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Sahinbegovic H, Andres S, Langer-Freitag S, Divane A, Ieremiadou F, Mehmedbasic S, Catic A. Genome wide noninvasive prenatal testing detects microduplication of the distal end of chromosome 15 in a fetus: a case report. Mol Cytogenet 2022; 15:16. [PMID: 35366924 PMCID: PMC8977037 DOI: 10.1186/s13039-022-00592-3] [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: 11/07/2021] [Accepted: 03/15/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Noninvasive prenatal testing (NIPT) is the most recent modality widely used in prenatal diagnostics. Commercially available NIPT has high sensitivity and specificity for the common fetal chromosomal aneuploidies. As future advancements in NIPT sequencing technology are becoming promising and more reliable, the ability to detect beyond aneuploidies and to expand detection of submicroscopic genomic alterations, as well as single-gene disorders might become possible.
Case presentation
Here we present a case of a 34-year-old pregnant woman, G2P1, who had NIPT screening which detected a terminal microduplication of 10.34 Mb on the long arm of chromosome 15 (15q26.1q26.3). Subsequent prenatal diagnostic testing including karyotype, microarray and fluorescence in situ hybridization (FISH) analyses were performed. Microarray testing confirmed and particularized a copy number gain of 10.66 Mb of the distal end of the long arm of chromosome 15. The G-banding cytogenetic studies yielded results consistent with unbalanced translocation between chromosome 15 and 18. To further characterize the abnormality involving the long arm of chromosome 18 and to map the genomic location of the duplicated 15q more precisely, FISH analysis using specific sub-telomeric probes was performed. FISH analysis confirmed that the extra duplicated segment of chromosome 15 is translocated onto the distal end of the long arm of chromosome 18 at band 18q23. Parental karyotype and FISH studies were performed to see if this unbalanced rearrangement was inherited from a healthy balanced translocation carrier versus being a de novo finding. Parental chromosomal analysis provided no evidence of a rearrangement between chromosome 15 and chromosome 18. The final fetal karyotype was reported as 46,XX,der(18)t(15;18)(q26.2;q23)dn.
Conclusions
In this case study, the microduplication of fetal chromosome 15q26.1q26.3 was accurately detected using NIPT. Our results suggest that further refinements in NIPT have the potential to evolve to a powerful and efficient screening method, which might be used to detect a broad range of chromosomal imbalances. Since microduplications and microdeletions are a potential reportable result with NIPT, this must be included in pre-test counseling. Prenatal diagnostic testing of such findings is strongly recommended.
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Gabriel H, Korinth D, Ritthaler M, Schulte B, Battke F, von Kaisenberg C, Wüstemann M, Schulze B, Friedrich-Freksa A, Pfeiffer L, Entezami M, Schröer A, Bürger J, Schwaibold EMC, Lebek H, Biskup S. Trio exome sequencing is highly relevant in prenatal diagnostics. Prenat Diagn 2021; 42:845-851. [PMID: 34958143 PMCID: PMC9305182 DOI: 10.1002/pd.6081] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/26/2022]
Abstract
Objective About 3% of newborns show malformations, with about 20% of the affected having genetic causes. Clarification of genetic diseases in postnatal diagnostics was significantly improved with high‐throughput sequencing, in particular through whole exome sequencing covering all protein‐coding regions. Here, we aim to extend the use of this technology to prenatal diagnostics. Method Between 07/2018 and 10/2020, 500 pregnancies with fetal ultrasound abnormalities were analyzed after genetic counseling as part of prenatal diagnostics using WES of the fetus and parents. Results Molecular genetic findings could explain ultrasound abnormalities in 38% of affected fetuses. In 47% of these, disease‐causing de novo variants were found. Pathogenic variants in genes with autosomal recessive or X‐linked inheritance were detected in more than one‐third (70/189 = 37%). The latter are associated with increased probability of recurrence, making their detection important for further pregnancies. Average time from sample receipt to report was 12 days in the recent cases. Conclusion Trio exome sequencing is a useful addition to prenatal diagnostics due to its high diagnostic yield and short processing time (comparable to chromosome analysis). It covers a wide spectrum of genetic changes. Comprehensive interdisciplinary counseling before and after diagnostics is indispensable.
What's already known about this topic?
It is known that about 20% of malformations in newborns can be associated with genetic causes. Whole‐exome sequencing, and especially trio exome sequencing, is an established and successful method in postnatal genetic diagnostics. Diagnostic yield for trio exome sequencing is around 37%.
What does this study add?
We show that trio exome sequencing is a fast and comprehensive method in prenatal diagnostics with diagnostic yield similar to that of postnatal trio exome sequencing. We provide case solution rates for different phenotypic observations from 19% for abnormalities of internal organs up to 52% for skeletal malformations.
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Affiliation(s)
| | - Dirk Korinth
- Praxis für Humangenetik Tübingen, Tübingen, Germany
| | | | | | | | | | - Max Wüstemann
- Zentrum für Pränatalmedizin Hannover, Hannover, Germany
| | | | | | - Lutz Pfeiffer
- Medicover Humangenetik Berlin-Lichtenberg, Berlin, Germany
| | | | | | | | | | - Holger Lebek
- Pränatale Diagnostik Berlin-Lichtenberg, Berlin, Germany
| | - Saskia Biskup
- Praxis für Humangenetik Tübingen, Tübingen, Germany.,CeGaT GmbH, Tübingen, Germany
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Dang Y, Wan S, Zheng Y, Song T, Li C, Li Y, Zhang J. The Prenatal Diagnosis of Seven Fetuses with 7q11.23 Microdeletion or Microduplication. Fetal Pediatr Pathol 2020; 39:269-276. [PMID: 31402733 DOI: 10.1080/15513815.2019.1651802] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Objective: There is scant information available about fetuses with 7q11.23 copy number variants (CNVs) found during pregnancy. We studied the clinical significance of 7q11.23 CNVs in prenatal diagnosis. Materials and methods: The amniocentesis was performed on pregnant women who underwent ultrasound (US) of fetal abnormalities. After karyotype analysis, CNVs were detected using BACs-on-Beads (BoBs) technique and chromosome microarray analysis (CMA). Results: Of seven fetuses with CNV of 7q11.23, five had microdeletions and two had microduplications. Case 1 had a 7q11.23 microdeletion along with other CNVs. Case 7 was a newborn with a normal phenotype and 7q11.23 microduplication. Conclusion: The CNVs in 7q11.23 results in many clinical manifestations, but the specificity of clinical features is not high. This study demonstrated that BoBs combined with CMA allows prenatal diagnosis of CNVs involving 7q11.23, and provide a clinical basis for prenatal diagnosis and genetic counseling of such CNVs.
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Affiliation(s)
- Yinghui Dang
- Department of Obstetrics and Gynecology, the First Affiliated Hospital Of AFMU (Air Force Medical University), Xi'an, China
| | - Shanning Wan
- Department of Obstetrics and Gynecology, the First Affiliated Hospital Of AFMU (Air Force Medical University), Xi'an, China
| | - Yunyun Zheng
- Department of Obstetrics and Gynecology, the First Affiliated Hospital Of AFMU (Air Force Medical University), Xi'an, China
| | - Tingting Song
- Department of Obstetrics and Gynecology, the First Affiliated Hospital Of AFMU (Air Force Medical University), Xi'an, China
| | - Chunyan Li
- Department of Obstetrics and Gynecology, the First Affiliated Hospital Of AFMU (Air Force Medical University), Xi'an, China
| | - Yu Li
- Department of Obstetrics and Gynecology, the First Affiliated Hospital Of AFMU (Air Force Medical University), Xi'an, China
| | - Jianfang Zhang
- Department of Obstetrics and Gynecology, the First Affiliated Hospital Of AFMU (Air Force Medical University), Xi'an, China
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4
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Farra C, Nassar AH, Mirza F, Abdouni L, Souaid M, Awwad J. BACs-on-Beads™ assay, a rapid aneuploidy test, improves the diagnostic yield of conventional karyotyping. Mol Biol Rep 2019; 47:169-177. [PMID: 31595440 DOI: 10.1007/s11033-019-05117-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 10/01/2019] [Indexed: 01/28/2023]
Abstract
BACs-on-Beads (BoBs™) assay is a rapid aneuploidy test (RAT) that detects numerical chromosomal aneuploidies and multiple microdeletion/microduplication syndromes. This study was conducted to appraise the usefulness of the BoB™ assay as a complementary diagnostic tool to conventional karyotyping for the rapid detection of chromosomal aneuploidies. A total of 485 prenatal (amniotic fluid and chorionic villi) and blood/products of conception samples were collected between July 2013 and August 2018, and analyzed by the BoBs™ assay and cytogenetic karyotyping and further validated by fluorescence in situ hybridization (FISH). Forty-three of 484 qualifying samples (8.9%) were identified as abnormal by the BoBs™ assay. The assay was comparable to karyotyping in the detection of common structural abnormalities (trisomy 21, trisomy 18, X, and Y), with a sensitivity of 96.0% and a specificity of 100%. BoBs™ assay detected 20 microdeletion and microduplication syndromes that were missed by karyotyping. BoBs™, however, missed 10 cases of polyploidies and chromosomal rearrangements which were identified by conventional karyotyping. Our findings suggest that BoBs™ is a reliable RAT which is suitable in combination with conventional karyotyping for the detection of common aneuploidies. The assay also improves the diagnostic yield by recognizing clinically relevant submicroscopic copy number gains and losses.
