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Levy M, Lifshitz S, Goldenberg-Fumanov M, Bazak L, Goldstein RJ, Hamiel U, Berger R, Lipitz S, Maya I, Shohat M. Exome sequencing in every pregnancy? Results of trio exome sequencing in structurally normal fetuses. Prenat Diagn 2024. [PMID: 38735835 DOI: 10.1002/pd.6585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 04/27/2024] [Accepted: 04/30/2024] [Indexed: 05/14/2024]
Abstract
OBJECTIVE This study aimed to assess the detection rate of clinically significant results of prenatal exome sequencing (pES) in low-risk pregnancies and apparently normal fetuses in non-consanguineous couples. METHODS A retrospective analysis of pES conducted at a single center from January 2020 to September 2023 was performed. Genetic counseling was provided, and detailed medical histories were obtained. High-risk pregnancies were excluded due to major ultrasound anomalies, sonographic soft markers, abnormal maternal biochemical screening, or family history suggestive of monogenic diseases as well as cases with pathogenic and likely pathogenic (P/LP) chromosomal microarray results. Exome analysis focused on ∼2100 genes associated with Mendelian genetic disorders. Variant analysis and classification followed the American College of Medical Genetics and Genomics (ACMG) guidelines. RESULTS Among 1825 pES conducted, 1020 low-risk cases revealed 28 fetuses (2.7%) with potentially clinically significant variants indicating known monogenic diseases, primarily de novo dominant variants (64%). Among these 28 cases, 9 fetuses (0.9%) had the potential for severe phenotypes, including shortened lifespan and intellectual disability, and another 12 had the potential for milder phenotypes. Seven cases were reported with variants of uncertain significance (VUS) that, according to the ACMG criteria, leaned toward LP, constituting 0.7% of the entire cohort. Termination of pregnancy was elected in 13 out of 1020 cases (1.2%) in the cohort, including 7/9 in the severe phenotypes group, 2/12 in the milder phenotype group, and 4/7 in the VUS group. CONCLUSION The 2.7% detection rate highlights the significant contribution of pES in low-risk pregnancies. However, it necessitates rigorous analysis, and comprehensive genetic counseling before and after testing.
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Affiliation(s)
- Michal Levy
- The Genetic Institute of Maccabi Health Services, Rehovot, Israel
- School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Raphael Recanati Genetics Institute, Beilinson Hospital, Rabin Medical Center, Petach Tikva, Israel
| | - Shira Lifshitz
- The Genetic Institute of Maccabi Health Services, Rehovot, Israel
| | | | - Lily Bazak
- The Genetic Institute of Maccabi Health Services, Rehovot, Israel
| | | | - Uri Hamiel
- The Genetic Institute of Maccabi Health Services, Rehovot, Israel
- School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Rachel Berger
- The Genetic Institute of Maccabi Health Services, Rehovot, Israel
| | - Shlomo Lipitz
- School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Idit Maya
- The Genetic Institute of Maccabi Health Services, Rehovot, Israel
- School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Raphael Recanati Genetics Institute, Beilinson Hospital, Rabin Medical Center, Petach Tikva, Israel
| | - Mordechai Shohat
- The Genetic Institute of Maccabi Health Services, Rehovot, Israel
- School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Bioinformatics Unit, Cancer Research Center, Chaim Sheba Medical Center, Tel-Hashomer, Israel
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Zhuang J, Zhang N, Chen Y, Jiang Y, Chen X, Chen W, Chen C. Prenatal diagnosis and molecular cytogenetic characterization of fetuses with central nervous system anomalies using chromosomal microarray analysis: a seven-year single-center retrospective study. Sci Rep 2024; 14:2271. [PMID: 38280885 PMCID: PMC10821898 DOI: 10.1038/s41598-024-52831-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 01/24/2024] [Indexed: 01/29/2024] Open
Abstract
Few existing reports have investigated the copy number variants (CNVs) in fetuses with central nervous system (CNS) anomalies. To gain further insights into the genotype-phenotype relationship, we conducted chromosomal microarray analysis (CMA) to reveal the pathogenic CNVs (pCNVs) that were associated with fetal CNS anomalies. We enrolled 5,460 pregnant women with different high-risk factors who had undergone CMA. Among them, 57 subjects with fetal CNS anomalies were recruited. Of the subjects with fetal CNS anomalies, 23 were given amniocentesis, which involved karyotype analysis and CMA to detect chromosomal abnormalities. The other 34 cases only underwent CMA detection using fetal abortive tissue. In this study, we identified five cases of chromosome aneuploid and nine cases of pCNVs in the fetuses, with a chromosomal aberration detection rate of 24.56% (14/57). In the 23 cases that were given both karyotype and CMA analysis, one case with trisomy 18 was detected by karyotyping. Moreover, CMA revealed a further three cases of pCNVs, including the 1p36.33p36.31, 7q11.23, and 1q21.1q21.2 microdeletions, with a 13.04% (3/23) increase in CMA yield over the karyotype analysis. Additionally, three cases of trisomy 13, one case of trisomy 21, and six cases of pCNVs were detected in the other 34 fetuses where only CMA was performed. Furthermore, a higher chromosomal aberration detection rate was observed in the extra CNS anomaly group than in the isolated CNS anomaly group (40.91% vs 14.29%). In conclude, several pathogenic CNVs were identified in the fetuses with CNS anomalies using CMA. Among the detected CNVs, ZIC2, GNB1, and NSUN5 may be the candidate genes that responsible for fetal CNS anomalies. Our findings provides an additional reference for genetic counseling regarding fetal CNS anomalies and offers further insight into the genotype-phenotype relationship.
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Affiliation(s)
- Jianlong Zhuang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, 362000, Fujian, China.
| | - Na Zhang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, 362000, Fujian, China.
| | - Yu'e Chen
- Department of Ultrasound, Quanzhou Women's and Children's Hospital, Quanzhou, 362000, Fujian, China
| | - Yuying Jiang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, 362000, Fujian, China
| | - Xinying Chen
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, 362000, Fujian, China
| | - Wenli Chen
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, 362000, Fujian, China
| | - Chunnuan Chen
- Department of Neurology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, 362000, Fujian, China.
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Mitrakos A, Kosma K, Makrythanasis P, Tzetis M. Prenatal Chromosomal Microarray Analysis: Does Increased Resolution Equal Increased Yield? Genes (Basel) 2023; 14:1519. [PMID: 37628571 PMCID: PMC10454647 DOI: 10.3390/genes14081519] [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: 06/26/2023] [Revised: 07/16/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Chromosomal microarray analysis (CMA) is considered a first-tier test for patients with developmental disabilities and congenital anomalies and is also routinely applied in prenatal diagnosis. The current consensus size cut-off for reporting copy number variants (CNVs) in the prenatal setting ranges from 200 Kb to 400 Kb, with the intention of minimizing the impact of variants of uncertain significance (VUS). Very limited data are currently available on the application of higher resolution platforms prenatally. The aim of this study is to investigate the feasibility and impact of applying high-resolution CMA in the prenatal setting. To that end, we report on the outcomes of applying CMA with a size cut-off of 20 Kb in 250 prenatal samples and discuss the findings and diagnostic yield and also provide follow-up for cases with variants of uncertain significance. Overall, 19.6% (49) showed one or more chromosomal abnormalities, with the findings classified as Pathogenic (P) or Likely Pathogenic (LP) in 15.6% and as VUS in 4%. When excluding the cases with known familial aberrations, the diagnostic yield was 12%. The smallest aberration detected was a 32 Kb duplication of the 16p11.2 region. In conclusion, this study demonstrates that prenatal diagnosis with a high-resolution aCGH platform can reliably detect smaller CNVs that are often associated with neurodevelopmental phenotypes while providing an increased diagnostic yield, regardless of the indication for testing, with only a marginal increase in the VUS incidence. Thus, it can be an important tool in the prenatal setting.
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Affiliation(s)
- Anastasios Mitrakos
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, St. Sophia’s Children’s Hospital, 11527 Athens, Greece; (K.K.); (P.M.)
| | | | | | - Maria Tzetis
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, St. Sophia’s Children’s Hospital, 11527 Athens, Greece; (K.K.); (P.M.)
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4
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Cai M, Lin N, Guo N, Su L, Wu X, Xie X, Li Y, He S, Fu X, Xu L, Huang H. Using single nucleotide polymorphism array for prenatal diagnosis in a large multicenter study in Southern China. Sci Rep 2023; 13:7242. [PMID: 37142625 PMCID: PMC10160013 DOI: 10.1038/s41598-023-33668-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 04/17/2023] [Indexed: 05/06/2023] Open
Abstract
Numerous studies have evaluated the use of single nucleotide polymorphism array (SNP-array) in prenatal diagnostics, but very few have evaluated its application under different risk conditions. Here, SNP-array was used for the retrospective analysis of 8386 pregnancies and the cases were categorized into seven groups. Pathogenic copy number variations (pCNVs) were found in 699 (8.3%, 699/8386) cases. Among the seven different risk factor groups, the non-invasive prenatal testing-positive group had the highest pCNVs rate (35.3%), followed by the abnormal ultrasound structure group (12.8%), and then the chromosomal abnormalities in the couples group (9.5%). Notably the adverse pregnancy history group presented with the lowest pCNVs rate (2.8%). Further evaluation of the 1495 cases with ultrasound abnormalities revealed that the highest pCNV rates were recorded in those cases with multiple system structure abnormalities (22.6%), followed by the groups with skeletal system (11.6%) and urinary system abnormalities (11.2%). A total of 3424 fetuses with ultrasonic soft markers were classified as having one, two, or three ultrasonic soft markers. The different pCNV rates in the three groups were statistically significant. There was little correlation between pCNVs and a previous history of adverse pregnancy outcomes, suggesting that genetic screening under these conditions should be evaluated on a case-by-case basis.
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Affiliation(s)
- Meiying Cai
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Nan Guo
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Linjuan Su
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Xiaoqing Wu
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Xiaorui Xie
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Ying Li
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Shuqiong He
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Xianguo Fu
- Department of Prenatal Diagnosis, Ningde Municipal Hospital, Ningde Normal University, Ningde, China.
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China.
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China.
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Pynaker C, Norris F, Hui L, Halliday J. Perinatal outcomes and genomic characteristics of fetal copy number variants: An individual record linkage study of 713 pregnancies. Prenat Diagn 2023; 43:516-526. [PMID: 36631928 PMCID: PMC10947476 DOI: 10.1002/pd.6305] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/23/2022] [Accepted: 01/05/2023] [Indexed: 01/13/2023]
Abstract
OBJECTIVE To determine the perinatal outcomes of fetuses diagnosed with a pathogenic copy number variant (CNV) or variant of uncertain significance (VUS); and to characterize these variants in terms of testing indication, genomic location, size, and inheritance. METHODS Retrospective study of singleton pregnancies with a pathogenic CNV or VUS from a single laboratory during 2012-2018. Probabilistic record linkage between the prenatal diagnosis dataset and perinatal outcome data for births from 20 weeks gestation was performed. If no birth record was found, this implied a pregnancy loss <20 weeks. RESULTS We included 6945 prenatal microarray results; a pathogenic CNV was detected in 230 (3.3%, 95% CI: 2.9%-3.8%) and a VUS in 483 (7.0%, 95% CI: 6.4%-7.6%). Of pregnancies with a pathogenic CNV, 20.0% (95% CI: 15.3%-25.6%) had a live birth, 3.0% (95% CI: 1.5%-6.2%) had a perinatal death (stillbirth or neonatal death), and 77% (95% CI: 71.1%-81.9%) had no birth record. Of those with a VUS, 64.4% (95% CI: 60.0%-68.5%) had a live birth, 1.8% (95% CI: 1.0%-3.5%) had a perinatal death, and no birth record was found for 33.7% (95% CI: 29.7%-38.1%). Most pathogenic CNVs (61.1%) were <7 Mb in size. The most common microdeletion syndromes were DiGeorge, Wolf-Hirschhorn, and Cri-du-chat syndromes. CONCLUSION This study provides an overview of perinatal outcomes and frequency of recurrent CNVs observed in the prenatal microarray era.
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Affiliation(s)
- Cecilia Pynaker
- Reproductive Epidemiology GroupMurdoch Children's Research InstituteParkvilleVictoriaAustralia
- Department of PaediatricsUniversity of MelbourneParkvilleVictoriaAustralia
| | - Fiona Norris
- Victorian Clinical Genetics ServicesMurdoch Children's Research InstituteParkvilleVictoriaAustralia
| | - Lisa Hui
- Reproductive Epidemiology GroupMurdoch Children's Research InstituteParkvilleVictoriaAustralia
- Department of Obstetrics and GynaecologyUniversity of MelbourneParkvilleVictoriaAustralia
- Department of Perinatal MedicineMercy Hospital for WomenHeidelbergVictoriaAustralia
- Department of Obstetrics and GynaecologyNorthern HealthEppingVictoriaAustralia
| | - Jane Halliday
- Reproductive Epidemiology GroupMurdoch Children's Research InstituteParkvilleVictoriaAustralia
- Department of PaediatricsUniversity of MelbourneParkvilleVictoriaAustralia
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Should Prenatal Chromosomal Microarray Analysis Be Offered for Pulmonary Atresia? A Single-Center Retrospective Study in China. Genes (Basel) 2023; 14:genes14030722. [PMID: 36980994 PMCID: PMC10047995 DOI: 10.3390/genes14030722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/06/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
(1) Objective: To evaluate the application of chromosomal microarray analysis (CMA) in fetuses with pulmonary atresia (PA) and to explore the risk factors for predicting chromosomal imbalances and adverse perinatal outcomes. (2) Methods: This study investigated 428 cases of PA singleton pregnancies that were tested using CMA and quantitative fluorescent polymerase chain reaction (QF-PCR) as first-line genetic testing. The PA cases were divided into two groups: an isolated group and a non-isolated group. (3) Results: CMA revealed clinically relevant copy number variations (CNVs) in 9/139 (6.47%) PA fetuses, i.e., pathogenic copy number variations (pCNVs) in 8/139 (5.76%) fetuses and likely pathogenic CNVs in 1/139 (0.72%) fetuses. Stratified analysis showed that the incidence of clinically significant variants was higher in non-isolated PA fetuses than in isolated PA fetuses (12.50%, 6/48 vs. 3.30%, 3/91, p = 0.036). Regression analysis showed that a combination of other structural abnormalities at diagnosis of PA represented the principal risk factor for chromosomal imbalances (OR = 2.672). A combination of other structural abnormalities and a high maternal age increased the risk of adverse pregnancy outcomes in PA cases, including intrauterine fetal death (IUFD), termination of pregnancy (TOP), and preterm delivery. (4) Conclusions: The value of CMA for locating imbalanced genetic variations in fetuses with PA was highlighted by this study, particularly when combined with additional structural abnormalities.
