% (60/2,247) had copy-number variations (CNVs) ≥10 Mb, 2.7% (61/2,247) had CNVs of terminal deletion and duplication, 2.8% (62/2,247) had CNVs <10 Mb, and 0.6% (14/2,247) had uniparental disomy. Furthermore, FISH confirmed 7 of the 60 POCs with mosaic aneuploids below 30% based on the SNP array results as tetraploid. Of the 52 POCs with CNVs of terminal deletion and duplication, 29 couples had balanced rearrangements based on chromosomal karyotyping. Conclusion: The integrated SNP array-based algorithm combined with optional FISH and parental chromosomal karyotyping is an effective laboratory testing strategy, providing a comprehensive and reliable genetic investigation for the etiology of miscarriage, regardless of the number of miscarriages and the method of conception.
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Affiliation(s)
- Na Liao
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Zhu Zhang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Xijing Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Jiamin Wang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Rui Hu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Like Xiao
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Yunyuan Yang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Yi Lai
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Hongmei Zhu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Lingping Li
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Shanling Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - He Wang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Ting Hu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
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30
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Jiao Z, Song T, Xu Y, Li J, Liu P, Zhang J, Yang H. Prenatal detection of chromosomal abnormalities and copy number variants in fetuses with corpus callosum agenesis. Ginekol Pol 2023:VM/OJS/J/85508. [PMID: 37162139 DOI: 10.5603/gp.a2022.0121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/29/2021] [Indexed: 05/11/2023] Open
Abstract
OBJECTIVES The corpus callosum is the main pathway that connects interhemispheric communication. Agenesis of corpus callosum (ACC) have not consistently detected replicate genetic risk factors, potentially due to Etiological heterogeneity of this trait. This study aimed to retrospectively analyze the molecular basis for the ACC and the potential genotyping-phenotyping association and provide the basis for genetic counselling. MATERIAL AND METHODS Karyotyping and chromosomal microarray analysis were performed for copy number variants. RESULTS Three cases had 1p36 deletions, two cases had 2q31.2 and 2p16.3 microdeletions, one case had microdeletion of Xq26.3q27.1, five cases involved derived chromosomes due to unbalanced translocations. These cases had variable deletions and duplications with partial overlapping. Phenotypically, besides agenesis of corpus callosum and other brain morphological abnormalities as well as heart abnormalities. CONCLUSIONS ACC may occur alone or be related to other abnormal clinical phenotypes, and its genetic mechanism is very complicated. These results revealed ACC is associated with a variety of chromosomal abnormalities. The findings of the present study expand the genotypes associated with ACC, and further delineation of the genotype-phenotype correlations for ACC. With current applications of chromosome microarray analysis, congenital submicroscopic copy-number variations in fetuses can be detected more effectively.
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Affiliation(s)
- Zheng Jiao
- Department of Gynecology and Obstetrics, Xijing Hospital, The Fourth Military Medical University, Xi'an Shaanxi, China.
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Wang Y, Fu F, Lei T, Zhen L, Deng Q, Zhou H, Ma C, Cheng K, Huang R, Li R, Yu Q, Li L, Han J, Yang X, Li D, Liao C. Genetic diagnosis of fetal microcephaly at a single tertiary center in China. Front Genet 2023; 14:1112153. [PMID: 37229200 PMCID: PMC10203430 DOI: 10.3389/fgene.2023.1112153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/21/2023] [Indexed: 05/27/2023] Open
Abstract
Background: Microcephaly is common in patients with neuropsychiatric problems, and it is usually closely related to genetic causes. However, studies on chromosomal abnormalities and single-gene disorders associated with fetal microcephaly are limited. Objective: We investigated the cytogenetic and monogenic risks of fetal microcephaly and evaluated their pregnancy outcomes. Methods: We performed a clinical evaluation, high-resolution chromosomal microarray analysis (CMA), and trio exome sequencing (ES) on 224 fetuses with prenatal microcephaly and closely followed the pregnancy outcome and prognosis. Results: Among 224 cases of prenatal fetal microcephaly, the diagnosis rate was 3.74% (7/187) for CMA and 19.14% (31/162) for trio-ES. Exome sequencing identified 31 pathogenic or likely pathogenic (P/LP) single nucleotide variants (SNVs) in 25 genes associated with fetal structural abnormalities in 37 microcephaly fetuses; 19 (61.29%) of which occurred de novo. Variants of unknown significance (VUS) was found in 33/162 (20.3%) fetuses. The gene variant involved included the single gene MPCH 2 and MPCH 11, which is associated with human microcephaly, and HDAC8, TUBGCP6, NIPBL, FANCI, PDHA1, UBE3A, CASK, TUBB2A, PEX1, PPFIBP1, KNL1, SLC26A4, SKIV2L, COL1A2, EBP, ANKRD11, MYO18B, OSGEP, ZEB2, TRIO, CLCN5, CASK, and LAGE3. The live birth rate of fetal microcephaly in the syndromic microcephaly group was significantly higher than that in the primary microcephaly group [62.9% (117/186) vs 31.56% (12/38), p = 0.000]. Conclusion: We conducted a prenatal study by conducting CMA and ES for the genetic analysis of fetal microcephaly cases. CMA and ES had a high diagnostic rate for the genetic causes of fetal microcephaly cases. In this study, we also identified 14 novel variants, which expanded the disease spectrum of microcephaly-related genes.
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Affiliation(s)
- You Wang
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Fang Fu
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Tingying Lei
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Li Zhen
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Qiong Deng
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Hang Zhou
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Chunling Ma
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Ken Cheng
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
- School of Medicine, South China University of Technology, Guangzhou, China
| | - Ruibin Huang
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Ru Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Qiuxia Yu
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Lushan Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Jin Han
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Xin Yang
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Dongzhi Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Can Liao
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
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Zhang S, Wang J, Pei Y, Han J, Xiong X, Yan Y, Zhang J, Liu Y, Su F, Xu J, Wu Q. Diagnostic Value of Chromosomal Microarray Analysis for Fetal Congenital Heart Defects with Different Cardiac Phenotypes and Extracardiac Abnormalities. Diagnostics (Basel) 2023; 13:diagnostics13081493. [PMID: 37189594 DOI: 10.3390/diagnostics13081493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/11/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
(1) Background: The objective of this study was to investigate the diagnostic value of chromosomal microarray analysis (CMA) for congenital heart defects (CHDs) with different cardiac phenotypes and extracardiac abnormalities (ECAs) and to explore the pathogenic genetic factors of CHDs. (2) Methods: We collected fetuses diagnosed with CHDs by echocardiography at our hospital from January 2012 to December 2021. We analyzed the CMA results of 427 fetuses with CHDs. We then categorized the CHD into different groups according to two dimensions: different cardiac phenotypes and whether it was combined with ECAs. The correlation between the numerical chromosomal abnormalities (NCAs) and copy number variations (CNVs) with CHDs was analyzed. Statistical analyses, including Chi-square tests and t-tests, were performed on the data using IBM SPSS and GraphPad Prism. (3) Results: In general, CHDs with ECAs increased the detection rate for CA, especially the conotruncal defects. CHD combined with the thoracic and abdominal walls and skeletal, thymic and multiple ECAs, were more likely to exhibit CA. Among the CHD phenotypes, VSD and AVSD were associated with NCA, while DORV may be associated with NCA. The cardiac phenotypes associated with pCNVs were IAA (type A and B), RAA, TAPVC, CoA and TOF. In addition, IAA, B, RAA, PS, CoA and TOF were also associated with 22q11.2DS. The length distribution of the CNV was not significantly different between each CHD phenotype. We detected twelve CNV syndromes, of which six syndromes may be related to CHDs. The pregnancy outcome in this study suggests that termination of pregnancy with fetal VSD and vascular abnormality is more dependent on genetic diagnosis, whereas the outcome in other phenotypes of CHDs may be associated with other additional factors. (4) Conclusions: CMA examination for CHDs is still necessary. We should identify the existence of fetal ECAs and specific cardiac phenotypes, which are helpful for genetic counseling and prenatal diagnosis.
