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Sun H, Li K, Wang L, Zhao L, Yan C, Kong X, Liu N. Fetal agenesis of the corpus callosum: Clinical and genetic analysis in a series of 40 patients. Eur J Obstet Gynecol Reprod Biol 2024; 298:146-152. [PMID: 38756055 DOI: 10.1016/j.ejogrb.2024.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 05/01/2024] [Accepted: 05/07/2024] [Indexed: 05/18/2024]
Abstract
OBJECTIVES This study aimed to explore the genetic causes of agenesis of the corpus callosum (ACC) and assess the utility of karyotype analysis, copy number variation sequencing (CNV-seq), and whole-exome sequencing (WES) to genetically diagnose fetal ACC. METHODS We retrospectively examined 40 fetuses diagnosed with ACC who underwent prenatal ultrasonography or magnetic resonance imaging between January 2019 and October 2023. Genetic tests were conducted on the fetuses using karyotype analysis or CNV-seq as the first-line diagnosis. WES was performed if aneuploid and pathogenic CNVs were excluded. RESULTS Among the 40 fetuses, 29 (72 %) had non-isolated ACC and 11 (28 %) had isolated ACC. Cerebellar dysplasia and hydrocephalus were the most common abnormal developments in the central nervous system. Twenty-eight patients underwent karyotype analysis, with a detection rate of 14 % (4/28). Twenty-six patients underwent CNV-seq; three patients were found to have pathogenic CNVs, with a detection rate of 12 % (3/26). Thirty-three fetuses with no findings of karyotype analysis or CNV-seq were subsequently tested using WES, with a detection rate of 36 % (12/33). Overall, the total diagnostic yield was 48 % (19/40), and monogenic etiology accounted for 30 % (12/40). The genetic detection rate of fetal non-isolated ACC (62 %, 18/29) was higher than that of isolated ACC (9 %, 1/11). CONCLUSION Prenatal genetic analysis of fetuses with ACC is clinically significant, with monogenic disorders being the main cause. WES may enhance the detection rate of fetuses with ACC with negative karyotype analysis or CNV-seq results.
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Affiliation(s)
- Hengqing Sun
- Department of Genetic and Prenatal Diagnosis Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Ke Li
- Department of Genetic and Prenatal Diagnosis Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Lu Wang
- Department of Ultrasound, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Lijuan Zhao
- Department of Ultrasound, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Chenyu Yan
- Department of MRI, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Xiangdong Kong
- Department of Genetic and Prenatal Diagnosis Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Ning Liu
- Department of Genetic and Prenatal Diagnosis Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.
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Engwerda A, Kerstjens-Frederikse WS, Corsten-Janssen N, Dijkhuizen T, van Ravenswaaij-Arts CMA. The phenotypic spectrum of terminal 6q deletions based on a large cohort derived from social media and literature: a prominent role for DLL1. Orphanet J Rare Dis 2023; 18:59. [PMID: 36935482 PMCID: PMC10024851 DOI: 10.1186/s13023-023-02658-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 02/27/2023] [Indexed: 03/21/2023] Open
Abstract
BACKGROUND Terminal 6q deletions are rare, and the number of well-defined published cases is limited. Since parents of children with these aberrations often search the internet and unite via international social media platforms, these dedicated platforms may hold valuable knowledge about additional cases. The Chromosome 6 Project is a collaboration between researchers and clinicians at the University Medical Center Groningen and members of a Chromosome 6 support group on Facebook. The aim of the project is to improve the surveillance of patients with chromosome 6 aberrations and the support for their families by increasing the available information about these rare aberrations. This parent-driven research project makes use of information collected directly from parents via a multilingual online questionnaire. Here, we report our findings on 93 individuals with terminal 6q deletions and 11 individuals with interstitial 6q26q27 deletions, a cohort that includes 38 newly identified individuals. RESULTS Using this cohort, we can identify a common terminal 6q deletion phenotype that includes microcephaly, dysplastic outer ears, hypertelorism, vision problems, abnormal eye movements, dental abnormalities, feeding problems, recurrent infections, respiratory problems, spinal cord abnormalities, abnormal vertebrae, scoliosis, joint hypermobility, brain abnormalities (ventriculomegaly/hydrocephaly, corpus callosum abnormality and cortical dysplasia), seizures, hypotonia, ataxia, torticollis, balance problems, developmental delay, sleeping problems and hyperactivity. Other frequently reported clinical characteristics are congenital heart defects, kidney problems, abnormalities of the female genitalia, spina bifida, anal abnormalities, positional foot deformities, hypertonia and self-harming behaviour. The phenotypes were comparable up to a deletion size of 7.1 Mb, and most features could be attributed to the terminally located gene DLL1. Larger deletions that include QKI (> 7.1 Mb) lead to a more severe phenotype that includes additional clinical characteristics. CONCLUSIONS Terminal 6q deletions cause a common but highly variable phenotype. Most clinical characteristics can be linked to the smallest terminal 6q deletions that include the gene DLL1 (> 500 kb). Based on our findings, we provide recommendations for clinical follow-up and surveillance of individuals with terminal 6q deletions.
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Affiliation(s)
- Aafke Engwerda
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | - Nicole Corsten-Janssen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Trijnie Dijkhuizen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Conny M A van Ravenswaaij-Arts
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
- ATN/Jonx, Groningen, The Netherlands.
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Genetic Analysis Algorithm for the Study of Patients with Multiple Congenital Anomalies and Isolated Congenital Heart Disease. Genes (Basel) 2022; 13:genes13071172. [PMID: 35885957 PMCID: PMC9317700 DOI: 10.3390/genes13071172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/16/2022] [Accepted: 06/27/2022] [Indexed: 11/20/2022] Open
Abstract
Congenital anomalies (CA) affect 3–5% of newborns, representing the second-leading cause of infant mortality in Argentina. Multiple congenital anomalies (MCA) have a prevalence of 2.26/1000 births in newborns, while congenital heart diseases (CHD) are the most frequent CA with a prevalence of 4.06/1000 births. The aim of this study was to identify the genetic causes in Argentinian patients with MCA and isolated CHD. We recruited 366 patients (172 with MCA and 194 with isolated CHD) born between June 2015 and August 2019 at public hospitals. DNA from peripheral blood was obtained from all patients, while karyotyping was performed in patients with MCA. Samples from patients presenting conotruncal CHD or DiGeorge phenotype (n = 137) were studied using MLPA. Ninety-three samples were studied by array-CGH and 18 by targeted or exome next-generation sequencing (NGS). A total of 240 patients were successfully studied using at least one technique. Cytogenetic abnormalities were observed in 13 patients, while 18 had clinically relevant imbalances detected by array-CGH. After MLPA, 26 patients presented 22q11 deletions or duplications and one presented a TBX1 gene deletion. Following NGS analysis, 12 patients presented pathogenic or likely pathogenic genetic variants, five of them, found in KAT6B, SHH, MYH11, MYH7 and EP300 genes, are novel. Using an algorithm that combines molecular techniques with clinical and genetic assessment, we determined the genetic contribution in 27.5% of the analyzed patients.
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Genotype–Phenotype Correlations for Putative Haploinsufficient Genes in Deletions of 6q26-q27: Report of Eight Patients and Review of Literature. Glob Med Genet 2022; 9:166-174. [PMID: 35707784 PMCID: PMC9192176 DOI: 10.1055/s-0042-1743568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 01/11/2022] [Indexed: 11/06/2022] Open
Abstract
Background
Cytogenomic analyses have been used to detect pathogenic copy number variants. Patients with deletions at 6q26-q27 present variable clinical features. We reported clinical and cytogenomic findings of eight unrelated patients with a deletion of 6q26-q27. A systematic review of the literature found 28 patients with a deletion of 6q26-q27 from 2010 to 2020.
Results
For these 36 patients, the sex ratio showed equal occurrence between males and females; 29 patients (81%) had a terminal deletion and seven patients (19%) had a proximal or distal interstitial deletion. Of the 22 patients with parental studies, deletions of de novo, maternal, paternal, and bi-parental inheritance accounted for 64, 18, 14, and 4% of patients, respectively. The most common clinical findings were brain abnormalities (100%) in fetuses observed by ultrasonography followed by developmental delay and intellectual disability (81%), brain abnormalities (72%), facial dysmorphism (66%), hypotonia (63%), learning difficulty or language delay (50%), and seizures (47%) in pediatric and adult patients. Anti-epilepsy treatment showed the effect on controlling seizures in these patients. Cytogenomic mapping defined one proximal critical region at 6q26 containing the putative haploinsufficient gene
PRKN
and one distal critical region at 6q27 containing two haploinsufficient genes
DLL1
and
TBP
. Deletions involving the
PRKN
gene could associate with early-onset Parkinson disease and autism spectrum disorder; deletions involving the
DLL1
gene correlate with the 6q terminal deletion syndrome.
Conclusion
The genotype–phenotype correlations for putative haploinsufficient genes in deletions of 6q26-q27 provided evidence for precise diagnostic interpretation, genetic counseling, and clinical management of patients with a deletion of 6q26-q27.
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Lesieur-Sebellin M, Till M, Khau Van Kien P, Herve B, Bourgon N, Dupont C, Tabet AC, Barrois M, Coussement A, Loeuillet L, Mousty E, Ea V, El Assal A, Mary L, Jaillard S, Beneteau C, Le Vaillant C, Coutton C, Devillard F, Goumy C, Delabaere A, Redon S, Laurent Y, Lamouroux A, Massardier J, Turleau C, Sanlaville D, Cantagrel V, Sonigo P, Vialard F, Salomon LJ, Malan V. Terminal 6q deletions cause brain malformations, a phenotype mimicking heterozygous DLL1 pathogenic variants: A multicenter retrospective case series. Prenat Diagn 2021; 42:118-135. [PMID: 34894355 DOI: 10.1002/pd.6074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 11/24/2021] [Accepted: 11/30/2021] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Terminal 6q deletion is a rare genetic condition associated with a neurodevelopmental disorder characterized by intellectual disability and structural brain anomalies. Interestingly, a similar phenotype is observed in patients harboring pathogenic variants in the DLL1 gene. Our study aimed to further characterize the prenatal phenotype of this syndrome as well as to attempt to establish phenotype-genotype correlations. METHOD We collected ultrasound findings from 22 fetuses diagnosed with a pure 6qter deletion. We reviewed the literature and compared our 22 cases with 14 fetuses previously reported as well as with patients with heterozygous DLL1 pathogenic variants. RESULTS Brain structural alterations were observed in all fetuses. The most common findings (>70%) were cerebellar hypoplasia, ventriculomegaly, and corpus callosum abnormalities. Gyration abnormalities were observed in 46% of cases. Occasional findings included cerebral heterotopia, aqueductal stenosis, vertebral malformations, dysmorphic features, and kidney abnormalities. CONCLUSION This is the first series of fetuses diagnosed with pure terminal 6q deletion. Based on our findings, we emphasize the prenatal sonographic anomalies, which may suggest the syndrome. Furthermore, this study highlights the importance of chromosomal microarray analysis to search for submicroscopic deletions of the 6q27 region involving the DLL1 gene in fetuses with these malformations.