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7
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Sakyu T, Stover SR, Wang Y, Ward P, Gandhi M, Braun MC, Van den Veyver IB, Bi W. Compound heterozygosity of a de novo submicroscopic deletion and an inherited frameshift pathogenic variant in the PKHD1 gene in a fetus with bilaterally enlarged and echogenic kidneys, enlarged abdomen and oligohydramnios. Clin Case Rep 2023; 11:e6692. [PMID: 36846174 PMCID: PMC9950036 DOI: 10.1002/ccr3.6692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/08/2022] [Indexed: 02/26/2023] Open
Abstract
We present a fetus with bilaterally enlarged and echogenic kidneys. Prenatal testing detected compound heterozygosity for a 0.676 Mb de novo deletion and an inherited pathogenic variant in PKHD1. This is the first case of autosomal recessive polycystic kidney disease (ARPKD) with a prenatally detected disease-causing PKHD1 deletion.
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Affiliation(s)
- Takuya Sakyu
- Baylor GeneticsHoustonTexasUSA,Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA,Present address:
H.U. Group Research Institute GKTokyoJapan
| | - Samantha R. Stover
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA,Department of Obstetrics and GynecologyBaylor College of MedicineHoustonTexasUSA,Texas Children's HospitalHoustonTexasUSA,Present address:
Department of Obstetrics and Gynecology, Division of Maternal Fetal MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Yue Wang
- Baylor GeneticsHoustonTexasUSA,Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
| | - Patricia Ward
- Baylor GeneticsHoustonTexasUSA,Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
| | - Manisha Gandhi
- Department of Obstetrics and GynecologyBaylor College of MedicineHoustonTexasUSA,Texas Children's HospitalHoustonTexasUSA
| | - Michael C. Braun
- Department of Obstetrics and GynecologyBaylor College of MedicineHoustonTexasUSA,Texas Children's HospitalHoustonTexasUSA,Division of Pediatrics NephrologyBaylor College of MedicineHoustonTexasUSA,Department of PediatricsBaylor College of MedicineHoustonTexasUSA
| | - Ignatia B. Van den Veyver
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA,Department of Obstetrics and GynecologyBaylor College of MedicineHoustonTexasUSA,Texas Children's HospitalHoustonTexasUSA
| | - Weimin Bi
- Baylor GeneticsHoustonTexasUSA,Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
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Akalın M, Demirci O, Dizdaroğulları GE, Çiftçi E, Karaman A. Contribution of chromosomal microarray analysis and next-generation sequencing to genetic diagnosis in fetuses with normal karyotype. J Obstet Gynaecol Res 2023; 49:519-529. [PMID: 36316250 DOI: 10.1111/jog.15486] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/08/2022] [Accepted: 10/20/2022] [Indexed: 11/07/2022]
Abstract
AIM The aim of this study was to investigate the contribution of chromosomal microarray analysis (CMA) and next-generation sequencing (NGS) to genetic diagnosis in fetuses with normal karyotype who underwent invasive testing for different indications. METHODS The results of invasive genetic testing performed at a tertiary center between September 2020 and March 2022 were retrospectively analyzed. Indications for invasive tests were classified as fetal structural malformation, presence of soft markers, and high risk in screening tests. CMA results were classified as pathogenic or likely pathogenic (pCNVs), benign (bCNVs), and variants of unknown clinical significance (VOUS). RESULTS A total of 830 invasive tests were performed and aneuploidy was detected in 11.2% of the fetuses. CMA was performed in 465 fetuses with normal karyotype, and pCNVs were detected in 6.9%. pCNVs were detected in 8.2% of fetuses with structural malformations, 6.5% in soft markers, and 4.7% in high risk in screening tests. Pathogenic variants were detected by NGS in 33.8% of fetuses with bCNVs. CONCLUSIONS pCNVs can be significantly detected not only in fetuses with structural malformations, but also in invasive testing with other indications. NGS significantly contributes to genetic diagnosis in fetuses with structural malformations.
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Affiliation(s)
- Münip Akalın
- Department of Perinatology, Marmara University Pendik Training and Research Hospital, Istanbul, Turkey
| | - Oya Demirci
- Department of Perinatology, University of Health Sciences Zeynep Kamil Women's and Children's Disease Training and Research Hospital, Istanbul, Turkey
| | - Gizem E Dizdaroğulları
- Department of Perinatology, University of Health Sciences Zeynep Kamil Women's and Children's Disease Training and Research Hospital, Istanbul, Turkey
| | - Erman Çiftçi
- Department of Obstetrics and Gynecology, University of Health Sciences Zeynep Kamil Women's and Children's Disease Training and Research Hospital, Istanbul, Turkey
| | - Ali Karaman
- Department of Medical Genetics, University of Health Sciences Zeynep Kamil Women's and Children's Disease Training and Research Hospital, Istanbul, Turkey
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Liu P, Vossaert L. Emerging technologies for prenatal diagnosis: The application of whole genome and RNA sequencing. Prenat Diagn 2022; 42:686-696. [PMID: 35416301 PMCID: PMC10014115 DOI: 10.1002/pd.6146] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 11/10/2022]
Abstract
DNA sequencing technologies for clinical genetic testing have been rapidly evolving in recent years, and steadily become more important within the field of prenatal diagnostics. This review aims to give an overview of recent developments and to describe how they have the potential to fill the gaps of the currently clinically implemented methods for prenatal diagnosis of various genetic disorders. It has been shown for postnatal testing that whole genome sequencing provides a set of added benefits compared to exome sequencing, and it is to be expected that this will be the case for prenatal testing as well. RNA-sequencing, already used postnatally, can provide valuable complementary data to DNA-based testing, and aid in variant interpretation. While not ready for clinical implementation, emerging technologies such as long-read and Hi-C sequencing analyses might add to the toolbox for interpreting the expanding genetic data sets generated by genome-wide sequencing. Lastly, we also discuss some more practical implications of introducing these emerging technologies, which generate larger and larger genomic data sets, in the prenatal field.
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Affiliation(s)
- Pengfei Liu
- Baylor College of Medicine and Baylor Genetics, Houston, Texas, USA
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10
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Comparative Genomic Hybridization to Microarrays in Fetuses with High-Risk Prenatal Indications: Polish Experience with 7400 Pregnancies. Genes (Basel) 2022; 13:genes13040690. [PMID: 35456496 PMCID: PMC9032831 DOI: 10.3390/genes13040690] [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: 03/19/2022] [Revised: 04/06/2022] [Accepted: 04/12/2022] [Indexed: 11/16/2022] Open
Abstract
The aim of this study was to determine the suitability of the comparative genomic hybridization to microarray (aCGH) technique for prenatal diagnosis, but also to assess the frequency of chromosomal aberrations that may lead to fetal malformations but are not included in the diagnostic report. We present the results of the aCGH in a cohort of 7400 prenatal cases, indicated for invasive testing due to ultrasound abnormalities, high-risk for serum screening, thickened nuchal translucency, family history of genetic abnormalities or congenital abnormalities, and advanced maternal age (AMA). The overall chromosomal aberration detection rate was 27.2% (2010/7400), including 71.2% (1431/2010) of numerical aberrations and 28.8% (579/2010) of structural aberrations. Additionally, the detection rate of clinically significant copy number variants (CNVs) was 6.8% (505/7400) and 0.7% (57/7400) for variants of unknown clinical significance. The detection rate of clinically significant submicroscopic CNVs was 7.9% (334/4204) for fetuses with structural anomalies, 5.4% (18/336) in AMA, 3.1% (22/713) in the group of abnormal serum screening and 6.1% (131/2147) in other indications. Using the aCGH method, it was possible to assess the frequency of pathogenic chromosomal aberrations, of likely pathogenic and of uncertain clinical significance, in the groups of cases with different indications for an invasive test.
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Mastromoro G, Guadagnolo D, Khaleghi Hashemian N, Marchionni E, Traversa A, Pizzuti A. Molecular Approaches in Fetal Malformations, Dynamic Anomalies and Soft Markers: Diagnostic Rates and Challenges-Systematic Review of the Literature and Meta-Analysis. Diagnostics (Basel) 2022; 12:575. [PMID: 35328129 PMCID: PMC8947110 DOI: 10.3390/diagnostics12030575] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/11/2022] [Accepted: 02/21/2022] [Indexed: 02/06/2023] Open
Abstract
Fetal malformations occur in 2-3% of pregnancies. They require invasive procedures for cytogenetics and molecular testing. "Structural anomalies" include non-transient anatomic alterations. "Soft markers" are often transient minor ultrasound findings. Anomalies not fitting these definitions are categorized as "dynamic". This meta-analysis aims to evaluate the diagnostic yield and the rates of variants of uncertain significance (VUSs) in fetuses undergoing molecular testing (chromosomal microarray (CMA), exome sequencing (ES), genome sequencing (WGS)) due to ultrasound findings. The CMA diagnostic yield was 2.15% in single soft markers (vs. 0.79% baseline risk), 3.44% in multiple soft markers, 3.66% in single structural anomalies and 8.57% in multiple structural anomalies. Rates for specific subcategories vary significantly. ES showed a diagnostic rate of 19.47%, reaching 27.47% in multiple structural anomalies. WGS data did not allow meta-analysis. In fetal structural anomalies, CMA is a first-tier test, but should be integrated with karyotype and parental segregations. In this class of fetuses, ES presents a very high incremental yield, with a significant VUSs burden, so we encourage its use in selected cases. Soft markers present heterogeneous CMA results from each other, some of them with risks comparable to structural anomalies, and would benefit from molecular analysis. The diagnostic rate of multiple soft markers poses a solid indication to CMA.
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Affiliation(s)
- Gioia Mastromoro
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (N.K.H.); (E.M.); (A.T.); (A.P.)
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12
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Prenatal Diagnosis by Array Comparative Genomic Hybridization in Fetuses with Cardiac Abnormalities. Genes (Basel) 2021; 12:genes12122021. [PMID: 34946970 PMCID: PMC8701951 DOI: 10.3390/genes12122021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 11/17/2022] Open
Abstract
Congenital heart defects (CHDs) appear in 8–10 out of 1000 live born newborns and are one of the most common causes of deaths. In fetuses, the congenital heart defects are found even 3–5 times more often. Currently, microarray comparative genomic hybridization (array CGH) is recommended by worldwide scientific organizations as a first-line test in the prenatal diagnosis of fetuses with sonographic abnormalities, especially cardiac defects. We present the results of the application of array CGH in 484 cases with prenatally diagnosed congenital heart diseases by fetal ultrasound scanning (256 isolated CHD and 228 CHD coexisting with other malformations). We identified pathogenic aberrations and likely pathogenic genetic loci for CHD in 165 fetuses and 9 copy number variants (CNVs) of unknown clinical significance. Prenatal array-CGH is a useful method allowing the identification of all unbalanced aberrations (number and structure) with a much higher resolution than the currently applied traditional assessment techniques karyotype. Due to this ability, we identified the etiology of heart defects in 37% of cases.
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13
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Stevens BK, Nunley PB, Wagner C, Murphy L, Wittman T, Ramdaney A, Jones M, Choates MG. Utility of expanded carrier screening in pregnancies with ultrasound abnormalities. Prenat Diagn 2021; 42:60-78. [PMID: 34792213 DOI: 10.1002/pd.6069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 09/15/2021] [Accepted: 11/05/2021] [Indexed: 11/09/2022]
Abstract
OBJECTIVE Explore the utility of expanded carrier screening in evaluating heritable causes of congenital anomalies detected by prenatal ultrasound. METHOD A retrospective chart review was conducted to collect structural abnormality and genetic testing data on infants who were evaluated postnatally by a medical geneticist. These were used to determine if expanded carrier screening could have determined the etiology prior to delivery. Additionally, recessive and X-linked conditions on clinically available carrier screening panels were evaluated to determine the number of conditions associated with abnormal ultrasound findings. RESULTS Our retrospective chart review found 222 patients with genetic etiologies, including eight unique autosomal recessive conditions and six X-linked conditions in the 23% who underwent exome sequencing. Of these 14 unique conditions detected, three were included on a list of 271 conditions for which screening was available in 2019 and five were included on a 500 condition panel available in 2020. A literature review was performed on the list of 271 conditions and 88 were reported to be associated with one or more ultrasound abnormalities. CONCLUSION This study demonstrates limited but potential utility for expanded carrier screening to determine the underlying etiology of congenital anomalies.