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Affiliation(s)
- Simin Zhang
- Department of Ultrasound, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing 100026, China
- Beijing Maternal and Child Health Care Hospital, Beijing 100026, China
| | - Jingjing Wang
- Department of Ultrasound, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing 100026, China
- Beijing Maternal and Child Health Care Hospital, Beijing 100026, China
| | - Yan Pei
- Beijing Maternal and Child Health Care Hospital, Beijing 100026, China
- Department of Obstetric, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing 100026, China
| | - Jijing Han
- Department of Ultrasound, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing 100026, China
- Beijing Maternal and Child Health Care Hospital, Beijing 100026, China
| | - Xiaowei Xiong
- Department of Ultrasound, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing 100026, China
- Beijing Maternal and Child Health Care Hospital, Beijing 100026, China
| | - Yani Yan
- Department of Obstetric, Peking University People's Hospital, Beijing 100032, China
| | - Juan Zhang
- Department of Ultrasound, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing 100026, China
- Beijing Maternal and Child Health Care Hospital, Beijing 100026, China
| | - Yan Liu
- Beijing Maternal and Child Health Care Hospital, Beijing 100026, China
- Prenatal Diagnosis Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing 100026, China
| | - Fangfei Su
- Department of Ultrasound, Beijing Friendship Hospital, Capital Medical University, Beijing 100032, China
| | - Jinyu Xu
- Department of Ultrasound, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100026, China
| | - Qingqing Wu
- Department of Ultrasound, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing 100026, China
- Beijing Maternal and Child Health Care Hospital, Beijing 100026, China
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33
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Zeng X, Liu F, Xu Y, Liu F. A rare case of uniparental isodisomy of chromosome 7 without phenotypic anomalies. Ginekol Pol 2023:VM/OJS/J/85137. [PMID: 36861877 DOI: 10.5603/gp.a2022.0045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 10/30/2021] [Accepted: 11/11/2021] [Indexed: 11/25/2022] Open
Abstract
Uniparental disomy (UPD) is a well-known epigenomic anomaly with both copies of a homologous pair of chromosomes (or part thereof) inherited from the same parent [1]. Unlike numerical or structural chromosomal aberrations, UPD has no effects on chromosome number or structure, thereby escaping cytogenetic detection [1, 2]. However, UPD detection could be performed by the microsatellite analysis or SNP-based chromosomal microarray analysis (CMA) method. UPD may cause diseases in humans by disrupting normal allelic expression of genes undergoing genomic imprinting, homozygosity in case of autosomal recessive traits, or mosaic aneuploidy [2]. Here we present the first case of parental UPD for chromosome 7 with a normal phenotype.
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Affiliation(s)
- Xiaoli Zeng
- Department of Maternal Health Care, Shiyan Maternal and Child Health Hospital, Shiyan, Hubei, China.
| | - Fang Liu
- Child Health Section, Shiyan Maternal and Child Health Hospital, Shiyan, Hubei, China
| | - Yunfan Xu
- Department of Emergency, Wuhan Jihe Hospital, Wuhan, Hubei, China
| | - Fangfang Liu
- Department of obstetrics, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei, China
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Zhuang J, Luo Q, Xie M, Chen Y, Jiang Y, Zeng S, Wang Y, Xie Y, Chen C. Etiological identification of recurrent male fatality due to a novel NSDHL gene mutation using trio whole-exome sequencing: A rare case report and literature review. Mol Genet Genomic Med 2023; 11:e2121. [PMID: 36504312 PMCID: PMC10009909 DOI: 10.1002/mgg3.2121] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 11/17/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Congenital hemidysplasia with ichthyosiform nevus and limb defects (CHILD) syndrome is a rare X-linked dominant, lethal male disorder caused by mutations to the NSDHL (NAD(P)H steroid dehydrogenase-like protein) gene. It primarily exhibits strictly unilateral congenital hemidysplasia with ichthyosiform erythroderma and ipsilateral limb defects in female individuals. METHODS A Chinese couple suffering from recurrent spontaneous abortion in male fetuses was enrolled in this study. Chromosomal microarray analysis and whole-exome sequencing were performed for genetic etiological diagnosis. RESULTS A 33-year-old pregnant woman with recurrent spontaneous abortion was experiencing her third pregnancy with a male embryo. In this pregnancy, a miscarriage occurred at a gestational age of 10+6 weeks with no copy number variants. However, a novel mutation c.790-6C>T in the NSDHL gene was observed in the fetus through whole-exome sequencing (WES). Parental verification indicated that the NSDHL gene variant was inherited from the mother. Additionally, the variant in the NSDHL gene was absent in her subsequent pregnancy with a female fetus. CONCLUSION In this study, we detected c.790-6C>T, a novel variant in the NSDHL gene that results in recurrent miscarriage in males. Our study may broaden the scope of research on the NSDHL gene in CHILD syndrome and strengthens the application value of WES for the genetic etiological identification of recurrent miscarriage.