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Affiliation(s)
- Marion Lesieur-Sebellin
- Service de Médecine Génomique des Maladies Rares, APHP-Centre, Hôpital Necker-Enfants Malades, Paris, France
- Faculté de Médecine, Sorbonne Université, Paris, France
| | - Marianne Till
- Laboratoire de Cytogénétique, service de Génétique, Hospices Civils de Lyon, Groupement Hospitalier Est, Bron, France
| | | | - Bérénice Herve
- Département de Génétique, CHI Poissy Saint-Germain, Saint-Germain, France
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France
| | - Nicolas Bourgon
- Service d'Obstétrique et de Médecine Fœtale, APHP-Centre, Hôpital Necker-Enfants Malades, Paris, France
| | - Céline Dupont
- Département de Génétique, Unité de Cytogénétique, Hôpital Robert Debré, APHP Nord, Paris, France
| | - Anne-Claude Tabet
- Département de Génétique, Unité de Cytogénétique, Hôpital Robert Debré, APHP Nord, Paris, France
- Génétique Humaine et Fonctions Cognitives, Institut Pasteur, UMR3571 CNRS, Université de Paris, Paris, France
| | - Mathilde Barrois
- Maternité Port Royal, APHP Centre, Hôpital Cochin, Paris, France
| | - Aurélie Coussement
- Service des Maladies Génétiques de système et d'organes, APHP-Centre, Hôpital Cochin, Paris, France
| | - Laurence Loeuillet
- Service de Médecine Génomique des Maladies Rares, APHP-Centre, Hôpital Necker-Enfants Malades, Paris, France
| | - Eve Mousty
- Service de Gynécologie Obstétrique, Hôpital Caremeau, Nîmes, France
| | - Vuthy Ea
- UF de Cytogénétique et Génétique Médicale, Hôpital Caremeau, Nîmes, France
| | - Amal El Assal
- Département de Gynécologie Obstétrique, CHI Poissy Saint-Germain, Saint-Germain, France
| | - Laura Mary
- Service d'Anatomie Pathologique, CHU Rennes, Rennes, France
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France
| | - Sylvie Jaillard
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France
- INSERM, EHESP, IRSET, Université Rennes 1, Rennes, France
| | - Claire Beneteau
- Service de Génétique Médicale, CHU Nantes, Nantes, France
- UF de Fœtopathologie et Génétique, CHU de Nantes, Nantes, France
| | | | - Charles Coutton
- Service de Génétique, Génomique et Procréation, Hôpital Couple Enfant, CHU Grenoble Alpes, Grenoble, France
- Université Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institut pour l'Avancée des Biosciences, Equipe Génétique, Epigénétique et Thérapies de l'infertilité, Grenoble, France
| | - Françoise Devillard
- Service de Génétique, Génomique et Procréation, Hôpital Couple Enfant, CHU Grenoble Alpes, Grenoble, France
| | - Carole Goumy
- Cytogénétique Médicale, CHU Clermont-Ferrand, CHU Estaing, Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, Clermont-Ferrand, France
| | | | - Sylvia Redon
- CHU Brest, Inserm, Université de Brest, Brest, France
| | - Yves Laurent
- Service de Gynécologie et Obstétrique, GHBS Lorient, Lorient, France
| | - Audrey Lamouroux
- Service de Génétique Clinique, CHU Montpellier, Université de Montpellier, Montpellier, France
- Service de Gynécologie Obstétrique, CHU Nîmes, Université de Montpellier, Nîmes, France
| | - Jérôme Massardier
- Service de Gynécologie et Obstétrique, Hôpital Femme-Mère-Enfant, Hospices Civils de Lyon, Bron, France
| | - Catherine Turleau
- Service de Médecine Génomique des Maladies Rares, APHP-Centre, Hôpital Necker-Enfants Malades, Paris, France
| | - Damien Sanlaville
- Laboratoire de Cytogénétique, service de Génétique, Hospices Civils de Lyon, Groupement Hospitalier Est, Bron, France
| | - Vincent Cantagrel
- Université de Paris, Institut Imagine, Laboratoire de génétique des troubles du neurodéveloppement, Paris, France
- Université de Paris, Paris, France
| | - Pascale Sonigo
- Service de Radiologie Pédiatrique, APHP-Centre, Hôpital Necker-Enfants Malades, Paris, France
| | - François Vialard
- Département de Génétique, CHI Poissy Saint-Germain, Saint-Germain, France
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France
| | - Laurent J Salomon
- Service d'Obstétrique et de Médecine Fœtale, APHP-Centre, Hôpital Necker-Enfants Malades, Paris, France
- Université de Paris, Paris, France
| | - Valérie Malan
- Service de Médecine Génomique des Maladies Rares, APHP-Centre, Hôpital Necker-Enfants Malades, Paris, France
- Université de Paris, Institut Imagine, Laboratoire de génétique des troubles du neurodéveloppement, Paris, France
- Université de Paris, Paris, France
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Lan L, Wu H, She L, Zhang B, He Y, Luo D, Wang H, Zheng Z. Analysis of copy number variation by sequencing in fetuses with nuchal translucency thickening. J Clin Lab Anal 2020; 34:e23347. [PMID: 32342531 PMCID: PMC7439336 DOI: 10.1002/jcla.23347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/30/2020] [Accepted: 04/03/2020] [Indexed: 12/20/2022] Open
Abstract
Objective Copy number variation sequencing (CNV‐seq) technique was used to analyze the genetic etiology of fetuses with increased nuchal translucency (NT). Methods A total of 139 women with gestational 11‐14 weeks whose fetuses were detected with increased NT (NT ≥ 2.5 mm) in our hospital from July 2016 to December 2018 were selected. Fetal specimens were performed for karyotyping analysis and CNV sequencing. Results According to the nuchal translucency thickness, 2.5‐3.4, 3.5‐4.4, 4.5‐5.4, and more than 5.5 mm, the rates of chromosomal abnormalities were 22.8% (13/57), 30.8% (12/39), 42.1% (8/19), and 62.5% (15/24), respectively. There was significant difference among the incidences of chromosomal abnormalities in four groups (χ2 = 37.69, P < .01) and the incidences increased with fetal NT thickness. Among 139 cases, there were 36 cases (25.9%) with abnormal chromosome karyotypes. Meanwhile, there were 45 cases (32.3%) with abnormal CNV. In the 12 cases with abnormal CNV and normal chromosome karyotypes, there were 2 cases of pathogenic CNV, 7 cases of CNV with unknown clinical significance, and 3 cases of possibly benign CNV. There was no significant difference in CNV between pregnant women in advanced maternal age and those in normal maternal age (χ2 = 1.389, P = .239). In the fetus who showed abnormalities in NT and ultrasonography (χ2 = 5.13, P < .05) and the fetus aborted (χ2 = 113.19, P < .05), the abnormal rate of CNV was higher with statistically significant difference. Conclusion CNV‐seq combined karyotype analysis should be performed simultaneously in fetuses with increased NT, providing a basis for genetic counseling, which is of great significance for prenatal diagnosis.
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Affiliation(s)
- Liubing Lan
- Prenatal Diagnosis Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Department of Obstetrics, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China
| | - Heming Wu
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China
| | - Lingna She
- Prenatal Diagnosis Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China
| | - Bosen Zhang
- Prenatal Diagnosis Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Department of Obstetrics, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China
| | - Yanhong He
- Prenatal Diagnosis Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Department of Obstetrics, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China
| | - Dandan Luo
- Prenatal Diagnosis Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Department of Obstetrics, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China
| | - Huaxian Wang
- Prenatal Diagnosis Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China
| | - Zhiyuan Zheng
- Prenatal Diagnosis Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China
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[Contribution of array CGH in the management of fetal nuchal translucency]. ACTA ACUST UNITED AC 2019; 48:174-180. [PMID: 31634590 DOI: 10.1016/j.gofs.2019.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Indexed: 11/23/2022]
Abstract
OBJECTIVES Increased nuchal translucency and cystic hygroma have a neonatal prognosis, when the karyotype is normal, which depends on the findings during the medical follow-up. Array comparative genomic hybridization (aCGH) has been systematically included in this follow-up by prenatal diagnosis teams. There are no guidelines and little information on the advantages of carrying out this test systematically. The aim of our study is to evaluate the contribution of the aCGH in the medical follow-up. METHODS Fifty-one patients were included during 18 months and followed till the end of their pregnancy in prenatal diagnosis centers in Brest and Amiens. Inclusion criterion was a nuchal translucency above 3,5mm on the first trimester ultrasound. A fetal DNA ChromoQuant and aCGH analysis on chorionic villi sampling, and an ultrasound at 18 weeks of gestation were performed during the follow-up. RESULTS The aCGH was decisive in only 2 cases. The ultrasound at 18 weeks gestation seemed to be more sensible in the detection of an abnormality. When the aCGH relieved an abnormality, the ultrasound permitted already to detect the presence of a deformity. In 10 cases, the aCGH could not be interpreted on the chorionic villi sampling. In 9 cases, an amniocentesis was performed in order to obtain this result. CONCLUSION Given the results of this study, the aCGH was rarely determinant or decisive on the realization of a therapeutic abortion. These elements make us reflect on the necessity of maintaining this test before 14 weeks of gestation or propose it as a second-line test after the ultrasound shows signs at 18weeks of gestation.