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Affiliation(s)
- Blair K Stevens
- Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas, USA
| | | | - Chelsea Wagner
- Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Lauren Murphy
- Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Theresa Wittman
- Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Aarti Ramdaney
- Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Malorie Jones
- Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Meagan Giles Choates
- Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas, USA
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14
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Cai M, Huang H, Xu L, Lin N. Clinical Utility and the Yield of Single Nucleotide Polymorphism Array in Prenatal Diagnosis of Fetal Central Nervous System Abnormalities. Front Mol Biosci 2021; 8:666115. [PMID: 34084776 PMCID: PMC8167038 DOI: 10.3389/fmolb.2021.666115] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/05/2021] [Indexed: 11/22/2022] Open
Abstract
Applying single nucleotide polymorphism (SNP) array to identify the etiology of fetal central nervous system (CNS) abnormality, and exploring its association with chromosomal abnormalities, copy number variations, and obstetrical outcome. 535 fetuses with CNS abnormalities were analyzed using karyotype analysis and SNP array. Among the 535 fetuses with CNS abnormalities, chromosomal abnormalities were detected in 36 (6.7%) of the fetuses, which were consistent with karyotype analysis. Further, additional 41 fetuses with abnormal copy number variations (CNVs) were detected using SNP array (the detection rate of additional abnormal CNVs was 7.7%). The rate of chromosomal abnormalities, but not that of pathogenic CNVs in CNS abnormalities with other ultrasound abnormalities was significantly higher than that in isolated CNS abnormalities. The rates of chromosomal abnormalities and pathogenic CNVs in fetuses with spine malformation (50%), encephalocele (50%), subependymal cyst (20%), and microcephaly (16.7%) were higher than those with other isolated CNS abnormalities. The pregnancies for 36 cases with chromosomal abnormalities, 18 cases with pathogenic CNVs, and three cases with VUS CNVs were terminated. SNP array should be used in the prenatal diagnosis of fetuses with CNS abnormalities, which can enable better prenatal assessment and genetic counseling, and affect obstetrical outcomes.
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Affiliation(s)
| | | | - Liangpu Xu
- Department of the Prenatal Diagnosis Center, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Na Lin
- Department of the Prenatal Diagnosis Center, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
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15
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Huang H, Cai M, Ma W, Lin N, Xu L. Chromosomal Microarray Analysis for the Prenatal Diagnosis in Fetuses with Nasal Bone Hypoplasia: A Retrospective Cohort Study. Risk Manag Healthc Policy 2021; 14:1533-1540. [PMID: 33889037 PMCID: PMC8054820 DOI: 10.2147/rmhp.s286038] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 01/27/2021] [Indexed: 01/03/2023] Open
Abstract
Background Previous studies have shown a strong correlation between fetal nasal bone hypoplasia and chromosomal anomaly; however, there is little knowledge on the associations of fetal nasal bone hypoplasia with chromosomal microdeletions and microduplications until now. Chromosomal microarray analysis (CMA) is a high-resolution molecular genetic tool that is effective to detect submicroscopic anomalies including chromosomal microdeletions and microduplications that cannot be detected by karyotyping. This study aimed to examine the performance of CMA for the prenatal diagnosis of nasal bone hypoplasia in the second and third trimesters. Subjects and Methods A total of 84 pregnant women in the second and third trimesters with fetal nasal bone hypoplasia, as revealed by ultrasound examinations, were enrolled, and all women underwent karyotyping and CMA with the Affymetrix CytoScan 750K GeneChip Platform. The subjects included 32 cases with fetal nasal bone hypoplasia alone and 52 cases with fetal nasal bone hypoplasia combined with other ultrasound abnormalities, and the prevalence of genomic abnormality was compared between these two groups. Results Karyotyping detected 21 cases of chromosomal anomaly in the 84 study subjects (21/84, 25%), including trisomy 21 (14 cases), trisomy 18 (3 cases), 46, del (4)(p16) karyotype (2 cases), 47, XYY syndrome (1 case) and 46, XY, del (5) (p15) karyotype (1 case). CMA detected additional four fetuses with pathogenic copy number variations (CNVs) and six fetuses with uncertain clinical significance (VOUS). No significant difference was detected in the prevalence of genomic abnormality in fetuses with nasal bone hypoplasia alone and in combination with other ultrasound abnormalities (13/32 vs 18/52; χ2 = 0.31, P > 0.05). The pregnancy was terminated in 21 fetuses detected with chromosomal abnormality and 4 fetuses detected with pathogenic CNVs. Among the other six fetuses detected with VOUS, the parents chose to continue the pregnancy, and the newborns all had normal clinical phenotypes. Conclusion In addition to chromosomal abnormalities identified in 21 fetuses by karyotyping, CMA detected additional 10 fetuses with abnormal CNVs (10/84, 11.9%) in the study population. CMA is a promising powerful tool for prenatal diagnosis that may provide valuable data for the accurate assessment of fetal prognosis and the decision of pregnancy continuation during the prenatal clinical counseling.
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Affiliation(s)
- Hailong Huang
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, People's Republic of China
| | - Meiying Cai
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, People's Republic of China
| | - Wei Ma
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, People's Republic of China.,School of Clinical Medicine, Fujian Medical University, Fuzhou City, Fujian Province, 350122, People's Republic of China
| | - Na Lin
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, People's Republic of China
| | - Liangpu Xu
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, People's Republic of China
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16
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The role of chromosomal microarray and exome sequencing in prenatal diagnosis. Curr Opin Obstet Gynecol 2021; 33:148-155. [PMID: 33620893 DOI: 10.1097/gco.0000000000000692] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
PURPOSE OF REVIEW Advancements in technologies have revolutionized prenatal diagnosis. Chromosomal microarray analysis (CMA) became a proven method and was implemented to detect gains and losses of DNA and absence of heterozygosity across the genome. Next-generation sequencing technologies have brought opportunities and challenges to genetic testing. Exome sequencing detects single-nucleotide variants (SNVs) across the exome and its prenatal application is an emerging field. We reviewed the literature to define the role of CMA and exome sequencing in prenatal diagnosis. RECENT FINDING The application of exome sequencing in genetic diagnosis shows increased diagnostic yield and could be potentially implemented for prenatal diagnosis of fetuses with one or more ultrasound structural abnormalities or suspected monogenetic conditions. Although CMA is a gold standard for copy number variant (CNV) detection, large clinical cohort studies emphasized integrated CNV and SNV analyses for precise molecular diagnosis. Recent studies also suggest low-pass genome sequencing-based CNV detection can identify genome-wide imbalances at higher resolutions. SUMMARY Data suggest exome sequencing for SNVs and CMA for CNV detection are the most effective approach for prenatal genetic diagnosis. Emerging evidences show genome sequencing has the potential to replace CMA and even exome sequencing to become a comprehensive genetic test in the clinical diagnostic laboratory.
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17
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Lewis C, Hammond J, Klapwijk JE, Harding E, Lou S, Vogel I, Szepe EJ, Hui L, Ingvoldstad-Malmgren C, Soller MJ, Ormond KE, Choolani M, Hill M, Riedijk S. Dealing with uncertain results from chromosomal microarray and exome sequencing in the prenatal setting: An international cross-sectional study with healthcare professionals. Prenat Diagn 2021; 41:720-732. [PMID: 33724493 PMCID: PMC8519283 DOI: 10.1002/pd.5932] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/26/2021] [Indexed: 12/20/2022]
Abstract
Objectives To conduct qualitative interviews with healthcare providers working in different countries to understand their experiences of dealing with uncertain results from prenatal chromosome microarray analysis (CMA) and exome sequencing (ES). Methods Semi‐structured interviews with 31 healthcare providers who report or return prenatal CMA and/or ES results (clinicians, genetic counsellors and clinical scientists) in six countries with differing healthcare systems; Australia (4), Denmark (5), Netherlands (6), Singapore (4), Sweden (6) and United Kingdom (6). The topic guide explored the main sources of uncertainty and their management. Results There was variation in reporting practices both between and across countries for variants of uncertain significance, however, there was broad agreement on reporting practices for incidental findings. There was also variation in who decides what results are reported (clinical scientists or clinicians). Technical limitations and lack of knowledge (to classify variants and of prenatal phenotypes) were significant challenges, as were turnaround times and lack of guidelines. Conclusion Health professionals around the globe are dealing with similar sources of uncertainty, but managing them in different ways, Continued dialogue with international colleagues on ways of managing uncertain results is important to compare and contrast the benefits and limitations of the different approaches.
What's already known about this topic?
Chromosome microarray analysis and exome sequencing have increased diagnostic yield over karyotyping but have increased the incidence of uncertain results.
What does this study add?
Our findings highlight variation in reporting practices both between and across countries for variants of uncertain significance, although there is broad agreement on reporting practices for incidental findings. International guidelines may help to standardise how we define and categorise variants, however, global uniformity on the management of uncertain results may not be a realistic or desirable goal.
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Affiliation(s)
- Celine Lewis
- Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, London, UK.,North Thames Genomic Laboratory Hub, Great Ormond Street Hospital, London, UK
| | - Jennifer Hammond
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital, London, UK.,Genetic and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | | | - Eleanor Harding
- BSc Paediatrics and Child Health, The UCL Great Ormond Street Institute of Child Health, London, UK
| | - Stina Lou
- Center for Fetal Diagnostics, Aarhus University Hospital, Aarhus, Denmark
| | - Ida Vogel
- Center for Fetal Diagnostics, Aarhus University Hospital, Aarhus, Denmark
| | - Emma J Szepe
- Reproductive Epidemiology, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia.,Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Lisa Hui
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Victoria, Australia.,Department of Perinatal Medicine, Mercy Hospital for Women, Heidelberg, Victoria, Australia.,Department of Obstetrics and Gynaecology, Northern Health, Epping, Victoria, Australia
| | - Charlotta Ingvoldstad-Malmgren
- Center for Fetal Medicine, Karolinska University Hospital, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska Hospital and Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Maria J Soller
- Department of Clinical Genetics, Karolinska Hospital and Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Kelly E Ormond
- Department of Genetics and Stanford Center for Biomedical Ethics, Stanford University School of Medicine, Stanford, California, USA
| | - Mahesh Choolani
- Department of Obstetrics & Gynaecology, National University Hospital, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Melissa Hill
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital, London, UK.,Genetic and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Sam Riedijk
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
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18
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Huang H, Cai M, Wang Y, Liang B, Lin N, Xu L. SNP Array as a Tool for Prenatal Diagnosis of Congenital Heart Disease Screened by Echocardiography: Implications for Precision Assessment of Fetal Prognosis. Risk Manag Healthc Policy 2021; 14:345-355. [PMID: 33542665 PMCID: PMC7851374 DOI: 10.2147/rmhp.s286001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/30/2020] [Indexed: 12/21/2022] Open
Abstract
Objective This study aimed to examine the effectiveness of the SNP array for the prenatal diagnosis of congenital heart disease (CHD) screened by echocardiography. Patients and Methods A total of 356 pregnant women with fetal congenital heart malformations revealed by echocardiography at the Center for Prenatal Diagnosis of Fujian Maternal and Children Hospital during the period from November 2016 through July 2019 were recruited. The fetuses were assigned into three cohorts, including 142 with a single cardiac malformation, 106 with multiple cardiac malformations and 108 with cardiac and extracardiac malformations. All fetuses underwent chromosomal karyotyping and SNP array simultaneously, and the effectiveness of the SNP array for the prenatal diagnosis of CHD was evaluated. Results The overall prevalence of abnormal karyotypes was 9.3% among the 356 fetuses with CHD, and a higher proportion was found in fetuses with cardiac and extracardiac malformations (18.5%) than in those with single (5.6%) or multiple cardiac malformations (4.7%) (P<0.05). Consistent with karyotype analysis, SNP array detected an additional 25 fetuses with pathogenic copy number variations (CNVs), seven with variant of unknown significance (VOUS) and seven with benign CNVs, and a lower proportion of abnormal CNV was found in fetuses with a single cardiac malformation (4.2%) than in those with multiple cardiac malformations (9.4%) or cardiac and extracardiac malformations (14.8%) (P<0.05). Among the 33 fetuses with chromosomal abnormality, postnatal follow-up showed termination of pregnancy in 25 with pathogenic CNVs, one with VOUS, and six with normal karyotypes and SNP array findings but severe multiple malformations by ultrasonography. Conclusion SNP array increases the overall detection of abnormal CNVs by 9%, which improves the detection of CNVs associated with CHD. SNP array may serve as a tool for prenatal diagnosis of CHD that facilitates the discovery of pathogenic genes associated with CHD and provide valuable insights into the precision assessment of fetal prognosis during the prenatal counseling.