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Affiliation(s)
- Jianlong Zhuang
- Center for Prenatal Diagnosis, Quanzhou Women's and Children's Hospital, Quanzhou, Fujian Province, China
| | - Qi Luo
- Department of Public Health for Women and Children, Quanzhou Women's and Children's Hospital, Quanzhou, Fujian, China
| | - Meihua Xie
- Prenatal Diagnosis Center, Yueyang Central Hospital, Yueyang, China
| | - Yu'e Chen
- Ultrasonography, Quanzhou Women's and Children's Hospital, Quanzhou, China
| | - Yuying Jiang
- Center for Prenatal Diagnosis, Quanzhou Women's and Children's Hospital, Quanzhou, Fujian Province, China
| | - Shuhong Zeng
- Center for Prenatal Diagnosis, Quanzhou Women's and Children's Hospital, Quanzhou, Fujian Province, China
| | - Yuanbai Wang
- Center for Prenatal Diagnosis, Quanzhou Women's and Children's Hospital, Quanzhou, Fujian Province, China
| | - Yingjun Xie
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, PR China.,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, PR China
| | - Chunnuan Chen
- Department of Neurology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, PR China
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35
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Akalın M, Demirci O, Dizdaroğulları GE, Çiftçi E, Karaman A. Contribution of chromosomal microarray analysis and next-generation sequencing to genetic diagnosis in fetuses with normal karyotype. J Obstet Gynaecol Res 2023; 49:519-529. [PMID: 36316250 DOI: 10.1111/jog.15486] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/08/2022] [Accepted: 10/20/2022] [Indexed: 11/07/2022]
Abstract
AIM The aim of this study was to investigate the contribution of chromosomal microarray analysis (CMA) and next-generation sequencing (NGS) to genetic diagnosis in fetuses with normal karyotype who underwent invasive testing for different indications. METHODS The results of invasive genetic testing performed at a tertiary center between September 2020 and March 2022 were retrospectively analyzed. Indications for invasive tests were classified as fetal structural malformation, presence of soft markers, and high risk in screening tests. CMA results were classified as pathogenic or likely pathogenic (pCNVs), benign (bCNVs), and variants of unknown clinical significance (VOUS). RESULTS A total of 830 invasive tests were performed and aneuploidy was detected in 11.2% of the fetuses. CMA was performed in 465 fetuses with normal karyotype, and pCNVs were detected in 6.9%. pCNVs were detected in 8.2% of fetuses with structural malformations, 6.5% in soft markers, and 4.7% in high risk in screening tests. Pathogenic variants were detected by NGS in 33.8% of fetuses with bCNVs. CONCLUSIONS pCNVs can be significantly detected not only in fetuses with structural malformations, but also in invasive testing with other indications. NGS significantly contributes to genetic diagnosis in fetuses with structural malformations.
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Affiliation(s)
- Münip Akalın
- Department of Perinatology, Marmara University Pendik Training and Research Hospital, Istanbul, Turkey
| | - Oya Demirci
- Department of Perinatology, University of Health Sciences Zeynep Kamil Women's and Children's Disease Training and Research Hospital, Istanbul, Turkey
| | - Gizem E Dizdaroğulları
- Department of Perinatology, University of Health Sciences Zeynep Kamil Women's and Children's Disease Training and Research Hospital, Istanbul, Turkey
| | - Erman Çiftçi
- Department of Obstetrics and Gynecology, University of Health Sciences Zeynep Kamil Women's and Children's Disease Training and Research Hospital, Istanbul, Turkey
| | - Ali Karaman
- Department of Medical Genetics, University of Health Sciences Zeynep Kamil Women's and Children's Disease Training and Research Hospital, Istanbul, Turkey
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36
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Dap M, Harter H, Lambert L, Perdriolle-Galet E, Bonnet C, Morel O. Genetic studies in isolated bilateral clubfoot detected by prenatal ultrasound. J Matern Fetal Neonatal Med 2022; 35:10384-10387. [PMID: 36167341 DOI: 10.1080/14767058.2022.2128654] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
OBJECTIVE To evaluate the contribution of genetic investigations in case of isolated bilateral clubfoot detected by routine prenatal ultrasound. Pathogenic Copy Number Variations is about 3.9% in fetuses with isolated clubfoot (uni- or bilateral). We hypothesize that this rate could be higher in a homogenous group of fetuses with bilateral clubfoot. METHODS This retrospective single-center study included all women referred to our fetal-medicine center between 2013 and 2020 after ultrasound detection of isolated bilateral clubfoot. Genetic counseling was offered in which the woman was offered an amniocentesis for CMA and targeted investigation for Prader-Willi Syndrome (PWS), Steinert's disease and Spinal Muscular Atrophy (SMA). RESULTS 34 women were referred, 18 of them consented to undergo genetic studies by amniocentesis (18/34; 52.9%). Pathogenic copy number variations (CNVs) were found in 2/18 (11.1%) of cases. One of these CNVs was directly linked to the clubfoot pathology (a deletion in 5q31.1 containing PITX1 gene). Four fetuses (4/18, 22.2%) had variants of unknown significance (VUS). No PWS, SMA or Steinert's disease was found. No case diagnosed with isolated clubfoot prenatally had additional anomalies postnatally. CONCLUSIONS In the case of bilateral isolated clubfoot detected at the antenatal ultrasound, invasive prenatal testing should be offered, and if accepted, a CMA should be done, as pathogenic variations were observed in up to 11.1% of women who got amniocentesis. The findings of this study do not support the systematic recommendation of molecular studies for PWS, SMA, Steinert's disease.
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Affiliation(s)
- Matthieu Dap
- Obstetrics and Fetal medicine Unit, CHRU of Nancy, Nancy, France.,Department of Fetopathology and Placental Pathology, CHRU of Nancy, Nancy, France
| | - Hélène Harter
- Obstetrics and Fetal medicine Unit, CHRU of Nancy, Nancy, France
| | | | | | - Céline Bonnet
- Department of Genetics, CHRU de Nancy, Vandoeuvre-lès-Nancy, Nancy, France
| | - Olivier Morel
- Obstetrics and Fetal medicine Unit, CHRU of Nancy, Nancy, France.,INSERM, Diagnostic and Interventional Adaptive Imaging, University of Lorraine, Nancy, France
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Zhou H, Wang Y, Huang R, Fu F, Li R, Cheng K, Wang D, Yu Q, Zhang Y, Jing X, Lei T, Han J, Yang X, Li D, Liao C. Prenatal Diagnosis and Outcomes in Fetuses with Hemivertebra. Genes (Basel) 2022; 13:genes13091623. [PMID: 36140791 PMCID: PMC9498835 DOI: 10.3390/genes13091623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/07/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Background: There are few studies on the burden of chromosomal abnormalities and single gene disorders in fetal hemivertebra (HV). We aim to investigate the cytogenetic and monogenic risk and evaluate prenatal outcomes of fetal HV. Method: This study included fetuses diagnosed with HV divided into two groups: isolated HV and non-isolated HV. Data on other sonographic structural anomalies, chromosomal and sub-chromosomal abnormalities, monogenic variations detected by WES, and prenatal outcomes are recorded and reviewed. Results: Among 109 fetal HV cases, forty-seven (43.1%) non-isolated HV cases were associated with structural anomalies. Chromosomal test results were available in 58 cases, identifying six (10.3%) chromosomal aberrations involved in four isolated and two non-isolated HV. WES identified four (likely) pathogenic variants in three cases among 16 fetuses with HV, involving three novel variants, 1250G > T and c.1277G> inherited from parents, respectively, in DLL3 and c.7213C > A ** in the FLNB. The live birth rate (LB) was higher in the isolated fetal HV group than in the non-isolated group (67.7% (42/62) vs. 12.5% (12/47), p < 0.001). Conclusion: This study emphasizes the risk of cytogenetic abnormalities in isolated HV. WES yields a diagnostic rate of 18.3% in HV with normal CMA, probably aiding the prenatal counseling and management of fetal HV.