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8
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Rudolf G, Lovrečić L, Tul N, Teran N, Peterlin B. The frequency of CNVs in a cohort population of consecutive fetuses with congenital anomalies after the termination of pregnancy. Mol Genet Genomic Med 2019; 7:e658. [PMID: 31004418 PMCID: PMC6565594 DOI: 10.1002/mgg3.658] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 03/01/2019] [Accepted: 03/04/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The implementation of molecular karyotyping has resulted in an improved diagnostic yield in the genetic diagnostics of congenital anomalies, detected prenatally or after the termination of pregnancy. However, the systematic epidemiologic ascertainment of copy number variations in the etiology of congenital anomalies has not yet been sufficiently explored. METHODS Consecutive fetuses, altogether 204, with major single or multiple congenital anomalies were ascertained by using the SLOCAT registry for the period from 2011 to 2015. After excluding aneuploidies by using conventional karyotyping or Quantitative Fluorescence-Polymerase Chain Reaction, array comparative genomic hybridization was performed for the detection of copy number variations. RESULTS We identified pathogenic or likely pathogenic copy number variations in 14 fetuses (6.8%); 2.9% in fetuses with isolated, and 3.9% in fetuses with multiple congenital anomalies. Additionally, aneuploidies and major structural chromosomal abnormalities were detected in 40.2%. CONCLUSION Our systematic approach of ascertaining congenital anomalies resulted in explaining the etiology of congenital anomalies in 47% of fetuses after the termination of pregnancy. By using array comparative genomic hybridization, we found that copy number variations represent an important part in the etiology of multiple, as well as isolated congenital anomalies, which indicates the importance of analyzing copy number variations in the diagnostic approach of fetuses with congenital anomalies after the termination of pregnancy.
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Affiliation(s)
- Gorazd Rudolf
- Clinical Institute of Medical Genetics (CIMG), University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Luca Lovrečić
- Clinical Institute of Medical Genetics (CIMG), University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Nataša Tul
- Department of Perinatology, Division of Gynaecology and Obstetrics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Nataša Teran
- Clinical Institute of Medical Genetics (CIMG), University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Medical Genetics (CIMG), University Medical Centre Ljubljana, Ljubljana, Slovenia
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Thakur M, Bronshtein E, Hankerd M, Adekola H, Puder K, Gonik B, Ebrahim S. Genomic detection of a familial 382 Kb 6q27 deletion in a fetus with isolated severe ventriculomegaly and her affected mother. Am J Med Genet A 2018; 176:1985-1990. [PMID: 30194807 DOI: 10.1002/ajmg.a.40376] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 04/26/2018] [Accepted: 06/03/2018] [Indexed: 12/12/2022]
Abstract
Terminal deletions of the chromosome 6q27 region are rare genomic abnormalities, linked to specific brain malformations and other neurological phenotypes. Reported cases have variable sized genomic deletions that harbor several genes including the DLL1 and TBP. We report on an inherited 0.38 Mb terminal deletion of chromosome 6q27 in a 22-week fetus with isolated bilateral ventriculomegaly and her affected mother using microarray-based comparative genomic hybridization and fluorescent in situ hybridization (FISH). The deleted region harbors at least seven genes including DLL1 and TBP. The affected mother had a history of hydrocephalus, developmental delay, and seizures commonly associated with DLL1 and TBP 6q27 deletions. This deletion is one of the smallest reported isolated 6q27 terminal deletions. Our data provides additional evidence that haploinsufficiency of the DLL1 and TBP genes may be sufficient to cause the ventriculomegaly, seizures, and developmental delays associated with terminal 6q27 deletions, indicating a plausible role in the abnormal development of the central nervous system.
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Affiliation(s)
- Mili Thakur
- Division of Genetic and Metabolic Disorders, Department of Pediatrics and Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan.,Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Wayne State University/Detroit Medical Center, Detroit, Michigan
| | - Elena Bronshtein
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Wayne State University/Detroit Medical Center, Detroit, Michigan
| | - Michael Hankerd
- Cytogenetics Laboratory, Detroit Medical Center University Laboratories, Detroit, Michigan
| | - Henry Adekola
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Wayne State University/Detroit Medical Center, Detroit, Michigan
| | - Karoline Puder
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Wayne State University/Detroit Medical Center, Detroit, Michigan
| | - Bernard Gonik
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Wayne State University/Detroit Medical Center, Detroit, Michigan
| | - Salah Ebrahim
- Cytogenetics Laboratory, Detroit Medical Center University Laboratories, Detroit, Michigan.,Department of Pathology, Wayne State University School of Medicine, Detroit, Michigan
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Guéant-Rodriguez RM, Chery C, Caillierez-Fofou BM, Voirin J, Foliguet B, Josse T, Tramoy D, Feillet F, Guéant JL. Association of combined GIF290T>C heterozygous mutation/FUT2 secretor variant with neural tube defects. Clin Genet 2018; 93:191-193. [PMID: 28742214 DOI: 10.1111/cge.13104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 07/18/2017] [Accepted: 07/19/2017] [Indexed: 01/22/2023]
Abstract
Folate and vitamin B12 are needed for the proper embryo-fetal development possibly through their interacting role in the 1-carbon metabolism. Folate fortification reduces the prevalence of complex birth defects, and more specifically neural tube defects (NTDs). GIF and FUT2 are 2 genes associated with the uptake and blood level of vitamin B12. We evaluated GIF and FUT2 as predictors of severe birth defects, in 183 aborted fetuses compared with 375 healthy newborns. The GIF290C allele frequency was estimated to 0.4% in healthy newborns and to 8.1% in NTD fetuses (odds ratio 17.8 [95% confidence interval CI: 4.0-77.6]). The frequency of FUT2 rs601338 secretor variant was not different among groups. The GIF 290C heterozygous/FUT2 rs601338 secretor variant combined genotype was reported in 6 of the 37 NTD fetuses, but not in other fetuses and healthy newborns (P < .0001). This GIF/FUT2 combined genotype has been previously reported in children with congenital gastric intrinsic factor (GIF) deficiency, with respective consequences on B12 binding activity and GIF secretion. In conclusion, a genotype reported in congenital GIF deficiency produces also severe forms of NTD. This suggests that vitamin B12 delivery to neural tissue by the CUBN/GIF pathway could play a role in the neural tube closure mechanisms.
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Affiliation(s)
- R M Guéant-Rodriguez
- Inserm-UMRS 954 (Nutrition-Genetics-Environmental Risks) and National Reference Centre for Inherited Metabolic Diseases, University of Lorraine and University Regional Hospital Center, Vandoeuvre lès Nancy, France
| | - C Chery
- Inserm-UMRS 954 (Nutrition-Genetics-Environmental Risks) and National Reference Centre for Inherited Metabolic Diseases, University of Lorraine and University Regional Hospital Center, Vandoeuvre lès Nancy, France
| | - B-M Caillierez-Fofou
- Inserm-UMRS 954 (Nutrition-Genetics-Environmental Risks) and National Reference Centre for Inherited Metabolic Diseases, University of Lorraine and University Regional Hospital Center, Vandoeuvre lès Nancy, France
| | - J Voirin
- Inserm-UMRS 954 (Nutrition-Genetics-Environmental Risks) and National Reference Centre for Inherited Metabolic Diseases, University of Lorraine and University Regional Hospital Center, Vandoeuvre lès Nancy, France
| | - B Foliguet
- Inserm-UMRS 954 (Nutrition-Genetics-Environmental Risks) and National Reference Centre for Inherited Metabolic Diseases, University of Lorraine and University Regional Hospital Center, Vandoeuvre lès Nancy, France
| | - T Josse
- Inserm-UMRS 954 (Nutrition-Genetics-Environmental Risks) and National Reference Centre for Inherited Metabolic Diseases, University of Lorraine and University Regional Hospital Center, Vandoeuvre lès Nancy, France
| | - D Tramoy
- Inserm-UMRS 954 (Nutrition-Genetics-Environmental Risks) and National Reference Centre for Inherited Metabolic Diseases, University of Lorraine and University Regional Hospital Center, Vandoeuvre lès Nancy, France
| | - F Feillet
- Inserm-UMRS 954 (Nutrition-Genetics-Environmental Risks) and National Reference Centre for Inherited Metabolic Diseases, University of Lorraine and University Regional Hospital Center, Vandoeuvre lès Nancy, France
| | - J-L Guéant
- Inserm-UMRS 954 (Nutrition-Genetics-Environmental Risks) and National Reference Centre for Inherited Metabolic Diseases, University of Lorraine and University Regional Hospital Center, Vandoeuvre lès Nancy, France
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Liu N, Yan J, Chen X, Song J, Wang B, Yao Y. Prenatal diagnosis of a de novo interstitial deletion of 11q (11q22.3 → q23.3) associated with abnormal ultrasound findings by array comparative genomic hybridization. Mol Cytogenet 2014; 7:62. [PMID: 25298785 PMCID: PMC4189608 DOI: 10.1186/s13039-014-0062-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 08/26/2014] [Indexed: 11/29/2022] Open
Abstract
Background Conventional G-band karyotyping offers low-resolution detection of chromosome abnormalities and cannot provide information about the involved genomic content. On the other hand, array comparative genomic hybridization can offer a rapid and comprehensive detection of genomewide gains and losses with higher resolution, thus providing the genetic basis for prenatal diagnosis of fetal abnormalities. Case presentation A 35-year-old primigravid underwent cordocentesis at 28 weeks gestation due to the presence of polyhydramnios, intrauterine growth retardation, persistent right umbilical vein and mild stenosis of aortic arch at the ultrasound scan. Conventional G-band chromosome analysis revealed an apparently normal karyotype whereas the array CGH detected a de novo 8.97 Mb deletion at chromosome 11q22.3 → q23.3 and offered a precise characterization of the genetic defect. Conclusions The array CGH detected a de novo interstitial 11q deletion with its precise location and size which could be missed or confused by G-band chromosome analysis. The breakpoint was close to the folate sensitive rare fragile site FRA11B and the aphidicolin inducible common fragile site FRA11G, the co-localization fragile site could have caused instability and constitutional chromosomal breakage. This case study indicates that array CGH is a useful technique for detecting small unbalanced chromosomal abnormalities and should be an integral part of prenatal diagnosis for fetal malformations.