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Affiliation(s)
- Hailong Huang
- Center for Prenatal Diagnosis, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou 350001, Fujian Province, People's Republic of China.,Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fuzhou 350001, Fujian Province, People's Republic of China
| | - Meiying Cai
- Center for Prenatal Diagnosis, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou 350001, Fujian Province, People's Republic of China.,Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fuzhou 350001, Fujian Province, People's Republic of China
| | - Yan Wang
- Center for Prenatal Diagnosis, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou 350001, Fujian Province, People's Republic of China.,Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fuzhou 350001, Fujian Province, People's Republic of China
| | - Bin Liang
- Center for Prenatal Diagnosis, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou 350001, Fujian Province, People's Republic of China.,Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fuzhou 350001, Fujian Province, People's Republic of China
| | - Na Lin
- Center for Prenatal Diagnosis, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou 350001, Fujian Province, People's Republic of China.,Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fuzhou 350001, Fujian Province, People's Republic of China
| | - Liangpu Xu
- Center for Prenatal Diagnosis, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou 350001, Fujian Province, People's Republic of China.,Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fuzhou 350001, Fujian Province, People's Republic of China
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19
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Characterization of Copy-Number Variations and Possible Candidate Genes in Recurrent Pregnancy Losses. Genes (Basel) 2021; 12:genes12020141. [PMID: 33499090 PMCID: PMC7911754 DOI: 10.3390/genes12020141] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/09/2021] [Accepted: 01/19/2021] [Indexed: 12/12/2022] Open
Abstract
It is well established that embryonic chromosomal abnormalities (both in the number of chromosomes and the structure) account for 50% of early pregnancy losses. However, little is known regarding the potential differences in the incidence and distribution of chromosomal abnormalities between patients with sporadic abortion (SA) and recurrent pregnancy loss (RPL), let alone the role of submicroscopic copy-number variations (CNVs) in these cases. The aim of the present study was to systematically evaluate the role of embryonic chromosomal abnormalities and CNVs in the etiology of RPL compared with SA. Over a 3-year period, 1556 fresh products of conception (POCs) from miscarriage specimens were investigated using single nucleotide polymorphism array (SNP-array) and CNV sequencing (CNV-seq) in this study, along with further functional enrichment analysis. Chromosomal abnormalities were identified in 57.52% (895/1556) of all cases. Comparisons of the incidence and distributions of chromosomal abnormalities within the SA group and RPL group and within the different age groups were performed. Moreover, 346 CNVs in 173 cases were identified, including 272 duplications, 2 deletions and 72 duplications along with deletions. Duplications in 16q24.3 and 16p13.3 were significantly more frequent in RPL cases, and thereby considered to be associated with RPL. There were 213 genes and 131 signaling pathways identified as potential RPL candidate genes and signaling pathways, respectively, which were centered primarily on six functional categories. The results of the present study may improve our understanding of the etiologies of RPL and assist in the establishment of a population-based diagnostic panel of genetic markers for screening RPL amongst Chinese women.
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20
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Chen Y, Xie Y, Jiang Y, Luo Q, Shi L, Zeng S, Zhuang J, Lyu G. The Genetic Etiology Diagnosis of Fetal Growth Restriction Using Single-Nucleotide Polymorphism-Based Chromosomal Microarray Analysis. Front Pediatr 2021; 9:743639. [PMID: 34722424 PMCID: PMC8555260 DOI: 10.3389/fped.2021.743639] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 09/06/2021] [Indexed: 11/13/2022] Open
Abstract
Background: An increase in pathogenic copy number variants (pCNVs) has been recognized to associate with fetal growth restriction (FGR). Here, we aim to explore the application value of chromosomal microarray analysis (CMA) in prenatal diagnosis of FGR. Methods: Prenatal ultrasound was applied to identify FGR. A total of 149 pregnant women with FGR were enrolled in our study. All subjects underwent karyotype analysis and CMA to reveal the chromosomal abnormalities. Results: In this study, all subjects were successfully detected by karyotype and CMA analyses. Of these subjects, the chromosomal abnormalities detection rate was 5.37% (8/149) for karyotyping and 13.42% (20/149) for CMA, respectively. Among them, an 8.05% (12/149) incremental yield of CMA over karyotype analysis was observed (p = 0.004). In addition, a significant difference of pCNV detection rate was observed between the groups with different high-risk factors (p = 0.005). The FGR with structural anomalies group showed the highest pCNV detection rate (33.33%), followed by the FGR with non-structural anomalies group (8.77%) and the isolated FGR group (8.06%). Conclusion: In conclusion, CMA technology showed an effective application value in etiology diagnosis of FGR. We believe that CMA should be recommended as first-line detection technology for prenatal diagnosis in FGR.
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Affiliation(s)
- Yu'e Chen
- Ultrasonography, Quanzhou Women's and Children's Hospital, Quanzhou, China
| | - Yingjun Xie
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yuying Jiang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, China
| | - Qi Luo
- Department of Public Health for Women and Children, Quanzhou Women's and Children's Hospital, Quanzhou, China
| | - Lijing Shi
- Ultrasonography, Quanzhou Women's and Children's Hospital, Quanzhou, China
| | - Shuhong Zeng
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, China
| | - Jianlong Zhuang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, China
| | - Guorong Lyu
- Ultrasonography, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
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21
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Tanner LM, Alitalo T, Stefanovic V. Prenatal array comparative genomic hybridization in a well-defined cohort of high-risk pregnancies. A 3-year implementation results in a public tertiary academic referral hospital. Prenat Diagn 2020; 41:422-433. [PMID: 33340112 DOI: 10.1002/pd.5877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 09/17/2020] [Accepted: 12/02/2020] [Indexed: 11/11/2022]
Abstract
OBJECTIVE To find out whether the diagnostic yield of prenatal array comparative genomic hybridization (aCGH) can be improved by targeting preselected high-risk pregnancies. METHOD All the in-house arrays ordered by the Fetomaternal Medical Center from February 2016 until December 2018 were retrospectively analyzed. The indications for array analysis included fetal structural abnormalities, increased nuchal translucency ≥3.5 mm and a chromosomal abnormality in a parent or a sibling. Common aneuploidies were excluded. RESULTS Diagnostic yield was 15.1% in the entire patient cohort and as high as 20% in fetuses with multiple structural anomalies. The diagnostic yield was lowest in the group with isolated growth retardation. A total of 76 copy number variants (CNVs) were reported from a total of 65 samples, including 16 CNVs associated with a well-described microdeletion/microduplication syndrome, six autosomal trisomies in mosaic form, and three pathogenic single-gene deletions with dominant inheritance and 12 CNVs known to be risk factors for eg developmental delay. CONCLUSION The diagnostic yield of aCGH was higher than what has previously been reported in less defined patient cohorts. However, the number of CNVs with unclear correlation to the fetal ultrasound findings was still relatively high. The importance of adequate pre- and posttest counseling must therefore be emphasized.
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Affiliation(s)
- Laura M Tanner
- HUSLAB Department of Clinical Genetics, Helsinki University Hospital, Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Department of Obstetrics and Gynecology, Fetomaternal Medical Center, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Tiina Alitalo
- HUSLAB Genetics Laboratory, Helsinki University Hospital, Helsinki, Finland
| | - Vedran Stefanovic
- Department of Obstetrics and Gynecology, Fetomaternal Medical Center, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
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22
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Copy number variations in ultrasonically abnormal late pregnancy fetuses with normal karyotypes. Sci Rep 2020; 10:15094. [PMID: 32934329 PMCID: PMC7493916 DOI: 10.1038/s41598-020-72157-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 08/06/2020] [Indexed: 11/22/2022] Open
Abstract
Many fetuses are found to have ultrasonic abnormalities in the late pregnancy. The association of fetal ultrasound abnormalities in late pregnancy with copy number variations (CNVs) is unclear. We attempted to explore the relationship between types of ultrasonically abnormal late pregnancy fetuses and CNVs. Fetuses (n = 713) with ultrasound-detected abnormalities in late pregnancy and normal karyotypes were analyzed. Of these, 237 showed fetal sonographic structural malformations and 476 showed fetal non-structural abnormalities. Single nucleotide polymorphism (SNP)-based chromosomal microarray (CMA) was performed on the Affymetrix CytoScan HD platform. Using the SNP array, abnormal CNVs were detected in 8.0% (57/713) of the cases, with pathogenic CNVs in 32 cases and variants of uncertain clinical significance (VUS) in 25 cases. The detection rate of abnormal CNVs in fetuses with sonographic structural malformations (12.7%, 30/237) was significantly higher (P = 0.001) than that in the fetuses with non-structural abnormalities (5.7%, 27/476). Overall, we observed that when fetal sonographic structural malformations or non-structural abnormalities occurred in the third trimester of pregnancy, the use of SNP analysis could improve the accuracy of prenatal diagnosis and reduce the rate of pregnancy termination.
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23
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The Necessity of Prenatal Diagnosis by CMA for the Women with NIPS-Positive Results. Int J Genomics 2020; 2020:2145701. [PMID: 32953872 PMCID: PMC7481948 DOI: 10.1155/2020/2145701] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/20/2020] [Accepted: 08/18/2020] [Indexed: 11/18/2022] Open
Abstract
Objective To retrospectively analyze the results of prenatal diagnoses of noninvasive prenatal screening- (NIPS) positive pregnant women and discuss whether there is a need for chromosomal microarray analysis (CMA). Methods The study recruited 1,019 NIPS-positive women from two prenatal diagnostic centers. Based on clinical advice, they opted for traditional karyotype analysis or CMA. Single nucleotide polymorphism array testing was performed on a commercial 750K microarray chip (Affymetrix CytoScan 750K Array). Results Of the NIPS-positive women, 761 (74.7%) accepted the prenatal diagnosis. There were 418 (54.9%) abnormal results, and most (99.5%) were chromosome aneuploidy or structural abnormalities. Only three cases were confirmed as pathogenic copy number variation (CNVs), which were found only with CMA and not by karyotype analysis. Fifteen women were variants of uncertain significance (VUS) CNV. In addition, 300 women selected opted for both karyotype analysis and CMA for prenatal diagnosis: in 275 (91.7%) cases, the results of the two modalities were consistent, while in the remaining 25, they were not. In three cases, the additional positive results obtained with CMA were potentially clinically significant. Conclusions CMA may not be useful for many women positive for trisomy 21/18/13 based on NIPS results, because traditional karyotype analysis can identify most problems. However, it can yield important additional findings in women positive for fetal sex chromosome aneuploidy (SCA). Further clinical studies are needed to confirm these findings.
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Cai M, Lin N, Lin Y, Huang H, Xu L. Evaluation of chromosomal abnormalities and copy number variations in late trimester pregnancy using cordocentesis. Aging (Albany NY) 2020; 12:15556-15565. [PMID: 32805723 PMCID: PMC7467360 DOI: 10.18632/aging.103575] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 06/09/2020] [Indexed: 01/30/2023]
Abstract
Because the numbers of detected fetal abnormalities increase as gestation progresses, we evaluated the safety and efficacy of cordocentesis for single nucleotide polymorphism (SNP) analysis tests in 754 women during third trimester pregnancy. Conventional karyotyping was performed on all fetuses, and Affymetrix CytoScan HD was used for SNP-array testing. In addition to the 24 cases with chromosomal abnormalities detected with conventional karyotyping analysis, the SNP-array test identified 56 (7.4%) cases with normal karyotypes but abnormal copy number variations (CNVs). Of those, 24 were pathogenic CNVs and 32 were of uncertain clinical significance. In 742 of the cases, there were abnormal sonographic findings, and cytogenetic abnormalities were detected in 76 cases (10.2%). The largest number of abnormalities involved multiple malformations (21.7%), followed by defects in the lymphatics or effusion (19.0%) or urogenital system (15.3%). The use of SNP-array test fully complemented chromosome karyotype analysis after late cordocentesis. It also improved the detection rate for fetal chromosomal abnormalities and was effective for preventing and controlling the occurrence of birth defects.
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Affiliation(s)
- Meiying Cai
- Department of the Prenatal Diagnosis Center, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Na Lin
- Department of the Prenatal Diagnosis Center, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Yuan Lin
- Department of the Prenatal Diagnosis Center, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Hailong Huang
- Department of the Prenatal Diagnosis Center, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Liangpu Xu
- Department of the Prenatal Diagnosis Center, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
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Wang Y, Zhang M, Chen L, Huang H, Xu L. Prenatal diagnosis of BACs-on-Beads assay in 1520 cases from Fujian Province, China. Mol Genet Genomic Med 2020; 8:e1446. [PMID: 32767744 PMCID: PMC7549593 DOI: 10.1002/mgg3.1446] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 07/08/2020] [Accepted: 07/16/2020] [Indexed: 11/25/2022] Open
Abstract
Background The aim of this study was to evaluate the application of BACs‐on‐Beads (BoBs™) assay for rapid detection of chromosomal abnormalities for prenatal diagnosis (PND). Methods A total of 1520 samples, including seven chorionic villi biopsy samples, 1328 amniotic fluid samples, and 185 umbilical cord samples from pregnant women were collected to detect the chromosomal abnormalities using BoBs™ assay and karyotyping. Furthermore, abnormal specimens were verified by chromosome microarray analysis (CMA) and fluorescence in situ hybridization (FISH). Results The results demonstrated that the success rate of karyotyping and BoBs™ assay in PND was 98.09% and 100%, respectively. BoBs™ assay was concordant with karyotyping for Trisomy 21, Trisomy 18, and Trisomy 13, sex chromosomal aneuploidy, Wolf–Hirschhorn syndrome, and mosaicism. BoBs™ assay also detected Smith–Magenis syndrome, Williams–Beuren syndrome, DiGeorge syndrome, Miller–Dieker syndrome, Prader–Willi syndrome, Xp22.31 microdeletions, 22q11.2, and 17p11.2 microduplications. However, karyotyping failed to show these chromosomal abnormalities. A case of 8q21.2q23.3 duplication which was found by karyotyping was not detected by BoBs™ assay. Furthermore, all these chromosomal abnormalities were consistent with CMA and FISH verifications. According to the reports, we estimated that the detection rates of karyotyping, BoBs™, and CMA in the present study were 4.28%, 4.93%, and 5%, respectively, which is consistent with the results of a previous study. The respective costs for the three methods were about $135–145, $270–290, and $540–580. Conclusion BoBs™ assay is considered a reliable, rapid test for use in PND. A variety of comprehensive technological applications can complement each other in PND, in order to maximize the diagnosis rate and reduce the occurrence of birth defects.