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Affiliation(s)
- Hang Zhou
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510620, China
| | - You Wang
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510620, China
- The First Clinical Medical College, Southern Medical University, Guangzhou 510515, China
| | - Ruibin Huang
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510620, China
| | - Fang Fu
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510620, China
| | - Ru Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510620, China
| | - Ken Cheng
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510620, China
- School of Medicine, South China University of Technology, Guangzhou 510641, China
| | - Dan Wang
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510620, China
| | - Qiuxia Yu
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510620, China
| | - Yongling Zhang
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510620, China
| | - Xiangyi Jing
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510620, China
| | - Tingying Lei
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510620, China
| | - Jin Han
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510620, China
| | - Xin Yang
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510620, China
| | - Dongzhi Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510620, China
| | - Can Liao
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510620, China
- Correspondence: ; Tel.: +86-(020)-38076346
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Qian Y, Xiao L, Zhang L, Hu T, Wang J, Hu R, Liao N, Liu Z, Wang H, Liu S, Zhang Z. Prenatal diagnosis with chromosome microarray and pregnancy outcomes of fetuses with biliary tract system abnormalities. Prenat Diagn 2022; 42:1390-1397. [PMID: 36068921 DOI: 10.1002/pd.6234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 08/22/2022] [Accepted: 08/29/2022] [Indexed: 11/06/2022]
Abstract
OBJECTIVES To investigate the prenatal diagnostic value of chromosome microarray analysis (CMA) in fetuses presenting with ultrasound-based biliary tract system (BTS) anomalies. METHODS Amniocentesis was performed and CMA was applied in 271 pregnant women carrying fetuses with BTS abnormalities between April 2015 and December 2020. Pregnancy outcomes and fetal prognosis were followed from 1 to 6 years. RESULTS Sixteen cases (5.9%, 16/271) of chromosomal anomalies were detected. The detection rate of chromosomal abnormalities was significantly higher for fetuses with nonisolated BTS anomalies than for those with isolated BTS anomalies (9.0% vs 0%, p=0.0017). Follow-up results were obtained from 267 fetuses, including 25 cases of termination of pregnancy (9.4%), 237 live births (88.8%) and 5 (1.9%) neonatal demises. The incidence of congenital biliary atresia in the small gallbladder and nonvisualized gallbladder groups were 3.0% (1/33) and 9.5% (7/74), respectively; however, none was detected on postnatal ultrasound reexamination in the gallbladder enlargement or the other BTS groups. CONCLUSIONS An isolated BTS abnormality is not an indication for invasive prenatal chromosomal analysis. When combined with other ultrasonographic abnormalities, prenatal CMA should be provided. When a small or non-visualized gallbladder is found prenatally, ultrasonography is limited in the differential diagnosis of congenital biliary atresia. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yanping Qian
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Sichuan, China
| | - Like Xiao
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Sichuan, China
| | - Lijuan Zhang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.,Department of Laboratory Medicine, The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - Ting Hu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Sichuan, China
| | - Jiamin Wang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Sichuan, China
| | - Rui Hu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Sichuan, China
| | - Na Liao
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Sichuan, China
| | - Zhushu Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Sichuan, China
| | - He Wang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Sichuan, China
| | - Shanling Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Sichuan, China
| | - Zhu Zhang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Sichuan, China
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Huang R, Yang X, Zhou H, Fu F, Cheng K, Wang Y, Ma C, Li R, Jing X, Han J, Zhen L, Pan M, Li D, Liao C. Prenatal Diagnosis of Talipes Equinovarus by Ultrasound and Chromosomal Microarray Analysis: A Chinese Single-Center Retrospective Study. Genes (Basel) 2022; 13. [PMID: 36140741 DOI: 10.3390/genes13091573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/24/2022] [Accepted: 08/29/2022] [Indexed: 12/03/2022] Open
Abstract
Background: There are few studies on the detection rate by chromosomal microarray analysis (CMA) of the prenatal diagnosis of talipes equinovarus (TE) compared to conventional karyotyping. We aimed to explore the molecular etiology of fetal TE and examine the detection rate by CMA, which provides more information for the clinical screening and genetic counseling of TE. Methods: In this retrospective study, pregnancies diagnosed with fetal TE were enrolled and clinical data for all cases were retrieved from our medical record database, including demographic data for pregnancies, ultrasound findings, karyotype/CMA results, and pregnant and perinatal outcomes. Results: Among the 164 patients, 17 (10.4%) clinically significant variants were detected by CMA. In 148 singleton pregnancies, the diagnostic rate of clinically significant variants was significantly higher in the non-isolated TE group than in the isolated TE group (10/37, 27.0% vs. 6/111, 5.4%, P < 0.001). In twin pregnancies, 1 (6.3%) pathogenic copy number variant was present in the other 16 twin pregnancies. Conclusions: This study demonstrates that CMA is useful for the prenatal genetic diagnosis of fetal TE. Fetal TE with the associated structural malformation correlates with a higher probability of clinically significant variants. This data may aid prenatal diagnosis and genetic counseling for fetal TE.
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40
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Xu C, Peng J, Zhang Y, Liang S, Wang D. Detection of partial deletion and mosaicism using quantitative fluorescent polymerase chain reaction: Case reports and a review of the literature. J Clin Lab Anal 2022; 36:e24574. [PMID: 35766446 PMCID: PMC9396200 DOI: 10.1002/jcla.24574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 05/09/2022] [Accepted: 06/05/2022] [Indexed: 11/12/2022] Open
Abstract
Background Aneuploidy of chromosomes 13, 18, 21, X, and Y can be detected by the quantitative fluorescence polymerase chain reaction (QF‐PCR) performed with short tandem repeat (STR) markers. Although QF‐PCR is designed to detect whole chromosome trisomy, the partial deletion or mosaic of chromosomes may also be detected. Methods Partial deletion or mosaic of chromosomes in three cases was detected by QF‐PCR. Karyotyping and chromosome microarray analysis(CMA) were performed. We further reviewed the clinical utility of QF‐PCR in detecting mosaicisms and deletions/duplications. Results QF‐PCR demonstrated structurally abnormal 21, X, and Y chromosomes in primary amniotic cells. QF‐PCR results in these three cases showed abnormal peak height/peak area, which could not be interpreted according to the kit instructions. QF‐PCR results suggested that there were partial deletions or mosaicism, which were confirmed by karyotyping and CMA. Conclusion In addition to detecting trisomies of whole chromosomes, QF‐PCR can also detect deletion and mosaicism of chromosomes 13, 18, 21, X, and Y, which could suggest the presence of copy number variants (CNVs). Additional testing with genetic technologies, such as karyotyping or microarrays, is recommended when an uninformative pattern is suspected.