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Affiliation(s)
- Nian Liu
- Prenatal Diagnosis Center, Hubei Maternal and Child Health Hospital, Wuhan, 430070 China
| | - Jiong Yan
- Prenatal Diagnosis Center, Hubei Maternal and Child Health Hospital, Wuhan, 430070 China
| | - Xinlin Chen
- Prenatal Diagnosis Center, Hubei Maternal and Child Health Hospital, Wuhan, 430070 China
| | - Jieping Song
- Prenatal Diagnosis Center, Hubei Maternal and Child Health Hospital, Wuhan, 430070 China
| | - Bo Wang
- Prenatal Diagnosis Center, Hubei Maternal and Child Health Hospital, Wuhan, 430070 China
| | - Yanyi Yao
- Prenatal Diagnosis Center, Hubei Maternal and Child Health Hospital, Wuhan, 430070 China
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Exome Sequencing in Fetuses with Structural Malformations. J Clin Med 2014; 3:747-62. [PMID: 26237476 PMCID: PMC4449643 DOI: 10.3390/jcm3030747] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 05/08/2014] [Accepted: 05/19/2014] [Indexed: 01/01/2023] Open
Abstract
Prenatal diagnostic testing is a rapidly advancing field. An accurate diagnosis of structural anomalies and additional abnormalities in fetuses with structural anomalies is important to allow “triage” and designation of prognosis. This will allow parents to make an informed decision relating to the pregnancy. This review outlines the current tests used in prenatal diagnosis, focusing particularly on “new technologies” such as exome sequencing. We demonstrate the utility of exome sequencing above that of conventional karyotyping and Chromosomal Microarray (CMA) alone by outlining a recent proof of concept study investigating 30 parent-fetus trios where the fetus is known to have a structural anomaly. This may allow the identification of pathological gene anomalies and consequently improved prognostic profiling, as well as excluding anomalies and distinguishing between de novo and inherited mutations, in order to estimate the recurrence risk in future pregnancies. The potential ethical dilemmas surrounding exome sequencing are also considered, and the future of prenatal genetic diagnosis is discussed.
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A de novo chromosomal abnormality in Cri du Chat syndrome. Indian J Pediatr 2014; 81:722-5. [PMID: 23900752 DOI: 10.1007/s12098-013-1134-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Accepted: 06/10/2013] [Indexed: 10/26/2022]
Abstract
OBJECTIVE To find the length and location of the deletions in the short arm of chromosome 5 in one case of Cri du Chat syndrome using oligo array comparative genomic hybridization. METHODS Metaphase chromosomes were prepared from peripheral blood lymphocyte cultures using standard cytogenetic protocols. Chromosomal analysis was done in G-banded metaphases. Oligo array comparative genomic hybridization and fluorescence in situ hybridization were performed by the commercially available kits. RESULTS Oligonucleotide array comparative genomic hybridization (CGH) analysis revealed a 23.263 Mb deletion at region 5p14.2-->qter, combined with a duplication of 14.602 Mb in size in the area 12p13.1-->pter. Chromosomal aberrations were confirmed by fluorescence in situ hybridization. The male neonate with Cri du Chat syndrome had an unbalanced translocation which was inherited from his father who was a balanced carrier with a karyotype 46, XY, t (5; 12) (p14.2; p13.1). CONCLUSIONS This report shows the clinical utility of the oligonucleotide array in the detection of submicroscopic chromosomal aberrations, thus improving the molecular diagnosis of Cri du Chat syndrome.
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Hillman SC, Barton PM, Roberts TE, Maher ER, McMullan DM, Kilby MD. BAC chromosomal microarray for prenatal detection of chromosome anomalies in fetal ultrasound anomalies: an economic evaluation. Fetal Diagn Ther 2014; 36:49-58. [PMID: 24943865 DOI: 10.1159/000358387] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 12/27/2013] [Indexed: 11/19/2022]
Abstract
INTRODUCTION To determine the cost-effectiveness of prenatal chromosomal microarray (CMA) when performed for structural anomalies on fetal ultrasound scan over conventional techniques. METHOD A decision tree was populated using data from a prospective cohort of women undergoing testing when a fetal ultrasound scan showed a structural abnormality. Nine strategies of testing were modeled including combinations of the tests: QFPCR, G-band karyotyping, CMA and FISH for DiGeorge (22q) microdeletion. RESULTS When CMA costs GBP 405 and using a 1-Mb BAC array it would cost GBP 24,600 for every additional case detected by CMA over a combination of QFPCR, followed by G-band karyotype, followed lastly by FISH (for DiGeorge syndrome). If CMA is performed instead of conventional karyotyping alone it costs GBP 33,000 for every additional case detected. However, if the cost of CMA is reduced to GBP 360 than when CMA is performed instead of conventional karyotyping alone it would cost GBP 9,768 for every additional case detected. DISCUSSION The use of a prenatal BAC CMA is not currently cost-effective when compared to other testing strategies. However, as CMA costs decrease and resolution (and detection rates) increase it is likely to become the cost-effective option of the future.
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Affiliation(s)
- Sarah C Hillman
- School of Clinical and Experimental Medicine, College of Medicine and Dentistry, Birmingham, UK
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Yin A, Lu J, Liu C, Guo L, Wu J, Mai M, Zhong Y, Zhang X. A prenatal missed diagnosed case of submicroscopic chromosomal abnormalities by karyotyping: the clinical utility of array-based CGH in prenatal diagnostics. Mol Cytogenet 2014; 7:26. [PMID: 24735551 PMCID: PMC4005634 DOI: 10.1186/1755-8166-7-26] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 03/26/2014] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Array-based comparative genomic hybridization possesses a number of significant advantages over conventional cytogenetic and other molecular cytogenetic techniques, providing a sensitive and comprehensive detection platform for unexpected imbalances in the genome wide. CASE PRESENTATION The newborn proband, demonstrated with craniofacial dysmorphism and multiple malformations, was born to a family with spontaneous abortions. This pregnancy was uneventful, except the prenatal ultrasound examination showed an increased nuchal translucency at 12(+) weeks of gestation. Cytogenetics revealed an apparently normal karyotype, and the couple decided to continue the pregnancy. Array-based CGH analysis was applied to the affected infant, identified a combination of 18p deletion and 7q duplication. Further study indicates that the unbalanced translocation was inherited from a balanced translocation carrier parent. CONCLUSIONS In review of the case, several overlooked points leading to the missed diagnosis should be discussed and certain quality control strategies should be adopted to avoid similar problems in the future. Array-based CGH and karyotyping techniques are complemented by diverse detection spectrum and resolutions, and a combination of these methods could help providing optimal genetic diagnosis. Given that the array-CGH analysis will not introduce additional risk to patients, it is reasonable to recommend those already undergoing invasive testing should take array-based CGH as an adjunct to conventional cytogenetic tests and other molecular cytogenetic analysis.
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Affiliation(s)
- Aihua Yin
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Jian Lu
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Chang Liu
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Li Guo
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Jing Wu
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Mingqin Mai
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Yanfang Zhong
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Xiaozhuang Zhang
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
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Vanakker O, Vilain C, Janssens K, Van der Aa N, Smits G, Bandelier C, Blaumeiser B, Bulk S, Caberg JH, De Leener A, De Rademaeker M, de Ravel T, Desir J, Destree A, Dheedene A, Gaillez S, Grisart B, Hellin AC, Janssens S, Keymolen K, Menten B, Pichon B, Ravoet M, Revencu N, Rombout S, Staessens C, Van Den Bogaert A, Van Den Bogaert K, Vermeesch JR, Kooy F, Sznajer Y, Devriendt K. Implementation of genomic arrays in prenatal diagnosis: The Belgian approach to meet the challenges. Eur J Med Genet 2014; 57:151-6. [DOI: 10.1016/j.ejmg.2014.02.002] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Accepted: 02/06/2014] [Indexed: 11/24/2022]
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de Wit MC, Srebniak MI, Govaerts LCP, Van Opstal D, Galjaard RJH, Go ATJI. Additional value of prenatal genomic array testing in fetuses with isolated structural ultrasound abnormalities and a normal karyotype: a systematic review of the literature. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2014; 43:139-146. [PMID: 23897843 DOI: 10.1002/uog.12575] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/19/2013] [Indexed: 06/02/2023]
Abstract
OBJECTIVE To establish the prevalence of submicroscopic genetic copy number variants (CNVs) in fetuses with a structural ultrasound anomaly (restricted to one anatomical system) and a normal karyotype. The aim was to determine the diagnostic and prognostic value of genomic array testing in these pregnancies. METHODS Embase and PubMed databases were systematically searched for all relevant articles on prevalence of pathogenic submicroscopic CNVs in fetuses with ultrasound anomalies. Reported cases were sorted into groups according to anatomical site of the detected ultrasound anomaly. The prevalence of causative submicroscopic CNVs was calculated for each group. RESULTS Combined data of the reviewed studies (n = 18) indicated that fetuses with an ultrasound anomaly restricted to one anatomical system (n = 2220) had a 3.1-7.9% chance of carrying a causative submicroscopic CNV, depending on the anatomical system affected. This chance increased to 9.1% for fetuses with multiple ultrasound anomalies (n = 1139). CONCLUSION This review indicates that 3.1-7.9% of fetuses with a structural ultrasound anomaly restricted to one anatomical system and a normal karyotype will show a submicroscopic CNV, which explains its phenotype and provides information for fetal prognosis. Therefore, we conclude that microarray has considerable diagnostic and prognostic value in these pregnancies.
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Affiliation(s)
- M C de Wit
- Department of Obstetrics and Gynecology, Erasmus Medical Centre, Rotterdam, The Netherlands
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Carss KJ, Hillman SC, Parthiban V, McMullan DJ, Maher ER, Kilby MD, Hurles ME. Exome sequencing improves genetic diagnosis of structural fetal abnormalities revealed by ultrasound. Hum Mol Genet 2014; 23:3269-77. [PMID: 24476948 PMCID: PMC4030780 DOI: 10.1093/hmg/ddu038] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The genetic etiology of non-aneuploid fetal structural abnormalities is typically investigated by karyotyping and array-based detection of microscopically detectable rearrangements, and submicroscopic copy-number variants (CNVs), which collectively yield a pathogenic finding in up to 10% of cases. We propose that exome sequencing may substantially increase the identification of underlying etiologies. We performed exome sequencing on a cohort of 30 non-aneuploid fetuses and neonates (along with their parents) with diverse structural abnormalities first identified by prenatal ultrasound. We identified candidate pathogenic variants with a range of inheritance models, and evaluated these in the context of detailed phenotypic information. We identified 35 de novo single-nucleotide variants (SNVs), small indels, deletions or duplications, of which three (accounting for 10% of the cohort) are highly likely to be causative. These are de novo missense variants in FGFR3 and COL2A1, and a de novo 16.8 kb deletion that includes most of OFD1. In five further cases (17%) we identified de novo or inherited recessive or X-linked variants in plausible candidate genes, which require additional validation to determine pathogenicity. Our diagnostic yield of 10% is comparable to, and supplementary to, the diagnostic yield of existing microarray testing for large chromosomal rearrangements and targeted CNV detection. The de novo nature of these events could enable couples to be counseled as to their low recurrence risk. This study outlines the way for a substantial improvement in the diagnostic yield of prenatal genetic abnormalities through the application of next-generation sequencing.
