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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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Noveski P, Terzic M, Vujovic M, Kuzmanovska M, Sukarova Stefanovska E, Plaseska-Karanfilska D. Multilevel regression modeling for aneuploidy classification and physical separation of maternal cell contamination facilitates the QF-PCR based analysis of common fetal aneuploidies. PLoS One 2019; 14:e0221227. [PMID: 31430300 PMCID: PMC6701765 DOI: 10.1371/journal.pone.0221227] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 08/01/2019] [Indexed: 11/19/2022] Open
Abstract
Background The quantitative fluorescent polymerase chain reaction (QF-PCR) has proven to be a reliable method for detection of common fetal chromosomal aneuploidies. However, there are some technical shortcomings, such as uncertainty of aneuploidy determination when the short tandem repeats (STR) height ratio is unusual due to a large size difference between alleles or failure due to the presence of maternal cell contamination (MCC). The aim of our study is to facilitate the implementation of the QF-PCR as a rapid diagnostic test for common fetal aneuploidies. Methods Here, we describe an in-house one-tube multiplex QF-PCR method including 20 PCR markers (15 STR markers and 5 fixed size) for rapid prenatal diagnosis of chromosome 13, 18, 21, X and Y aneuploidies. In order to improve the aneuploidy classification of a given diallelic STR marker, we have employed a multilevel logistic regression analysis using "height-ratio" and "allele-size-difference" as fixed effects and "marker" as a random effect. We employed two regression models, one for the 2:1 height ratio (n = 48 genotypes) and another for the 1:2 height ratio (n = 41 genotypes) of the trisomic diallelic markers while using the same 9015 genotypes with normal 1:1 height ratio in both models. Furthermore, we have described a simple procedure for the treatment of the MCC, prior DNA isolation and QF-PCR analysis. Results For both models, we have achieved 100% specificity for the marker aneuploidy classification as compared to 98.60% (2:1 ratio) and 98.04% (1:2 ratio) specificity when using only the height ratio for classification. Treatment of the MCC enables a successful diagnosis rate of 76% among truly contaminated amniotic fluids. Conclusions Adjustment for the allele size difference and marker type improves the STR aneuploidy classification, which, complemented with appropriate treatment of contaminated amniotic fluids, eliminates sample re-testing and reinforces the robustness of the QF-PCR method for prenatal testing.
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Affiliation(s)
- Predrag Noveski
- Research Center for Genetic Engineering and Biotechnology “Georgi D. Efremov”, Macedonian Academy of Science and Arts, Skopje, Republic of Macedonia
| | - Marija Terzic
- Research Center for Genetic Engineering and Biotechnology “Georgi D. Efremov”, Macedonian Academy of Science and Arts, Skopje, Republic of Macedonia
| | - Marija Vujovic
- Research Center for Genetic Engineering and Biotechnology “Georgi D. Efremov”, Macedonian Academy of Science and Arts, Skopje, Republic of Macedonia
| | - Maja Kuzmanovska
- Research Center for Genetic Engineering and Biotechnology “Georgi D. Efremov”, Macedonian Academy of Science and Arts, Skopje, Republic of Macedonia
| | - Emilija Sukarova Stefanovska
- Research Center for Genetic Engineering and Biotechnology “Georgi D. Efremov”, Macedonian Academy of Science and Arts, Skopje, Republic of Macedonia
| | - Dijana Plaseska-Karanfilska
- Research Center for Genetic Engineering and Biotechnology “Georgi D. Efremov”, Macedonian Academy of Science and Arts, Skopje, Republic of Macedonia
- * E-mail:
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Mann K, Petek E, Pertl B. Prenatal Detection of Chromosome Aneuploidy by Quantitative Fluorescence PCR. Methods Mol Biol 2019; 1885:139-160. [PMID: 30506196 DOI: 10.1007/978-1-4939-8889-1_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Autosomal chromosome aneuploid pregnancies that survive to term, namely, trisomies 13, 18, and 21, account for 89% of chromosome abnormalities with a severe phenotype identified in prenatal samples. They are traditionally detected by full karyotype analysis of cultured cells. The average reporting time for a prenatal karyotype analysis is approximately 14 days, and in recent years, there has been increasing demand for more rapid prenatal results with respect to the common chromosome aneuploidies, to relieve maternal anxiety and facilitate options in pregnancy. The rapid tests that have been developed negate the requirement for cultured cells, instead directly testing cells from the amniotic fluid or chorionic villus sample, with the aim of generating results within 48 h of sample receipt. Interphase fluorescence in situ hybridization is the method of choice in some genetic laboratories, usually because the expertise and equipment are readily available. However, a quantitative fluorescence (QF)-PCR-based approach is now widely used and reported as a clinical diagnostic service in many studies. It may be used as a stand-alone test or as an adjunct test to full karyotype or array CGH analysis, which scan for other chromosome abnormalities not detected by the QF-PCR assay.
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Affiliation(s)
- Kathy Mann
- Viapath Analytics, Guy's Hospital, London, UK.
| | - Erwin Petek
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
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Sanguansermsri C, Tanpaiboon P, Charoenkwan P, Phusua A. Brief communication (Original). Rapid diagnosis of trisomy 21 by relative gene copy using real-time quantitative polymerase chain reaction. ASIAN BIOMED 2017. [DOI: 10.5372/1905-7415.0803.306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
AbstractBackground: Trisomy 21 or Down syndrome (DS) is the most common aneuploidy disorder. Fetal karyotypic analysis remains the criterion standard for prenatal diagnosis of DS, although the method is time consuming and requires skilled personnel. Real-time quantitative polymerase chain reaction (qPCR) can be used to determine a difference in the amount of gene copy by calculation of the difference between the cycle threshold (ΔCT) of a tested gene and a reference gene.Objectives: To develop a rapid qPCR diagnostic method for trisomy 21.Methods: Ten DS patients with the known karyotype of trisomy 21 were enrolled. Their parents were included as controls. D21S11 locus on chromosome 21 and SM locus on chromosome 16 from each subject were amplified by qPCR. The D21S11/SM ΔCT and 2-ΔΔCTvalues were compared between DS patients and their parents.Results: The D21S11/SM ΔCT values of the DS patients were higher than their respective controls except for one family. The mean 2-ΔΔCTvalue between patients and mothers was 1.88 ± 0.95 (95% CI 1.20-2.56), and between fathers and mothers as controls was 1.06 ± 0.68 (95% CI 0.58-1.54).Conclusion: The diagnostic method of trisomy 21 by using qPCR is feasible, although false negative results may occur. Using more index genes is recommended to increase the sensitivity and specificity.