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Affiliation(s)
- Chenxia Xu
- Prenatal Diagnosis Center, Boai Hospital of Zhongshan, Zhongshan, China
| | - Jianming Peng
- Prenatal Diagnosis Center, Boai Hospital of Zhongshan, Zhongshan, China
| | - Yanfang Zhang
- Prenatal Diagnosis Center, Boai Hospital of Zhongshan, Zhongshan, China
| | - Shaoxia Liang
- Prenatal Diagnosis Center, Boai Hospital of Zhongshan, Zhongshan, China
| | - Degang Wang
- Prenatal Diagnosis Center, Boai Hospital of Zhongshan, Zhongshan, China.,The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
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41
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Similuk MN, Yan J, Ghosh R, Oler AJ, Franco LM, Setzer M, Kamen M, Jodarski C, DiMaggio T, Davis J, Gore R, Jamal L, Borges A, Gentile N, Niemela J, Lowe C, Jevtich K, Yu Y, Hullfish H, Hsu AP, Hong C, Littel P, Seifert BA, Milner J, Johnston JJ, Cheng X, Li Z, Veltri D, Huang K, Kaladi K, Barnett J, Zhang L, Vlasenko N, Fan Y, Karlins E, Ganakammal SR, Gilmore R, Tran E, Yun A, Mackey J, Yazhuk S, Lack J, Kuram V, Cao W, Huse S, Frank K, Fahle G, Rosenzweig S, Su Y, Hwang S, Bi W, Bennett J, Myles IA, De Ravin SS, Fussm I, Strober W, Bielekova B, Almeida de Jesus A, Goldbach-Mansky R, Williamson P, Kumar K, Dempsy C, Frischmeyer-Guerrerio P, Eisch R, Bolan H, Metcalfe DD, Komarow H, Carter M, Druey KM, Sereti I, Dropulic L, Klion AD, Khoury P, O' Connell EM, Holland-Thomas NC, Brown T, McDermott DH, Murphy PM, Bundy V, Keller MD, Peng C, Kim H, Norman S, Delmonte OM, Kang E, Su HC, Malech H, Freeman A, Zerbe C, Uzel G, Bergerson JRE, Rao VK, Olivier KN, Lyons JJ, Lisco A, Cohen JI, Lionakis MS, Biesecker LG, Xirasagar S, Notarangelo L, Holland SM, Walkiewicz MA. Clinical Exome Sequencing of 1000 Families with Complex Immune Phenotypes: Towards comprehensive genomic evaluations. J Allergy Clin Immunol 2022; 150:947-954. [PMID: 35753512 PMCID: PMC9547837 DOI: 10.1016/j.jaci.2022.06.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 05/07/2022] [Accepted: 06/02/2022] [Indexed: 10/17/2022]
Abstract
BACKGROUND Prospective genetic evaluation of patients at our referral research hospital presents clinical research challenges. OBJECTIVE This study sought not only a single-gene explanation for participants' immune-related presentations, but viewed each participant holistically, with the potential to have multiple genetic contributions to their immune-phenotype and other heritable comorbidities relevant to their presentation and health. METHODS We developed a program integrating exome sequencing, chromosomal microarray, phenotyping, results return with genetic counseling, and reanalysis in 1505 individuals from 1000 families with suspected or known inborn errors of immunity. RESULTS Probands were 50.8% female, 71.5% >18 years, and had diverse immune presentations. Overall, 327/1000 probands (32.7%) received 361 molecular diagnoses. These included 17 probands with diagnostic copy number variants, 32 probands with secondary findings, and 31 probands with multiple molecular diagnoses. Reanalysis added 22 molecular diagnoses, predominantly due to new disease-gene associations (9/22, 40.9%). One-quarter of the molecular diagnoses (92/361) did not involve immune-associated genes. Molecular diagnosis was correlated with younger age, male sex, and a higher number of organ systems involved. This program also facilitated the discovery of new gene-disease associations such as SASH3-related immunodeficiency. A review of treatment options and ClinGen actionability curations suggest that at least 251/361 (69.5%) of these molecular diagnoses could translate into >1 management option. CONCLUSION This program contributes to our understanding of the diagnostic and clinical utility whole exome analysis on a large scale. CLINICAL Implication: Comprehensive analysis of exome data has diagnostic and clinical utility for patients with suspected inborn errors of immunity.
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Affiliation(s)
| | - Jia Yan
- Centralized Sequencing Program
- DIR
- NIAID
| | | | - Andrew J Oler
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Luis M Franco
- Functional Immunogenomics Unit
- Systemic Autoimmunity Branch
- National Institute of Arthritis and Musculoskeletal and Skin Diseases
| | | | | | | | - Thomas DiMaggio
- Fungal Pathogenesis Section
- Laboratory of Clinical Immunology and Microbiology
| | - Joie Davis
- Immunopathogenesis Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | | | - Leila Jamal
- Johns Hopkins/NIH Genetic Counseling Training Program; Genetics Branch, Center for Cancer Research, National Cancer Institute; NIH Clinical Center Department of Bioethics
| | | | | | | | - Chenery Lowe
- Health, Behavior, and Society
- Johns Hopkins Bloomberg School of Public Health
| | - Kathleen Jevtich
- School of Medicine
- Uniformed Services University of Health Sciences
| | | | | | - Amy P Hsu
- Immunopathogenesis Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | | | - Patricia Littel
- Genetic Immunotherapy Section
- Laboratory of Clinical Immunology and Microbiology
| | | | | | | | - Xi Cheng
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Zhiwen Li
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Daniel Veltri
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Ke Huang
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Krishnaveni Kaladi
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Jason Barnett
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Lingwen Zhang
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Nikita Vlasenko
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Yongjie Fan
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Eric Karlins
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | | | - Robert Gilmore
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Emily Tran
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Alvin Yun
- Operations and Engineering Branch
- Office of Cyber Infrastructure and Computational Biology
- NIAID
| | - Joseph Mackey
- Operations and Engineering Branch
- Office of Cyber Infrastructure and Computational Biology
- NIAID
| | - Svetlana Yazhuk
- Operations and Engineering Branch
- Office of Cyber Infrastructure and Computational Biology
- NIAID
| | - Justin Lack
- NIAID Collaborative Bioinformatics Resource
- Leidos Biomedical Research, Inc
| | - Vasu Kuram
- NIAID Collaborative Bioinformatics Resource
- Leidos Biomedical Research, Inc
| | - Wen Cao
- NIAID Collaborative Bioinformatics Resource
- Leidos Biomedical Research, Inc
| | - Susan Huse
- NIAID Collaborative Bioinformatics Resource
- Leidos Biomedical Research, Inc
| | | | | | | | - Yan Su
- Immunology Service
- Laboratory Medicine
- NIH
| | - SuJin Hwang
- Tumor Vaccines and Biotechnology Branch, Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration
| | - Weimin Bi
- Department of Molecular and Human Genetics
- Baylor Genetics
| | - John Bennett
- Clinical Mycology
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Ian A Myles
- Epithelial Therapeutics Unit
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Suk See De Ravin
- Laboratory of Host Defenses
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Ivan Fussm
- Mucosal Immunity Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Warren Strober
- Mucosal Immunity Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Bibiana Bielekova
- Neuroimmunological Diseases Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Adriana Almeida de Jesus
- Translational Autoinflammatory Disease Studies Unit