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Affiliation(s)
- Chantal Farra
- Medical Genetics, Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Anwar H Nassar
- Department of Obstetrics and Gynecology, American University of Beirut Medical Center, Beirut, Lebanon
| | - Fadi Mirza
- Department of Obstetrics and Gynecology, American University of Beirut Medical Center, Beirut, Lebanon
| | - Lina Abdouni
- Medical Genetics, Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Mirna Souaid
- Medical Genetics, Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Johnny Awwad
- Department of Obstetrics and Gynecology, American University of Beirut Medical Center, Beirut, Lebanon. .,Department of Obstetrics and Gynecology, Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon.
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5
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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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Wu T, Zhu Y, Hong L, Lin Q, Chen C, Yang J, Ye L, Huang W, Zeng Y. Evaluation of two aneuploidy screening tests for chorionic villus samples: Multiplex ligation-dependent probe amplification and fluorescence in situ hybridization. Mol Cell Probes 2019; 46:101422. [PMID: 31319160 DOI: 10.1016/j.mcp.2019.101422] [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] [Received: 05/26/2019] [Revised: 07/09/2019] [Accepted: 07/15/2019] [Indexed: 10/26/2022]
Abstract
The vast majority of first-trimester pregnancy losses are the consequence of numerical aberrations in fetal chromosomes, which may involve nearly all chromosomes. Although commercial probes for all chromosomes are available for multiplex ligation-dependent probe amplification (MLPA) and fluorescence in situ hybridization (FISH) analyses, their use has rarely been reported for screening all 24 chromosomes for early fetal demise, especially by FISH. Here, we validated the ability of MLPA and FISH techniques as two low-cost aneuploidy screening methods for 24 chromosomes in 165 chorionic villus samples (CVSs). The results obtained by two methods were compared by the Chi-square test and the Kappa agreement test. Both methods gave conclusive results for all CVSs tested and showed highly consistent results (kappa = 0.890, p < 0.001). There was no statistically significant difference between the aneuploidy rate of the CVSs tested by the two methods (p = 0.180). Most of the samples showed fully concordant molecular karyotyping results (81.21%) between the two analytical methods, 10.91% had incompletely concordant results, and 7.88% had discordant results. The inconsistencies included segmental abnormalities, mosaicism, and polyploidy. Both assays used to screen 24 chromosomes were powerful techniques for detecting aneuploidy in CVSs. In terms of cost-effectiveness and diagnostic accuracy, the combination of subtelomeric (P036, P070) and centromeric (P181) MLPA assays is the better analytic strategy and follow-up analysis by FISH is recommended for MLPA-negative samples.
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Affiliation(s)
- Tonghua Wu
- Shenzhen Key Laboratory for Reproductive Immunology of Preimplantation, Shenzhen Zhongshan Institute for Reproduction and Genetics, Fertility Center, Shenzhen Zhongshan Urology Hospital, Shenzhen, Guangdong, 518045, China
| | - Yuanchang Zhu
- Shenzhen Key Laboratory for Reproductive Immunology of Preimplantation, Shenzhen Zhongshan Institute for Reproduction and Genetics, Fertility Center, Shenzhen Zhongshan Urology Hospital, Shenzhen, Guangdong, 518045, China
| | - Ling Hong
- Shenzhen Key Laboratory for Reproductive Immunology of Preimplantation, Shenzhen Zhongshan Institute for Reproduction and Genetics, Fertility Center, Shenzhen Zhongshan Urology Hospital, Shenzhen, Guangdong, 518045, China
| | - Qi Lin
- Shenzhen Key Laboratory for Reproductive Immunology of Preimplantation, Shenzhen Zhongshan Institute for Reproduction and Genetics, Fertility Center, Shenzhen Zhongshan Urology Hospital, Shenzhen, Guangdong, 518045, China
| | - Chunmei Chen
- Shenzhen Key Laboratory for Reproductive Immunology of Preimplantation, Shenzhen Zhongshan Institute for Reproduction and Genetics, Fertility Center, Shenzhen Zhongshan Urology Hospital, Shenzhen, Guangdong, 518045, China
| | - Jing Yang
- Shenzhen Key Laboratory for Reproductive Immunology of Preimplantation, Shenzhen Zhongshan Institute for Reproduction and Genetics, Fertility Center, Shenzhen Zhongshan Urology Hospital, Shenzhen, Guangdong, 518045, China
| | - Lijun Ye
- Shenzhen Key Laboratory for Reproductive Immunology of Preimplantation, Shenzhen Zhongshan Institute for Reproduction and Genetics, Fertility Center, Shenzhen Zhongshan Urology Hospital, Shenzhen, Guangdong, 518045, China
| | - Wensi Huang
- Shenzhen Key Laboratory for Reproductive Immunology of Preimplantation, Shenzhen Zhongshan Institute for Reproduction and Genetics, Fertility Center, Shenzhen Zhongshan Urology Hospital, Shenzhen, Guangdong, 518045, China
| | - Yong Zeng
- Shenzhen Key Laboratory for Reproductive Immunology of Preimplantation, Shenzhen Zhongshan Institute for Reproduction and Genetics, Fertility Center, Shenzhen Zhongshan Urology Hospital, Shenzhen, Guangdong, 518045, China.
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7
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Henry MP, Hawkins JR, Boyle J, Bridger JM. The Genomic Health of Human Pluripotent Stem Cells: Genomic Instability and the Consequences on Nuclear Organization. Front Genet 2019; 9:623. [PMID: 30719030 PMCID: PMC6348275 DOI: 10.3389/fgene.2018.00623] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/23/2018] [Indexed: 12/11/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) are increasingly used for cell-based regenerative therapies worldwide, with embryonic and induced pluripotent stem cells as potential treatments for debilitating and chronic conditions, such as age-related macular degeneration, Parkinson's disease, spinal cord injuries, and type 1 diabetes. However, with the level of genomic anomalies stem cells generate in culture, their safety may be in question. Specifically, hPSCs frequently acquire chromosomal abnormalities, often with gains or losses of whole chromosomes. This review discusses how important it is to efficiently and sensitively detect hPSC aneuploidies, to understand how these aneuploidies arise, consider the consequences for the cell, and indeed the individual to whom aneuploid cells may be administered.
