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Chai H, DiAdamo A, Grommisch B, Xu F, Zhou Q, Wen J, Mahoney M, Bale A, McGrath J, Spencer-Manzon M, Li P, Zhang H. A Retrospective Analysis of 10-Year Data Assessed the Diagnostic Accuracy and Efficacy of Cytogenomic Abnormalities in Current Prenatal and Pediatric Settings. Front Genet 2019; 10:1162. [PMID: 31850057 PMCID: PMC6902283 DOI: 10.3389/fgene.2019.01162] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 10/23/2019] [Indexed: 01/01/2023] Open
Abstract
Background: Array comparative genomic hybridization (aCGH), karyotyping and fluorescence in situ hybridization (FISH) analyses have been used in a clinical cytogenetic laboratory. A systematic analysis on diagnostic findings of cytogenomic abnormalities in current prenatal and pediatric settings provides approaches for future improvement. Methods: A retrospective analysis was performed on abnormal findings by aCGH, karyotyping, and FISH from 3,608 prenatal cases and 4,509 pediatric cases during 2008–2017. The diagnostic accuracy was evaluated by comparing the abnormality detection rate (ADR) and the relative frequency (RF) of different types of cytogenomic abnormalities between prenatal and pediatric cases. A linear regression correlation between known prevalence and ADR of genomic disorders was used to extrapolate the prevalence of other genomic disorders. The diagnostic efficacy was estimated as percentage of detected abnormal cases by expected abnormal cases from served population. Results: The composite ADR for numerical chromosome abnormalities, structural chromosome abnormalities, recurrent genomic disorders, and sporadic pathogenic copy number variants (pCNVs) in prenatal cases were 13.03%, 1.77%, 1.69%, and 0.9%, respectively, and were 5.13%, 2.84%, 7.08%, and 2.69% in pediatric cases, respectively. The chromosomal abnormalities detected in prenatal cases (14.80%) were significantly higher than that of pediatric cases (7.97%) (p < 0.05), while the pCNVs detected in prenatal cases (2.59%) were significantly lower than that of pediatric cases (9.77%) (p < 0.05). The prevalence of recurrent genomic disorders and total pCNVs was estimated to be 1/396 and 1/291, respectively. Approximately, 29% and 35% of cytogenomic abnormalities expected from the population served were detected in current prenatal and pediatric diagnostic practice, respectively. Conclusion: For chromosomal abnormalities, effective detection of Down syndrome (DS) and Turner syndrome (TS) and under detection of sex chromosome numerical abnormalities in both prenatal and pediatric cases were noted. For pCNVs, under detection of pCNVs in prenatal cases and effective detection of DiGeorge syndrome (DGS) and variable efficacy in detecting other pCNVs in pediatric cases were noted. Extend aCGH analysis to more prenatal cases with fetal ultrasonographic anomalies, enhanced non-invasive prenatal (NIPT) testing screening for syndromic genomic disorders, and better clinical indications for pCNVs are approaches that could improve diagnostic yield of cytogenomic abnormalities.
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Affiliation(s)
- Hongyan Chai
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Autumn DiAdamo
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Brittany Grommisch
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Fang Xu
- Prevention Genetics, Marshfield, WI, United States
| | - Qinghua Zhou
- The First Affiliated Hospital, Biomedical Translational Research Institute, Jinan University, Guangzhou, China
| | - Jiadi Wen
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Maurice Mahoney
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Allen Bale
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - James McGrath
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Michele Spencer-Manzon
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Peining Li
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Hui Zhang
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
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Integrated FISH, Karyotyping and aCGH Analyses for Effective Prenatal Diagnosis of Common Aneuploidies and Other Cytogenomic Abnormalities. Med Sci (Basel) 2019; 7:medsci7020016. [PMID: 30678103 PMCID: PMC6410168 DOI: 10.3390/medsci7020016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/10/2019] [Accepted: 01/21/2019] [Indexed: 01/18/2023] Open
Abstract
Current prenatal genetic evaluation showed a significantly increase in non-invasive screening and the reduction of invasive diagnostic procedures. To evaluate the diagnostic efficacy on detecting common aneuploidies, structural chromosomal rearrangements, and pathogenic copy number variants (pCNV), we performed a retrospective analysis on a case series initially analyzed by aneuvysion fluorescence in situ hybridization (FISH) and karyotyping then followed by array comparative genomic hybridization (aCGH). Of the 386 cases retrieved from the past decade, common aneuploidies were detected in 137 cases (35.5%), other chromosomal structural rearrangements were detected in four cases (1%), and pCNV were detected in five cases (1.3%). The relative frequencies for common aneuploidies suggested an under detection of sex chromosome aneuploidies. Approximately 9.5% of cases with common aneuploidies showed a mosaic pattern. Inconsistent results between FISH and karyotyping were noted in cases with pseudo-mosaicism introduced by culture artifact or variable cellular proliferation from cells with mosaic karyotypic complements under in vitro cell culture. Based on findings from this case series, cell-based FISH and karyotyping should be performed to detect common aneuploidies, structural chromosomal abnormalities, and mosaic pattern. DNA-based aCGH and reflex FISH should be performed to detect and confirm genomic imbalances and pCNV. Practice points to ensure the diagnostic accuracy and efficacy were summarized.