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Raphaela Goldbach-Mansky
- Translational Autoinflammatory Disease Studies Unit
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Peter Williamson
- Translational Mycology Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | | | - Caeden Dempsy
- Food Allergy Research Unit
- Laboratory of Allergic Diseases
- NIAID
| | | | - Robin Eisch
- Mast Cell Biology Section
- Laboratory of Allergic Diseases
- NIAID
| | - Hyejeong Bolan
- Mast Cell Biology Section
- Laboratory of Allergic Diseases
- NIAID
| | - Dean D Metcalfe
- Mast Cell Biology Section
- Laboratory of Allergic Diseases
- NIAID
| | - Hirsh Komarow
- Mast Cell Biology Section
- Laboratory of Allergic Diseases
- NIAID
| | - Melody Carter
- Mast Cell Biology Section
- Laboratory of Allergic Diseases
- NIAID
| | - Kirk M Druey
- Lung and Vascular Inflammation Section
- Laboratory of Allergic Diseases
- NIAID
| | - Irini Sereti
- HIV Pathogenesis Section
- Laboratory of Immunoregulation
- NIAID
| | - Lesia Dropulic
- Medical Virology Section
- Laboratory of Immunoregulation
- NIAID
| | - Amy D Klion
- Human Eosinophil Section
- Laboratory of Parasitic Diseases
- NIAID
| | - Paneez Khoury
- Human Eosinophil Section
- Laboratory of Parasitic Diseases
- NIAID
| | | | | | - Thomas Brown
- Human Eosinophil Section
- Laboratory of Parasitic Diseases
- NIAID
| | | | - Philip M Murphy
- Molecular Signaling Section
- Laboratory of Molecular Immunology
- NIAID
| | - Vanessa Bundy
- Division of Allergy and Immunology
- Children's National Health System
| | - Michael D Keller
- Division of Allergy and Immunology
- Children's National Health System
| | - Christine Peng
- Division of Allergy and Immunology
- Children's National Health System
| | - Helen Kim
- Division of Allergy and Immunology
- Children's National Health System
| | - Stephanie Norman
- Division of Allergy and Immunology
- Children's National Health System
| | - Ottavia M Delmonte
- Immune Deficiency Genetics Diseases Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Elizabeth Kang
- Genetic Immunotherapy Section
- Laboratory of Clinical Immunology and Microbiology
| | - Helen C Su
- Human Immunological Diseases Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Harry Malech
- Genetic Immunotherapy Section
- Laboratory of Clinical Immunology and Microbiology
| | - Alexandra Freeman
- Immunopathogenesis Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Christa Zerbe
- Immunopathogenesis Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Gulbu Uzel
- Immunopathogenesis Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Jenna R E Bergerson
- Primary Immune Deficiency Clinic
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - V Koneti Rao
- Primary Immune Deficiency Clinic
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | | | - Jonathan J Lyons
- Translational Allergic Immunopathology Unit
- Laboratory of Allergic Diseases
- NIAID
| | - Andrea Lisco
- HIV Pathogenesis Section
- Laboratory of Immunoregulation
- NIAID
| | - Jeffrey I Cohen
- Medical Virology Section
- Laboratory of Infectious Diseases
- NIAID
| | - Michail S Lionakis
- Fungal Pathogenesis Section
- Laboratory of Clinical Immunology and Microbiology
| | | | - Sandhya Xirasagar
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Luigi Notarangelo
- Immune Deficiency Genetics Diseases Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Steven M Holland
- Immunopathogenesis Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
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Cui W, Li X, Jin Y, Zhang J. Prenatal Diagnosis and Molecular Cytogenetic Characterization of Xp22.32p22.31 microduplication in a Chinese family. Ginekol Pol 2022; 94:VM/OJS/J/85248. [PMID: 35315014 DOI: 10.5603/gp.a2021.0225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/14/2021] [Accepted: 11/19/2021] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVES To explore the relationship between Xp22.32p22.31 microduplication and mental retardation identifiable by chromosomal G-banding and chromosomal microarray analysis (CMA). MATERIAL AND METHODS Chromosomal G-banding, CMA, and physical and mental examinations were performed on four members of a Chinese family. RESULTS The mother and one baby had the same microduplication (arr[GRCh37] Xp22.32p22.31(5970505-6075215)x2), and the baby had mental retardation. CONCLUSIONS Xp22.32p22.31 microduplication in males could cause mental retardation. Combination of NIPT, prenatal ultrasound, chromosomal G-banding and CMA has high accuracy in risk assessment for prenatal diagnosis.
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Affiliation(s)
- Weixin Cui
- Department of Obstetrics, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, PR China
| | - Xi Li
- Department of Gastroenterology, Peking University Shenzhen Hospital, Shenzhen, Guangdong, PR China
| | - Yan Jin
- Department of of child Health Care, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, PR China
| | - Juan Zhang
- Department of Stomatology, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, PR China.
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Ma Y, Lei E, Liu F, Chen Z. Prenatal diagnosis of chromosome 3q25.32 and 12p11.22p11.1 microduplication with a favorable outcome. Ginekol Pol 2022; 93:937-938. [PMID: 35315027 DOI: 10.5603/gp.a2021.0253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 10/26/2021] [Accepted: 10/26/2021] [Indexed: 01/26/2023] Open
Affiliation(s)
- Yan Ma
- Transfusin Research Department, Wuhan Blood Center, Wuhan, Hubei, PR China
| | - E Lei
- Surgical Anesthesiology Department, Shiyan Maternal and Child Health Hospital, Shiyan, Hubei, PR China
| | - Fang Liu
- Child Health Section, Shiyan Maternal and Child Health Hospital, Shiyan, Hubei, PR China
| | - Zhijun Chen
- Department of Stomatology, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, PR China.
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Song T, Zheng J, Li Y, Li J, Guo F, Zhao S, Zhang W, Xu Y, Yang H. Prenatal diagnosis of pure 1p36 terminal deletion by chromosome microarry analysis - clinical report of 3 new cases and review of the literature. Ginekol Pol 2022:VM/OJS/J/75604. [PMID: 35072240 DOI: 10.5603/gp.a2021.0173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 12/07/2021] [Accepted: 06/12/2021] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVES Our objective was to present the experience on prenatal diagnosis of 1p36 terminal deletion, and further delineated the fetal presentation of the syndrome. MATERIAL AND METHODS This was a retrospective analysis of three new prenatal cases with pure 1p36 terminal deletion detected by chromosome microarray analysis (CMA) at a single Chinese medical center. We also reviewed 11 published prenatal cases with similar deletion sizes. Clinical data of all cases including indications for invasive testing, sonographic findings, maternal factors, and pregnancy outcomes were reviewed and analyzed. RESULTS Three new cases with pure 1p36 terminal deletion were prenatal diagnosed by CMA, the sizes of the deletion were 1.3 Mb, 5.0 Mb, and 4.9 Mb respectively. All cases were detected because of abnormal ultrasound findings, including central nervous system (CNS) abnormalities, congenital heart disease (CHD) and fetal growth restriction. Two pregnancies were terminated, and one was live-born but died three months after birth. CONCLUSIONS The 1p36 terminal deletion results in many clinical manifestations, but the specificity of clinical features are not high. Prenatal sonographic findings such as CNS, CHD may act as suggestive signs of 1p36 deletion or other microdeletion/duplication syndromes.