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Affiliation(s)
- Marianne P Henry
- Advanced Therapies Division, National Institute for Biological Standards and Control, Potters Bar, United Kingdom.,Laboratory of Nuclear and Genomic Health, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, United Kingdom
| | - J Ross Hawkins
- Advanced Therapies Division, National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | - Jennifer Boyle
- Advanced Therapies Division, National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | - Joanna M Bridger
- Laboratory of Nuclear and Genomic Health, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, United Kingdom
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Mao Y, Su L, Li H, Yang Y, Weng B. Desirable quality-control materials for the establishment of qualified external quality assessment on prenatal diagnosis of chromosomal aneuploidies. Clin Chim Acta 2018; 487:80-83. [PMID: 30213462 DOI: 10.1016/j.cca.2018.09.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 08/20/2018] [Accepted: 09/07/2018] [Indexed: 10/28/2022]
Abstract
OBJECTIVE To prepare desirable quality-control materials for the establishement of qualified external quality assessment on fluorescence in situ hybridization (FISH)-detected prenatal diagnosis of chromosomal aneuploidies. METHODS Four types of amniotic fluid cell suspensions (13-trisomy, 18-trisomy, 21-trisomy and 47,XXY) were mixed together by ratio to produce mosaicism with the percentages of each aneuploidy as 10%, 20%, 30% and 40%, respectively. After being stored in liquid nitrogen of -196 °C for six months, randomly selected samples were incubated in 37 °C water, followed by cultivation, hypo-osmosis and fixation. Finally, FISH detetion was applied on them before and after external laboratory mailing, in step with detection on conventional case samples. RESULTS Before mailing, the positive rates of each aneuploidy described above were 12.8%, 23.6%, 33.8%, 44.0%, while 12.6%, 23.8%, 34.0%, 43.5% after mailing. t-test, criteria for stability assessment of quality-control materials in CANS-GL03:2006, showed no significant effect of external mailing on mosaicism since corresponding t values are lower than threshold with significance level α as 0.05 and degree of freedom as 10. CONCLUSION As FISH detection showed, the mosaic cell strains prepared in current study exhibited excellent stabilities after cryopreservation in -196 °C, subculture, hypo-osmosis, fixation and external laboratory mailing, demonstrating them as reliable and promising quality-control materials for the establishment of a qualified external quality assessment on prenatal diagnosis of chromosomal aneuploidies.
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Affiliation(s)
- Yuchan Mao
- The Key Laboratory of Reproductive Genetics, Ministry of Education(Zhejiang University), Department of Obstetrics and Gynecology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310006, China
| | - Lan Su
- The Key Laboratory of Reproductive Genetics, Ministry of Education(Zhejiang University), Department of Obstetrics and Gynecology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310006, China
| | - Hongge Li
- The Key Laboratory of Reproductive Genetics, Ministry of Education(Zhejiang University), Department of Obstetrics and Gynecology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310006, China
| | - Yanmei Yang
- The Key Laboratory of Reproductive Genetics, Ministry of Education(Zhejiang University), Department of Obstetrics and Gynecology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310006, China
| | - Binghuan Weng
- The Key Laboratory of Reproductive Genetics, Ministry of Education(Zhejiang University), Department of Obstetrics and Gynecology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310006, China.
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Huang H, Zhang M, Wang Y, Lin N, He D, Chen M, Chen L, Lin Y, Xu L. Application of the BACs-on-Beads™ assay for rapid prenatal detection application of BoBs™ for PND of aneuploidies and microdeletions. Mol Reprod Dev 2018; 85:146-154. [PMID: 29247566 DOI: 10.1002/mrd.22945] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 12/01/2017] [Indexed: 01/24/2023]
Abstract
Prenatal diagnosis focuses on the detection of anatomic and physiologic problems with a foetus before birth. Karyotyping is currently considered the gold standard for prenatal diagnosis of chromosomal abnormalities, but this method can be time consuming. This study evaluated the diagnostic accuracy of the BACs-on-BeadsTM (BoBs™) assay for the rapid diagnosis of aneuploidies and microdeletions. A total of 625 samples from pregnant women in Fujian province, in southeastern China-including three chorionic villus biopsies, 523 amniotic fluid samples, and 99 umbilical-cord centesis samples-were assessed for chromosomal abnormalities by karyotyping and by the BoBs™ assay. A diagnosis was successfully achieved by karyotyping for 98.8% (618/625) and by the BoBs™ assay for 100% (625/625) of the samples. Both assays were concordant for trisomy 21 (2.72%, 17/625), trisomy 18 (1.12%, 7/625), trisomy 13 (0.48%, 3/625), and sex chromosome aneuploidies (0.8%, 5/625). Unlike karyotyping, the BoBs™ assay detected 22q11.2 microdeletion (0.64%, 4/625), 22q11.2 microduplication (0.16%, 1/625), Smith-Magenis syndrome microdeletion (0.16%, 1/625), and Miller-Dieker syndrome microdeletion (0.16%, 1/625). Thus, the BoBs™ assay is a reliable and rapid test for detecting common aneuploidies and microdeletions for prenatal diagnosis, and could be used instead of karyotyping for detection of common aneuploidies as well as to provide additional information regarding microdeletions.
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Affiliation(s)
- Hailong Huang
- Fujian Provincial Maternity and Children's Hospital, Affiliated hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Min Zhang
- Fujian Provincial Maternity and Children's Hospital, Affiliated hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Yan Wang
- Fujian Provincial Maternity and Children's Hospital, Affiliated hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Na Lin
- Fujian Provincial Maternity and Children's Hospital, Affiliated hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Deqin He
- Fujian Provincial Maternity and Children's Hospital, Affiliated hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Meihuan Chen
- Fujian Provincial Maternity and Children's Hospital, Affiliated hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Lingji Chen
- Fujian Provincial Maternity and Children's Hospital, Affiliated hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Yuan Lin
- Fujian Provincial Maternity and Children's Hospital, Affiliated hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Liangpu Xu
- Fujian Provincial Maternity and Children's Hospital, Affiliated hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
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10
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Weida J, Patil AS, Schubert FP, Vance G, Drendel H, Reese A, Dlouhy S, Bai S, Lee MJ. Prevalence of maternal cell contamination in amniotic fluid samples. J Matern Fetal Neonatal Med 2016; 30:2133-2137. [DOI: 10.1080/14767058.2016.1240162] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Jennifer Weida
- Division of Maternal–Fetal Medicine, Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN, USA,
| | - Avinash S. Patil
- Division of Maternal–Fetal Medicine, Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN, USA,
- Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA,
| | - Frank P. Schubert
- Division of Maternal–Fetal Medicine, Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN, USA,
| | - Gail Vance
- Division of Diagnostic Genomics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA, and
| | - Holli Drendel
- Division of Diagnostic Genomics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA, and
| | - Angela Reese
- Division of Diagnostic Genomics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA, and
| | - Stephen Dlouhy
- Division of Diagnostic Genomics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA, and
| | - Shaochun Bai
- Division of Diagnostic Genomics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA, and
| | - Men-Jean Lee
- Division of Maternal–Fetal Medicine, Department of Obstetrics and Gynecology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Donate A, Estop AM, Giraldo J, Templado C. Paternal Age and Numerical Chromosome Abnormalities in Human Spermatozoa. Cytogenet Genome Res 2016; 148:241-8. [PMID: 27322585 DOI: 10.1159/000446724] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2016] [Indexed: 11/19/2022] Open
Abstract
This study explores the relationship between numerical chromosome abnormalities in sperm and age in healthy men. We performed FISH in the spermatozoa of 10 donors from the general population: 5 men younger than 40 years of age and 5 fertile men older than 60 years of age. For each chromosome, 1,000 sperm nuclei were analyzed, with a total of 15,000 sperm nuclei for each donor. We used a single sperm sample per donor, thus minimizing intra-donor variability and optimizing consistent analysis. FISH with a TelVysion assay, which provides data on aneuploidy of 19 chromosomes, was used in order to gain a more genome-wide perspective of the level of aneuploidy. Aneuploidy and diploidy rates observed in the younger and older groups were compared. There were no significant differences in the incidence of autosomal disomy, sex chromosome disomy, total chromosome disomy, diploidy, nor total numerical abnormalities between younger and older men. This work confirms that aneuploidy of the sex chromosomes is more common than that of autosomes and that this does not change with age. Our results suggest that some probe combinations have a tendency to indicate higher levels of diploidy, thus potentially affecting FISH results and highlighting the limitations of FISH.