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Affiliation(s)
- Keren J Carss
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Sarah C Hillman
- School of Clinical and Experimental Medicine (Birmingham Centre for Women's and Children's Health), College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Vijaya Parthiban
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Dominic J McMullan
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Trust, Edgbaston, Birmingham B15 2TG, UK
| | - Eamonn R Maher
- School of Clinical and Experimental Medicine (Birmingham Centre for Women's and Children's Health), College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Mark D Kilby
- School of Clinical and Experimental Medicine (Birmingham Centre for Women's and Children's Health), College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK Fetal Medicine Centre, Birmingham Women's Foundation Trust, Edgbaston, Birmingham B15 2TG, UK
| | - Matthew E Hurles
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
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Strassberg M, Fruhman G, Van den Veyver IB. Copy-number changes in prenatal diagnosis. Expert Rev Mol Diagn 2014; 11:579-92. [DOI: 10.1586/erm.11.43] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Lonardo F. Genomic microarrays in prenatal diagnosis. World J Med Genet 2013; 3:14-21. [DOI: 10.5496/wjmg.v3.i4.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 07/13/2013] [Accepted: 08/09/2013] [Indexed: 02/06/2023] Open
Abstract
The application of microarray-based techniques for the diagnosis of genomic rearrangements has been steadily growing in popularity since its introduction in 2004. Given the many advantages of these techniques over conventional cytogenetics, there is increasing pressure towards their application in prenatal diagnosis. However, there remain several important issues that must be addressed. For example, microarray-based techniques (comparative genomic hybridization-based arrays and single nucleotide polymorphism-based arrays) allow detection of even very small genomic imbalances that can determine pathological clinical conditions. In addition, there are other copy number variations which represent normal variation, with no detectable effects on phenotype. Given the still incomplete knowledge of the changes in our genome and the associated phenotypes, microarray-based diagnosis is likely to find variants of uncertain and unknown clinical significance. The interpretation of these variants is now a major challenge for the medical geneticist, who often find it difficult to establish precise correlations between genotype and phenotype. There is sufficient available evidence to justify the use of microarray-based diagnostics for a select number of specific conditions, but there is also an inevitable trend towards ever wider application. It is very important that this drift does not progress in an unchecked and uncontrolled manner under the thrust of commercial interests. Therefore, we recommend that scientific societies be vigilant and take an advisory role in the adopting of these technologies as new scientific knowledge becomes available.
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Shaffer LG, Rosenfeld JA. Microarray-based prenatal diagnosis for the identification of fetal chromosome abnormalities. Expert Rev Mol Diagn 2013; 13:601-11. [PMID: 23895129 DOI: 10.1586/14737159.2013.811912] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The goal of prenatal cytogenetic testing is to provide reassurance to the couple seeking testing for their pregnancy, identify chromosome abnormalities in the fetus, if present, and provide treatments and medical management for affected babies. Cytogenetic analysis of banded chromosomes has been the standard for identifying chromosome abnormalities in the fetus for over 40 years. With chromosome analysis, whole chromosome aneuploidies and large structural rearrangements can be identified. The sequencing of the human genome has provided the resources to develop molecular tools that allow higher resolution observations of human chromosomes. The future holds the promise of sequencing that may identify chromosomal imbalances and deleterious single nucleotide variants. This review will focus on the use of genomic microarrays for the testing and identification of chromosome anomalies in prenatal diagnosis and will discuss the future directions of fetal testing.
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Affiliation(s)
- Lisa G Shaffer
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., Spokane, WA, USA.
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Callaway JLA, Shaffer LG, Chitty LS, Rosenfeld JA, Crolla JA. The clinical utility of microarray technologies applied to prenatal cytogenetics in the presence of a normal conventional karyotype: a review of the literature. Prenat Diagn 2013; 33:1119-23. [PMID: 23983223 PMCID: PMC4285999 DOI: 10.1002/pd.4209] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 06/24/2013] [Accepted: 07/22/2013] [Indexed: 12/22/2022]
Abstract
ABSTRACT The clinical utility of microarray technologies when used in the context of prenatal diagnosis lies in the technology's ability to detect submicroscopic copy number changes that are associated with clinically significant outcomes. We have carried out a systematic review of the literature to calculate the utility of prenatal microarrays in the presence of a normal conventional karyotype. Amongst 12 362 cases in studies that recruited cases from all prenatal ascertainment groups, 295/12 362 (2.4%) overall were reported to have copy number changes with associated clinical significance (pCNC), 201/3090 (6.5%) when ascertained with an abnormal ultrasound, 50/5108 (1.0%) when ascertained because of increased maternal age and 44/4164 (1.1%) for all other ascertainment groups (e.g. parental anxiety and abnormal serum screening result). When additional prenatal microarray studies are included in which ascertainment was restricted to fetuses with abnormal ultrasound scans, 262/3730 (7.0%) were reported to have pCNCs. © 2013 The Authors. Prenatal Diagnosis published by John Wiley & Sons Ltd.
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Hillman SC, McMullan DJ, Hall G, Togneri FS, James N, Maher EJ, Meller CH, Williams D, Wapner RJ, Maher ER, Kilby MD. Use of prenatal chromosomal microarray: prospective cohort study and systematic review and meta-analysis. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2013; 41:610-620. [PMID: 23512800 DOI: 10.1002/uog.12464] [Citation(s) in RCA: 189] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 02/25/2013] [Accepted: 03/01/2013] [Indexed: 06/01/2023]
Abstract
OBJECTIVES Chromosomal microarray analysis (CMA) is utilized in prenatal diagnosis to detect chromosomal abnormalities not visible by conventional karyotyping. A prospective cohort of women undergoing fetal CMA and karyotyping following abnormal prenatal ultrasound findings is presented in the context of a systematic review and meta-analysis of the literature describing detection rates by CMA and karyotyping. METHODS We performed a prospective cohort study of 243 women undergoing CMA alongside karyotyping when a structural abnormality was detected on prenatal ultrasound. A systematic review of the literature was also performed. MEDLINE (1970-Dec 2012), EMBASE (1980-Dec 2012) and CINAHL (1982-June 2012) databases were searched electronically. Selected studies included > 10 cases and prenatal CMA in addition to karyotyping. The search yielded 560 citations. Full papers were retrieved for 86, and 25 primary studies were included in the systematic review. RESULTS Our cohort study found an excess detection rate of abnormalities by CMA of 4.1% over conventional karyotyping when the clinical indication for testing was an abnormal fetal ultrasound finding; this was lower than the detection rate of 10% (95% CI, 8-13%) by meta-analysis. The rate of detection for variants of unknown significance (VOUS) was 2.1% (95% CI, 1.3-3.3%) when the indication for CMA was an abnormal scan finding. The VOUS detection rate was lower (1.4%; 95% CI, 0.5-3.7%) when any indication for prenatal CMA was meta-analyzed. CONCLUSION We present evidence for a higher detection rate by CMA than by karyotyping not just in the case of abnormal ultrasound findings but also in cases of other indications for invasive testing. It is likely that CMA will replace karyotyping in high-risk pregnancies.
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Affiliation(s)
- S C Hillman
- School of Clinical and Experimental Medicine, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham, UK
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An improved method to extract DNA from 1 ml of uncultured amniotic fluid from patients at less than 16 weeks' gestation. PLoS One 2013; 8:e59956. [PMID: 23565177 PMCID: PMC3614959 DOI: 10.1371/journal.pone.0059956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 02/20/2013] [Indexed: 11/30/2022] Open
Abstract
The aim of this study was to develop an improved technique for DNA extraction from 1 ml of uncultured AF from patients with a gestational age less than 16 weeks and to allow the use of array-CGH without DNA amplification. The DNA extraction protocol was tested in a series of 90 samples including 41 of uncultured AF at less than 16 weeks of gestation. Statistical analyses were performed using linear regression. To evaluate the sensitivity and the specificity of array-CGH on 1 ml of uncultured AF, five samples with an abnormal karyotype (three with aneuploidy, two with structural abnormalities) and five with a normal karyotype were studied. This protocol was reproducible and we were able to show a great improvement with higher yield of DNA obtained from all patients, including those with a gestational age less than 16 weeks (p = 0.003). All chromosomal abnormalities were detected and characterized by array-CGH and normal samples showed normal profiles. This new DNA extraction protocol associated with array-CGH analysis could be used in prenatal testing even when gestational age is less than 16 weeks, especially in cases with abnormal ultrasound findings.
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Mademont-Soler I, Morales C, Soler A, Martínez-Crespo JM, Shen Y, Margarit E, Clusellas N, Obón M, Wu BL, Sánchez A. Prenatal diagnosis of chromosomal abnormalities in fetuses with abnormal cardiac ultrasound findings: evaluation of chromosomal microarray-based analysis. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2013; 41:375-382. [PMID: 23233332 DOI: 10.1002/uog.12372] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/06/2012] [Indexed: 06/01/2023]
Abstract
OBJECTIVES To assess the frequency of karyotype abnormalities and chromosome 22q11.2 deletion syndrome among fetuses with abnormal cardiac ultrasound findings, and to evaluate the clinical value of chromosomal microarray-based analysis (CMA) in the study of such pregnancies. METHODS First, we carried out retrospective analysis of karyotype abnormalities and 22q11.2 deletion syndrome cases diagnosed between January 2009 and December 2011 in our center among fetuses with abnormal cardiac ultrasound findings (n = 276). Second, CMA was performed in 51 of the fetuses with such findings, normal karyotype and negative or no 22q11.2 deletion syndrome study, and in the only fetus with a heart defect and an apparently balanced de novo chromosomal rearrangement. RESULTS Out of the 276 pregnancies with abnormal cardiac ultrasound findings, karyotyping revealed a chromosomal abnormality in 44 (15.9%). Of fetuses with normal karyotype in which 22q11.2 deletion syndrome studies were performed, 6.4% (5/78) had this microdeletion syndrome. Among fetuses with abnormal cardiac findings, normal karyotype and negative or no 22q11.2 deletion syndrome study that underwent CMA, the detection rate of pathogenic copy number variants not detected by conventional cytogenetics was 2.0% (1/51), and no variants of uncertain clinical significance were found. In the fetus with a heart defect and an apparently balanced de novo chromosomal rearrangement, CMA revealed that the rearrangement was not truly balanced. CONCLUSIONS In the assessment of genetic abnormalities in pregnancies with abnormal cardiac ultrasound findings, the diagnostic yield may be increased by 2% if CMA is used as a complementary tool to conventional cytogenetics. Our results suggest that CMA could be a good alternative to karyotyping in these pregnancies.