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Affiliation(s)
- Chinnuwat Sanguansermsri
- Department of Pediatrics, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Pranoot Tanpaiboon
- Division of Genetics and Metabolism, Children’s National Medical Center, Washington DC, United States of America
| | - Pimlak Charoenkwan
- Department of Pediatrics, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Arunee Phusua
- Department of Pediatrics, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
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Non‐invasive prenatal screening for chromosomal abnormalities using circulating cell-free fetal DNA in maternal plasma: Current applications, limitations and prospects. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2017. [DOI: 10.1016/j.ejmhg.2016.07.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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Mačkić-Đurović M, Projić P, Ibrulj S, Cakar J, Marjanović D. A comparative analysis of the effectiveness of cytogenetic and molecular genetic methods in the detection of Down syndrome. Bosn J Basic Med Sci 2014; 14:94-8. [PMID: 24856381 DOI: 10.17305/bjbms.2014.2271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The goal of this study was to examine the effectiveness of 6 STR markers application (D21S1435, D21S11, D21S1270, D21S1411, D21S226 and IFNAR) in molecular genetic diagnostics of Down syndrome (DS) and to compare it with cytogenetic method. Testing was performed on 73 children, with the previously cytogenetically confirmed Down syndrome. DNA isolated from the buccal swab was used. Previously mentioned loci located on chromosome 21 were simultaneously amplified using quantitative fluorescence PCR (QF PCR). Using this method, 60 previously cytogenetically diagnosed DS with standard type of trisomy 21 were confirmed. Furthermore, six of eight children with mosaic type of DS were detected. Two false negative results for mosaic type of DS were obtained. Finally, five children with the translocation type of Down syndrome were also confirmed with this molecular test. In conclusion, molecular genetic analysis of STR loci is fast, cheap and simple method that could be used in detection of DS. Regarding possible false results detected for certain number of mosaic types, cytogenetic analysis should be used as a confirmatory test.
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Affiliation(s)
- Mirela Mačkić-Đurović
- Center for genetics, Faculty of Medicine, University of Sarajevo, Čekaluša 90, 71 000 Sarajevo, Bosnia and Herzegovina
| | - Petar Projić
- Genos LTD, Hondlova 2, 10000 Zagreb, Croatia. 3Institute for Genetic Engineering and Biotechnology, Zmaja od Bosne 8, 71000 Sarajevo, Bosnia and Herzegovina
| | - Slavka Ibrulj
- Center for genetics, Faculty of Medicine, University of Sarajevo, Čekaluša 90, 71 000 Sarajevo, Bosnia and Herzegovina
| | - Jasmina Cakar
- Institute for Genetic Engineering and Biotechnology, Zmaja od Bosne 8, 71000 Sarajevo, Bosnia and Herzegovina
| | - Damir Marjanović
- Institute for Genetic Engineering and Biotechnology, Zmaja od Bosne 8, 71000 Sarajevo, Bosnia and Herzegovina
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Mann K, Ogilvie CM. QF-PCR: application, overview and review of the literature. Prenat Diagn 2012; 32:309-14. [PMID: 22467160 DOI: 10.1002/pd.2945] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Quantitative fluorescent polymerase chain reaction has been in diagnostic use in the UK for over 10 years and has proved to be a cost-effective, robust and accurate rapid prenatal test for common aneuploidies. Specific advantages include detection of triploidy, mosaicism and maternal cell contamination. Its application at our centre is described, with developments including stand-alone testing and improvements in strategies for the preparation and testing of chorionic villus biopsies.
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Affiliation(s)
- Kathy Mann
- Cytogenetics Department, GSTS Pathology, Guy's and St Thomas' Hospital, London, UK.
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Pires S, Nogueira AJA, Pinho O, Delgado T, Sousa M, Santos R, Jorge P. Statistical Approach to Prenatal Zygosity Assessment Following a Decade of Molecular Aneuploidy Screening. Twin Res Hum Genet 2012; 14:221-7. [DOI: 10.1375/twin.14.3.221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
In twin pregnancy studies, molecular genetic techniques have rarely been used to determine zygosity, despite their known precision and accuracy. The present work aimed to assess the power of discrimination in zygosity assessment, using a set of microsatellite markers that were routinely used for aneuploidy screening by multiplex-PCR in a prenatal context. Rapid aneuploidy screening using a group of 20 microsatellite markers (STRs) located on chromosomes 13, 18, 21 and X has been performed in our lab for over 10 years, with a total of approximately 1,500 samples studied to date. A retrospective analysis of the 257 prenatal samples from multiple pregnancies was carried out. A subset of 14 cases presenting theoretical monozygosity were re-evaluated by the use of biostatistics tools accessed via the ZygProb website. Further monozygosity determination relative to dizygosity was calculated, given an estimated overall error value of 0.093%. The results show that monozygosity had been correctly determined in all our previously studied twins. This work demonstrates that accurate zygosity assessment can be achieved with the same STRs applied in aneuploidy screening with a high power of discrimination and a matching probability of over 99.999999%.
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Crkvenac Gornik K, Grubić Z, Stingl K, Tonković Durisević I, Begović D. Application of microsatellite loci on the chromosome X for rapid prenatal detection of the chromosome X numerical abnormalities. Croat Med J 2011; 52:392-5. [PMID: 21674836 PMCID: PMC3118710 DOI: 10.3325/cmj.2011.52.392] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Aim To determine the value of short-tandem repeat markers on the chromosome X (X-STR) for prenatal diagnostics of the chromosome X numerical disorders. Methods We investigated the genetic variability of 5 X-markers (DXS9895, DXS6810, DXS6803, GATA172D05, and HPRTB) in 183 healthy Croatian individuals (90 men and 93 women). We also tested 13 patients with X chromosome disorders (Turner syndrome – 6 cases; Klinefelter syndrome – 5 cases, and Triple X syndrome – 2 cases). The analysis was performed using polymerase chain reaction amplification with specific primers and electrophoresis on a polyacrylamide gel. The study was performed in 2010. Results Our sample showed no significant differences in allelic frequencies of the investigated X-markers from other European populations. A set of 5 X-STR markers was sufficiently informative for a successful determination of the chromosome X numerical abnormalities. Conclusion Since no false positive or negative results were observed, diagnostic value of the investigated X-STR loci for prenatal detection of chromosome X numerical disorders was confirmed. Our study represents an important step toward an improved prenatal diagnostics in Croatia.
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Mann K, Petek E, Pertl B. Prenatal detection of chromosome aneuploidy by quantitative-fluorescence PCR. Methods Mol Biol 2011; 688:207-226. [PMID: 20938841 DOI: 10.1007/978-1-60761-947-5_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
QF-PCR refers to the amplification of chromosome-specific polymorphic microsatellite markers using fluorescence-labelled primers, followed by semi-quantitative analysis of the products on a genetic analyser to determine copy number and/or imbalances of specific chromosomal material. This approach is now widely used for rapid prenatal diagnosis of the common trisomies. In addition, it can successfully detect maternal cell contamination and mosaicism in prenatal material.
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Affiliation(s)
- Kathy Mann
- Cytogenetics Department, Guy's Hospital, London, UK.
