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Lee D, Na S, Park S, Go S, Ma J, Yang S, Kim K, Lee S, Hwang D. Clinical experience with multiplex ligation-dependent probe amplification for microdeletion syndromes in prenatal diagnosis: 7522 pregnant Korean women. Mol Cytogenet 2019; 12:10. [PMID: 30891099 PMCID: PMC6390335 DOI: 10.1186/s13039-019-0422-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 02/07/2019] [Indexed: 11/20/2022] Open
Abstract
Background Conventional cytogenetic analysis using G-band karyotyping has been the method of choice for prenatal diagnosis, accurately detecting chromosomal abnormalities larger than 5 Mb. However, the method is inefficient for detecting the submicroscopic deletions and duplications that are associated with malformations and mental retardation. This study evaluated the results of the multiplex ligation-dependent probe amplification (MLPA) P245 assay used for prenatal diagnosis in cases with unusual ultrasonographic findings or specifically where parents wanted to be tested. The objective was to compare the results from MLPA with those from conventional cytogenetic testing in order to determine their concordance and the additional diagnostic yield of MLPA over G-band karyotyping. Results Of the 7522 prenatal cases analyzed, 124 were found to have genomic imbalances (1.6%). Of those 124 cases, 41 had gene loss (33.6%), and 83 had gene gain (66.4%). Most of the cases with genomic imbalances (64.5%) showed no abnormal karyotype. In particular, all cases with a 4p16.3 deletion (Wolf-Hirschhorn syndrome) showed an abnormal karyotype, whereas all of those with a 22q11–13 deletion showed a normal karyotype. In most of the cases with pathogenic deletions, the indication for invasive prenatal testing was an increase in the nuchal translucency (NT) alone (51.2%). Other indications observed in the remaining cases were abnormal serum screening markers (14.6%), other ultrasonographic findings (9.8%), pregnancy through in vitro fertilization and fertility assistance (9.8%), and advanced maternal age(2.4%). Conclusions These results show that for fetuses with an enlarged NT or abnormal ultrasonographic findings and normal conventional karyotype, additional genetic investigation like molecular testing would be for identifying the microscopic genomic aberrations (microdeletions, microduplications) responsible for syndromic associations including structural anomalies and mental retardation.
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Affiliation(s)
- Dongsook Lee
- Research Center of Fertility and Genetics, Hamchoon Women's Clinic, 10, Seochojungang-ro 8-gil, Seocho-gu, Seoul, South Korea.,2Department of Health and Environmental Science, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, South Korea
| | - Sohyun Na
- Research Center of Fertility and Genetics, Hamchoon Women's Clinic, 10, Seochojungang-ro 8-gil, Seocho-gu, Seoul, South Korea
| | - Surim Park
- Research Center of Fertility and Genetics, Hamchoon Women's Clinic, 10, Seochojungang-ro 8-gil, Seocho-gu, Seoul, South Korea
| | - Sanghee Go
- Research Center of Fertility and Genetics, Hamchoon Women's Clinic, 10, Seochojungang-ro 8-gil, Seocho-gu, Seoul, South Korea
| | - Jinyoung Ma
- Research Center of Fertility and Genetics, Hamchoon Women's Clinic, 10, Seochojungang-ro 8-gil, Seocho-gu, Seoul, South Korea
| | - Soonha Yang
- Research Center of Fertility and Genetics, Hamchoon Women's Clinic, 10, Seochojungang-ro 8-gil, Seocho-gu, Seoul, South Korea
| | - Kichul Kim
- Research Center of Fertility and Genetics, Hamchoon Women's Clinic, 10, Seochojungang-ro 8-gil, Seocho-gu, Seoul, South Korea
| | - Seunggwan Lee
- 2Department of Health and Environmental Science, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, South Korea
| | - Doyeong Hwang
- Research Center of Fertility and Genetics, Hamchoon Women's Clinic, 10, Seochojungang-ro 8-gil, Seocho-gu, Seoul, South Korea
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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 Obstet Gynecol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Srebniak MI, Van Opstal D, Joosten M, Diderich KEM, de Vries FAT, Riedijk S, Knapen MFCM, Go ATJI, Govaerts LCP, Galjaard RJH. Whole-genome array as a first-line cytogenetic test in prenatal diagnosis. Ultrasound Obstet Gynecol 2015; 45:363-372. [PMID: 25488734 DOI: 10.1002/uog.14745] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 11/17/2014] [Accepted: 11/21/2014] [Indexed: 06/04/2023]
Affiliation(s)
- M I Srebniak
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, The Netherlands
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Xu Z, Geng Q, Luo F, Xu F, Li P, Xie J. Multiplex ligation-dependent probe amplification and array comparative genomic hybridization analyses for prenatal diagnosis of cytogenomic abnormalities. Mol Cytogenet 2014; 7:84. [PMID: 25530804 PMCID: PMC4271441 DOI: 10.1186/s13039-014-0084-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Accepted: 11/03/2014] [Indexed: 08/19/2023] Open
Abstract