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Affiliation(s)
- I Mademont-Soler
- Servei de Bioquímica i Genètica Molecular, Hospital Clínic, Barcelona, Spain
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Implementation of high resolution whole genome array CGH in the prenatal clinical setting: advantages, challenges, and review of the literature. BIOMED RESEARCH INTERNATIONAL 2013; 2013:346762. [PMID: 23555083 PMCID: PMC3603644 DOI: 10.1155/2013/346762] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 01/17/2013] [Indexed: 11/17/2022]
Abstract
Array Comparative Genomic Hybridization analysis is replacing postnatal chromosomal analysis in cases of intellectual disabilities, and it has been postulated that it might also become the first-tier test in prenatal diagnosis.
In this study, array CGH was applied in 64 prenatal samples with whole genome oligonucleotide arrays (BlueGnome, Ltd.) on DNA extracted from chorionic villi, amniotic fluid, foetal blood, and skin samples. Results were confirmed with Fluorescence In Situ Hybridization or Real-Time PCR. Fifty-three cases had normal karyotype and abnormal ultrasound findings, and seven samples had balanced rearrangements, five of which also had ultrasound findings. The value of array CGH in the characterization of previously known aberrations in five samples is also presented. Seventeen out of 64 samples carried copy number alterations giving a detection rate of 26.5%. Ten of these represent benign or variables of unknown significance, giving a diagnostic capacity of the method to be 10.9%. If karyotype is performed the additional diagnostic capacity of the method is 5.1% (3/59). This study indicates the ability of array CGH to identify chromosomal abnormalities which cannot be detected during routine prenatal cytogenetic analysis, therefore increasing the overall detection rate. In addition a thorough review of the literature is presented.
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Schmid M, Stary S, Springer S, Bettelheim D, Husslein P, Streubel B. Prenatal microarray analysis as second-tier diagnostic test: single-center prospective study. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2013; 41:267-273. [PMID: 23292918 DOI: 10.1002/uog.12389] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/06/2012] [Indexed: 06/01/2023]
Abstract
OBJECTIVE To evaluate the usefulness of chromosome microarrays as a second-tier test in prenatal genetic testing. METHODS We prospectively analyzed 75 high-risk pregnancies undergoing invasive prenatal genetic testing in which the karyotype either was normal or had findings other than a common non-mosaic autosomal aneuploidy. RESULTS Chromosomal microarray analysis (CMA) was performed successfully in all cases. Pathological copy-number variations (CNVs) explaining the phenotypes were found in 11 cases (14.7%). Four cases were detected with an unbalanced translocation. In three of these cases, subsequent genetic analysis demonstrated that a parent was an unknown carrier of a balanced translocation. Among the 67 cases with normal karyo-types, submicroscopic rearrangements with pathological significance were detected in five (7.5%) and CNVs of unclear significance were detected in one (1.5%). CMA was able to discriminate correctly between true mosaicism and confined or pseudomosaicism in all six mosaic cases. CONCLUSION CMA is a valuable second-tier test in high-risk pregnancies for which identification or further delineation of genetic aberrations is important. Its higher resolution results in a higher detection rate of aberrant cases, with a clear clinical benefit for estimation of risk of recurrence.
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Affiliation(s)
- M Schmid
- Department of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
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Rooryck C, Toutain J, Cailley D, Bouron J, Horovitz J, Lacombe D, Arveiler B, Saura R. Prenatal diagnosis using array-CGH: a French experience. Eur J Med Genet 2013; 56:341-5. [PMID: 23454632 DOI: 10.1016/j.ejmg.2013.02.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 02/07/2013] [Indexed: 01/19/2023]
Abstract
Array-CGH or Chromosomal Microarray Analysis (CMA) is increasingly used in prenatal diagnosis throughout the world. However, routine practices are very different among centers and countries, regarding CMA indications, design and resolution of microarrays, notification and interpretation of Copy Number Alterations (CNA). We present our data and experience from our Fetal Medicine Center on 224 prospective prenatal diagnoses. Our approach is practical, and aims to propose a strategy to offer Chromosomal Microarray Analysis (CMA) to selected fetuses and to help to interpret CNA. We hope that this publication could encourage development of CMA in centers that have not started yet this activity in prenatal routine, and could contribute to edict guidelines in this field.
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Wei Y, Xu F, Li P. Technology-Driven and Evidence-Based Genomic Analysis for Integrated Pediatric and Prenatal Genetics Evaluation. J Genet Genomics 2013; 40:1-14. [DOI: 10.1016/j.jgg.2012.12.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Accepted: 12/14/2012] [Indexed: 10/27/2022]
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Coughlin CR, Scharer GH, Shaikh TH. Clinical impact of copy number variation analysis using high-resolution microarray technologies: advantages, limitations and concerns. Genome Med 2012; 4:80. [PMID: 23114084 PMCID: PMC3580449 DOI: 10.1186/gm381] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Copy number variation (CNV) analysis has had a major impact on the field of medical genetics, providing a mechanism to identify disease-causing genomic alterations in an unprecedented number of diseases and phenotypes. CNV analysis is now routinely used in the clinical diagnostic laboratory, and has led to a significant increase in the detection of chromosomal abnormalities. These findings are used for prenatal decision making, clinical management and genetic counseling. Although a powerful tool to identify genomic alterations, CNV analysis may also result in the detection of genomic alterations that have unknown clinical significance or reveal unintended information. This highlights the importance of informed consent and genetic counseling for clinical CNV analysis. This review examines the advantages and limitations of CNV discovery in the clinical diagnostic laboratory, as well as the impact on the clinician and family.
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Affiliation(s)
- Curtis R Coughlin
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado Denver, Aurora, CO 80045, USA
| | - Gunter H Scharer
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado Denver, Aurora, CO 80045, USA ; Intellectual and Developmental Disabilities Research Center, University of Colorado Denver, Aurora, CO 80045, USA
| | - Tamim H Shaikh
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado Denver, Aurora, CO 80045, USA ; Intellectual and Developmental Disabilities Research Center, University of Colorado Denver, Aurora, CO 80045, USA
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Wadt K, Jensen LN, Bjerglund L, Lundstrøm M, Kirchhoff M, Kjaergaard S. Fetal ventriculomegaly due to familial submicroscopic terminal 6q deletions. Prenat Diagn 2012; 32:1212-7. [PMID: 23065819 DOI: 10.1002/pd.3981] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Submicroscopic terminal 6q deletions are rare. We report on two familial submicroscopic terminal 6q deletions ascertained because of prenatally detected isolated ventriculomegaly and further delineate the variable prenatal and postnatal phenotype. We review published cases of <5 Mb terminal 6q deletions.
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Serra-Juhé C, Rodríguez-Santiago B, Cuscó I, Vendrell T, Camats N, Torán N, Pérez-Jurado LA. Contribution of rare copy number variants to isolated human malformations. PLoS One 2012; 7:e45530. [PMID: 23056206 PMCID: PMC3463597 DOI: 10.1371/journal.pone.0045530] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 08/21/2012] [Indexed: 11/18/2022] Open
Abstract
Background Congenital malformations are present in approximately 2–3% of liveborn babies and 20% of stillborn fetuses. The mechanisms underlying the majority of sporadic and isolated congenital malformations are poorly understood, although it is hypothesized that the accumulation of rare genetic, genomic and epigenetic variants converge to deregulate developmental networks. Methodology/Principal Findings We selected samples from 95 fetuses with congenital malformations not ascribed to a specific syndrome (68 with isolated malformations, 27 with multiple malformations). Karyotyping and Multiplex Ligation-dependent Probe Amplification (MLPA) discarded recurrent genomic and cytogenetic rearrangements. DNA extracted from the affected tissue (46%) or from lung or liver (54%) was analyzed by molecular karyotyping. Validations and inheritance were obtained by MLPA. We identified 22 rare copy number variants (CNV) [>100 kb, either absent (n = 7) or very uncommon (n = 15, <1/2,000) in the control population] in 20/95 fetuses with congenital malformations (21%), including 11 deletions and 11 duplications. One of the 9 tested rearrangements was de novo while the remaining were inherited from a healthy parent. The highest frequency was observed in fetuses with heart hypoplasia (8/17, 62.5%), with two events previously related with the phenotype. Double events hitting candidate genes were detected in two samples with brain malformations. Globally, the burden of deletions was significantly higher in fetuses with malformations compared to controls. Conclusions/Significance Our data reveal a significant contribution of rare deletion-type CNV, mostly inherited but also de novo, to human congenital malformations, especially heart hypoplasia, and reinforce the hypothesis of a multifactorial etiology in most cases.