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Cirigliano V, Voglino G, Ordoñez E, Marongiu A, Paz Cañadas M, Ejarque M, Rueda L, Lloveras E, Fuster C, Adinolfi M. Rapid prenatal diagnosis of common chromosome aneuploidies by QF-PCR, results of 9 years of clinical experience. Prenat Diagn 2009; 29:40-9. [PMID: 19173345 DOI: 10.1002/pd.2192] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND Despite being deliberately targeted to common chromosome aneuploidies, the rapid quantitative fluorescent polymerase chain reaction (QF-PCR) tests can detect the majority of chromosome abnormalities in prenatal diagnosis. The main advantages of this assay are low cost, speed and automation allowing large-scale application. METHODS We developed a QF-PCR test that was applied on 43 000 clinical samples reporting results in 24 h. Most common indications were biochemical risk (32%) and advanced maternal age (30%). Samples were also tested by cytogenetic analysis and the results compared. RESULTS Aneuploidies involving chromosomes 21, 18, 13, X and Y were detected with 100% specificity. Several cases of partial trisomies and mosaicism were also identified. Overall 95% of clinically relevant abnormalities were readily detected and termination of affected pregnancies could be performed without waiting for the cytogenetic results. CONCLUSIONS Our study supports the possibility of reducing the load of prenatal cytogenetic tests if the pregnancies are carefully monitored by non-invasive screening. In case of abnormal QF-PCR results, medical action can be taken within few hours from sampling. In cases of negative QF-PCR results, cytogenetic analyses might only be performed for fetuses with ultrasound abnormalities. In countries where large-scale cytogenetic tests are not available, QF-PCR may be used as the only prenatal diagnostic procedure.
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Fan HC, Blumenfeld YJ, El-Sayed YY, Chueh J, Quake SR. Microfluidic digital PCR enables rapid prenatal diagnosis of fetal aneuploidy. Am J Obstet Gynecol 2009; 200:543.e1-7. [PMID: 19375573 DOI: 10.1016/j.ajog.2009.03.002] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2008] [Revised: 02/20/2009] [Accepted: 03/10/2009] [Indexed: 01/23/2023]
Abstract
OBJECTIVE The purpose of this study was to demonstrate that digital polymerase chain reaction (PCR) enables rapid, allele independent molecular detection of fetal aneuploidy. STUDY DESIGN Twenty-four amniocentesis and 16 chorionic villus samples were used for microfluidic digital PCR analysis. Three thousand and sixty PCR reactions were performed for each of the target chromosomes (X, Y, 13, 18, and 21), and the number of single molecule amplifications was compared to a reference. The difference between target and reference chromosome counts was used to determine the ploidy of each of the target chromosomes. RESULTS Digital PCR accurately identified all cases of fetal trisomy (3 cases of trisomy 21, 3 cases of trisomy 18, and 2 cases of triosmy 13) in the 40 specimens analyzed. The remaining specimens were determined to have normal ploidy for the chromosomes tested. CONCLUSION Microfluidic digital PCR allows detection of fetal chromosomal aneuploidy utilizing uncultured amniocytes and chorionic villus tissue in less than 6 hours.
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Siala O, Kammoun Feki F, Louhichi N, Hadj Salem I, Gribaa M, Elghzel H, Saad A, Triki C, Fakhfakh F. Molecular prenatal diagnosis of muscular dystrophies in Tunisia and postnatal follow-up role. ACTA ACUST UNITED AC 2009; 12:581-6. [PMID: 19072569 DOI: 10.1089/gte.2008.0061] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We undertook in this study the first successful prenatal diagnoses of MDC1A and LGMD2C forms in Africa, with a subsequent postnatal clinical follow-up of the newborns. Genetic and molecular studies were performed on cultured amniotic fluid cells after exclusion of maternal cell contamination. Immunofluorescence on the patients' muscle biopsies was performed so as to study the expression of muscular laminins. Results showed that normal and affected fetuses were diagnosed according to the presence or the absence of the responsible mutation in LAMA2 or SGCG genes. Postnatal molecular and clinical outcome was concordant with all prenatal diagnoses. However, a patient with MDC1A form of congenital muscular dystrophy who was diagnosed as affected was normal at birth, and developed later clinical features different from those observed in his severely affected elder brother. This intrafamilial clinical variability in two siblings occurring with the same mutation in LAMA2 gene emphasizes the importance of the postnatal follow-up in the confirmation of prenatal diagnosis, and suggests that other genetic or epigenetic factors can monitor the course of the MDC1A form.
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Affiliation(s)
- Olfa Siala
- Laboratoire de Génétique Moléculaire Humaine, Faculté de Médecine de Sfax, Sfax, Tunisia.
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Putzova M, Pecnova L, Dvorakova L, Soldatova I, Goetz P, Stejskal D. OmniPlex-a new QF-PCR assay for prenatal diagnosis of common aneuploidies based on evaluation of the heterozygosity of short tandem repeat loci in the Czech population. Prenat Diagn 2008; 28:1214-20. [DOI: 10.1002/pd.2151] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Abstract
Autosomal chromosome aneuploid pregnancies that survive to term, namely, trisomies 13, 18, and 21, account for 89% of chromosome abnormalities with a severe phenotype. They are normally detected by full karyotype analysis of cultured cells. The average reporting time for a prenatal karyotype analysis is approximately 14 days, and in recent years, there has been increasing demand for more rapid prenatal results with respect to the common chromosome aneuploidies, to relieve maternal anxiety and facilitate options in pregnancy. The rapid tests that have been developed negate the requirement for cultured cells, instead directly testing cells from the amniotic fluid or chorionic villus sample, with the aim of generating results within 48 h of sample receipt. Interphase fluorescence in situ hybridization is the method of choice in some genetic laboratories, usually because the expertise and equipment are readily available. However, a quantitative fluorescence (QF)-PCR-based approach is more suited to a high-throughput diagnostic service. This approach has been investigated in a small number of pilot studies and reported as a clinical diagnostic service in many studies. It may be used as a stand-alone test or as an adjunct test to full karyotype analysis, which subsequently confirms the rapid result and scans for other chromosome abnormalities not detected by the QF-PCR assay.
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QF-PCR-based prenatal detection of common aneuploidies in the Czech population: Five years of experience. Eur J Med Genet 2008; 51:209-18. [PMID: 18378202 DOI: 10.1016/j.ejmg.2008.02.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2008] [Accepted: 02/04/2008] [Indexed: 11/17/2022]
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Brown L, Abigania M, Warburton D, Brown S. Validation of QF-PCR for prenatal aneuploidy screening in the United States. Prenat Diagn 2007; 26:1068-74. [PMID: 16952193 DOI: 10.1002/pd.1558] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
OBJECTIVE QF-PCR is an inexpensive and reliable method for aneuploidy screening; however, despite its obvious advantages, it is not in routine use in the United States. Our objective in the present study was to validate QF-PCR as a means for prenatal aneuploidy screening in our institution. METHODS A QF-PCR assay using 15 primer pairs located on chromosomes 13, 18, 21 X and Y was established for aneuploidy screening. Amniotic fluid (AF) and chorionic villus sampling (CVS) samples consisting only of the cells recovered from the plasticware discarded by our institutional cytogenetics laboratory were collected and DNA was prepared by a simple and inexpensive microwave procedure. QF-PCR was then performed and interpreted using established criteria. RESULTS 687 consecutive prenatal samples were screened in a blinded prospective manner, and results were compared to those obtained by conventional cytogenetics. 100% of autosomal trisomies were detected, and there were zero false positives. A single case each of XXY and 45X were missed. CONCLUSIONS QF-PCR for prenatal aneuploidy screening was validated in our laboratory and has now been approved by the New York State Clinical Laboratory Evaluation Program. We propose a simple protocol for integrating QF-PCR into the normal cytogenetics laboratory workflow.