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Affiliation(s)
- Tingting Song
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Air Force Medical University, China.
| | - Jiao Zheng
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Air Force Medical University, China
| | - Yu Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Air Force Medical University, China
| | - Jia Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Air Force Medical University, China
| | - Fenfen Guo
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Air Force Medical University, China
| | - Shuhua Zhao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Air Force Medical University, China
| | | | - Ying Xu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Air Force Medical University, China
| | - Hong Yang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Air Force Medical University, China
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Zhuang J, Chen C, Chen Y, Luo Q, Wang Y, Jiang Y, Zeng S, Xie Y, Chen D. Identification of a Rare Variant of c.1777G>A (p.G593S) in the COL1A1 Gene as the Etiology of Recurrent Osteogenesis Imperfecta by Whole-Exome Sequencing. Front Pediatr 2022; 10:816090. [PMID: 35463886 PMCID: PMC9028459 DOI: 10.3389/fped.2022.816090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 02/11/2022] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Osteogenesis imperfecta (OI) is a rare heterogeneous disorder typically featured by fragile bones and susceptibility to fracture. The aim of the present study was to explore the genetic etiology of familial recurrent OI and the genotype-phenotype correlation. METHODS Karyotyping, chromosomal microarray analysis, and whole-exome sequencing (WES) were performed to determine the genetic etiology of OI in the enrolled family. Western blotting analysis was carried out using the fetal skin tissue for type I collagen production analysis. RESULTS At the first pregnancy, a c.1777G>A mutation in the COL1A1 gene was detected in the fetus who exhibited skeletal dysplasia. In this second pregnancy, severe fetal skeletal dysplasia was also presented without significant chromosomal abnormality detected by karyotype and chromosomal microarray analysis in the fetus. Further WES results demonstrated a de novo missense mutation of c.1777G>A (p.G593S) in the fetus, which was classified as a pathogenic variant according to the ACMG guidelines. The recurrent mutation in the two fetuses hinted at the possible existence of gonadal mosaicism in the parents, while no mutation in the COL1A1 gene was identified in the DNA from the father's sperm. In addition, Western blot results demonstrated no reduced type I procollagen production in the affected fetus compared with the age-matched controls. CONCLUSIONS To the best of our knowledge, this is the first study that identified a rare variant of c.1777G>A in the COL1A1 gene that led to recurrent OI in the Chinese population. Additionally, we believe that this rare variant of c.1777G>A in the COL1A1 gene will lead to OI type II. The results of the present study further verify the application value of WES in identifying fetuses with ultrasound anomalies.
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Affiliation(s)
- Jianlong Zhuang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, China
| | - Chunnuan Chen
- Department of Neurology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Yu'e Chen
- Department of Ultrasound, Quanzhou Women's and Children's Hospital, Quanzhou, China
| | - Qi Luo
- Department of Public Health for Women and Children, Quanzhou Women's and Children's Hospital, Quanzhou, China
| | - Yuanbai Wang
- 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
| | - Yingjun Xie
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Dongmei Chen
- Department of Neonatal Intensive Care Unit, Quanzhou Women's and Children's Hospital, Quanzhou, China
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Wu X, Su L, Shen Q, Guo Q, Li Y, Xu S, Lin N, Huang H, Xu L. Chromosomal Abnormalities and Pregnancy Outcomes for Fetuses With Gastrointestinal Tract Obstructions. Front Pediatr 2022; 10:918130. [PMID: 35783302 PMCID: PMC9245709 DOI: 10.3389/fped.2022.918130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/09/2022] [Indexed: 11/23/2022] Open
Abstract
Fetal gastrointestinal tract obstruction (GITO) is the most frequently encountered gastrointestinal defect in the prenatal period. This study aimed to investigate the genetic disorders and pregnancy outcomes of fetal GITO. We reviewed data from 70 pregnancies that were referred for invasive prenatal testing because of fetal GITO. According to the level of obstruction, they were classified into esophageal atresia/stenosis, duodenal atresia/stenosis, jejunal or ileal atresia/stenosis, or anal atresia. Traditional karyotyping was performed on all the 70 pregnancies, and chromosomal microarray analysis (CMA) was performed on 32 of them in parallel. Traditional karyotyping revealed twelve (17.1%) chromosomal abnormalities, including 11 cases of trisomy 21 (Down syndrome), and one case of a supernumerary marker chromosome related to Cat eye syndrome. According to the absence or presence of other ultrasound anomalies, they were categorized into isolated GITO (n = 36) and non-isolated GITO (n = 34). The rate of chromosomal abnormalities in the non-isolated GITO pregnancies was significantly higher than that in the isolated GITO pregnancies (29.4 vs. 5.5%, p < 0.05); the survival rate in the isolated group was significantly higher than that in the non-isolated group (67.6 vs. 34.4%, p < 0.05). Among the 32 cases where CMA was performed, an additional one (3.1%) copy number variant with clinical significance was noted in a fetus with normal karyotype. The microduplication on 7q12 was considered to be the genetic etiology of duodenal stenosis, although it was inherited from a phenotypically normal mother. Our study supports the strong association between Down syndrome and fetal GITO, especially duodenal stenosis. Our findings suggested that the risk of chromosomal abnormalities was increased when GITO was accompanied by other ultrasound anomalies; thus, chromosomal abnormalities and fetal anatomy should be carefully evaluated for pregnancy management of fetal GITO.
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Affiliation(s)
- Xiaoqing Wu
- Department of Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China.,Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China.,Department of Laboratory Medicine, Fujian Medical University, Fuzhou, China
| | - Linjuan Su
- Department of Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China.,Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Qingmei Shen
- Department of Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China.,Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Qun Guo
- Department of Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China.,Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Ying Li
- Department of Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China.,Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Shiyi Xu
- Department of Pediatrics, Guangxi Medical University, Nanning, China
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center of Fujian Provincial Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Hailong Huang
- Department of Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China.,Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Liangpu Xu
- Department of Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China.,Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
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Wu X, Su L, Shen Q, Guo Q, Li Y, Xu S, Lin N, Huang H, Xu L. Corrigendum: Chromosomal abnormalities and pregnancy outcomes for fetuses with gastrointestinal tract obstructions. Front Pediatr 2022; 10:976997. [PMID: 36389373 PMCID: PMC9644240 DOI: 10.3389/fped.2022.976997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/06/2022] [Indexed: 11/28/2022] Open
Abstract
[This corrects the article DOI: 10.3389/fped.2022.918130.].