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Affiliation(s)
- Clara Serra-Juhé
- Unitat de Genètica, Universitat Pompeu Fabra, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
| | | | - Ivon Cuscó
- Unitat de Genètica, Universitat Pompeu Fabra, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Teresa Vendrell
- Programa de Medicina Molecular i Genètica, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Núria Camats
- Servei d'Anatomia Patològica, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Núria Torán
- Servei d'Anatomia Patològica, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Luis A. Pérez-Jurado
- Unitat de Genètica, Universitat Pompeu Fabra, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
- * E-mail:
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Shaffer LG, Rosenfeld JA, Dabell MP, Coppinger J, Bandholz AM, Ellison JW, Ravnan JB, Torchia BS, Ballif BC, Fisher AJ. Detection rates of clinically significant genomic alterations by microarray analysis for specific anomalies detected by ultrasound. Prenat Diagn 2012; 32:986-95. [PMID: 22847778 PMCID: PMC3509216 DOI: 10.1002/pd.3943] [Citation(s) in RCA: 178] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 06/01/2012] [Accepted: 06/26/2012] [Indexed: 12/18/2022]
Abstract
OBJECTIVE The aim of this study is to understand the diagnostic utility of comparative genomic hybridization (CGH)-based microarrays for pregnancies with abnormal ultrasound findings. METHODS We performed a retrospective analysis of 2858 pregnancies with abnormal ultrasounds and normal karyotypes (when performed) tested in our laboratory using CGH microarrays targeted to known chromosomal syndromes with later versions providing backbone coverage of the entire genome. Abnormalities were stratified according to organ system involvement. Detection rates for clinically significant findings among these categories were calculated. RESULTS Clinically significant genomic alterations were identified in cases with a single ultrasound anomaly (n = 99/1773, 5.6%), anomalies in two or more organ systems (n = 77/808, 9.5%), isolated growth abnormalities (n = 2/76, 2.6%), and soft markers (n = 2/77, 2.6%). The following anomalies in isolation or with additional anomalies had particularly high detection rates: holoprosencephaly (n = 9/85, 10.6%), posterior fossa defects (n = 21/144, 14.6%), skeletal anomalies (n = 15/140, 10.7%), ventricular septal defect (n = 14/132, 10.6%), hypoplastic left heart (n = 11/68, 16.2%), and cleft lip/palate (n = 14/136, 10.3%). CONCLUSIONS Microarray analysis identified clinically significant genomic alterations in 6.5% of cases with one or more abnormal ultrasound findings; the majority were below the resolution of karyotyping. Larger data sets such as this allow for sub-stratification by specific anomalies to determine risks for genomic alterations detectable by microarray analysis.
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Affiliation(s)
- Lisa G Shaffer
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, Washington, USA.
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Hillman SC, McMullan DJ, Williams D, Maher ER, Kilby MD. Microarray comparative genomic hybridization in prenatal diagnosis: a review. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2012; 40:385-391. [PMID: 22887694 DOI: 10.1002/uog.11180] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/13/2012] [Indexed: 06/01/2023]
Abstract
G-band chromosomal karyotyping of fetal cells obtained by invasive prenatal testing has been used since the 1960s to identify structural chromosomal anomalies. Prenatal testing is usually performed in response to parental request, increased risk of fetal chromosomal abnormality associated with advanced maternal age, a high-risk screening test and/or the presence of a congenital malformation identified by ultrasonography. The results of karyotyping may inform the long-term prognosis (e.g. aneuploidy being associated with a poor outcome or microscopic chromosomal anomalies predicting global neurodevelopmental morbidity). Relatively recent advances in microarray technology are now enabling high-resolution genome-wide evaluation for DNA copy number abnormalities (e.g. deletions or duplications). While such technological advances promise increased sensitivity and specificity they can also pose difficult challenges of interpretation and clinical management. This review aims to give interested clinicians without an extensive prior knowledge of microarray technology, an overview of its use in prenatal diagnosis, the literature to date, advantages, potential pitfalls and experience from our own tertiary center.
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Affiliation(s)
- S C Hillman
- School of Clinical and Experimental Medicine, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham, UK
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Breman A, Pursley AN, Hixson P, Bi W, Ward P, Bacino CA, Shaw C, Lupski JR, Beaudet A, Patel A, Cheung SW, Van den Veyver I. Prenatal chromosomal microarray analysis in a diagnostic laboratory; experience with >1000 cases and review of the literature. Prenat Diagn 2012; 32:351-61. [PMID: 22467166 DOI: 10.1002/pd.3861] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
OBJECTIVE To evaluate the results of prenatal chromosomal microarray analysis (CMA) on >1000 fetal samples referred for testing at our institution and to compare these data to published reports. METHODS High resolution CMA was offered to women undergoing amniocentesis or chorionic villus sampling. Parental samples were obtained concurrently to exclude maternal cell contamination and assist interpretation of copy number variations. RESULTS Clinically significant copy number variations were observed in 85/1115 cases (7.6%) overall, and in 45/1075 cases (4.2 %) if 40 abnormal cases with known chromosome abnormalities or familial genomic imbalances were excluded. Eighteen of the 1115 cases had variants of unclear clinical significance (1.6%). Indications yielding the most clinically significant findings were abnormal karyotype/fluorescence in situ hybridization (26/61, 42.6%), family history of chromosomal abnormality (13/137, 9.5%), abnormal ultrasound (38/410, 9.3%), abnormal serum screening (2/37, 5.4%) and advanced maternal age (5/394, 1.3%). Of 1075 cases having no previously known cytogenetic abnormality or family history, 18 (1.7%) had clinically significant genomic changes undetectable by conventional prenatal chromosome analysis. CONCLUSION Current experience confirms that the detection rate of CMA for prenatal chromosomal abnormalities surpasses that of conventional karyotype analysis and continues to improve with higher resolution arrays, while maintaining a low frequency of results of unclear clinical significance.
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Affiliation(s)
- Amy Breman
- Medical Genetics Laboratories, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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Shaffer LG, Dabell MP, Rosenfeld JA, Neill NJ, Ballif BC, Coppinger J, Diwan NR, Chong K, Shohat M, Chitayat D. Referral patterns for microarray testing in prenatal diagnosis. Prenat Diagn 2012; 32:344-50. [PMID: 22467165 DOI: 10.1002/pd.3856] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
OBJECTIVE To understand the prenatal referral patterns from the United States, Canada, and Israel for two whole-genome microarray platforms, each with a different resolution. METHOD Physicians selected one of the two array designs to be performed on 1483 prenatal specimens for a 1-year period. We retrospectively examined detection rates, indications for study, and physician array selection. RESULTS The lower resolution array (55 K) showed an ~32% decrease in the detection of results of unclear clinical significance while retaining the ability to detect all but one significant abnormality identified by the higher resolution array (135 K). A majority of samples were referred for abnormal ultrasound findings. Whereas the United States and Canada utilized the higher resolution array more often for this indication, Israel preferred the 55 K array. Referral patterns for parental anxiety were similar for the United States and Israel, with most cases being tested on the 55 K array. Few cases were referred for advanced maternal age or family history of a genetic condition from either Canada or Israel. CONCLUSION Referral patterns varied between the countries and between indications for study. Understanding these differences will provide laboratories the critical information needed to develop array designs to meet the medical needs and patient desires for prenatal testing.
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Affiliation(s)
- Lisa G Shaffer
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA, USA.
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Repnikova EA, Astbury C, Reshmi SC, Ramsey SN, Atkin JF, Thrush DL, Mitchell AL, Pyatt RE, Reber K, Slavin T, Gastier-Foster JM. Microarray comparative genomic hybridization and cytogenetic characterization of tissue-specific mosaicism in three patients. Am J Med Genet A 2012; 158A:1924-33. [DOI: 10.1002/ajmg.a.35477] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 04/13/2012] [Indexed: 11/08/2022]
Affiliation(s)
- Elena A Repnikova
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, and The Ohio State University College of Medicine, Columbus, Ohio 43205, USA
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Abstract
BACKGROUND Chromosome microarray (CMA) testing allows automatic and easy identification of large chromosomal abnormalities detectable by conventional cytogenetics as well as the detection of submicroscopic chromosomal imbalances. METHODS A PubMed search was performed in order to review the current use of CMA testing in the field of human reproduction. Articles discussing the use of CMA in the preimplantation setting, ongoing pregnancies, miscarriages and patients with reproductive disorders were considered. RESULTS A high rate of concordance between conventional methods of detecting chromosomal abnormalities [e.g. fluorescence in situ hybridization (FISH), karyotyping] and CMA was reported in the prenatal setting with CMA providing more comprehensive and detailed results as it investigates the whole genome at higher resolution. In preimplantation genetic screening, CMA is replacing FISH and the selection of embryos based on CMA has already resulted in live births. For ongoing pregnancies and miscarriages, CMA eliminates tissue culture failures and artifacts and allows a quick turnaround time. The detection of submicroscopic imbalances [or copy number variants (CNVs)] is beneficial when the imbalance has a clear clinical consequence but is challenging for previously undescribed imbalances, particularly for ongoing pregnancies. Recurrent CNVs have been documented in patients with reproductive disorders; however, the application of CMA in this field is still limited. CONCLUSIONS CMA enhances reproductive medicine as it facilitates better understanding of the genetic aspects of human development and reproduction and more informed patient management. Further clinical validation of CMA in the prenatal setting, creation of practice guidelines and catalogs of newly discovered submicroscopic imbalances with clinical outcomes are areas that will require attention in the future.
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Affiliation(s)
- Evica Rajcan-Separovic
- Department of Pathology and Laboratory Medicine (Cytogenetics), University of British Columbia, Children's and Women's Health Centre of BC and Child and Family Research Institute, Vancouver, BC, Canada V5Z 4H4.
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Malan V, Romana S. Analyse chromosomique sur puce à ADN (CGH array) : principe et application en diagnostic prénatal. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/s12611-012-0181-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Vetro A, Bouman K, Hastings R, McMullan DJ, Vermeesch JR, Miller K, Sikkema-Raddatz B, Ledbetter DH, Zuffardi O, van Ravenswaaij-Arts CMA. The introduction of arrays in prenatal diagnosis: a special challenge. Hum Mutat 2012; 33:923-9. [PMID: 22508381 DOI: 10.1002/humu.22050] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Accepted: 02/03/2012] [Indexed: 01/14/2023]
Abstract
Genome-wide arrays are rapidly replacing conventional karyotyping in postnatal cytogenetic diagnostics and there is a growing request for arrays in the prenatal setting. Several studies have documented 1-3% additional abnormal findings in prenatal diagnosis with arrays compared to conventional karyotyping. A recent meta-analysis demonstrated that 5.2% extra diagnoses can be expected in fetuses with ultrasound abnormalities. However, no consensus exists as to whether the use of genome-wide arrays should be restricted to pregnancies with ultrasound abnormalities, performed in all women undergoing invasive prenatal testing or offered to all pregnant women. Moreover, the interpretation of array results in the prenatal situation is challenging due to the large numbers of copy number variants with no major phenotypic effect. This also raises the question of what, or what not to report, for example, how to deal with unsolicited findings. These issues were discussed at a working group meeting that preceded the European Society of Human Genetics 2011 Conference in Amsterdam. This article is the result of this meeting and explores the introduction of genome-wide arrays into routine prenatal diagnosis. We aim to give some general recommendations on how to develop practical guidelines that can be implemented in the local setting and that are consistent with the emerging international consensus.