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Affiliation(s)
- Lucia Brown
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
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Huang DJ, Nelson MR, Zimmermann B, Dudarewicz L, Wenzel F, Spiegel R, Nagy B, Holzgreve W, Hahn S. Reliable detection of Trisomy 21 using MALDI-TOF mass spectrometry. Genet Med 2006; 8:728-34. [PMID: 17108765 DOI: 10.1097/01.gim.0000245573.42908.34] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
PURPOSE Current diagnostic methods for chromosomal abnormalities rely mainly on karyotyping and occasionally fluorescent in situ hybridization or quantitative polymerase chain reaction. We describe an alternative molecular method for the detection of trisomy 21 involving mass spectrometric analysis of single nucleotide polymorphisms. METHODS In collaboration with Sequenom, Inc., 350 blinded amniotic fluid, amniocyte culture, chorionic villus, or amniotic fluid supernatant samples were analyzed for trisomy 21 using SNP analysis and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. Peak ratios were calculated for heterozygous genotypes and compared to control values generated from known euploid samples. An analytical algorithm using standard deviations from control values was used to determine the probability of a sample being affected or unaffected. RESULTS Seventy-three trisomy 21 samples from among the 350 blinded samples were correctly identified. There were no false-positive or false-negative results among the complete trisomy 21 samples. One sample exhibiting mosaicism for trisomy 21 was identified as being unaffected. CONCLUSIONS MALDI-TOF mass spectrometry is a robust and reproducible method for the detection of trisomy 21. Its amenability to high-throughput analysis and high degree of multiplexing make it a potential future diagnostic tool for the detection of other aneuploidies as well.
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Affiliation(s)
- Dorothy J Huang
- Laboratory for Prenatal Medicine University Women's Hospital, Department of Research Spitalstrasse 21, CH4031 Basel, Switzerland
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Ochshorn Y, Bar-Shira A, Jonish A, Yaron Y. Rapid Prenatal Diagnosis of Aneuploidy for Chromosomes 21, 18, 13, and X by Quantitative Fluorescence Polymerase Chain Reaction. Fetal Diagn Ther 2006; 21:326-31. [PMID: 16757905 DOI: 10.1159/000092459] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2005] [Accepted: 07/02/2005] [Indexed: 11/19/2022]
Abstract
OBJECTIVE Quantitative fluorescence polymerase chain reaction (QF-PCR) is a rapid method for detection of chromosome copy number by amplification of repeat sequences at polymorphic loci. Our objective was to assess the performance of QF-PCR in detecting common aneuploidies in prenatal diagnosis. STUDY DESIGN The study group consisted of pregnant women referred for amniocentesis or chorionic villus sampling (CVS) due to increased risk of fetal aneuploidy. Samples were collected from known affected and normal pregnancies. These were blindly screened for trisomy of chromosomes 21, 18, 13, and sex chromosome abnormalities, using QF-PCR. DNA from uncultured amniocytes was directly extracted using a modified alkaline lysis method. DNA from CVS was extracted by the phenol-chloroform procedure. Ten short tandem repeat (STR) markers were used for detection of fetal aneuploidy and gender. The STRs were selected for high heterozygosity rates and efficiency of the PCR amplification. The forward primer of each pair was labeled with a unique fluorescent dye. Amplified products were detected by an ABI Prism 310 Genetic Analyzer and results were analyzed using GeneScan Analysis Software. RESULTS A total of 65 amniotic fluid and CVS samples were collected from affected and normal pregnancies. Two samples were contaminated with blood and were therefore excluded from the analysis. All 29 cases of aneuploidy were correctly diagnosed by QF-PCR, including 17 cases of trisomy 21, 7 cases of trisomy 18, and 5 cases with trisomy 13. The 34 normal samples were also correctly diagnosed as such. Thus, all results were in agreement with the standard cytogenetic results. There were no false-positive or false-negative results. CONCLUSION We conclude that QF-PCR is a rapid, reliable, and reproducible method that may be used to provide rapid results in prenatal diagnosis of aneuploidy.
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Affiliation(s)
- Yifat Ochshorn
- Department of Obstetrics and Gynecology, Sourasky Medical Center, Tel Aviv University, Israel
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Yan J, Wu J, Li Y, Wang H, Huang Z, Zhou X, Zhang W, Hou Y. A novel diagnostic strategy for trisomy 21 using short tandem repeats. Electrophoresis 2006; 27:416-22. [PMID: 16342319 DOI: 10.1002/elps.200500349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Molecular technique with STRs can rapidly diagnose aneuploidy. In order to improve its fidelity, we developed a novel STR-based strategy for fast diagnosis of trisomy 21 and constructed a multimarker diagnostic system according to it. The system is based on nine STRs, of which two were previously known and seven were newly identified from the genomic sequence of the long arm of chromosome 21. They were confirmed to be highly polymorphic in the Chinese population by PCR amplification and gel electrophoresis. The combination of nine STR markers, when applied to DNA from 102 Chinese individuals with normal karyotype, did not yield any false-positives, and clearly revealed three different alleles in DNA from 15 out of 18 trisomy 21 patients. The results show that our new strategy can provide an alternative molecular technique for the rapid detection of aneuploidy.
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Affiliation(s)
- Jing Yan
- Department of Forensic Genetics, Institute of Preliminary and Forensic Medicine, Chengdu, Sichuan, China
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22
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Choueiri MB, Makhoul NJ, Zreik TG, Mattar F, Adra AM, Eid R, Mroueh AM, Zalloua PA. The consanguinity effect on QF-PCR diagnosis of autosomal anomalies. Prenat Diagn 2006; 26:409-14. [PMID: 16532522 DOI: 10.1002/pd.1424] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
OBJECTIVES Quantitative Fluorescent PCR (QF-PCR) is a simpler and faster method of detecting common chromosomal abnormalities when compared to cytogenetic analysis. The aim of our study is to investigate the applicability of this methodology in a population where consanguineous marriages are common and to estimate the heterozygous frequency of the PCR markers used. METHODS Four hundred and twenty-three DNA samples were extracted from uncultured amniocytes and amplified with 18 short tandem repeats (STR) markers specific to chromosomes 13, 18 and 21. Amplification products were analyzed using the GeneScan software. RESULTS QF-PCR correctly identified all the numerical abnormalities related to chromosomes 13, 18 and 21. A total of 24 autosomal trisomies (5.7%) were detected. The markers D21S1432 and D21S11 were the most consistent in providing unequivocal positive results for chromosome 21 and the heterozygosity percentages of the markers used were lower than the values reported in Western populations. CONCLUSION QF-PCR is reliable for the prenatal diagnosis of numerical anomalies of the chromosomes 13, 18 and 21 in our study population. The absence of STR heterozygosity data from Lebanon and surrounding countries makes our study very useful for the development of a reliable QF-PCR trisomy detection test.