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Affiliation(s)
- Yan Wang
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Min Zhang
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Lingji Chen
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Hailong Huang
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Liangpu Xu
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, China
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26
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Van den Veyver IB. Prenatally diagnosed developmental abnormalities of the central nervous system and genetic syndromes: A practical review. Prenat Diagn 2019; 39:666-678. [PMID: 31353536 DOI: 10.1002/pd.5520] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 07/05/2019] [Accepted: 07/08/2019] [Indexed: 12/15/2022]
Abstract
Developmental brain abnormalities are complex and can be difficult to diagnose by prenatal imaging because of the ongoing growth and development of the brain throughout pregnancy and the limitations of ultrasound, often requiring fetal magnetic resonance imaging as an additional tool. As for all major structural congenital anomalies, amniocentesis with chromosomal microarray and a karyotype is the first-line recommended test for the genetic work-up of prenatally diagnosed central nervous system (CNS) abnormalities. Many CNS defects, especially neuronal migration defects affecting the cerebral and cerebellar cortex, are caused by single-gene mutations in a large number of different genes. Early data suggest that prenatal diagnostic exome sequencing for fetal CNS defects will have a high diagnostic yield, but interpretation of sequencing results can be complex. Yet a genetic diagnosis is important for prognosis prediction and recurrence risk counseling. The evaluation and management of such patients is best done in a multidisciplinary team approach. Here, we review general principles of the genetic work-up for fetuses with CNS defects and review categories of genetic causes of prenatally diagnosed CNS phenotypes.
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Shi Y, Ma J, Xue Y, Wang J, Yu B, Wang T. The assessment of combined karyotype analysis and chromosomal microarray in pregnant women of advanced maternal age: a multicenter study. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:318. [PMID: 31475188 DOI: 10.21037/atm.2019.06.63] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Background Retrospectively analyzed the results of prenatal diagnosis and hoped to provide scientific clinical guidance of prenatal screening and diagnosis for the women in advanced maternal age (AMA). Methods In total, 4,224 women of AMA who accepted prenatal diagnosis by amniocentesis (AC) from two prenatal diagnosis centers were recruited for this study. After genetic counseling and informed consent, 3,475 women received karyotype analysis only, 703 were examined by both karyotype analysis and chromosomal microarray (CMA), while 46 cases selected CMA only. Both centers used the same detection platform, experimental scheme, and quality control standards. Results A total of 164 women with chromosomal abnormal results were found, the abnormality rate was 3.88% (164/4,224). Among them, 145 (3.4%, 145/4,224) cases were detected as abnormal chromosome number, 19 cases (0.4%, 19/4,224) as abnormal chromosome structure. Compared with simple AMA women, the abnormality rate was significantly increased in the AMA women who combined with other indications, particularly in number abnormalities (22.5% vs. 1.0%, P<0.001). Forty-eight copy number variations (CNVs) were detected, moreover 10 cases (0.24%, 10/4,224) were proved as pathogenic or likely pathogenic CNVs. With the CMA technology, the rate of additional abnormalities with clinical significance was 1.42% (10/703). Chromosome number abnormalities significantly increased with age (P<0.001), while there were no such trends in chromosomal structural abnormalities (P=0.624). Conclusions About 3.88% fetuses of AMA women had chromosomal abnormalities, the abnormality rate increased with their age. The application of CMA could increase the diagnostic rate by about 1.4% for AMA women, and greatly reduce their tension.
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Affiliation(s)
- Ye Shi
- Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou 213003, China
| | - Jun Ma
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou 215000, China
| | - Ying Xue
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou 215000, China
| | - Jing Wang
- Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou 213003, China
| | - Bin Yu
- Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou 213003, China
| | - Ting Wang
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou 215000, China
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Lin CZ, Qi BR, Hu JS, Huang YD, Huang XQ. Chromosome 15q13 microduplication in a fetus with cardiac rhabdomyoma: a case report. Mol Cytogenet 2019; 12:24. [PMID: 31149030 PMCID: PMC6537215 DOI: 10.1186/s13039-019-0437-1] [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: 10/05/2018] [Accepted: 05/17/2019] [Indexed: 01/10/2023] Open
Abstract
Background Copy number variation (CNV) is a complex genomic rearrangement that has been linked to a large number of human diseases. Chromosome 15q13 microduplication is a rare form of CNV, which has been proved to be associated with multiple human disorders; however, the association between chromosome 15q13 microduplication and cardiac disorders has not been fully understood. Case presentation A fetus with fetal cardiac developmental defects was detected by Color Doppler ultrasound imaging; however, further chromosomal G-banding revealed no abnormal karyotype. Then, chromosomal microarray analysis (CMA) was performed and revealed a 1.8 Mb-duplication of the chromosome 15q13.2q13.3 region containing 7 genes (TRPM1, KLF13, OTUD7A, CHRNA7, FAN1, MIR211 and RAHGAP11A). Cardiac ultrasound follow-up displayed significant enlargement of the space-occupying lesion in the fetal heart with extension of the gestational age, and the space-occupying lesion was finally pathologically diagnosed as cardiac rhabdomyoma. Next-generation sequencing revealed no mutations in the TSC1 or TSC2 gene in the fetus, the mother or the father. Conclusions This is the first report to demonstrate the potential association between chromosome 15q13 microduplication and fetal cardiac rhabdomyoma. It is recommended that CMA be employed in fetuses with abnormal cardiac development diagnosed by routine cardiac color Doppler ultrasound imaging for early detection of congenital genetic abnormality, which may provide valuable information for prenatal diagnostic consultation and the decision on pregnancy termination.
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Affiliation(s)
- Chen-Zhao Lin
- 1Department of Obstetrics and Gynecology, Affiliated Fuzhou First Hospital of Fujian Medical University, No. 190 Dadao Road, Taijiang District, Fuzhou, Fujian Province 350009 People's Republic of China
| | - Bi-Ru Qi
- 1Department of Obstetrics and Gynecology, Affiliated Fuzhou First Hospital of Fujian Medical University, No. 190 Dadao Road, Taijiang District, Fuzhou, Fujian Province 350009 People's Republic of China
| | - Jian-Su Hu
- 2Department of Ultrasound, Affiliated Fuzhou First Hospital of Fujian Medical University, Fuzhou, 350009 Fujian Province People's Republic of China
| | - Yu-Dian Huang
- 3Department of Pathology, Affiliated Fuzhou First Hospital of Fujian Medical University, Fuzhou, 350009 Fujian Province People's Republic of China
| | - Xiu-Qiong Huang
- 4Department of Laboratory Medicine, Affiliated Fuzhou First Hospital of Fujian Medical University, Fuzhou, 350009 Fujian Province People's Republic of China
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29
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Durham L, Papanna R, Stevens B, Noblin S, Rodriguez-Buritica D, Hashmi SS, Krstic N. The utilization of prenatal microarray: A survey of current genetic counseling practices and barriers. Prenat Diagn 2019; 39:351-360. [PMID: 30734934 DOI: 10.1002/pd.5435] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 02/01/2019] [Accepted: 02/01/2019] [Indexed: 12/29/2022]
Abstract
OBJECTIVE We evaluated what prenatal genetic counselor's (GCs) practices, attitudes, and barriers are in regards to prenatal microarray since the publication of the American College of Obstetricians and Gynecologists (ACOG) and the Society for Maternal-Fetal Medicine (SMFM) guidelines for microarray use. METHODS This was a survey-based cross-sectional study of English-speaking, board certified or eligible GCs who currently practice prenatal genetic counseling. RESULTS Of 192 respondents, 183 (95%) have incorporated chromosome microarray (CMA) into clinical practice, with 64% believing that the benefits of CMA outweigh the harms and 52% agreeing that CMA should be offered to all women regardless of indication. Those who reported being experts/comfortable in their knowledge of CMA (85%) and familiar with current clinical guidelines (86%) were significantly more likely to offer CMA to patients undergoing invasive testing and patients with fetal anomalies. Patient-specific concerns were the largest reported barrier (51%) when GCs do not offer CMA to patients. CONCLUSION Our study demonstrates GCs follow guidelines for CMA use when specific indications are involved, but further guidelines are needed regarding CMA use for other routine indications where utility of CMA is not clearly understood. On this basis, ACOG and SMFM should continue revising their guidelines as more information comes to light regarding utility of prenatal CMA for all indications, and organizations like the National Society of Genetic Counselors (NSGC) should consider publishing guidelines on prenatal CMA that are specialized to the GCs sphere of practice.
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Affiliation(s)
- Leslie Durham
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas, Houston, Texas.,Department of Pediatric Development and Rehabilitation, Randall Children's Hospital at Legacy Emanuel, Portland, Oregon
| | - Ramesha Papanna
- Department of Obstetrics, Gynecology, and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas
| | - Blair Stevens
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas, Houston, Texas.,Department of Obstetrics, Gynecology, and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas
| | - Sarah Noblin
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas, Houston, Texas.,Department of Obstetrics, Gynecology, and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas
| | - David Rodriguez-Buritica
- Department of Obstetrics, Gynecology, and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas
| | - S Shahrukh Hashmi
- Department of Obstetrics, Gynecology, and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas
| | - Nevena Krstic
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas, Houston, Texas.,Department of Obstetrics, Gynecology, and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas.,Department of Obstetrics and Gynecology, Morsani College of Medicine, University of South Florida, Tampa, FL
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30
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Cytogenetic microarray in structurally normal and abnormal foetuses: a five years experience elucidating increasing acceptance and clinical utility. J Genet 2019. [DOI: 10.1007/s12041-018-1050-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Zhang R, Chen X, Wang D, Chen X, Wang C, Zhang Y, Xu M, Yu J. Prevalence of chromosomal abnormalities identified by copy number variation sequencing in high-risk pregnancies, spontaneous abortions, and suspected genetic disorders. J Int Med Res 2019; 47:1169-1178. [PMID: 30732499 PMCID: PMC6421393 DOI: 10.1177/0300060518818020] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Objective High-throughput sequencing based on copy number variation (CNV-seq) is
commonly used to detect chromosomal abnormalities including aneuploidy. This
study provides evidence for the prevalence of chromosomal abnormalities in
target populations. Methods A total of 160 samples, including 83 high-risk pregnancies, 37 spontaneous
abortions, and 40 suspected genetic disorders, were analyzed by CNV-seq.
Relationships between the incidence of these chromosomal abnormalities and
risk factors (e.g. advanced maternal age, abnormal pregnancy history, and
family history of congenital disease) were further analyzed by subgroup. Results A total of 37 (44.6%) high-risk pregnancies, 25 (67.6%) spontaneous
abortions, and 22 (55%) suspected genetic disorders had chromosomal
abnormalities including aneuploidy and CNVs. There was an increased risk
association between the prevalence of aneuploidy and pathogenic-relevant CNV
in the fetus or abortive tissue and advanced maternal age. Moreover, a
family history of congenital disease was also positively correlated with
fetal chromosomal abnormalities in high-risk pregnancies. Conclusion A relatively high prevalence of chromosomal abnormalities was detected in
high-risk pregnancies, spontaneous abortions, and suspected genetic
disorders, indicating the importance of CNV detection in such
populations.
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Affiliation(s)
- Rui Zhang
- 1 Prenatal Diagnosis Center, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.,2 Scientific Research Centre, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | | | - Dong Wang
- 2 Scientific Research Centre, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xuan Chen
- 4 Department of Obstetrics, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Chao Wang
- 1 Prenatal Diagnosis Center, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yuhong Zhang
- 1 Prenatal Diagnosis Center, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | | | - Jingcui Yu
- 2 Scientific Research Centre, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
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Walker L, Watson CM, Hewitt S, Crinnion LA, Bonthron DT, Cohen KE. An alternative to array-based diagnostics: a prospectively recruited cohort, comparing arrayCGH to next-generation sequencing to evaluate foetal structural abnormalities. J OBSTET GYNAECOL 2019; 39:328-334. [PMID: 30714504 DOI: 10.1080/01443615.2018.1522529] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Molecular diagnostic investigations, following the identification of foetal abnormalities, are routinely performed using array comparative genomic hybridisation (aCGH). Despite the utility of this technique, contemporary approaches for the detection of copy number variation are typically based on next-generation sequencing (NGS). We sought to compare an in-house NGS-based workflow (CNVseq) with aCGH, for invasively obtained foetal samples from pregnancies complicated by foetal structural abnormality. DNA from 40 foetuses was screened using both 8 × 60 K aCGH oligoarrays and low-coverage whole genome sequencing. Sequencer-compatible libraries were combined in a ten-sample multiplex and sequenced using an Illumina HiSeq2500. The mean resolution of CNVseq was 29 kb, compared to 60 kb for aCGH analyses. Four clinically significant, concordant, copy number imbalances were detected using both techniques, however, genomic breakpoints were more precisely defined by CNVseq. This data indicates CNVseq is a robust and sensitive alternative to aCGH, for the prenatal investigation of foetuses with structural abnormalities. Impact statement What is already known about this subject? Copy number variant analysis using next-generation sequencing has been successfully applied to investigations of tumour specimens and patients with developmental delays. The application of our approach, to a prospective prenatal diagnosis cohort, has not hitherto been assessed. What do the results of this study add? Next-generation sequencing has a comparable turnaround time and assay sensitivity to copy number variant analysis performed using array CGH. We demonstrate that having established a next-generation sequencing facility, high-throughput CNVseq sample processing and analysis can be undertaken within the framework of a regional diagnostic service. What are the implications of these findings for clinical practice and/or further research? Array CGH is a legacy technology which is likely to be superseded by low-coverage whole genome sequencing, for the detection of copy number variants, in the prenatal diagnosis of structural abnormalities.