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Affiliation(s)
- Anna Donate
- Unitat de Biologia Celx00B7;lular i Genx00E8;tica Mx00E8;dica, Departament de Biologia Celx00B7;lular, Fisiologia i Immunologia, Facultat de Medicina, Barcelona, Spain
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12
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Leavitt K, Goldwaser T, Bhat G, Kalia I, Klugman SD, Dolan SM. Chromosomal microarray in prenatal diagnosis: case studies and clinical challenges. Per Med 2016; 13:249-255. [PMID: 29767605 DOI: 10.2217/pme-2015-0003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Chromosomal microarray analysis (CMA) is a diagnostic tool used in the evaluation of pediatric patients with congenital anomalies or developmental and intellectual disability. In both the pediatric and prenatal patient population, CMA has been shown to have a higher detection rate of chromosomal abnormalities than conventional karyotype alone. Currently, the diagnostic yield of prenatal CMA is highest when applied to the evaluation of a fetus with multiple ultrasound anomalies. Challenges arise when CMA yields isolated findings not associated with a phenotype on ultrasound or variants of uncertain significance, which warrants evaluation of the risks, benefits, limitations and optimal incorporation of CMA into prenatal care. The clinical cases presented here will be used to illustrate these issues.
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Affiliation(s)
- Karla Leavitt
- Division of Reproductive Genetics, Department of Obstetrics & Gynecology & Women's Health, Montefiore Medical Center/Albert Einstein College of Medicine 1695 Eastchester Road Suite 301, Bronx, NY 10463, USA
| | - Tamar Goldwaser
- Division of Reproductive Genetics, Department of Obstetrics & Gynecology & Women's Health, Montefiore Medical Center/Albert Einstein College of Medicine 1695 Eastchester Road Suite 301, Bronx, NY 10463, USA
| | - Gifty Bhat
- Genetics Division, Department of Pediatrics, Montefiore Medical Center/Albert Einstein College of Medicine, The Children's Hospital at Montefiore, 3415 Bainbridge Ave., Bronx, NY 10467, USA
| | - Isha Kalia
- Division of Reproductive Genetics, Department of Obstetrics & Gynecology & Women's Health, Montefiore Medical Center/Albert Einstein College of Medicine 1695 Eastchester Road Suite 301, Bronx, NY 10463, USA
| | - Susan D Klugman
- Division of Reproductive Genetics, Department of Obstetrics & Gynecology & Women's Health, Montefiore Medical Center/Albert Einstein College of Medicine 1695 Eastchester Road Suite 301, Bronx, NY 10463, USA
| | - Siobhan M Dolan
- Division of Reproductive Genetics, Department of Obstetrics & Gynecology & Women's Health, Montefiore Medical Center/Albert Einstein College of Medicine 1695 Eastchester Road Suite 301, Bronx, NY 10463, USA
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Pan M, Han J, Zhen L, Yang X, Li R, Liao C, Li DZ. Prenatal diagnosis of fetuses with increased nuchal translucency using an approach based on quantitative fluorescent polymerase chain reaction and genomic microarray. Eur J Obstet Gynecol Reprod Biol 2015; 197:164-7. [PMID: 26771907 DOI: 10.1016/j.ejogrb.2015.12.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 11/28/2015] [Accepted: 12/21/2015] [Indexed: 01/29/2023]
Abstract
OBJECTIVE To assess the clinical value of prenatal diagnosis of fetuses with increased nuchal translucency (NT) using an approach based on quantitative fluorescent polymerase chain reaction (QF-PCR) and chromosomal microarray (CMA). STUDY DESIGN From January 2013 to October 2014, we included 175 pregnancies with fetal NT ≥ 3.5mm at 11-13 weeks' gestation who received chorionic villus sampling. QF-PCR was first used to rapidly detect common aneuploidies. The cases with a normal QF-PCR result were analyzed by CMA. RESULTS Of the 175 cases, common aneuploidies were detected by QF-PCR in 53 (30.2%) cases (30 cases of trisomy 21, 12 cases of monosomy X, 7 cases of trisomy 18, 3 cases of trisomy 13 and 1 case of 47, XXY). Among the 122 cases with a normal QF-PCR result, microarray detected additional pathogenic copy number variants (CNVs) in 5.7% (7/122) of cases. Four cases would have expected to be detectable by conventional karyotyping because of large deletions/duplications (>10 Mb), leaving three cases (2.5%; 3/118) with pathogenic CNVs only detectable by CMA. CONCLUSION It is rational to use a diagnostic strategy in which CMA is preceded by the less expensive, rapid, QF-PCR to detect common aneuploidies. CMA allows detection of a number of pathogenic chromosomal aberrations in fetuses with a high NT.
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Affiliation(s)
- Min Pan
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jin Han
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Li Zhen
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xin Yang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Ru Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Can Liao
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Dong-Zhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, Guangdong, China.
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14
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Byeon Y, Ki CS, Han KH. Isolation of nucleated red blood cells in maternal blood for Non-invasive prenatal diagnosis. Biomed Microdevices 2015; 17:118. [DOI: 10.1007/s10544-015-0021-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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15
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Grati FR, Molina Gomes D, Ferreira JCPB, Dupont C, Alesi V, Gouas L, Horelli-Kuitunen N, Choy KW, García-Herrero S, de la Vega AG, Piotrowski K, Genesio R, Queipo G, Malvestiti B, Hervé B, Benzacken B, Novelli A, Vago P, Piippo K, Leung TY, Maggi F, Quibel T, Tabet AC, Simoni G, Vialard F. Prevalence of recurrent pathogenic microdeletions and microduplications in over 9500 pregnancies. Prenat Diagn 2015; 35:801-9. [PMID: 25962607 DOI: 10.1002/pd.4613] [Citation(s) in RCA: 199] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 05/01/2015] [Accepted: 05/04/2015] [Indexed: 12/23/2022]
Abstract
OBJECTIVES The implementation of chromosomal microarray analysis (CMA) in prenatal testing for all patients has not achieved a consensus. Technical alternatives such as Prenatal BACs-on-Beads(TM) (PNBoBs(TM) ) have thus been applied. The aim of this study was to provide the frequencies of the submicroscopic defects detectable by PNBoBs(TM) under different prenatal indications. METHODS A total of 9648 prenatal samples were prospectively analyzed by karyotyping plus PNBoBs(TM) and classified by prenatal indication. The frequencies of the genomic defects and their 95%CIs were calculated for each indication. RESULTS The overall incidence of cryptic imbalances was 0.7%. The majority involved the DiGeorge syndrome critical region (DGS). The additional diagnostic yield of PNBoBs(TM) in the population with a low a priori risk was 1/298. The prevalences of DGS microdeletion and microduplication in the low-risk population were 1/992 and 1/850, respectively. CONCLUSIONS The constant a priori risk for common pathogenic cryptic imbalances detected by this technology is estimated to be ~0.3%. A prevalence higher than that previously estimated was found for the 22q11.2 microdeletion. Their frequencies were independent of maternal age. These data have implications for cell-free DNA screening tests design and justify prenatal screening for 22q11 deletion, as early recognition of DGS improves its prognosis.