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Affiliation(s)
- Xiaoqing Wu
- Department of Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China.,Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China.,Department of Laboratory Medicine, Fujian Medical University, Fuzhou, China
| | - Linjuan Su
- Department of Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China.,Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Qingmei Shen
- Department of Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China.,Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Qun Guo
- Department of Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China.,Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Ying Li
- Department of Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China.,Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Shiyi Xu
- Department of Pediatrics, Guangxi Medical University, Nanning, China
| | - Na Lin
- Department of Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China.,Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Hailong Huang
- Department of Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China.,Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Liangpu Xu
- Department of Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China.,Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
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Cheng MC, Chien WH, Huang YS, Fang TH, Chen CH. Translational Study of Copy Number Variations in Schizophrenia. Int J Mol Sci 2021; 23:ijms23010457. [PMID: 35008879 PMCID: PMC8745588 DOI: 10.3390/ijms23010457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/11/2021] [Accepted: 12/29/2021] [Indexed: 11/16/2022] Open
Abstract
Rare copy number variations (CNVs) are part of the genetics of schizophrenia; they are highly heterogeneous and personalized. The CNV Analysis Group of the Psychiatric Genomic Consortium (PGC) conducted a large-scale analysis and discovered that recurrent CNVs at eight genetic loci were pathogenic to schizophrenia, including 1q21.1, 2p16.3 (NRXN1), 3q29, 7q11.23, 15q13.3, distal 16p11.2, proximal 16p11.2, and 22q11.2. We adopted a two-stage strategy to translate this knowledge into clinical psychiatric practice. As a screening test, we first developed a real-time quantitative PCR (RT-qPCR) panel that simultaneously detected these pathogenic CNVs. Then, we tested the utility of this screening panel by investigating a sample of 557 patients with schizophrenia. Chromosomal microarray analysis (CMA) was used to confirm positive cases from the screening test. We detected and confirmed thirteen patients who carried CNVs at these hot loci, including two patients at 1q21.1, one patient at 7q11.2, three patients at 15q13.3, two patients at 16p11.2, and five patients at 22q11.2. The detection rate in this sample was 2.3%, and the concordance rate between the RT-qPCR test panel and CMA was 100%. Our results suggest that a two-stage approach is cost-effective and reliable in achieving etiological diagnosis for some patients with schizophrenia and improving the understanding of schizophrenia genetics.
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Affiliation(s)
- Min-Chih Cheng
- Department of Psychiatry, Yuli Branch, Taipei Veterans General Hospital, Hualien 981, Taiwan;
| | - Wei-Hsien Chien
- Department of Occupational Therapy, College of Medicine, Fu Jen Catholic University, New Taipei City 242, Taiwan;
| | - Yu-Shu Huang
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan 333, Taiwan;
- School of Medicine, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan;
| | - Ting-Hsuan Fang
- School of Medicine, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan;
| | - Chia-Hsiang Chen
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan 333, Taiwan;
- Department and Institute of Biomedical Sciences, Chang Gung University, Taoyuan 333, Taiwan
- Correspondence:
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Sagi-Dain L, Singer A, Petersen OB, Lou S, Vogel I. Trends in Non-invasive Prenatal Screening and Invasive Testing in Denmark (2000-2019) and Israel (2011-2019). Front Med (Lausanne) 2021; 8:768997. [PMID: 34869484 PMCID: PMC8635699 DOI: 10.3389/fmed.2021.768997] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/26/2021] [Indexed: 11/15/2022] Open
Abstract
Introduction: Following the wide distribution of non-invasive prenatal genetic screening (NIPS), numerous studies have reported a decline in total invasive tests in the recent years, up to 50–70% in some countries. However, in Denmark and Israel we have not experienced these declines. The objective of our study was to evaluate the trends in NIPS and chromosomal microarray analysis (CMA) use in Denmark and Israel. Methods: This retrospective study was performed by data acquisition from the Danish Cytogenetics Central Registry throughout the years 2000–2019, and Israeli Public Health Services, Ministry of Health computerized database (from 2011). Results: Of the 1,243,956 live births registered in Denmark over the years 2000–2019, a relatively steady level of invasive testing around 6% was noted since 2004, as opposed to 13.0% in Israel based on 1,594,962 live births between 2011 and 2019. The average uptake of NIPS was 1.1 ± 0.5% in Denmark vs. 4.3% in Israel (2013–2019). Relatively steady rates of invasive testing were noted in both countries, compared to a slight decline in NIPS in the recent years. Discussion: The recent decrease in the rates of invasive testing in the NIPS era was not observed in Denmark or in Israel. These results imply that Danish and Israeli women and/or health providers might favor the high resolution and yield of CMA testing over the non-invasiveness of NIPS. We explore and discuss this phenomenon, based on five central factors.
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Affiliation(s)
- Lena Sagi-Dain
- Prenatal Genetics, Genetics Institute, Carmel Medical Center, Affiliated to the Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Amihood Singer
- Community Genetics, Public Health Services, Ministry of Health, Jerusalem, Israel
| | - Olav B Petersen
- Department of Obstetrics, Center for Fetal Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Stina Lou
- Center for Fetal Diagnostics, Aarhus University, Aarhus, Denmark
| | - Ida Vogel
- Center for Fetal Diagnostics, Aarhus University, Aarhus, Denmark.,Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
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Shi X, Tang H, Lu J, Yang X, Ding H, Wu J. Prenatal genetic diagnosis of omphalocele by karyotyping, chromosomal microarray analysis and exome sequencing. Ann Med 2021; 53:1285-1291. [PMID: 34374610 PMCID: PMC8366676 DOI: 10.1080/07853890.2021.1962966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/27/2021] [Indexed: 01/12/2023] Open
Abstract
OBJECTIVES The aim of this study is to share our experience in the prenatal diagnosis of omphalocele by karyotyping, chromosomal microarray analysis (CMA) and whole exome sequencing (WES). METHODS In this retrospective study, 81 cases of omphalocele were identified from 2015 to 2020. Associated anomalies and prenatal diagnosis based on karyotyping, CMA and WES were analysed. RESULTS Fifty-eight (71.6%) of the 81 foetuses had other ultrasound anomalies. Giant omphalocele was present in 11 cases (13.6%) and small omphalocele was present in 70 cases (86.4%). Chromosomal abnormalities were found in 24 foetuses (29.6%, 24/81), the most common of which were trisomy 18 (58.8%, 11/24) and trisomy 13 (29.2%, 7/24). Compared to isolated omphalocele, non-isolated omphalocele was accompanied by an increased prevalence of chromosomal abnormalities (4.3% (1/23) vs. 39.7% (23/58), χ2 = 8.226, p = .004). All chromosomal abnormalities were found in small omphalocele. Aside from aneuploidy, CMA showed one pathogenic copy number variants (CNVs) for a detection rate of 1.2%, one variants of unknown significance (VOUS) and one instance of loss of heterozygosity (LOH). WES was performed on 3 non-isolated cases, and one was found to have pathogenic variants. CONCLUSIONS The most common genetic cause of omphalocele is aneuploidy and the prevalence of chromosomal abnormalities is increased with non-isolated and small omphalocele. CMA and WES can be useful for providing further genetic information to assist in prenatal counselling and pregnancy management.
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Affiliation(s)
- Xiaomei Shi
- Gentic Medical Center, Guangdong Women and Children Hospital, Guangzhou, PR China
| | - Hui Tang
- Gentic Medical Center, Guangdong Women and Children Hospital, Guangzhou, PR China
| | - Jian Lu
- Gentic Medical Center, Guangdong Women and Children Hospital, Guangzhou, PR China
| | - Xiue Yang
- Gentic Medical Center, Guangdong Women and Children Hospital, Guangzhou, PR China
| | - Hongke Ding
- Gentic Medical Center, Guangdong Women and Children Hospital, Guangzhou, PR China
| | - Jing Wu
- Gentic Medical Center, Guangdong Women and Children Hospital, Guangzhou, PR China
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