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Affiliation(s)
- Michel B Choueiri
- Department of Obstetrics and Gynecology, Medical Center, American University of Beirut, Riad el Solh/Beirut 1107 2020, Lebanon
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Cha DH, Khosrotehrani K, Bianchi DW, Johnson KL. The utility of an erythroblast scoring system and gender-independent short tandem repeat (STR) analysis for the detection of aneuploid fetal cells in maternal blood. Prenat Diagn 2005; 25:586-91. [PMID: 16032770 DOI: 10.1002/pd.1199] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
OBJECTIVE The aim of this study was to determine whether fetal nucleated red blood cells (NRBCs) could be distinguished from maternal cells in peripheral blood using an erythroblast scoring system based on the unique morphological and hemoglobin staining characteristics of this cell type. Presumptive fetal NRBCs were further analyzed for the presence of paternally inherited DNA polymorphisms to prove fetal origin. METHODS NRBCs were isolated by density gradient separation, CD15/45 depletion, and gamma hemoglobin positive selection from peripheral blood of nine women following termination of pregnancy for trisomy 21 (n=4), 18 (n=1), 13 (n=2), and other genetic abnormalities (n=2). Candidate fetal NRBCs, based on four discrete morphological and hemoglobin staining criteria, were then subjected to fluorescent PCR (polymerase chain reaction) amplification of chromosome 21 (D21S1411, D21S11) and chromosome 18 (D18S535) short tandem repeat (STR) DNA polymorphisms. RESULTS In all cases, candidate fetal NRBCs were accurately identified on the basis of morphologic and hemoglobin staining characteristics and confirmed to be fetal in origin based on the presence of shared and nonshared polymorphic DNA alleles when compared to DNA isolated from maternal cells. CONCLUSIONS Using the erythroblast scoring system and subsequent analysis of inherited DNA polymorphisms, we were able to distinguish fetal NRBCs from maternal cells and prove fetal origin independent of gender. These results suggest that this novel combined approach to fetal cell isolation and genetic analysis is a promising method for noninvasive prenatal diagnostic applications.
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Affiliation(s)
- Dong Hyun Cha
- Department of Obstetrics and Gynecology, CHA Hospital, Pochon CHA University, College of Medicine, Seoul, South Korea
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24
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Goddijn M, van Stralen M, Schuring-Blom H, Redeker B, van Leeuwen L, Repping S, Leschot N, van der Veen F. Detection of chromosome abnormalities by quantitative fluorescent PCR in ectopic pregnancies. Gynecol Obstet Invest 2005; 60:139-44. [PMID: 15925891 DOI: 10.1159/000086131] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2004] [Accepted: 04/02/2005] [Indexed: 11/19/2022]
Abstract
OBJECTIVE To evaluate the potential value of quantitative fluorescent polymerase chain reaction (QF-PCR) in the detection of chromosome abnormalities in ectopic pregnancies. METHODS Seventy chorionic villi samples of ectopic pregnancies were studied by QF-PCR. Primers for chromosomes 16, 21, X and Y in chorionic villi were evaluated. Fluorescence in situ hybridization (FISH) was performed when results of QF-PCR showed aneuploidy, in case of unexplicable QF-PCR peaks, and in 10 cases with normal QF-PCR results. RESULTS QF-PCR produced a result for chromosomes X and Y in 66 cases (94%), for chromosome 16 in 62 cases (89%) and for chromosome 21 in 55 cases (79%). Overall, QF-PCR produced a result for the chromosomes tested in 54 ectopic pregnancy cases (77%). Fifty-two of these results were normal disomic (96%) and two were abnormal, one trisomy 16 (2%) and one triploidy (2%). In 16 cases (23%) no definite QF-PCR results could be obtained for all chromosomes, 11 due to amplification failure, and 5 due to unexplicable QF-PCR peaks. In 10 cases with normal QF-PCR results, disomy was confirmed by FISH. The trisomy 16 was also confirmed by FISH. Furthermore, a result was obtained with FISH in 5 of the cases without definite QF-PCR results. CONCLUSION Although QF-PCR can establish the chromosomal status in ectopic pregnancies for chromosomes 16, 21, X and Y in the majority of cases, the technical failure rate is still considerable and does not improve results when compared to cytogenetic techniques.
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MESH Headings
- Adult
- Aneuploidy
- Chorionic Villi/metabolism
- Chromosome Aberrations
- Chromosomes, Human, Pair 16
- Chromosomes, Human, Pair 21
- Chromosomes, Human, X
- Chromosomes, Human, Y
- Down Syndrome/diagnosis
- Female
- Humans
- In Situ Hybridization, Fluorescence
- Middle Aged
- Polymerase Chain Reaction
- Predictive Value of Tests
- Pregnancy
- Pregnancy, Ectopic/diagnosis
- Pregnancy, Ectopic/genetics
- Prenatal Diagnosis
- Risk Factors
- Trisomy/diagnosis
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Affiliation(s)
- Mariette Goddijn
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
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25
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Diego-Alvarez D, Garcia-Hoyos M, Trujillo MJ, Gonzalez-Gonzalez C, Rodriguez de Alba M, Ayuso C, Ramos-Corrales C, Lorda-Sanchez I. Application of quantitative fluorescent PCR with short tandem repeat markers to the study of aneuploidies in spontaneous miscarriages. Hum Reprod 2005; 20:1235-43. [PMID: 15760965 DOI: 10.1093/humrep/deh781] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Aneuploidies involve approximately 80% of chromosomal anomalies found in spontaneous miscarriages. Since cytogenetic studies show high rates of failure, we have incorporated the quantitative fluorescent polymerase chain reaction (QF-PCR) technique to the study of numerical chromosome anomalies in miscarriages. METHODS Multiplex and simple QF-PCR assays have been performed on 160 miscarriage and 34 parental DNA samples analysing specific short tandem repeat (STR) markers for chromosomes 2, 7, 13, 15, 16, 18, 21, 22 and X. Cases successfully karyotyped were used as controls in our study. RESULTS While maternal contamination could be detected in such cases, a molecular result was obtained for 94% of miscarriages without a cytogenetic one. Thirty-six per cent of them were diagnosed with numerical chromosome anomalies. Parental origin of the extra chromosome and the error stage of meiosis could be also determined. CONCLUSIONS QF-PCR represents a useful and reliable tool to diagnose aneuploidies in spontaneous miscarriages. It provides information about parental and meiotic origin of anomaly, allowing an appropriate genetic counselling.
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Affiliation(s)
- Dan Diego-Alvarez
- Fundacion Jimenez Diaz - Human Genetics, Avda. Reyes Catolicos, Madrid, Spain.
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26
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Katz-Jaffe MG, Mantzaris D, Cram DS. DNA identification of fetal cells isolated from cervical mucus: potential for early non-invasive prenatal diagnosis. BJOG 2005; 112:595-600. [PMID: 15842283 DOI: 10.1111/j.1471-0528.2004.00506.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVES To develop a reliable method to isolate fetal cells for genetic diagnosis. DESIGN Aspiration of cervical mucus from pregnant women in the first trimester. SETTING Pregnant women were recruited before an elective termination of pregnancy. POPULATION Sixty pregnant women (7-10 weeks of gestation). METHODS Fetal cells were isolated from aspirated cervical mucus of pregnant women using a combination of enzymatic digestion, fluorescent immunohistochemistry, micromanipulation and single-cell DNA allelic profiling. MAIN OUTCOME MEASURES The isolation and identification of fetal cells. RESULTS The transformation of the tenacious cervical mucus into a single-cell suspension enabled the isolation and identification of fetal cells by fluorescent immunohistochemistry. Confirmation of fetal origin was accomplished by single-cell DNA allelic profiling alongside known maternal cells. CONCLUSIONS This novel non-invasive method is rapid and efficient with results attainable within 24 hours as early as seven weeks of gestation. The technique would offer earlier reassurance and the option of first trimester therapeutic abortions to both high and low risk pregnant women.