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Affiliation(s)
| | - Denise Molina Gomes
- CHI Poissy St Germain, Département de Cytogénétique, Obstétrique et Gynécologie, Poissy, France
| | | | - Celine Dupont
- Unité de Cytogénétique-Département de Génétique, Hôpital Robert Debré-AP-HP, GHU Nord, Paris, France
| | - Viola Alesi
- Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Laetitia Gouas
- CHU de Clermont Ferrand, Unit of Cytogenetics, Clermont Ferrand, France
| | | | - Kwong Wai Choy
- Chinese University of Hong Kong, Department of Obstetrics and Gynecology, Hong Kong, China
| | | | | | - Krzysztof Piotrowski
- Cytogenetic Unit, Department of Pathology and Genetics, Pomeranian Medical University, Szczecin, Poland
| | - Rita Genesio
- University 'Federico II', Department of Molecular Medicine and Medical Biotechnology, Naples, Italy
| | - Gloria Queipo
- Hospital General de México Eduardo Liceaga-Facultada de Medicina UNAM, NanoLab, Mexico, Mexico
| | | | - Bérénice Hervé
- CHI Poissy St Germain, Département de Cytogénétique, Obstétrique et Gynécologie, Poissy, France.,UPCG, UVSQ, Versaille, France
| | - Brigitte Benzacken
- Unité de Cytogénétique-Département de Génétique, Hôpital Robert Debré-AP-HP, GHU Nord, Paris, France
| | | | - Philippe Vago
- CHU de Clermont Ferrand, Unit of Cytogenetics, Clermont Ferrand, France
| | - Kirsi Piippo
- United Medix Laboratories Ltd., Department of Genetics, Helsinki, Finland
| | - Tak Yeung Leung
- Chinese University of Hong Kong, Department of Obstetrics and Gynecology, Hong Kong, China
| | - Federico Maggi
- TOMA Advanced Biomedical Assays S.p.A, Busto Arsizio, Italy
| | - Thibault Quibel
- CHI Poissy St Germain, Département de Cytogénétique, Obstétrique et Gynécologie, Poissy, France
| | - Anne Claude Tabet
- Unité de Cytogénétique-Département de Génétique, Hôpital Robert Debré-AP-HP, GHU Nord, Paris, France
| | | | - François Vialard
- CHI Poissy St Germain, Département de Cytogénétique, Obstétrique et Gynécologie, Poissy, France.,UPCG, UVSQ, Versaille, France
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Konialis C, Pangalos C. Dilemmas in Prenatal Chromosomal Diagnosis Revealed Through a Single Center's 30 Years' Experience and 90,000 Cases. Fetal Diagn Ther 2015; 38:218-32. [PMID: 25659342 DOI: 10.1159/000368604] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 09/21/2014] [Indexed: 11/19/2022]
Abstract
INTRODUCTION The aim of this article is to provide a perspective of prenatal chromosomal diagnosis (PCD) derived from a single center's evolving experience from ∼90,000 consecutive prenatal cases and to highlight important issues and current dilemmas. MATERIALS AND METHODS Prenatal cases in this study (1985-2013) were referred for various indications, and PCD was performed by standard karyotype in 84,255 cases, multiplex ligation-dependent probe amplification (MLPA) panel in 3,010 cases and standalone array comparative genomic hybridization (aCGH) in 3,122 cases. RESULTS Classic karyotype revealed 1.7 and 7.9% of pathological cases in amniotic fluid and CVS samples, respectively, with common aneuploidies accounting for 59.6 and 64.3% of the total abnormal. Molecular approaches increased the diagnostic yield by 0.6% for MLPA and 1.6% for aCGH, uncovering pathogenic chromosomal abnormalities undetectable by karyotype analysis. CONCLUSIONS Current molecular diagnostic capabilities and the recent introduction of noninvasive prenatal testing (NIPT) point to one current major dilemma in PCD, with serious implications in genetic counseling, relating on the one hand to reaping the benefits from the high detection rate afforded through aCGH but accepting an invasive risk, and on the other hand, offering a lower detection rate practically only for Down syndrome, with minimal invasive risk.
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Affiliation(s)
- Christopher Konialis
- Department of Molecular Genetics and Genomics, InterGenetics - Diagnostic Genetic Centre, Athens, Greece
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17
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Choy KW, Kwok YK, Cheng YKY, Wong KM, Wong HK, Leung KO, Suen KW, Adler K, Wang CC, Lau TK, Schermer MJ, Lao TT, Leung TY. Diagnostic accuracy of the BACs-on-Beads™ assay versus karyotyping for prenatal detection of chromosomal abnormalities: a retrospective consecutive case series. BJOG 2014; 121:1245-52. [PMID: 24893808 DOI: 10.1111/1471-0528.12873] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/04/2014] [Indexed: 01/23/2023]
Abstract
OBJECTIVE To evaluate the diagnostic performance of the BACs-on-Beads(™) (BoBs(™)) assay for prenatal detection of chromosomal abnormalities. DESIGN Retrospective study. SETTING Tertiary prenatal diagnosis centre. POPULATION Women referred for prenatal diagnosis. METHODS We retrieved 2153 archived DNA samples collected between January 2010 and August 2011 for the BoBs(™) assay. These samples had previously been tested by quantitative fluorescence polymerase chain reaction (QF-PCR) and karyotyping. In the BoBs(™) assay a sample was defined as normal disomic when the ratio of the fluorescence intensities in a chromosome locus lay within the threshold (mean ratio ± 2SD), and as deleted or duplicated when the ratio was below the lower threshold (0.6-0.8) or above the upper threshold (1.3-1.4), respectively. The BoBs(™) results were further validated by microarray and compared in a blinded manner with the original QF-PCR and karyotyping results. MAIN OUTCOME MEASURES Concordance of any numerical, structural, and submicroscopic chromosomal abnormalities between the methods. RESULTS BACs-on-Beads(™) was similar to karyotyping and QF-PCR in detecting trisomy 13, trisomy 18, trisomy 21, and sex chromosomal aneuploidies, and superior to QF-PCR in detecting major structural abnormalities (53.3 versus 13.3%) and mosaicism (28.6 versus 0%) involving chromosomal abnormalities other than the common aneuploidies. BoBs(™) detected six microdeletion syndromes missed by karyotyping and QF-PCR; however, BoBs(™) missed two cases of triploidy identified by QF-PCR. Therefore, the sensitivity of BoBs(™) is 96.7% (95% CI 92.6-98.7%), and its specificity is 100% (95% CI 99.8-100%). CONCLUSIONS BACs-on-Beads(™) can replace QF-PCR for triaging in prenatal diagnosis, and gives a better diagnostic yield than current rapid aneuploidy tests.
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Affiliation(s)
- K W Choy
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China; Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China; School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
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18
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Placental mosaicism for Trisomy 13: a challenge in providing the cell-free fetal DNA testing. J Assist Reprod Genet 2014; 31:589-94. [PMID: 24497298 DOI: 10.1007/s10815-014-0182-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 01/22/2014] [Indexed: 10/25/2022] Open
Abstract
PURPOSE We investigated the disagreement between the positive cell-free fetal DNA test for trisomy 13 and the standard cytogenetic diagnosis of one case. METHODS Cell-free fetal DNA testing was performed by massively parallel sequencing. We used conventional cytogenetic analysis to confirm the commercial cell-free fetal DNA testing. Additionally, postnatal fluorescent in situ hybridization (FISH) testing was performed on placental tissues. RESULTS The cell-free fetal DNA testing result was positive for trisomy 13. G-banded analysis of amniotic fluid was normal, 46, XY. FISH testing of tissues from four quadrants of the placenta demonstrated mosaicism for trisomy 13. CONCLUSIONS A positive cell-free fetal DNA testing result may not be representative of the fetal karyotype because of placental mosaicism. Cytogenetic analysis should be performed when abnormal cell-free fetal DNA test results are obtained.
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19
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The prevalence of non-detectable chromosomal abnormalities by QF-PCR in amniocentesis for certain referral indications: experience at a mainland Chinese hospital. Arch Gynecol Obstet 2013; 289:75-8. [DOI: 10.1007/s00404-013-2951-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 07/01/2013] [Indexed: 10/26/2022]
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20
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Sillence KA, Madgett TE, Roberts LA, Overton TG, Avent ND. Non-Invasive Screening Tools for Down's Syndrome: A Review. Diagnostics (Basel) 2013; 3:291-314. [PMID: 26835682 PMCID: PMC4665531 DOI: 10.3390/diagnostics3020291] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 05/14/2013] [Accepted: 05/16/2013] [Indexed: 01/16/2023] Open
Abstract
Down's syndrome (DS) is the most common genetic cause of developmental delay with an incidence of 1 in 800 live births, and is the predominant reason why women choose to undergo invasive prenatal diagnosis. However, as invasive tests are associated with around a 1% risk of miscarriage new non-invasive tests have been long sought after. Recently, the most promising approach for non-invasive prenatal diagnosis (NIPD) has been provided by the introduction of next generation sequencing (NGS) technologies. The clinical application of NIPD for DS detection is not yet applicable, as large scale validation studies in low-risk pregnancies need to be completed. Currently, prenatal screening is still the first line test for the detection of fetal aneuploidy. Screening cannot diagnose DS, but developing a more advanced screening program can help to improve detection rates, and therefore reduce the number of women offered invasive tests. This article describes how the prenatal screening program has developed since the introduction of maternal age as the original "screening" test, and subsequently discusses recent advances in detecting new screening markers with reference to both proteomic and bioinformatic techniques.