Background The aims of this study were to evaluate the clinical utility of multiplex ligation-dependent probe amplification (MLPA) and array comparative genomic hybridization (aCGH) analyses on prenatal cases and to review prenatal ultrasound findings of cytogenomic syndromes. Results Of the 54 prenatal cases analyzed, cytogenomic abnormalities were characterized in 14 cases. In four fetuses with abnormal ultrasound findings, a 40.701 Mb duplication of 8q22.3-q24.3 and a 23.839 Mb deletion of 7q33-q36.3 derived from a paternal balanced translocation, a de novo 13.062 Mb deletion of 11q24.1-q25 for Jacobsen syndrome, a de novo 19.971 Mb deletion of 7q11.23-q21.3 for type 1 split-hand/foot malformation (SHFM1), and a de novo 28.909 Mb duplication of 3q21.1-q25.1 were detected. A 699.8 Kb deletion at 5p15.33 for Cri du Chat syndrome was confirmed in a fetus with abnormal MLPA result. A fetus with abnormal maternal screening was detected with a de novo distal 1.747 Mb duplication at 2q37.1-q37.2 and a 6.664 Mb deletion at 2q37.2-q37.3. Of the eight cases referred by history of spontaneous abortions, derivative chromosomes 11 from paternal carriers of a balanced 8q/11q and a 10q/11q translocation were noted in two cases, simple aneuploids of trisomy 2 and trisomy 21 were seen in three cases, and compound aneuploids of two or three chromosomes were found in three cases. Post-test genetic counseling was performed with detailed genomic information and well characterized postnatal syndromic features. Conclusions These results demonstrated that coupling MLPA screening and aCGH analysis are a cost-effective approach to detect cytogenomic abnormalities in a prenatal setting. The aCGH analysis provided not only genomic maps of breakpoints and gene content of imbalanced regions but also better inference of related phenotypes for genetic counseling. Prenatal ultrasound findings reported in the literature for Jacobsen syndrome, SHFM and Cri du Chat syndrome were summarized for use as diagnostic references.
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Affiliation(s)
- Zhiyong Xu
- Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong China
| | - Qian Geng
- Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong China
| | - Fuwei Luo
- Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong China
| | - Fang Xu
- Department of Genetics, Yale University School of Medicine, New Haven, CT USA
| | - Peining Li
- Department of Genetics, Yale University School of Medicine, New Haven, CT USA
| | - Jiansheng Xie
- Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong China
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de Wit MC, Srebniak MI, Govaerts LCP, Van Opstal D, Galjaard RJH, Go ATJI. Additional value of prenatal genomic array testing in fetuses with isolated structural ultrasound abnormalities and a normal karyotype: a systematic review of the literature. Ultrasound Obstet Gynecol 2014; 43:139-146. [PMID: 23897843 DOI: 10.1002/uog.12575] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/19/2013] [Indexed: 06/02/2023]
Abstract
OBJECTIVE To establish the prevalence of submicroscopic genetic copy number variants (CNVs) in fetuses with a structural ultrasound anomaly (restricted to one anatomical system) and a normal karyotype. The aim was to determine the diagnostic and prognostic value of genomic array testing in these pregnancies. METHODS Embase and PubMed databases were systematically searched for all relevant articles on prevalence of pathogenic submicroscopic CNVs in fetuses with ultrasound anomalies. Reported cases were sorted into groups according to anatomical site of the detected ultrasound anomaly. The prevalence of causative submicroscopic CNVs was calculated for each group. RESULTS Combined data of the reviewed studies (n = 18) indicated that fetuses with an ultrasound anomaly restricted to one anatomical system (n = 2220) had a 3.1-7.9% chance of carrying a causative submicroscopic CNV, depending on the anatomical system affected. This chance increased to 9.1% for fetuses with multiple ultrasound anomalies (n = 1139). CONCLUSION This review indicates that 3.1-7.9% of fetuses with a structural ultrasound anomaly restricted to one anatomical system and a normal karyotype will show a submicroscopic CNV, which explains its phenotype and provides information for fetal prognosis. Therefore, we conclude that microarray has considerable diagnostic and prognostic value in these pregnancies.
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Affiliation(s)
- M C de Wit
- Department of Obstetrics and Gynecology, Erasmus Medical Centre, Rotterdam, The Netherlands
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Callaway JLA, Shaffer LG, Chitty LS, Rosenfeld JA, Crolla JA. The clinical utility of microarray technologies applied to prenatal cytogenetics in the presence of a normal conventional karyotype: a review of the literature. Prenat Diagn 2013; 33:1119-23. [PMID: 23983223 PMCID: PMC4285999 DOI: 10.1002/pd.4209] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 06/24/2013] [Accepted: 07/22/2013] [Indexed: 12/22/2022]
Abstract
ABSTRACT The clinical utility of microarray technologies when used in the context of prenatal diagnosis lies in the technology's ability to detect submicroscopic copy number changes that are associated with clinically significant outcomes. We have carried out a systematic review of the literature to calculate the utility of prenatal microarrays in the presence of a normal conventional karyotype. Amongst 12 362 cases in studies that recruited cases from all prenatal ascertainment groups, 295/12 362 (2.4%) overall were reported to have copy number changes with associated clinical significance (pCNC), 201/3090 (6.5%) when ascertained with an abnormal ultrasound, 50/5108 (1.0%) when ascertained because of increased maternal age and 44/4164 (1.1%) for all other ascertainment groups (e.g. parental anxiety and abnormal serum screening result). When additional prenatal microarray studies are included in which ascertainment was restricted to fetuses with abnormal ultrasound scans, 262/3730 (7.0%) were reported to have pCNCs. © 2013 The Authors. Prenatal Diagnosis published by John Wiley & Sons Ltd.
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