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Affiliation(s)
- Mandy G Katz-Jaffe
- Monash Institute of Reproduction and Development, Monash University and Monash IVF, Melbourne, Australia
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27
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Chiu RWK, Lo YMD. The biology and diagnostic applications of fetal DNA and RNA in maternal plasma. Curr Top Dev Biol 2004; 61:81-111. [PMID: 15350398 DOI: 10.1016/s0070-2153(04)61004-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Affiliation(s)
- Rossa W K Chiu
- Department of Chemical Pathology The Chinese University of Hong Kong Prince of Wales Hospital Shatin, Hong Kong SAR, China
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Lee MH, Ryu HM, Kim DJ, Lee BY, Cho EH, Yang JH, Kim MY, Han JY, Park SY. Rapid prenatal diagnosis of Down Syndrome using quantitative fluorescent PCR in uncultured amniocytes. J Korean Med Sci 2004; 19:341-4. [PMID: 15201497 PMCID: PMC2816832 DOI: 10.3346/jkms.2004.19.3.341] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rapid prenatal diagnosis of common chromosome aneuploidies have been successful through quantitative fluorescent PCR (QF-PCR) assays and small tandem repeat (STR) markers. The purpose of our study was to investigate the clinical feasibility for rapid prenatal detection of Down syndrome using the quantitative fluorescent PCR in uncultured amniocytes. DNA was extracted from uncultured amniotic fluid of normal karyotype (n=200) and of Down syndrome (n=21). It was amplified using QF-PCR with four STR markers located on chromosome 21. Among normal samples, the ranges of diallelic peaks for at least one STR marker were 1.0-1.3 for D21S11, 1.0-1.4 for D21S1411 and 1.0-1.5 for D21S1270. Down syndrome samples showed trisomic triallelic patterns or trisomic diallelic patterns. The sensitivity, specificity, and efficiency of the assay for detecting Down syndrome were 95.4%, 100%, and 99.5%, respectively. Rapid prenatal diagnosis of Down syndrome using QF-PCR is a reliable technique that aids clinical management of pregnancy.
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Affiliation(s)
- Moon-Hee Lee
- Laboratory of Medical Genetics, Samsung Cheil Hospital & Women's Healthcare Center, Sungkyunkwan University, School of Medicine, Seoul, Korea.
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Abstract
Ventriculomegaly is an excess of fluid in the lateral ventricles within the developing cerebrum. It is usually diagnosed at a routine fetal anomaly scan at 18-22 weeks gestation. Management of the condition and counselling of parents are difficult, as the cause, absolute risk, and degree of resulting handicap cannot be determined with confidence.
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Affiliation(s)
- M Wyldes
- Princess of Wales Maternity Unit, Birmingham Heartlands Hospital, Birmingham, UK
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30
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Pont-Kingdon G, Lyon E. Rapid detection of aneuploidy (trisomy 21) by allele quantification combined with melting curves analysis of single-nucleotide polymorphism loci. Clin Chem 2003; 49:1087-94. [PMID: 12816905 DOI: 10.1373/49.7.1087] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Molecular approaches for the detection of chromosomal abnormalities will allow the development of rapid, cost-effective screening strategies. We present here a molecular alternative for the detection of aneuploidies and, more specifically, trisomy 21. METHODS We used the quantitative value of melting curve analysis of heterozygous genetic loci to establish a relative allelic count. The two alleles of a given single-nucleotide polymorphism (SNP) were differentiated by thermodynamic stability with a fluorescently labeled hybridization probe and were quantified by relative areas of derivative melting curves detected after fluorescence resonance energy transfer. Heterozygous SNPs provided internal controls for the assay. RESULTS We selected six SNPs, heterozygous in at least 30% of a random population, to form a panel of informative loci in the majority of a random population. After normalization to a heterozygous control, samples segregated into three categories; nontrisomic samples had mean allele ratios of 0.96-1.09, whereas trisomic samples had mean ratios of 1.84-2.09 or 0.46-0.61, depending on which allele was duplicated. Within-run mean CVs of ratios were 6.5-27%, and between-assay mean CVs were 13-24%. CONCLUSIONS The use of melting curve analysis of multiple SNPs is an alternative to the use of small tandem repeats for the detection of trisomies. Because of the high density of SNPs, the approach may be specifically useful for very fine mapping of the regions of chromosome 21 that are critical for Down syndrome; it is also applicable to aneuploidies other than trisomy 21 and to specimens that are not amenable to cytogenetic analysis.
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Affiliation(s)
- Genevieve Pont-Kingdon
- ARUP Institute for Clinical and Experimental Pathology, 500 Chipeta Way, Salt Lake City, UT 84108, USA.
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Ogilvie CM. Prenatal diagnosis for chromosome abnormalities: past, present and future. PATHOLOGIE-BIOLOGIE 2003; 51:156-60. [PMID: 12781797 DOI: 10.1016/s0369-8114(03)00017-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Prenatal diagnosis for chromosome abnormalities has been available for over 30 years. The most common referral indication is a raised risk of Down's syndrome, and diagnosis has, until recently, been carried out by culture of cells from invasive prenatal sampling, followed by full karyotype analysis, with a waiting time of around 2 weeks for results. More recent developments in fluorescence in situ hybridisation (FISH) and quantitative fluorescence-PCR techniques have led to rapid 1-2 d reporting for Down's syndrome, opening the way to the possibility of targeted testing based on referral indication, thus reducing the incidence of difficult counselling issues and potentially unnecessary pregnancy terminations following the unexpected discovery of anomalies such as balanced chromosome rearrangements. The future of prenatal diagnosis must lie in the non-invasive diagnosis of Down's syndrome using fetal cells from maternal circulation.
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Donaghue C, Roberts A, Mann K, Ogilvie CM. Development and targeted application of a rapid QF-PCR test for sex chromosome imbalance. Prenat Diagn 2003; 23:201-10. [PMID: 12627420 DOI: 10.1002/pd.569] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
OBJECTIVES A QF-PCR test has been developed to diagnose sex chromosome imbalances in prenatal samples and has been applied to a diagnostic service. METHODS The test uses a PCR multiplex with eight primer pairs: six X-chromosome polymorphic markers, including two markers from Xp (a region not included in previously published sex chromosome aneuploidy tests), one polymorphic marker for a locus common to the long arms of the X and Y chromosomes, and the non-polymorphic amelogenin marker. Homozygosity for all X-chromosome markers and the absence of the Y-chromosome amelogenin marker is highly likely (907 : 1) to represent monosomy X (Turner syndrome), but interphase FISH is always used to confirm such a result. RESULTS Blind studies were carried out to validate the test and the first year of clinical use has been reported. Results are usually issued within one working day, and the test is more efficient than interphase FISH. CONCLUSIONS The sex chromosome imbalance test has been targeted to prenatal samples displaying a clear ultrasound indication consistent with Turner syndrome, and has also been used to identify fetal sex in pregnancies at risk of inheriting a sex-linked molecular disorder. No misdiagnoses were made. It is concluded that QF-PCR can rapidly and accurately diagnose sex chromosome status and imbalances, reducing maternal anxiety and aiding in efficient pregnancy management.