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Affiliation(s)
- Kelly A Sillence
- School of Biomedical and Biological Sciences, Plymouth University Peninsula School of Medicine and Dentistry, Plymouth University, Plymouth, PL4 8AA, UK.
| | - Tracey E Madgett
- School of Biomedical and Biological Sciences, Plymouth University Peninsula School of Medicine and Dentistry, Plymouth University, Plymouth, PL4 8AA, UK.
| | - Llinos A Roberts
- School of Biomedical and Biological Sciences, Plymouth University Peninsula School of Medicine and Dentistry, Plymouth University, Plymouth, PL4 8AA, UK.
| | - Timothy G Overton
- Department of Obstetrics, St Michael's Hospital, Southwell Street, Bristol, BS2 8EG, UK.
| | - Neil D Avent
- School of Biomedical and Biological Sciences, Plymouth University Peninsula School of Medicine and Dentistry, Plymouth University, Plymouth, PL4 8AA, UK.
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Mademont-Soler I, Morales C, Soler A, Martínez-Crespo JM, Shen Y, Margarit E, Clusellas N, Obón M, Wu BL, Sánchez A. Prenatal diagnosis of chromosomal abnormalities in fetuses with abnormal cardiac ultrasound findings: evaluation of chromosomal microarray-based analysis. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2013; 41:375-382. [PMID: 23233332 DOI: 10.1002/uog.12372] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/06/2012] [Indexed: 06/01/2023]
Abstract
OBJECTIVES To assess the frequency of karyotype abnormalities and chromosome 22q11.2 deletion syndrome among fetuses with abnormal cardiac ultrasound findings, and to evaluate the clinical value of chromosomal microarray-based analysis (CMA) in the study of such pregnancies. METHODS First, we carried out retrospective analysis of karyotype abnormalities and 22q11.2 deletion syndrome cases diagnosed between January 2009 and December 2011 in our center among fetuses with abnormal cardiac ultrasound findings (n = 276). Second, CMA was performed in 51 of the fetuses with such findings, normal karyotype and negative or no 22q11.2 deletion syndrome study, and in the only fetus with a heart defect and an apparently balanced de novo chromosomal rearrangement. RESULTS Out of the 276 pregnancies with abnormal cardiac ultrasound findings, karyotyping revealed a chromosomal abnormality in 44 (15.9%). Of fetuses with normal karyotype in which 22q11.2 deletion syndrome studies were performed, 6.4% (5/78) had this microdeletion syndrome. Among fetuses with abnormal cardiac findings, normal karyotype and negative or no 22q11.2 deletion syndrome study that underwent CMA, the detection rate of pathogenic copy number variants not detected by conventional cytogenetics was 2.0% (1/51), and no variants of uncertain clinical significance were found. In the fetus with a heart defect and an apparently balanced de novo chromosomal rearrangement, CMA revealed that the rearrangement was not truly balanced. CONCLUSIONS In the assessment of genetic abnormalities in pregnancies with abnormal cardiac ultrasound findings, the diagnostic yield may be increased by 2% if CMA is used as a complementary tool to conventional cytogenetics. Our results suggest that CMA could be a good alternative to karyotyping in these pregnancies.
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Affiliation(s)
- I Mademont-Soler
- Servei de Bioquímica i Genètica Molecular, Hospital Clínic, Barcelona, Spain
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22
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Shaffer LG, Ballif BC, Theisen A, Rorem E, Bejjani BA, Torchia BA. In the middle of it all: a centered approach to chromosome analysis. ACTA ACUST UNITED AC 2013; 2:221-9. [PMID: 23485141 DOI: 10.1517/17530059.2.2.221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND The pericentromeric areas immediately flanking the centromeres are prone to instability owing to their high levels of repetitive sequences. This genomic instability makes the pericentromeric regions ideal candidates for the investigation of chromosomal abnormalities resulting in genetic disease. However, it is this instability that confounds attempts to analyze these regions of the genome. The sequencing of the human genome, while illuminating the complexity of the pericentromeric regions, has enabled the development of high-resolution microarrays for the characterization of chromosomal abnormalities. OBJECTIVE The MarkerChip(™) was developed specifically to target the pericentromeres for the identification and characterization of pericentromeric chromosomal abnormalities. METHODS The authors' experience with this microarray is reviewed in their clinical diagnostic laboratory. RESULTS/DISCUSSION The MarkerChip demonstrates the utility of constructing a microarray for the analysis of chromosome abnormalities with coverage concentrated on areas of the genome particularly susceptible to rearrangement.
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Affiliation(s)
- Lisa G Shaffer
- Signature Genomic Laboratories, 120 N Pine St, Spokane, WA 99202, USA +1 509 474 6840 ; +1 509 474 6839 ;
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Zeng H, Weier JF, Wang M, Kassabian HJ, Polyzos AA, Baumgartner A, O'Brien B, Weier HUG. Bioinformatic Tools Identify Chromosome-Specific DNA Probes and Facilitate Risk Assessment by Detecting Aneusomies in Extra-embryonic Tissues. Curr Genomics 2013; 13:438-45. [PMID: 23450259 PMCID: PMC3426778 DOI: 10.2174/138920212802510510] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 06/11/2012] [Accepted: 06/13/2012] [Indexed: 02/03/2023] Open
Abstract
Despite their non-diseased nature, healthy human tissues may show a surprisingly large fraction of aneusomic or aneuploid cells. We have shown previously that hybridization of three to six non-isotopically labeled, chromosome-specific DNA probes reveals different proportions of aneuploid cells in individual compartments of the human placenta and the uterine wall. Using fluorescence in situ hybridization, we found that human invasive cytotrophoblasts isolated from anchoring villi or the uterine wall had gained individual chromosomes. Chromosome losses in placental or uterine tissues, on the other hand, were detected infrequently. A more thorough numerical analysis of all possible aneusomies occurring in these tissues and the investigation of their spatial as well as temporal distribution would further our understanding of the underlying biology, but it is hampered by the high cost of and limited access to DNA probes. Furthermore, multiplexing assays are difficult to set up with commercially available probes due to limited choices of probe labels. Many laboratories therefore attempt to develop their own DNA probe sets, often duplicating cloning and screening efforts underway elsewhere. In this review, we discuss the conventional approaches to the preparation of chromosome-specific DNA probes followed by a description of our approach using state-of-the-art bioinformatics and molecular biology tools for probe identification and manufacture. Novel probes that target gonosomes as well as two autosomes are presented as examples of rapid and inexpensive preparation of highly specific DNA probes for applications in placenta research and perinatal diagnostics.