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Affiliation(s)
- Lesley Walker
- a Department of Fetal Medicine , Leeds General Infirmary , Leeds , United Kingdom
| | - Christopher M Watson
- b Yorkshire Regional Genetics Service , St. James's University Hospital , Leeds , United Kingdom.,c School of Medicine , University of Leeds, St. James's University Hospital , Leeds , United Kingdom
| | - Sarah Hewitt
- b Yorkshire Regional Genetics Service , St. James's University Hospital , Leeds , United Kingdom
| | - Laura A Crinnion
- b Yorkshire Regional Genetics Service , St. James's University Hospital , Leeds , United Kingdom.,c School of Medicine , University of Leeds, St. James's University Hospital , Leeds , United Kingdom
| | - David T Bonthron
- b Yorkshire Regional Genetics Service , St. James's University Hospital , Leeds , United Kingdom.,c School of Medicine , University of Leeds, St. James's University Hospital , Leeds , United Kingdom
| | - Kelly E Cohen
- a Department of Fetal Medicine , Leeds General Infirmary , Leeds , United Kingdom
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Levy B, Wapner R. Prenatal diagnosis by chromosomal microarray analysis. Fertil Steril 2018; 109:201-212. [PMID: 29447663 DOI: 10.1016/j.fertnstert.2018.01.005] [Citation(s) in RCA: 162] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 01/05/2018] [Indexed: 02/07/2023]
Abstract
Chromosomal microarray analysis (CMA) is performed either by array comparative genomic hybridization or by using a single nucleotide polymorphism array. In the prenatal setting, CMA is on par with traditional karyotyping for detection of major chromosomal imbalances such as aneuploidy and unbalanced rearrangements. CMA offers additional diagnostic benefits by revealing sub-microscopic imbalances or copy number variations that are too small to be seen on a standard G-banded chromosome preparation. These submicroscopic imbalances are also referred to as microdeletions and microduplications, particularly when they include specific genomic regions that are associated with clinical sequelae. Not all microdeletions/duplications are associated with adverse clinical phenotypes and in many cases, their presence is benign. In other cases, they are associated with a spectrum of clinical phenotypes that may range from benign to severe, while in some situations, the clinical significance may simply be unknown. These scenarios present a challenge for prenatal diagnosis, and genetic counseling prior to prenatal CMA greatly facilitates delivery of complex results. In prenatal diagnostic samples with a normal karyotype, chromosomal microarray will diagnose a clinically significant subchromosomal deletion or duplication in approximately 1% of structurally normal pregnancies and 6% with a structural anomaly. Pre-test counseling is also necessary to distinguish the primary differences between the benefits, limitations and diagnostic scope of CMA versus the powerful but limited screening nature of non-invasive prenatal diagnosis using cell-free fetal DNA.
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Affiliation(s)
- Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York.
| | - Ronald Wapner
- Department of Obstetrics & Gynecology, Columbia University Medical Center, New York, New York
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Normand EA, Braxton A, Nassef S, Ward PA, Vetrini F, He W, Patel V, Qu C, Westerfield LE, Stover S, Dharmadhikari AV, Muzny DM, Gibbs RA, Dai H, Meng L, Wang X, Xiao R, Liu P, Bi W, Xia F, Walkiewicz M, Van den Veyver IB, Eng CM, Yang Y. Clinical exome sequencing for fetuses with ultrasound abnormalities and a suspected Mendelian disorder. Genome Med 2018; 10:74. [PMID: 30266093 PMCID: PMC6162951 DOI: 10.1186/s13073-018-0582-x] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 09/12/2018] [Indexed: 12/11/2022] Open
Abstract
Background Exome sequencing is now being incorporated into clinical care for pediatric and adult populations, but its integration into prenatal diagnosis has been more limited. One reason for this is the paucity of information about the clinical utility of exome sequencing in the prenatal setting. Methods We retrospectively reviewed indications, results, time to results (turnaround time, TAT), and impact of exome results for 146 consecutive “fetal exomes” performed in a clinical diagnostic laboratory between March 2012 and November 2017. We define a fetal exome as one performed on a sample obtained from a fetus or a product of conception with at least one structural anomaly detected by prenatal imaging or autopsy. Statistical comparisons were performed using Fisher’s exact test. Results Prenatal exome yielded an overall molecular diagnostic rate of 32% (n = 46/146). Of the 46 molecular diagnoses, 50% were autosomal dominant disorders (n = 23/46), 41% were autosomal recessive disorders (n = 19/46), and 9% were X-linked disorders (n = 4/46). The molecular diagnostic rate was highest for fetuses with anomalies affecting multiple organ systems and for fetuses with craniofacial anomalies. Out of 146 cases, a prenatal trio exome option designed for ongoing pregnancies was performed on 62 fetal specimens, resulting in a diagnostic yield of 35% with an average TAT of 14 days for initial reporting (excluding tissue culture time). The molecular diagnoses led to refined recurrence risk estimates, altered medical management, and informed reproductive planning for families. Conclusion Exome sequencing is a useful diagnostic tool when fetal structural anomalies suggest a genetic etiology, but other standard prenatal genetic tests did not provide a diagnosis. Electronic supplementary material The online version of this article (10.1186/s13073-018-0582-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elizabeth A Normand
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Alicia Braxton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Salma Nassef
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Patricia A Ward
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | | | | | | | | | - Lauren E Westerfield
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Samantha Stover
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Donna M Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Xia Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Rui Xiao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Magdalena Walkiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA.,Present address: The National Institute of Allergy and Infectious Disease, NIH, Bethesda, MD, USA
| | - Ignatia B Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. .,Baylor Genetics, Houston, TX, USA.
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Gu S, Jernegan M, Van den Veyver IB, Peacock S, Smith J, Breman A. Chromosomal microarray analysis on uncultured chorionic villus sampling can be complicated by confined placental mosaicism for aneuploidy and microdeletions. Prenat Diagn 2018; 38:858-865. [PMID: 30094853 DOI: 10.1002/pd.5342] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 07/27/2018] [Accepted: 07/30/2018] [Indexed: 12/18/2022]
Abstract
OBJECTIVE This study aims to establish the incidence and implications of confined placental mosaicism (CPM) in the context of prenatal chromosomal microarray analysis (CMA). METHODS We retrospectively reviewed prenatal array data on 1382 consecutive chorionic villus sampling (CVS) specimens spanning the past 6 years, focusing on those for which whole CVS biopsy (both cytotrophoblast and mesenchymal cells) was used for CMA and cultured cells (primarily mesenchyme) was also analyzed or amniotic fluid (AF)/newborn blood was used for confirmation, to determine the frequency of mosaic abnormal findings that were the result of CPM. RESULTS Out of a total of 1382 consecutive CVS cases, we identified 42 (42/1382 = 3.0%) cases with abnormal array findings suggestive of mosaicism. Among them, 10 cases were unequivocally interpreted as CPM based on a normal AF/newborn blood confirmatory result. In addition, another 10 cases were interpreted as provisional CPM based on normal results on cultured cells. Notably, 40% (8/20) of the cases revealed complex findings, including multiple mosaic aneuploidies, mosaic submicroscopic copy number variation (CNV), and mosaic aneuploidy plus mosaic CNV. CONCLUSION Abnormal CMA results from CVS specimens should be interpreted with caution when mosaicism is evident or suspected. Furthermore, confirmatory testing on amniotic fluid, which contains cells derived from the fetus, is recommended in these cases.
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Affiliation(s)
- Shen Gu
- Baylor Genetics Laboratories, Houston, Texas.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Madison Jernegan
- Department of Nursing, Northeastern Oklahoma A&M College, Miami, Oklahoma
| | - Ignatia B Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, Texas
| | | | - Janice Smith
- Baylor Genetics Laboratories, Houston, Texas.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Amy Breman
- Baylor Genetics Laboratories, Houston, Texas.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
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Lumaka A, Race V, Peeters H, Corveleyn A, Coban-Akdemir Z, Jhangiani SN, Song X, Mubungu G, Posey J, Lupski JR, Vermeesch JR, Lukusa P, Devriendt K. A comprehensive clinical and genetic study in 127 patients with ID in Kinshasa, DR Congo. Am J Med Genet A 2018; 176:1897-1909. [PMID: 30088852 DOI: 10.1002/ajmg.a.40382] [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: 05/26/2018] [Accepted: 06/06/2018] [Indexed: 12/21/2022]
Abstract
Pathogenic variants account for 4 to 41% of patients with intellectual disability (ID) or developmental delay (DD). In Sub-Saharan Africa, the prevalence of ID is thought to be higher, but data in Central Africa are limited to some case reports. In addition, clinical descriptions of some syndromes are not available for this population. This study aimed at providing an estimate for the fraction of ID/DD for which an underlying etiological genetic cause may be elucidated and provide insights into their clinical presentation in special institutions in a Central African country. A total of 127 patients (33 females and 94 males, mean age 10.03 ± 4.68 years), were recruited from six institutions across Kinshasa. A clinical diagnosis was achieved in 44 but molecular confirmation was achieved in 21 of the 22 patients with expected genetic defect (95% clinical sensitivity). Identified diseases included Down syndrome (15%), submicroscopic copy number variants (9%), aminoacylase deficiency (0.8%), Partington syndrome in one patient (0.8%) and his similarly affected brother, X-linked syndromic Mental Retardation type 33 (0.8%), and two conditions without clear underlying molecular genetic etiologies (Oculo-Auriculo-Vertebral and Amniotic Bands Sequence). We have shown that genetic etiologies, similar to those reported in Caucasian subjects, are a common etiologic cause of ID in African patients from Africa. We have confirmed the diagnostic utility of clinical characterization prior to genetic testing. Finally, our clinical descriptions provide insights into the presentation of these genetic diseases in African patients.
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Affiliation(s)
- Aimé Lumaka
- Centre for Human Genetics, Faculty of Medicine, University of Kinshasa, Kinshasa, DR, Congo.,Département des Sciences Biomédicales et Précliniques, GIGA-R, Laboratoire de Génétique Humaine, University of Liège, Liège, Belgium.,Institut National de Recherche Biomédicale, Kinshasa, DR, Congo.,Department of Pediatrics, Faculty of Medicine, University of Kinshasa, Kinshasa, DR, Congo
| | - Valerie Race
- Centre for Human Genetics, University Hospital, University of Leuven, Leuven, Belgium
| | - Hilde Peeters
- Centre for Human Genetics, University Hospital, University of Leuven, Leuven, Belgium
| | - Anniek Corveleyn
- Centre for Human Genetics, University Hospital, University of Leuven, Leuven, Belgium
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Shalini N Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Xiaofei Song
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Gerrye Mubungu
- Centre for Human Genetics, Faculty of Medicine, University of Kinshasa, Kinshasa, DR, Congo.,Institut National de Recherche Biomédicale, Kinshasa, DR, Congo.,Department of Pediatrics, Faculty of Medicine, University of Kinshasa, Kinshasa, DR, Congo.,Centre for Human Genetics, University Hospital, University of Leuven, Leuven, Belgium
| | - Jennifer Posey
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Genetics Clinic service, Texas Children's Hospital, Houston, Texas
| | - Joris R Vermeesch
- Centre for Human Genetics, University Hospital, University of Leuven, Leuven, Belgium
| | - Prosper Lukusa
- Centre for Human Genetics, Faculty of Medicine, University of Kinshasa, Kinshasa, DR, Congo.,Département des Sciences Biomédicales et Précliniques, GIGA-R, Laboratoire de Génétique Humaine, University of Liège, Liège, Belgium.,Institut National de Recherche Biomédicale, Kinshasa, DR, Congo.,Centre for Human Genetics, University Hospital, University of Leuven, Leuven, Belgium
| | - Koenraad Devriendt
- Centre for Human Genetics, University Hospital, University of Leuven, Leuven, Belgium
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Li H, Liu M, Xie M, Zhang Q, Xiang J, Duan C, Ding Y, Liu Y, Mao J, Wang T, Li H. Submicroscopic chromosomal imbalances contribute to early abortion. Mol Cytogenet 2018; 11:41. [PMID: 30038665 PMCID: PMC6054741 DOI: 10.1186/s13039-018-0386-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 05/24/2018] [Indexed: 12/13/2022] Open
Abstract
Background Chromosomal abnormalities are one of the genetic mechanisms associated with abortion. However, the roles of submicroscopic chromosomal imbalances in early abortion are still unclear. This study aims to find out whether submicroscopic chromosomal imbalances contribute to early abortion. Methods A total of 78 chorionic villus specimens from early spontaneous abortion patients with no obvious abnormality are collected after miccroassay analysis (the case group). At the same time, 60 chorionic villus specimens from induced abortion patients with no obvious abnormality are selected as the control group. The submicroscopic structures of chromosomes from two groups are analyzed using an array-based comparative genomic hybridization (aCGH). Results In the case group, 15 specimens show submicroscopic chromosomal abnormalities including 14 micro-deletion/micro-duplication in chromosomes 2, 4, 5, 6, 7, 8, 9, 12, 15, 16, 18, and 22, and 1 uniparental disomy (UPD) in chromosome 19. Moreover, no pathogenic copy number variations are found in the control group. The results between these two groups exhibit significantly statistical difference. Conclusion Submicroscopic chromosomal imbalances may be one of the main reasons for early abortion.