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Querejeta ME, Nieva B, Navajas J, Cigudosa JC, Suela J. Diagnóstico prenatal y array-CGH II: gestaciones de bajo riesgo. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.diapre.2012.01.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Novelli A, Grati FR, Ballarati L, Bernardini L, Bizzoco D, Camurri L, Casalone R, Cardarelli L, Cavalli P, Ciccone R, Clementi M, Dalprà L, Gentile M, Gelli G, Grammatico P, Malacarne M, Nardone AM, Pecile V, Simoni G, Zuffardi O, Giardino D. Microarray application in prenatal diagnosis: a position statement from the cytogenetics working group of the Italian Society of Human Genetics (SIGU), November 2011. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2012; 39:384-388. [PMID: 22262341 DOI: 10.1002/uog.11092] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A precise guideline establishing chromosomal microarray analysis (CMA) applications and platforms in the prenatal setting does not exist. The controversial question is whether CMA technologies can or should soon replace standard karyotyping in prenatal diagnostic practice. A review of the recent literature and survey of the knowledge and experience of all members of the Italian Society of Human Genetics (SIGU) Committee were carried out in order to propose recommendations for the use of CMA in prenatal testing. The analysis of datasets reported in the medical literature showed a considerable 6.4% incidence of pathogenic copy number variations (CNVs) in the group of pregnancies with sonographically detected fetal abnormalities and normal karyotype. The reported CNVs are likely to have a relevant role in terms of nosology for the fetus and in the assessment of reproductive risk for the couple. Estimation of the frequency of copy number variations of uncertain significance (VOUS) varied depending on the different CMA platforms used, ranging from 0-4%, obtained using targeted arrays, to 9-12%, obtained using high-resolution whole genome single nucleotide polymorphism (SNP) arrays. CMA analysis can be considered a second-tier diagnostic test to be used after standard karyotyping in selected groups of pregnancies, namely those with single (apparently isolated) or multiple ultrasound fetal abnormalities, those with chromosomal rearrangements, even if apparently balanced, and those with supernumerary marker chromosomes.
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Affiliation(s)
- A Novelli
- Mendel Laboratory, Casa Sollievo della Sofferenza Hospital, IRCCS, San Giovanni Rotondo, Italy.
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Mori MDLÁ, Mansilla E, García-Santiago F, Vallespín E, Palomares M, Martín R, Rodríguez R, Martínez-Payo C, Gil-Fournier B, Ramiro S, Lapunzina P, Nevado J. Diagnóstico prenatal y array-hibridación genómica comparada (CGH) (I). Gestaciones de elevado riesgo. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.diapre.2012.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Kremer V, Girard F, Gasser B, Marcellin L, Christmann D, Nisand I, Schmitt E, Florent S, Flori E. Prenatal diagnosis of a 12q22q23.2 interstitial deletion by array CGH in a malformed fetus. Eur J Med Genet 2012; 55:269-73. [PMID: 22425634 DOI: 10.1016/j.ejmg.2012.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 02/06/2012] [Indexed: 11/13/2022]
Abstract
We report the prenatal diagnosis of a 12q22q23.2 de novo interstitial deletion performed by array based comparative genomic hybridization (array CGH) in a fetus with cystic hygroma colli, intrauterine growth retardation, microcephaly and micrognathism. Haploinsufficiency for insuline-like growth factor 1 gene (IGF1), which is mapped in the deleted region, is suggested because of its implication in prenatal and postnatal growth and in neuronal maturation. This case demonstrates the contribution of array CGH in prenatal diagnosis for detecting small unbalanced chromosomal abnormalities in malformed fetuses and, subsequently, for genetic counselling.
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Affiliation(s)
- Valérie Kremer
- Service de Cytogénétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.
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Srebniak MI, Boter M, Oudesluijs GO, Cohen-Overbeek T, Govaerts LC, Diderich KE, Oegema R, Knapen MF, van de Laar IM, Joosten M, Van Opstal D, Galjaard RJH. Genomic SNP array as a gold standard for prenatal diagnosis of foetal ultrasound abnormalities. Mol Cytogenet 2012; 5:14. [PMID: 22413963 PMCID: PMC3328283 DOI: 10.1186/1755-8166-5-14] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 03/13/2012] [Indexed: 01/10/2023] Open
Abstract
Background We have investigated whether replacing conventional karyotyping by SNP array analysis in cases of foetal ultrasound abnormalities would increase the diagnostic yield and speed of prenatal diagnosis in clinical practice. Findings/results From May 2009 till June 2011 we performed HumanCytoSNP-12 array (HCS) (http://www.Illumina.com) analysis in 207 cases of foetal structural abnormalities. HCS allows detecting unbalanced genomic abnormalities with a resolution of about 150/200 kb. All cases were selected by a clinical geneticist after excluding the most common aneuploidies by RAD (rapid aneuploidy detection). Pre-test genetic counselling was offered in all cases. In 24/207 (11,6%) foetuses a clinically relevant genetic abnormality was detected. Only 8/24 abnormalities would have been detected if only routine karyotyping was performed. Submicroscopic abnormalities were found in 16/207 (7,7%) cases. The array results were achieved within 1-2 weeks after amniocentesis. Conclusions Prenatal SNP array testing is faster than karyotyping and allows detecting much smaller aberrations (~0.15 Mb) in addition to the microscopic unbalanced chromosome abnormalities detectable with karyotyping (~ > 5 Mb). Since karyotyping would have missed 66% (16/24) of genomic abnormalities in our cohort, we propose to perform genomic high resolution array testing assisted by pre-test counselling as a primary prenatal diagnostic test in cases of foetal ultrasound abnormalities.
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Arlt MF, Wilson TE, Glover TW. Replication stress and mechanisms of CNV formation. Curr Opin Genet Dev 2012; 22:204-10. [PMID: 22365495 DOI: 10.1016/j.gde.2012.01.009] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 01/24/2012] [Accepted: 01/25/2012] [Indexed: 12/11/2022]
Abstract
Copy number variants (CNVs) are widely distributed throughout the human genome, where they contribute to genetic variation and phenotypic diversity. De novo CNVs are also a major cause of numerous genetic and developmental disorders. However, unlike many other types of mutations, little is known about the genetic and environmental risk factors for new and deleterious CNVs. DNA replication errors have been implicated in the generation of a major class of CNVs, the nonrecurrent CNVs. We have found that agents that perturb normal replication and create conditions of replication stress, including hydroxyurea and aphidicolin, are potent inducers of nonrecurrent CNVs in cultured human cells. These findings have broad implications for identifying CNV risk factors and for hydroxyurea-related therapies in humans.
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Affiliation(s)
- Martin F Arlt
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-5618, United States
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Lee CN, Lin SY, Lin CH, Shih JC, Lin TH, Su YN. Clinical utility of array comparative genomic hybridisation for prenatal diagnosis: a cohort study of 3171 pregnancies. BJOG 2012; 119:614-25. [PMID: 22313859 DOI: 10.1111/j.1471-0528.2012.03279.x] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
OBJECTIVE To evaluate the clinical value of prenatal array comparative genomic hybridisation (CGH) in screening for submicroscopic genomic imbalances. DESIGN Cross-sectional study. SETTING Tertiary referral centre. POPULATION From June 2008 to February 2011, 3171 fetuses underwent prenatal array CGH testing and karyotyping at the National Taiwan University Hospital. Indications for invasive prenatal diagnosis included abnormal karyotype, abnormal ultrasound, advanced maternal age and parental anxiety. METHODS In all, 2497 fetuses were screened with 1-Mb resolution bacterial artificial chromosome array-based CGH, and 674 fetuses with 60-K oligonucleotide array-based CGH. Multiplex ligation-dependent probe amplification, fluorescence in situ hybridization, or 105-K oligonucleotide array CGH provided further confirmation. MAIN OUTCOME MEASURE Copy number variations identified by array CGH. RESULTS Array CGH detected numerical chromosome anomalies in 37 (1.2%) fetuses, microdeletion/duplication in 34 (1.1%) fetuses, large deletion/duplication in 13 (0.4%) fetuses, benign copy number changes in 13 (0.4%) fetuses and variation of unknown clinical significance in five (0.2%) fetuses. Array CGH was effective in identifying submicroscopic genomic imbalance in fetuses with de novo balance translocations (2/17, 1.8%), supernumerary marker chromosomes (3/6, 50%), and abnormal prenatal ultrasound findings (33/194, 17.0%). Array CGH detected microdeletions/duplications in 12 fetuses with normal karyotype. CONCLUSION Prenatal array CGH is effective in screening for submicroscopic genomic imbalance. Array CGH may add 8.2% to the diagnostic field, compared with conventional karyotyping, for fetuses with abnormal ultrasound results, and is particularly useful in fetuses with karyotypic balanced translocation or marker chromosomes. There is a 0.52% baseline risk of submicroscopic genomic imbalance, even in women with an uneventful prenatal examination.
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Affiliation(s)
- C-N Lee
- Department of Obstetrics and Gynaecology, National Taiwan University Hospital, Taipei, Taiwan
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Use of Array Genomic Hybridization Technology in Prenatal Diagnosis in Canada. JOURNAL OF OBSTETRICS AND GYNAECOLOGY CANADA 2011. [DOI: 10.1016/s1701-2163(16)35112-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Schmid M, Stary S, Blaicher W, Gollinger M, Husslein P, Streubel B. Prenatal genetic diagnosis using microarray analysis in fetuses with congenital heart defects. Prenat Diagn 2011; 32:376-82. [DOI: 10.1002/pd.2862] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Revised: 08/08/2011] [Accepted: 08/08/2011] [Indexed: 02/02/2023]
Affiliation(s)
- Maximilian Schmid
- Department of Obstetrics and Feto-maternal Medicine; Medical University of Vienna; Vienna; Austria
| | - Susanne Stary
- Clinical Institute of Pathology; Medical University of Vienna; Vienna; Austria
| | - Wibke Blaicher
- Department of Obstetrics and Feto-maternal Medicine; Medical University of Vienna; Vienna; Austria
| | - Michaela Gollinger
- Clinical Institute of Pathology; Medical University of Vienna; Vienna; Austria
| | - Peter Husslein
- Department of Obstetrics and Feto-maternal Medicine; Medical University of Vienna; Vienna; Austria
| | - Berthold Streubel
- Clinical Institute of Pathology; Medical University of Vienna; Vienna; Austria
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