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Affiliation(s)
- Celia Donaghue
- Cytogenetics Department, Genetics Centre, Guy's and St Thomas' Hospital Trust, 5th Floor Guy's Tower, St Thomas' Street, London SE1 9RT, UK.
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Bozzette M. Recent advances in prenatal screening and diagnosis of genetic disorders. AACN CLINICAL ISSUES 2002; 13:501-10. [PMID: 12473913 DOI: 10.1097/00044067-200211000-00004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In any pregnancy, there is an approximate 3% to 5% chance that a fetal complication will occur. The most familiar prenatal diagnostics cannot be performed until the fetus is well into gestation, and most involve invasive procedures along with their inherent risks. In light of these facts, many noninvasive prenatal screening and diagnostic tests have been developed, the newest using recombinant deoxyribonucleic acid (DNA) technology in the examination of fetal cells. Through these procedures, genetic coding errors and chromosomal disruptions may be detected. This article discusses the currently available prenatal and screening diagnostic tests for genetic disorders with a focus on the latest technology.
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Affiliation(s)
- Maryann Bozzette
- Universityof Illinois at Chicago, College of Nursing, Chicago, Illinois 60612, USA.
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Bili C, Divane A, Apessos A, Konstantinos T, Apostolos A, Ioannis B, Periklis T, Florentin L. Prenatal diagnosis of common aneuploidies using quantitative fluorescent PCR. Prenat Diagn 2002; 22:360-5. [PMID: 12001187 DOI: 10.1002/pd.301] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
OBJECTIVE Quantitative fluorescence-polymerase chain reaction (QF-PCR) has recently been used for the detection of common chromosomal aneuploidies in prenatal diagnosis. Here we describe our experience in prenatal diagnosis of 1100 samples. METHODS Extraction of DNA was performed from amniotic fluid, chorionic villus samples (CVS), fetal blood and fetal tissue samples, using a simple, rapid protocol. Fluorescent multiplex PCR products of single tandem repeats (STRs) located on chromosomes 13, 18, 21, X and Y were then analyzed on an automated laser fluorescent sequencer. All samples were analyzed with at least two polymorphic markers for chromosomes 13, 18 and 21 and one for the X chromosome. The amelogenin locus was used for sexing. Analysis was performed twice on affected samples. When miscellaneous results were obtained extra markers were used. RESULTS We evaluated the usefulness of different markers in the Greek population. In a total of 1100 samples, 25 chromosome aberrations were identified, including trisomy 13, 18 and 21, XYY, triploidies 69,XXX and 69,XXY and one Turner mosaic. All results but three were consistent with conventional cytogenetic analysis. One mosaic was missed. Most bloodstained samples were successfully analyzed. CONCLUSION Successful analysis of a large number of prenatal samples proves QF-PCR to be an efficient adjunct in routine prenatal diagnosis.
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Affiliation(s)
- Chrysanthy Bili
- Alfalab, Molecular Biology and Cytogenetics Center, Athens, Greece.
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35
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Mann K, Fox SP, Abbs SJ, Yau SC, Scriven PN, Docherty Z, Ogilvie CM. Development and implementation of a new rapid aneuploidy diagnostic service within the UK National Health Service and implications for the future of prenatal diagnosis. Lancet 2001; 358:1057-61. [PMID: 11589937 DOI: 10.1016/s0140-6736(01)06183-9] [Citation(s) in RCA: 158] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
BACKGROUND Prenatal diagnosis for chromosome abnormality is routinely undertaken by full karyotype analysis of chromosomes from cultured cells; pregnant women must wait on average 13-14 days for their results. Autosomal trisomies, which account for around 80% of significant abnormalities, can be detected by quantitative fluorescence (QF) PCR. We report on the development and implementation of this technique as the first such routine service within a diagnostic department of the UK National Health Service (NHS). METHODS We designed a "one-tube test" comprising four primer pairs for polymorphic tetranucleotide repeat sequences on chromosome 21, four primer pairs for sequences on chromosome 18, three primer pairs for sequences on chromosome 13, and one primer pair to identify the sex chromosomes. All prenatal samples received by our NHS diagnostic department between April, 2000, and April, 2001, were tested. After DNA extraction, PCR amplification was done and the products separated on a capillary-based genetic analyser; the results were interpreted with dedicated software. Follow-up karyotype analysis was done on all samples. FINDINGS 1148 amniotic fluid samples, 188 chorionic villus samples, and 37 fetal tissue samples were tested; the amplification failure rate was zero with our current protocol. QF-PCR results were obtained and reported on 1314 (98%) of the prenatal samples; the remaining 22 (2%) were uninformative because of maternal-cell contamination. One case of mosaicism in a chorionic villus sample, and two cases indicating somatic expansion of a tetranucleotide repeat were found. No false positive or false negative results were obtained. The mean reporting time for the last 4 months of data collection was 1.25 working days. INTERPRETATION QF-PCR aneuploidy testing is an efficient and accurate technique for the detection of autosomal trisomies in prenatal samples. Implementation of this service has led to the rapid diagnosis of abnormalities and early reassurance for women with normal results.
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Affiliation(s)
- K Mann
- Genetics Centre, Guy's and St Thomas' Hospital Trust, London, UK
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36
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Affiliation(s)
- M Adinolfi
- Galton Laboratory and Department Obstetrics and Gynaecology, University College London, NW1 2HE, London, UK.
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37
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Samura O, Sohda S, Johnson KL, Pertl B, Ralston S, Delli-Bovi LC, Bianchi DW. Diagnosis of Trisomy 21 in Fetal Nucleated Erythrocytes from Maternal Blood by Use of Short Tandem Repeat Sequences. Clin Chem 2001. [DOI: 10.1093/clinchem/47.9.1622] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Background: The purpose of this study was to determine whether aneuploid fetal nucleated erythrocytes (NRBCs) could be detected in maternal blood through the use of fluorescent PCR amplification with polymorphic short tandem repeat (STR) markers as an alternative or complementary method to analysis by fluorescent in situ hybridization (FISH).
Methods: Peripheral blood samples were obtained from women who had just undergone termination of pregnancy because of fetal trisomy 21 (three cases, 47,XY,+21; four cases, 47,XX,+21). Candidate fetal cells were isolated by flow-sorting by antibodies to the γ chain of fetal hemoglobin and Hoechst 33342. FISH analysis was performed by the use of chromosome-specific probes for X, Y, and 21. Fetal NRBCs, as defined by the presence of γ staining, characteristic morphology, and three chromosome 21 signals, along with maternal leukocytes, defined as γ negative and two chromosome 21 signals, were micromanipulated separately and subjected to fluorescent PCR amplification of chromosome 21 STR markers (D21S11, D21S1411, and/or D21S1412).
Results: In five of seven cases analyzed, fetal NRBCs were aneuploid, as determined by the presence of triallelic or diallelic peaks of chromosome 21 sequences when compared with sequences from the maternal leukocytes.