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Affiliation(s)
- Haibo Li
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, NO. 26 Daoqian Street, Suzhou, 215002 Jiangsu Province China
| | - Minjuan Liu
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, NO. 26 Daoqian Street, Suzhou, 215002 Jiangsu Province China
| | - Min Xie
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, NO. 26 Daoqian Street, Suzhou, 215002 Jiangsu Province China
| | - Qin Zhang
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, NO. 26 Daoqian Street, Suzhou, 215002 Jiangsu Province China
| | - Jingjing Xiang
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, NO. 26 Daoqian Street, Suzhou, 215002 Jiangsu Province China
| | - Chengying Duan
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, NO. 26 Daoqian Street, Suzhou, 215002 Jiangsu Province China
| | - Yang Ding
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, NO. 26 Daoqian Street, Suzhou, 215002 Jiangsu Province China
| | - Yinghua Liu
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, NO. 26 Daoqian Street, Suzhou, 215002 Jiangsu Province China
| | - Jun Mao
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, NO. 26 Daoqian Street, Suzhou, 215002 Jiangsu Province China
| | - Ting Wang
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, NO. 26 Daoqian Street, Suzhou, 215002 Jiangsu Province China
| | - Hong Li
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, NO. 26 Daoqian Street, Suzhou, 215002 Jiangsu Province China
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Non invasive prenatal diagnosis of fetal aneuploidy using cell free fetal DNA. Eur J Obstet Gynecol Reprod Biol 2018; 225:5-8. [DOI: 10.1016/j.ejogrb.2018.03.033] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 02/13/2018] [Accepted: 03/19/2018] [Indexed: 01/21/2023]
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Cheung SW, Bi W. Novel applications of array comparative genomic hybridization in molecular diagnostics. Expert Rev Mol Diagn 2018; 18:531-542. [PMID: 29848116 DOI: 10.1080/14737159.2018.1479253] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
INTRODUCTION In 2004, the implementation of array comparative genomic hybridization (array comparative genome hybridization [CGH]) into clinical practice marked a new milestone for genetic diagnosis. Array CGH and single-nucleotide polymorphism (SNP) arrays enable genome-wide detection of copy number changes in a high resolution, and therefore microarray has been recognized as the first-tier test for patients with intellectual disability or multiple congenital anomalies, and has also been applied prenatally for detection of clinically relevant copy number variations in the fetus. Area covered: In this review, the authors summarize the evolution of array CGH technology from their diagnostic laboratory, highlighting exonic SNP arrays developed in the past decade which detect small intragenic copy number changes as well as large DNA segments for the region of heterozygosity. The applications of array CGH to human diseases with different modes of inheritance with the emphasis on autosomal recessive disorders are discussed. Expert commentary: An exonic array is a powerful and most efficient clinical tool in detecting genome wide small copy number variants in both dominant and recessive disorders. However, whole-genome sequencing may become the single integrated platform for detection of copy number changes, single-nucleotide changes as well as balanced chromosomal rearrangements in the near future.
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Affiliation(s)
- Sau W Cheung
- a Department of Molecular and Human Genetics , Baylor College of Medicine , Houston , TX , USA
| | - Weimin Bi
- a Department of Molecular and Human Genetics , Baylor College of Medicine , Houston , TX , USA.,b Baylor Genetics , Houston , TX , USA
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Srebniak MI, Joosten M, Knapen MFCM, Arends LR, Polak M, van Veen S, Go ATJI, Van Opstal D. Frequency of submicroscopic chromosomal aberrations in pregnancies without increased risk for structural chromosomal aberrations: systematic review and meta-analysis. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2018; 51:445-452. [PMID: 28556491 DOI: 10.1002/uog.17533] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 05/08/2017] [Accepted: 05/18/2017] [Indexed: 06/07/2023]
Abstract
OBJECTIVE To establish, based on a systematic literature review, the frequency of pathogenic submicroscopic chromosomal aberrations in fetuses that are not at increased risk for unbalanced structural chromosomal aberrations, with the aim of determining whether high-resolution testing for submicroscopic aberrations is beneficial in a general pregnant population. METHODS EMBASE, PubMed, Web of Science and CENTRAL databases were searched systematically on 3 June 2016 for all relevant articles on the prevalence of pathogenic submicroscopic copy number variants (CNVs) in fetuses referred for prenatal invasive testing because of advanced maternal age (AMA) or parental anxiety (ANX). Relevant full-text articles were analyzed and the prevalence of submicroscopic CNVs was calculated based on the extracted data. Meta-analysis was conducted in a pooled cohort of 10 614 fetuses based on the 10 largest studies (n > 300) of a total of 19 that were relevant. RESULTS Pooled estimate analysis indicated that 0.84% (95% CI, 0.55-1.30%) of fetuses that had invasive testing because of AMA/ANX carried a pathogenic clinically significant submicroscopic aberration. The onset/penetrance of submicroscopic findings was studied in 10 314 fetuses reported in eight papers that presented aberrant cases with all necessary details to allow assessment of the findings. The pooled estimates resulting from meta-analysis of the data indicated that an early-onset syndromic disorder was detected in 0.37% (95% CI, 0.27-0.52%) of cases, a susceptibility CNV was found in 0.30% (95% CI, 0.14-0.67%) and late-onset diseases were reported in 0.11% (95% CI, 0.05%-0.21%). The prevalence of early-onset syndromic disorders caused by a submicroscopic aberration was calculated to be 1:270. When the risk for submicroscopic aberrations is added to the individual risk for microscopic chromosomal aberrations, all pregnant women have a risk of higher than 1 in 180 for a relevant chromosomal aberration, and pregnant women under 36 years of age have a higher risk for submicroscopic pathogenic aberrations than for Down syndrome. CONCLUSION This systematic review shows that a significant proportion of fetuses in a general pregnant population carry a submicroscopic pathogenic CNV. Based on these figures, all women should be informed on their individual risk for all pathogenic chromosomal aberrations and not only for common trisomies. Copyright © 2017 ISUOG. Published by John Wiley & Sons Ltd.
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Affiliation(s)
- M I Srebniak
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - M Joosten
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - M F C M Knapen
- Department of Obstetrics and Gynecology, Erasmus MC, Rotterdam, The Netherlands
- Foundation Prenatal Screening Southwest Region of the Netherlands, Rotterdam, The Netherlands
| | - L R Arends
- Department of Psychology, Education & Child Studies (DPECS), Erasmus University Rotterdam, Rotterdam, The Netherlands
- Department of Biostatistics, Erasmus MC, Rotterdam, The Netherlands
| | - M Polak
- Department of Psychology, Education & Child Studies (DPECS), Erasmus University Rotterdam, Rotterdam, The Netherlands
| | - S van Veen
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - A T J I Go
- Department of Obstetrics and Gynecology, Erasmus MC, Rotterdam, The Netherlands
| | - D Van Opstal
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
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Brabbing-Goldstein D, Reches A, Svirsky R, Bar-Shira A, Yaron Y. Dilemmas in genetic counseling for low-penetrance neuro-susceptibility loci detected on prenatal chromosomal microarray analysis. Am J Obstet Gynecol 2018; 218:247.e1-247.e12. [PMID: 29146387 DOI: 10.1016/j.ajog.2017.11.559] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 10/14/2017] [Accepted: 11/06/2017] [Indexed: 01/03/2023]
Abstract
BACKGROUND Chromosomal microarray analysis is standard of care in fetuses with malformations, detecting clinically significant copy number variants in 5-7% of cases over conventional karyotyping. However, it also detects variants of uncertain significance in 1.6-4.2% of the cases, some of which are low-penetrance neuro-susceptibility loci. The interpretation of these variants in pregnancy is particularly challenging because the significance is often unclear and the clinical implications may be difficult to predict. OBJECTIVE The purpose of this study was to describe counseling dilemmas regarding low-penetrance neuro-susceptibility loci that are detected by prenatal chromosomal microarray analysis. STUDY DESIGN During the study period (January 2014 to December 2015), 700 prenatal chromosomal microarray analyses were performed. Cases were categorized as "indicated" (n=375) if there were abnormal sonographic findings or suggestive medical history and "patient choice" (n=325) in the presence of a structurally normal fetus with no other particular indication. The laboratory reported on copy number variants ≥400 Kb in size in loci known to be associated with genetic syndromes and ≥1 Mb in other areas of genome. Results were classified as gross aneuploidy, copy number variants, and normal. Copy number variants were categorized according to the American College of Medical Genetics standards and guidelines: pathogenic, variants of uncertain significance, or benign. Variants of uncertain significance were further subdivided into categories of likely pathogenic, variants of uncertain significance with no subclassification, and likely benign. Statistical analysis was performed with the use of Chi square test and Fisher's exact test to compare intergroup differences in incidence of the different result categories and demographic data. RESULTS Patient choice cases became more prevalent with time (35.5% in the beginning of the study, compared with 48.4% at the end of the study period). Clinically significant copy number variants were found in 14 of 375 (3.7%) of indicated cases vs only 2 of 325 (0.6%) of patient choice cases (P=.009). All "likely benign" variants consisted of low-penetrance neuro-susceptibility loci. The incidence thereof was similar between the indicated and patient choice groups (3.7% vs 3.4%; P=.85). In the indicated group, some variants of uncertain significance may have contributed to the abnormal anatomic findings. Conversely, in the patient choice group, the finding of low-penetrance neuro-susceptibility loci was often unexpected and confounding for prospective parents. CONCLUSION Prenatal chromosomal microarray analysis added clinically significant information in both groups. However, it also detected low-penetrance neuro-susceptibility loci in approximately 3.5% of the cases. This fact should be conveyed during pretest counseling to allow patients to make informed choices, particularly when chromosomal microarray is to be performed for patient choice.
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Qu S, Wang L, Cai A, Cui S, Bai N, Liu N, Kong X. Exploring the cause of early miscarriage with SNP-array analysis and karyotyping. J Matern Fetal Neonatal Med 2017; 32:1-10. [PMID: 29034762 DOI: 10.1080/14767058.2017.1367379] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
OBJECTIVE The aim of this study is to explore the cause of miscarriage, providing risk assessment to guide the next pregnancy. METHODS Four hundred eighty-four products-of-conception (POC) samples were analyzed by single nucleotide polymorphism (SNP) array, and peripheral blood samples of couples were collected for karyotyping or fluorescence in situ hybridization (FISH) analysis. RESULTS Four hundred sixty-eight of the 484 (96.7%) fresh POC samples were successfully analyzed using SNP-array. The rate of clinically significant chromosomal abnormalities were 58.3% (274/468), in which rates of aneuploidy, polyploidy, partial aneuploidy, uniparental isodisomy (isoUPD), and pathogenic microdeletion/microduplication were 43.4% (203/468), 8.8% (41/468), 3.6% (17/468), 1.9% (9/48), and 0.9% (4/468), respectively. The percentage of embryonic chromosomal abnormalities significantly increased with maternal age of patients older than 35 years old. Among 468 couples, 12 major chromosomal rearrangements were detected by G-banding, including nine reciprocal translocations, two Robertsonian translocations, and one superfemale. CONCLUSIONS Chromosome abnormality is the main causes of early miscarriage, and aneuploidies are the most common type of chromosomal abnormalities. Application of SNP array and karyotyping in early miscarriage can provide more genetic information about miscarriage, providing risk assessment to guide the next pregnancy.
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Affiliation(s)
- Suzhen Qu
- a Center for Genetics and Prenatal Diagnosis , the First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , China
| | - Li Wang
- a Center for Genetics and Prenatal Diagnosis , the First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , China
| | - Aojie Cai
- a Center for Genetics and Prenatal Diagnosis , the First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , China
| | - Siying Cui
- a Center for Genetics and Prenatal Diagnosis , the First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , China
| | - Nan Bai
- a Center for Genetics and Prenatal Diagnosis , the First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , China
| | - Ning Liu
- a Center for Genetics and Prenatal Diagnosis , the First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , China
| | - Xiangdong Kong
- a Center for Genetics and Prenatal Diagnosis , the First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , China
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Vermeesch JR, Voet T, Devriendt K. Prenatal and pre-implantation genetic diagnosis. Nat Rev Genet 2017; 17:643-56. [PMID: 27629932 DOI: 10.1038/nrg.2016.97] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The past decade has seen the development of technologies that have revolutionized prenatal genetic testing; that is, genetic testing from conception until birth. Genome-wide single-cell arrays and high-throughput sequencing analyses are dramatically increasing our ability to detect embryonic and fetal genetic lesions, and have substantially improved embryo selection for in vitro fertilization (IVF). Moreover, both invasive and non-invasive mutation scanning of the genome are helping to identify the genetic causes of prenatal developmental disorders. These advances are changing clinical practice and pose novel challenges for genetic counselling and prenatal care.