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Affiliation(s)
- Hui Zeng
- Department of Cancer & DNA Damage Responses, Life Sciences Division, University of California, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Zimmermann B, Hill M, Gemelos G, Demko Z, Banjevic M, Baner J, Ryan A, Sigurjonsson S, Chopra N, Dodd M, Levy B, Rabinowitz M. Noninvasive prenatal aneuploidy testing of chromosomes 13, 18, 21, X, and Y, using targeted sequencing of polymorphic loci. Prenat Diagn 2012; 32:1233-41. [PMID: 23108718 PMCID: PMC3548605 DOI: 10.1002/pd.3993] [Citation(s) in RCA: 221] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
OBJECTIVE This study aims to develop a noninvasive prenatal test on the basis of the analysis of cell-free DNA in maternal blood to detect fetal aneuploidy at chromosomes 13, 18, 21, X, and Y. METHODS A total of 166 samples from pregnant women, including 11 trisomy 21, three trisomy 18, two trisomy 13, two 45,X, and two 47,XXY samples, were analyzed using an informatics-based method. Cell-free DNA from maternal blood was isolated, amplified using a multiplex polymerase chain reaction (PCR) assay targeting 11,000 single nucleotide polymorphisms on chromosomes 13, 18, 21, X, and Y in a single reaction, and sequenced. A Bayesian-based maximum likelihood statistical method was applied to determine the chromosomal count of the five chromosomes interrogated in each sample, along with a sample-specific calculated accuracy for each test result. RESULTS The algorithm correctly reported the chromosome copy number at all five chromosomes in 145 samples that passed a DNA quality test, for a total of 725/725 correct calls. The average calculated accuracy for these samples was 99.92%. Twenty-one samples did not pass the DNA quality test. CONCLUSIONS This informatics-based method noninvasively detected fetuses with trisomy 13, 18, and 21, 45,X, and 47,XXY with high sample-specific calculated accuracies for each individual chromosome and across all five chromosomes.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia, New York
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Cheng YKY, Wong C, Wong HK, Leung KO, Kwok YK, Suen A, Wang CC, Leung TY, Choy KW. The detection of mosaicism by prenatal BoBs™. Prenat Diagn 2012; 33:42-9. [PMID: 23168997 DOI: 10.1002/pd.4006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
OBJECTIVE The objective of the study was to evaluate the ability of a new prenatal diagnostic platform - prenatal BACs-on-Beads™ (BoBs™) in detecting mosaicism by comparison to quantitative fluorescence-polymerase chain reaction (QF-PCR). METHODS A validation study of prenatal BoBs™ was firstly performed using 18 artificially constructing mosaic samples involving various aneuploidies and microdeletion conditions. Additionally, we compared the accuracy between prenatal BoBs™ and QF-PCR for 18 archived clinical mosaic cases and nine chromosomally abnormal cell lines with reference to conventional karyotype results. RESULTS In the validation study, BoBs™ allowed the detection of mosaicism at a level of 20-40%. Among the clinical mosaic cases, 14/18 cases were within the detection of BoBs™, 8/14 (57.1%) could be identified by BoBs™ and 6/9 (66.7%) by QF-PCR, but 6/14 (42.9%) were missed by both tests. Three cases (16.7%) were detected by prenatal BoBs™ but missed by QF-PCR, whereas QF-PCR detected one case that was missed by BoBs™. The overall sensitivity of BoBs™ in detecting mosaicism is 44.4% (8/18), which is slightly higher than that of QF-PCR (33.3%; 6/18). CONCLUSION Prenatal BoBs™ has a sensitivity of 57.1% in the detection clinical mosaic cases. According to the validation test, mosaicism of 20% or greater is detectable by the BoBs™ assay.
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Affiliation(s)
- Yvonne K Y Cheng
- Department of Obstetrics and Gynaecology, Prince of Wales Hospital, Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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26
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Hui L, Bianchi DW. Recent advances in the prenatal interrogation of the human fetal genome. Trends Genet 2012; 29:84-91. [PMID: 23158400 DOI: 10.1016/j.tig.2012.10.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 10/10/2012] [Accepted: 10/15/2012] [Indexed: 02/07/2023]
Abstract
The amount of genetic and genomic information obtainable from the human fetus during pregnancy is accelerating at an unprecedented rate. Two themes have dominated recent technological advances in prenatal diagnosis: interrogation of the fetal genome in increasingly high resolution and the development of non-invasive methods of fetal testing using cell-free DNA in maternal plasma. These two areas of advancement have now converged with several recent reports of non-invasive assessment of the entire fetal genome from maternal blood. However, technological progress is outpacing the ability of the healthcare providers and patients to incorporate these new tests into existing clinical care, and further complicates many of the economic and ethical dilemmas in prenatal diagnosis. This review summarizes recent work in this field and discusses the integration of these new technologies into the clinic and society.
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Affiliation(s)
- Lisa Hui
- Mother Infant Research Institute at Tufts Medical Center, 800 Washington St, Box 394, Boston, MA 02111, USA.
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27
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Abstract
Genomic microarrays are now widely used diagnostically for the molecular karyotyping of patients with intellectual disability, congenital anomalies and autistic spectrum disorder and have more recently been applied for the detection of genomic imbalances in prenatal genetic diagnosis. We present an overview of the different arrays, protocols used and discuss methods of genomic array data analysis.
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Affiliation(s)
- Paul D Brady
- Laboratory for Cytogenetics and Genome Research, Centre for Human Genetics, University Hospital Leuven, K.U. Leuven, Leuven, Belgium
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28
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Defining the impact of maternal cell contamination on the interpretation of prenatal microarray analysis. Genet Med 2012; 14:914-21. [DOI: 10.1038/gim.2012.77] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
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29
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Armengol L, Nevado J, Serra-Juhé C, Plaja A, Mediano C, García-Santiago FA, García-Aragonés M, Villa O, Mansilla E, Preciado C, Fernández L, Mori MÁ, García-Pérez L, Lapunzina PD, Pérez-Jurado LA. Clinical utility of chromosomal microarray analysis in invasive prenatal diagnosis. Hum Genet 2012; 131:513-23. [PMID: 21975797 PMCID: PMC3277707 DOI: 10.1007/s00439-011-1095-5] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2011] [Accepted: 09/16/2011] [Indexed: 01/19/2023]
Abstract
Novel methodologies for detection of chromosomal abnormalities have been made available in the recent years but their clinical utility in prenatal settings is still unknown. We have conducted a comparative study of currently available methodologies for detection of chromosomal abnormalities after invasive prenatal sampling. A multicentric collection of a 1-year series of fetal samples with indication for prenatal invasive sampling was simultaneously evaluated using three screening methodologies: (1) karyotype and quantitative fluorescent polymerase chain reaction (QF-PCR), (2) two panels of multiplex ligation-dependent probe amplification (MLPA), and (3) chromosomal microarray-based analysis (CMA) with a targeted BAC microarray. A total of 900 pregnant women provided informed consent to participate (94% acceptance rate). Technical performance was excellent for karyotype, QF-PCR, and CMA (~1% failure rate), but relatively poor for MLPA (10% failure). Mean turn-around time (TAT) was 7 days for CMA or MLPA, 25 for karyotype, and two for QF-PCR, with similar combined costs for the different approaches. A total of 57 clinically significant chromosomal aberrations were found (6.3%), with CMA yielding the highest detection rate (32% above other methods). The identification of variants of uncertain clinical significance by CMA (17, 1.9%) tripled that of karyotype and MLPA, but most alterations could be classified as likely benign after proving they all were inherited. High acceptability, significantly higher detection rate and lower TAT, could justify the higher cost of CMA and favor targeted CMA as the best method for detection of chromosomal abnormalities in at-risk pregnancies after invasive prenatal sampling.