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Vuillaume ML, Moizard MP, Rossignol S, Cottereau E, Vonwill S, Alessandri JL, Busa T, Colin E, Gérard M, Giuliano F, Lambert L, Lefevre M, Kotecha U, Nampoothiri S, Netchine I, Raynaud M, Brioude F, Toutain A. Mutation update for the GPC3 gene involved in Simpson-Golabi-Behmel syndrome and review of the literature. Hum Mutat 2018; 39:790-805. [PMID: 29637653 DOI: 10.1002/humu.23428] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 03/22/2018] [Accepted: 04/02/2018] [Indexed: 11/08/2022]
Abstract
Simpson-Golabi-Behmel syndrome (SGBS) is an X-linked multiple congenital anomalies and overgrowth syndrome caused by a defect in the glypican-3 gene (GPC3). Until now, GPC3 mutations have been reported in isolated cases or small series and the global genotypic spectrum of these mutations has never been delineated. In this study, we review the 57 previously described GPC3 mutations and significantly expand this mutational spectrum with the description of 29 novel mutations. Compiling our data and those of the literature, we provide an overview of 86 distinct GPC3 mutations identified in 120 unrelated families, ranging from single nucleotide variations to complex genomic rearrangements and dispersed throughout the entire coding region of GPC3. The vast majority of them are deletions or truncating mutations (frameshift, nonsense mutations) predicted to result in a loss-of-function. Missense mutations are rare and the two which were functionally characterized, impaired GPC3 function by preventing GPC3 cleavage and cell surface addressing respectively. This report by describing for the first time the wide mutational spectrum of GPC3 could help clinicians and geneticists in interpreting GPC3 variants identified incidentally by high-throughput sequencing technologies and also reinforces the need for functional validation of non-truncating mutations (missense, in frame mutations, duplications).
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Affiliation(s)
- Marie-Laure Vuillaume
- Service de Génétique, CHU de Tours, Hôpital Bretonneau, Tours, France.,INSERM UMR_U930, Faculté de Médecine, Université de Tours, Tours, France
| | - Marie-Pierre Moizard
- Service de Génétique, CHU de Tours, Hôpital Bretonneau, Tours, France.,INSERM UMR_U930, Faculté de Médecine, Université de Tours, Tours, France
| | - Sylvie Rossignol
- Unité d'explorations fonctionnelles endocriniennes, CHU Paris Est, Hôpital d'Enfants Armand-Trousseau, Paris, France.,Service de génétique médicale, CHU de Strasbourg, Hôpital de Hautepierre, Strasbourg, France
| | - Edouard Cottereau
- Service de Génétique, CHU de Tours, Hôpital Bretonneau, Tours, France
| | - Sandrine Vonwill
- Service de Génétique, CHU de Tours, Hôpital Bretonneau, Tours, France.,INSERM UMR_U930, Faculté de Médecine, Université de Tours, Tours, France
| | | | - Tiffany Busa
- Unité de Génétique Clinique, Département de génétique médicale, Hôpital de la Timone, CHU de Marseille, Marseille, France
| | - Estelle Colin
- Département de biochimie et génétique, CHU d'Angers, Angers, France
| | - Marion Gérard
- Service de génétique, CHU de Caen, Hôpital Clémenceau, Avenue Georges Clémenceau, Caen, France
| | - Fabienne Giuliano
- Service de génétique médicale, CHU de Nice, Hôpital l'Archet 2, Nice, France
| | - Laetitia Lambert
- Service de Génétique Clinique, Hôpital d'Enfants, CHU de Nancy, Rue du Morvan, Vandoeuvre-Lès-Nancy, France
| | - Mathilde Lefevre
- Centre de génétique, Hôpital d'enfants, CHU Dijon Bourgogne, Dijon, France
| | - Udhaya Kotecha
- Center of Medical Genetics, Sir Ganga Ram Hospital, Rajinder Nagar, New Delhi, India
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences and Research Center, AIMS Poneakara P O, Cochin, Kerala, India
| | - Irène Netchine
- Unité d'explorations fonctionnelles endocriniennes, CHU Paris Est, Hôpital d'Enfants Armand-Trousseau, Paris, France
| | - Martine Raynaud
- Service de Génétique, CHU de Tours, Hôpital Bretonneau, Tours, France.,INSERM UMR_U930, Faculté de Médecine, Université de Tours, Tours, France
| | - Frédéric Brioude
- Unité d'explorations fonctionnelles endocriniennes, CHU Paris Est, Hôpital d'Enfants Armand-Trousseau, Paris, France
| | - Annick Toutain
- Service de Génétique, CHU de Tours, Hôpital Bretonneau, Tours, France.,INSERM UMR_U930, Faculté de Médecine, Université de Tours, Tours, France
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