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Affiliation(s)
- Joris Robert Vermeesch
- Centre for Human Genetics, Department of Human Genetics, University of Leuven, 49 Herestraat, Leuven 3000, Belgium
| | - Thierry Voet
- Centre for Human Genetics, Department of Human Genetics, University of Leuven, 49 Herestraat, Leuven 3000, Belgium
| | - Koenraad Devriendt
- Centre for Human Genetics, Department of Human Genetics, University of Leuven, 49 Herestraat, Leuven 3000, Belgium
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Wu Y, Wang Y, Tao J, Han X, Zhao X, Liu C, Gao L, Cheng W. The clinical use of chromosomal microarray analysis in detection of fetal chromosomal rearrangements: a study from China Mainland. Eur J Obstet Gynecol Reprod Biol 2017; 212:44-50. [DOI: 10.1016/j.ejogrb.2017.03.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Revised: 02/19/2017] [Accepted: 03/04/2017] [Indexed: 10/20/2022]
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Pons L, Till M, Alix E, Abel C, Boggio D, Bordes A, Caloone J, Raskin FC, Chatron N, Cordier MP, Fichez A, Labalme A, Lajeunesse C, Liaras É, Massoud M, Miribel J, Ollagnon E, Schluth-Bolard C, Vichier-Cerf A, Edery P, Attia J, Huissoud C, Rudigoz RC, Massardier J, Gaucherand P, Sanlaville D. Prenatal microarray comparative genomic hybridization: Experience from the two first years of activity at the Lyon university-hospital. J Gynecol Obstet Hum Reprod 2017; 46:275-283. [PMID: 28403926 DOI: 10.1016/j.jogoh.2016.11.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 11/07/2016] [Accepted: 11/17/2016] [Indexed: 11/17/2022]
Abstract
OBJECTIVES This study aims to describe how microarray comparative genomic hybridization (aCGH) has shifted to become a prenatal diagnosis tool at the Lyon university-hospital. MATERIALS AND METHODS This retrospective study included all patients who were referred in the 3 pluridisciplinary centers for prenatal diagnosis of the Lyon university-hospital and who received a prenatal aCGH between June 2013 and June 2015. aCGH was systematically performed in parallel with a karyotype, using the PréCytoNEM array design. RESULTS A total of 260 microarrays were performed for the following indications: 249 abnormal ultrasounds (95.8%), 7 characterizations of chromosomal rearrangements (2.7%), and 4 twins with no abnormal ultrasounds (1.5%). With a resolution of 1 mega base, we found 235 normal results (90.4%), 23 abnormal results (8.8%) and 2 non-returns (0.8%). For the chromosomal rearrangements visible on the karyotype, aCGH identified all of the 12 unbalanced rearrangements and did not identify the 2 balanced rearrangements. Among the fetuses with normal karyotypes, 11 showed abnormal microarray results, corresponding to unbalanced cryptic chromosomal rearrangements (4.2%). CONCLUSION Transferring aCGH to a prenatal diagnosis at the Lyon university-hospital has increased the detection rate of chromosomal abnormalities by 4.2% compared to the single karyotype.
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Affiliation(s)
- L Pons
- Service de génétique, groupement hospitalier Est, HCL, 59, boulevard Pinel, 69677 Bron, France; Université Claude-Bernard Lyon 1, 69008 Lyon, France.
| | - M Till
- Service de génétique, groupement hospitalier Est, HCL, 59, boulevard Pinel, 69677 Bron, France
| | - E Alix
- Service de génétique, groupement hospitalier Est, HCL, 59, boulevard Pinel, 69677 Bron, France
| | - C Abel
- Service de génétique, groupement hospitalier Est, HCL, 59, boulevard Pinel, 69677 Bron, France
| | - D Boggio
- Service de génétique, groupement hospitalier Est, HCL, 59, boulevard Pinel, 69677 Bron, France
| | - A Bordes
- Département d'obstétrique et de gynécologie, groupement hospitalier Est, HCL, 69500 Bron, France
| | - J Caloone
- Département d'obstétrique et de gynécologie, centre hospitalier de la Croix-Rousse, HCL, 69004 Lyon, France
| | - F C Raskin
- Département d'obstétrique et de gynécologie, centre hospitalier Lyon Sud, HCL, 69310 Pierre-Bénite, France
| | - N Chatron
- Service de génétique, groupement hospitalier Est, HCL, 59, boulevard Pinel, 69677 Bron, France; Université Claude-Bernard Lyon 1, 69008 Lyon, France; Équipe Gendev, CNRS UMR 5292, Inserm U1028, centre de recherche en neuroscience de Lyon, 69500 Bron, France
| | - M-P Cordier
- Service de génétique, groupement hospitalier Est, HCL, 59, boulevard Pinel, 69677 Bron, France
| | - A Fichez
- Département d'obstétrique et de gynécologie, centre hospitalier de la Croix-Rousse, HCL, 69004 Lyon, France
| | - A Labalme
- Service de génétique, groupement hospitalier Est, HCL, 59, boulevard Pinel, 69677 Bron, France
| | - C Lajeunesse
- Département d'obstétrique et de gynécologie, groupement hospitalier Est, HCL, 69500 Bron, France
| | - É Liaras
- Département d'obstétrique et de gynécologie, centre hospitalier Lyon Sud, HCL, 69310 Pierre-Bénite, France
| | - M Massoud
- Département d'obstétrique et de gynécologie, groupement hospitalier Est, HCL, 69500 Bron, France
| | - J Miribel
- Département d'obstétrique et de gynécologie, groupement hospitalier Est, HCL, 69500 Bron, France
| | - E Ollagnon
- Service de génétique, groupement hospitalier Est, HCL, 59, boulevard Pinel, 69677 Bron, France
| | - C Schluth-Bolard
- Service de génétique, groupement hospitalier Est, HCL, 59, boulevard Pinel, 69677 Bron, France; Université Claude-Bernard Lyon 1, 69008 Lyon, France; Équipe Gendev, CNRS UMR 5292, Inserm U1028, centre de recherche en neuroscience de Lyon, 69500 Bron, France
| | - A Vichier-Cerf
- Service de génétique, groupement hospitalier Est, HCL, 59, boulevard Pinel, 69677 Bron, France
| | - P Edery
- Service de génétique, groupement hospitalier Est, HCL, 59, boulevard Pinel, 69677 Bron, France; Université Claude-Bernard Lyon 1, 69008 Lyon, France; Équipe Gendev, CNRS UMR 5292, Inserm U1028, centre de recherche en neuroscience de Lyon, 69500 Bron, France
| | - J Attia
- Université Claude-Bernard Lyon 1, 69008 Lyon, France; Département d'obstétrique et de gynécologie, centre hospitalier Lyon Sud, HCL, 69310 Pierre-Bénite, France
| | - C Huissoud
- Département d'obstétrique et de gynécologie, centre hospitalier de la Croix-Rousse, HCL, 69004 Lyon, France
| | - R C Rudigoz
- Université Claude-Bernard Lyon 1, 69008 Lyon, France; Département d'obstétrique et de gynécologie, centre hospitalier de la Croix-Rousse, HCL, 69004 Lyon, France
| | - J Massardier
- Département d'obstétrique et de gynécologie, groupement hospitalier Est, HCL, 69500 Bron, France
| | - P Gaucherand
- Université Claude-Bernard Lyon 1, 69008 Lyon, France; Département d'obstétrique et de gynécologie, groupement hospitalier Est, HCL, 69500 Bron, France
| | - D Sanlaville
- Service de génétique, groupement hospitalier Est, HCL, 59, boulevard Pinel, 69677 Bron, France; Université Claude-Bernard Lyon 1, 69008 Lyon, France; Équipe Gendev, CNRS UMR 5292, Inserm U1028, centre de recherche en neuroscience de Lyon, 69500 Bron, France
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47
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Chen Y, Bartanus J, Liang D, Zhu H, Breman AM, Smith JL, Wang H, Ren Z, Patel A, Stankiewicz P, Cram DS, Cheung SW, Wu L, Yu F. Characterization of chromosomal abnormalities in pregnancy losses reveals critical genes and loci for human early development. Hum Mutat 2017; 38:669-677. [PMID: 28247551 DOI: 10.1002/humu.23207] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 02/19/2017] [Accepted: 02/21/2017] [Indexed: 11/09/2022]
Abstract
Detailed characterization of chromosomal abnormalities, a common cause for congenital abnormalities and pregnancy loss, is critical for elucidating genes for human fetal development. Here, 2,186 product-of-conception samples were tested for copy-number variations (CNVs) at two clinical diagnostic centers using whole-genome sequencing and high-resolution chromosomal microarray analysis. We developed a new gene discovery approach to predict potential developmental genes and identified 275 candidate genes from CNVs detected from both datasets. Based on Mouse Genome Informatics (MGI) and Zebrafish model organism database (ZFIN), 75% of identified genes could lead to developmental defects when mutated. Genes involved in embryonic development, gene transcription, and regulation of biological processes were significantly enriched. Especially, transcription factors and gene families sharing specific protein domains predominated, which included known developmental genes such as HOX, NKX homeodomain genes, and helix-loop-helix containing HAND2, NEUROG2, and NEUROD1 as well as potential novel developmental genes. We observed that developmental genes were denser in certain chromosomal regions, enabling identification of 31 potential genomic loci with clustered genes associated with development.
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Affiliation(s)
- Yiyun Chen
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Justin Bartanus
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Desheng Liang
- State Key Lab of Medical Genetics of China Central South University, Changsha, Hunan, China
| | | | - Amy M Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Cytogenetics Laboratory, Baylor Miraca Genetics Laboratories, Houston, Texas
| | - Janice L Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Cytogenetics Laboratory, Baylor Miraca Genetics Laboratories, Houston, Texas
| | - Hua Wang
- Hunan Maternal and Child Health Care Hospital, Changsha, Hunan, China
| | - Zhilin Ren
- Berry Genomics Corporation, Beijing, China
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Cytogenetics Laboratory, Baylor Miraca Genetics Laboratories, Houston, Texas
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Cytogenetics Laboratory, Baylor Miraca Genetics Laboratories, Houston, Texas
| | | | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Cytogenetics Laboratory, Baylor Miraca Genetics Laboratories, Houston, Texas
| | - Lingqian Wu
- State Key Lab of Medical Genetics of China Central South University, Changsha, Hunan, China
| | - Fuli Yu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Berry Genomics Corporation, Beijing, China
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48
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Oneda B, Rauch A. Microarrays in prenatal diagnosis. Best Pract Res Clin Obstet Gynaecol 2017; 42:53-63. [PMID: 28215395 DOI: 10.1016/j.bpobgyn.2017.01.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 12/13/2016] [Accepted: 01/04/2017] [Indexed: 01/09/2023]
Abstract
In prenatal diagnosis, chromosomal microarray (CMA) has not yet fully replaced conventional karyotyping but has rapidly become the recommended test in pregnancies with ultrasound abnormalities. In this review, we provide an overview of the published data concerning this technology and the controversies concerning its use in the prenatal setting. There is abundant evidence indicating the added detection of pathogenic abnormalities with CMA in comparison to the traditional karyotyping, especially in fetuses with multiple or isolated ultrasound abnormalities such as congenital heart disease, increased nuchal translucency, or oral cleft. On the other hand, there is also a risk to detect variants of unknown significance, late-onset disorders, and variants in susceptibility loci. However, it has been shown that pregnant couples tend to prefer a maximum of information about the health of their unborn child. Taken together, CMA has considerable diagnostic and prognostic values during pregnancy and should therefore be the test of choice.
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Affiliation(s)
- Beatrice Oneda
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland.
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
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49
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Govaerts L, Srebniak M, Diderich K, Joosten M, Riedijk S, Knapen M, Go A, Papatsonis D, de Graaf K, Toolenaar T, van der Steen S, Huijbregts G, Knijnenburg J, de Vries F, Van Opstal D, Galjaard RJ. Prenatal diagnosis of susceptibility loci for neurodevelopmental disorders - genetic counseling and pregnancy outcome in 57 cases. Prenat Diagn 2016; 37:73-80. [DOI: 10.1002/pd.4979] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/15/2016] [Accepted: 11/26/2016] [Indexed: 12/23/2022]
Affiliation(s)
- Lutgarde Govaerts
- Department of Clinical Genetics; Erasmus Medical Center; Rotterdam The Netherlands
| | - Malgorzata Srebniak
- Department of Clinical Genetics; Erasmus Medical Center; Rotterdam The Netherlands
| | - Karin Diderich
- Department of Clinical Genetics; Erasmus Medical Center; Rotterdam The Netherlands
| | - Marieke Joosten
- Department of Clinical Genetics; Erasmus Medical Center; Rotterdam The Netherlands
| | - Sam Riedijk
- Department of Clinical Genetics; Erasmus Medical Center; Rotterdam The Netherlands
| | - Maarten Knapen
- Department of Obstetrics and Gynecology; Erasmus Medical Center; Rotterdam The Netherlands
- Foundation Prenatal Screening Southwest region of the Netherlands; Rotterdam The Netherlands
| | - Attie Go
- Department of Obstetrics and Gynecology; Erasmus Medical Center; Rotterdam The Netherlands
| | - Dimitri Papatsonis
- Department of Obstetrics and Gynecology; Amphia Hospital; Breda The Netherlands
| | - Katja de Graaf
- Department of Obstetrics and Gynecology; Reinier de Graaf Gasthuis; Delft The Netherlands
| | - Toon Toolenaar
- Department of Gynecology; Albert Schweitzer Hospital Dordrecht; Dordrecht The Netherlands
| | - Sanne van der Steen
- Department of Clinical Genetics; Erasmus Medical Center; Rotterdam The Netherlands
| | - Gido Huijbregts
- Department of Clinical Genetics; Erasmus Medical Center; Rotterdam The Netherlands
| | - Jeroen Knijnenburg
- Department of Clinical Genetics; Erasmus Medical Center; Rotterdam The Netherlands
| | - Femke de Vries
- Department of Clinical Genetics; Erasmus Medical Center; Rotterdam The Netherlands
| | - Diane Van Opstal
- Department of Clinical Genetics; Erasmus Medical Center; Rotterdam The Netherlands
| | - Robert-Jan Galjaard
- Department of Clinical Genetics; Erasmus Medical Center; Rotterdam The Netherlands
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50
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Abstract
The introduction of new technologies has dramatically changed the current practice of prenatal screening and testing for genetic abnormalities in the fetus. Expanded carrier screening panels and non-invasive cell-free fetal DNA-based screening for aneuploidy and single-gene disorders, and more recently for subchromosomal abnormalities, have been introduced into prenatal care. More recently introduced technologies such as chromosomal microarray analysis and whole-exome sequencing can diagnose more genetic conditions on samples obtained through amniocentesis or chorionic villus sampling, including many disorders that cannot be screened for non-invasively. All of these options have benefits and limitations, and genetic counseling has become increasingly complex for providers who are responsible for guiding patients in their decisions about screening and testing before and during pregnancy.
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Affiliation(s)
- Ignatia B Van den Veyver
- Department of Obstetrics and Gynecology and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
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