Conclusions: Fluorescent PCR amplification of STRs can detect fetal aneuploidy and may be useful in the setting of poor hybridization efficiency with FISH analysis. These results suggest that combined fetal aneuploidy and single-gene diagnoses by the use of DNA microarrays may be feasible in the near future.
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Affiliation(s)
- Osamu Samura
- Division of Genetics, Department of Pediatrics, and
| | | | | | - Barbara Pertl
- Department of Obstetrics and Gynecology, University of Graz, A-8036 Graz, Austria
| | - Steven Ralston
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, New England Medical Center and Tufts University School of Medicine, Boston, MA 02111
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Chen CP, Chern SR, Chang CL, Lee CC, Chen WL, Chen LF, Wang W. Prenatal diagnosis and genetic analysis of X chromosome polysomy 49, XXXXY. Prenat Diagn 2000; 20:754-7. [PMID: 11015707 DOI: 10.1002/1097-0223(200009)20:9<754::aid-pd896>3.0.co;2-n] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We report on the prenatal diagnosis, genetic analysis and clinical manifestations of a 49,XXXXY fetus. A 31-year-old, primigravida woman was referred for genetic counselling at 17 weeks' gestation with the sonographic findings of intrauterine growth retardation, generalized oedema, a large septated cystic hygroma colli measuring 5x4 cm, and abnormal posturing of the lower extremities. Quantitative fluorescent polymerase chain reaction (QF-PCR) with small tandem repeat (STR) markers specific for chromosome X and a pentanucleotide marker X22 for the Xq/Yq pseudoautosomal region PAR2 rapidly detected the X-chromosome polysomy from amniotic fluid cells. This abnormality appeared to arise from successive non-disjunction during maternal meiosis I and meiosis II. Cytogenetic analysis revealed a karyotype of 49,XXXXY. Our case shows that a 49,XXXXY fetus in the second trimester may demonstrate hydrops fetalis and a large septated cystic hygroma colli by prenatal ultrasound. Our case also shows that QF-PCR assays with sex chromosome specific STR markers provide rapid prenatal diagnosis of numerical sex chromosome aneuploidy as well as its genetic cause in fetal cystic hygroma.
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Affiliation(s)
- C P Chen
- Department of Obstetrics and Gynecology, Mackay Memorial Hospital, Taipei, Taiwan, Republic of China.
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Abstract
The advent of molecular genetic technology has significantly advanced knowledge about the structure of chromosomes and their behaviour during meiosis and mitosis, as well as delineating cytogenetic aberrations that cannot be identified by conventional chromosome analysis. Molecular cytogenetics, the visualization of genetic loci using the dynamic recombinant technology of fluorescence in situ hybridization (FISH), now provides the obstetrician and gynaecologist with increasingly important diagnostic and prognostic information heretofore unavailable. The technical principles underlying FISH are briefly discussed. Emphasis is placed on the clinical applications of FISH and technologies derived from FISH, in particular comparative genome hybridization, microdissection FISH and multiplex FISH. These technologies play increasingly significant roles in preimplantation and prenatal genetic diagnosis, in the identification of microdeletion syndromes, cryptic translocations and marker chromosomes, and in defining chromosome mosaicism. FISH and related technologies also constitute essential diagnostic modalities in follow-up of organ transplantation, in a variety of haematological disorders and in determining the amplification of oncogenes associated with specific forms of cancer and neoplasia.
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Affiliation(s)
- E Pergament
- Northwestern University Medical School, Prentice Women's Hospital and Maternity Center, 333 East Superior Street, Chicago, IL, USA
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Cirigliano V, Sherlock J, Conway G, Quilter C, Rodeck C, Adinolfi M. Rapid detection of chromosomes X and Y aneuploidies by quantitative fluorescent PCR. Prenat Diagn 1999; 19:1099-103. [PMID: 10590424 DOI: 10.1002/(sici)1097-0223(199912)19:12<1099::aid-pd709>3.0.co;2-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Quantitative fluorescent polymerase chain reaction (QF-PCR) assays and small tandem repeat (STR) markers have been successfully employed for the rapid detection of major numerical aneuploidies affecting human autosomes. So far, the analysis of chromosomes X and Y disorders has been hampered by the rarity of highly polymorphic markers which could distinguish normal female homozygous PCR patterns from those seen in patients with Turner's syndrome. A new marker (X22) of the X/Y chromosomes has been identified which maps in the Xq/Yq pseudoautosomal region PAR2; used together with the HPRT it allows the rapid diagnosis of numerical aneuploidies of the sex chromosomes. Blood samples from normal male and female subjects and from patients with X and Y chromosome disorders (45,X and 47, XXY) have been tested by QF-PCR with the X22 polymorphic pentanucleotide (12 alleles) together with the HPRT and P39 markers. The samples were also tested by multiplex QF-PCR with STRs specific for chromosomes 21,18,13 and amelogenin (AMXY). Tested by QF-PCR, all samples from normal females were heterozygous for either the X22 or the HPRT marker with fluorescent peak ratios near 1:1, thus allowing a correct, rapid diagnosis of their chromosome complement. Turner's patients (45,X) showed only one X22 and one HPRT fluorescent peak, thus documenting the presence of a single X chromosome. Turner's patients with mosaicism showed a major fluorescent peak for the X22 and HPRT markers and a minor peak revealing the presence of a second minor population of cells. Two 47, XXY cases could also be diagnosed. Multiplex analyses can be performed using simultaneously STR markers for chromosomes 21,18,13 X and Y. The diagnostic value of a third X-linked marker (P39) was also investigated. These results suggest that rapid diagnosis of major numerical anomalies of the X and Y chromosomes can be performed using QF-PCR with a new highly polymorphic X-linked marker, X22, which maps in the Xq/Yq pseudoautosomal region PAR 2. Multiplex QF-PCR tests-using the X22 STR in association with HPRT and, in rare cases, a third P39 marker-allow the rapid diagnosis of major aneuploidies affecting chromosomes 21, 18, 13, X and Y. The X22 marker can also be employed for the detection of fetal cells present in maternal peripheral blood or the endocervical canal.
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Affiliation(s)
- V Cirigliano
- Galton Laboratory and Department of Obstetric and Gynaecology, University College London, London, U.K
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Cirigliano V, Sherlock J, Petrou M, Ward RH, Rodeck C, Adinolfi M. Transcervical cells and the prenatal diagnosis of haemoglobin (Hb) mutations. Clin Genet 1999; 56:357-61. [PMID: 10668925 DOI: 10.1034/j.1399-0004.1999.560503.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Prenatal diagnoses of haemoglobin (Hb) mutations were performed using transcervical cells, retrieved by aspiration from the endocervical canal of ten selected pregnant women at about 10 weeks of gestation, prior to chorionic villus sampling (CVS). Both parents were carriers of haemoglobinopathies (thalassaemia or HbS). Clumps of fetal cells were isolated by micromanipulation under an inverted microscope and aliquots of the extracted DNA tested separately for the presence of paternally derived chromosome markers and Hb mutations by quantitative fluorescent polymerase chain reaction (PCR). The correct prenatal diagnosis of Hb diseases, using selected single clumps of trophoblastic cellular elements free of maternal contaminating cells, was achieved in six out of ten cases.
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Affiliation(s)
- V Cirigliano
- Department of Obstetrics and Gynaecology, University College London, UK
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