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Affiliation(s)
- Lluís Armengol
- qGenomics Laboratory, Doctor Aiguader, 88, 08003 Barcelona, Spain
| | - Julián Nevado
- Instituto de Genética Médica y Molecular, Hospital Universitario La Paz, Paseo de la Castellana, 261, 28046 Madrid, Spain
- Centro de Investigación en Red en Enfermedades Raras (CIBERER), Spain, http://www.ciberer.es
| | - Clara Serra-Juhé
- Centro de Investigación en Red en Enfermedades Raras (CIBERER), Spain, http://www.ciberer.es
- Unitat de Genètica, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona (PRBB), Doctor Aiguader, 88, 08003 Barcelona, Spain
| | - Alberto Plaja
- Programa de Medicina Molecular i Genètica, Hospital Universitari Vall d’Hebron, Passeig de la Vall d’Hebron, 119-129, 08035 Barcelona, Spain
| | - Carmen Mediano
- Programa de Medicina Molecular i Genètica, Hospital Universitari Vall d’Hebron, Passeig de la Vall d’Hebron, 119-129, 08035 Barcelona, Spain
| | - Fe Amalia García-Santiago
- Instituto de Genética Médica y Molecular, Hospital Universitario La Paz, Paseo de la Castellana, 261, 28046 Madrid, Spain
- Centro de Investigación en Red en Enfermedades Raras (CIBERER), Spain, http://www.ciberer.es
| | | | - Olaya Villa
- Centro de Investigación en Red en Enfermedades Raras (CIBERER), Spain, http://www.ciberer.es
- Unitat de Genètica, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona (PRBB), Doctor Aiguader, 88, 08003 Barcelona, Spain
| | - Elena Mansilla
- Instituto de Genética Médica y Molecular, Hospital Universitario La Paz, Paseo de la Castellana, 261, 28046 Madrid, Spain
- Centro de Investigación en Red en Enfermedades Raras (CIBERER), Spain, http://www.ciberer.es
| | - Cristina Preciado
- Centro de Investigación en Red en Enfermedades Raras (CIBERER), Spain, http://www.ciberer.es
- Unitat de Genètica, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona (PRBB), Doctor Aiguader, 88, 08003 Barcelona, Spain
| | - Luis Fernández
- Instituto de Genética Médica y Molecular, Hospital Universitario La Paz, Paseo de la Castellana, 261, 28046 Madrid, Spain
- Centro de Investigación en Red en Enfermedades Raras (CIBERER), Spain, http://www.ciberer.es
| | - María Ángeles Mori
- Instituto de Genética Médica y Molecular, Hospital Universitario La Paz, Paseo de la Castellana, 261, 28046 Madrid, Spain
- Centro de Investigación en Red en Enfermedades Raras (CIBERER), Spain, http://www.ciberer.es
| | - Lidia García-Pérez
- Fundación Canaria de Investigación y Salud (FUNCIS), Unidad Central de Coordinación de Ensayos Clínicos, Servicio Canario de la Salud, Pérez de Rozas, 5, 4ª Planta, 38004 Santa Cruz de Tenerife, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Pablo Daniel Lapunzina
- Instituto de Genética Médica y Molecular, Hospital Universitario La Paz, Paseo de la Castellana, 261, 28046 Madrid, Spain
- Centro de Investigación en Red en Enfermedades Raras (CIBERER), Spain, http://www.ciberer.es
| | - Luis Alberto Pérez-Jurado
- Centro de Investigación en Red en Enfermedades Raras (CIBERER), Spain, http://www.ciberer.es
- Unitat de Genètica, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona (PRBB), Doctor Aiguader, 88, 08003 Barcelona, Spain
- Programa de Medicina Molecular i Genètica, Hospital Universitari Vall d’Hebron, Passeig de la Vall d’Hebron, 119-129, 08035 Barcelona, Spain
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Novelli A, Grati FR, Ballarati L, Bernardini L, Bizzoco D, Camurri L, Casalone R, Cardarelli L, Cavalli P, Ciccone R, Clementi M, Dalprà L, Gentile M, Gelli G, Grammatico P, Malacarne M, Nardone AM, Pecile V, Simoni G, Zuffardi O, Giardino D. Microarray application in prenatal diagnosis: a position statement from the cytogenetics working group of the Italian Society of Human Genetics (SIGU), November 2011. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2012; 39:384-388. [PMID: 22262341 DOI: 10.1002/uog.11092] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A precise guideline establishing chromosomal microarray analysis (CMA) applications and platforms in the prenatal setting does not exist. The controversial question is whether CMA technologies can or should soon replace standard karyotyping in prenatal diagnostic practice. A review of the recent literature and survey of the knowledge and experience of all members of the Italian Society of Human Genetics (SIGU) Committee were carried out in order to propose recommendations for the use of CMA in prenatal testing. The analysis of datasets reported in the medical literature showed a considerable 6.4% incidence of pathogenic copy number variations (CNVs) in the group of pregnancies with sonographically detected fetal abnormalities and normal karyotype. The reported CNVs are likely to have a relevant role in terms of nosology for the fetus and in the assessment of reproductive risk for the couple. Estimation of the frequency of copy number variations of uncertain significance (VOUS) varied depending on the different CMA platforms used, ranging from 0-4%, obtained using targeted arrays, to 9-12%, obtained using high-resolution whole genome single nucleotide polymorphism (SNP) arrays. CMA analysis can be considered a second-tier diagnostic test to be used after standard karyotyping in selected groups of pregnancies, namely those with single (apparently isolated) or multiple ultrasound fetal abnormalities, those with chromosomal rearrangements, even if apparently balanced, and those with supernumerary marker chromosomes.
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Affiliation(s)
- A Novelli
- Mendel Laboratory, Casa Sollievo della Sofferenza Hospital, IRCCS, San Giovanni Rotondo, Italy.
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31
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Mori MDLÁ, Mansilla E, García-Santiago F, Vallespín E, Palomares M, Martín R, Rodríguez R, Martínez-Payo C, Gil-Fournier B, Ramiro S, Lapunzina P, Nevado J. Diagnóstico prenatal y array-hibridación genómica comparada (CGH) (I). Gestaciones de elevado riesgo. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.diapre.2012.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Lin SY, Lee CN, Chen TC, Tu MP, Lin CY, Chang TY, Su YN. A fetus with 19q13.11 microdeletion presenting with intrauterine growth restriction and multiple cystic kidney a. CASE REPORTS IN PERINATAL MEDICINE 2012. [DOI: 10.1515/crpm-2012-0001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Background: Constitutional deletions of chromosome 19q were rarely reported in the literature. The array-comparative genome hybridization (CGH) helps to identify four children with 19q13 microdeletion and the microdeletion of 19q13.11 is a recent emerging syndrome. We report one fetus with 19q12q13.12 deletion diagnosed prenatally and compare with five cases in the literature.
Case: The 29 year-old woman was at the 27th week of gestation. Prenatal ultrasound revealed severe intrauterine growth restriction and left side multiple cystic kidney with normal amniotic fluid index. Cordocentesis was performed for karyotyping and array CGH.
Results: The karyotype of the fetus was considered as normal male. The BAC array CGH identified one deletion at chromosome 19q12q13.12. The oligonucleotide array CGH further characterized the size of the breakpoint (chr19:35,116, 199-42,994,905). After counselling, the pregnancy was terminated at the 28th week of gestation. The aborted fetus had hypospadias and facial dysmorphisms.
Conclusions: Although a complete genotype-phenotype may not be established in these patients with 19q13 deletions, they shared some unique phenotypes and facial dysmorphisms. The clinician should keep in mind when anomalies are detected prenatally, array CGH may help to identify the etiology, which is critical for counselling.
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Affiliation(s)
- Shin-Yu Lin
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chien-Nan Lee
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei, Taiwan
| | - Tai-Chang Chen
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, Hsin Chu branch, Hsin Chu, Taiwan
| | - Mei-Ping Tu
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei, Taiwan
| | - Chiou-Ya Lin
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei, Taiwan
| | | | - Yi-Ning Su
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
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33
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Kooper AJ, Pieters JJ, Faas BH, Hoefsloot LH, van der Burgt I, Zondervan HA, Smits AP. Is routine karyotyping required in prenatal samples with a molecular or metabolic referral? Mol Cytogenet 2012; 5:7. [PMID: 22281113 PMCID: PMC3293020 DOI: 10.1186/1755-8166-5-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2011] [Accepted: 01/27/2012] [Indexed: 11/17/2022] Open
Abstract
As a routine, karyotyping of invasive prenatal samples is performed as an adjunct to referrals for DNA mutation detection and metabolic testing. We performed a retrospective study on 500 samples to assess the diagnostic value of this procedure. These samples included 454 (90.8%) chorionic villus (CV) and 46 (9.2%) amniocenteses specimens. For CV samples karyotyping was based on analyses of both short-term culture (STC) and long-term culture (LTC) cells. Overall, 19 (3.8%) abnormal karyotypes were denoted: four with a common aneuploidy (trisomy 21, 18 and 13), two with a sex chromosomal aneuploidy (Klinefelter syndrome), one with a sex chromosome mosaicism and twelve with various autosome mosaicisms. In four cases a second invasive test was performed because of an abnormal finding in the STC. Taken together, we conclude that STC and LTC karyotyping has resulted in a diagnostic yield of 19 (3.8%) abnormal cases, including 12 cases (2.4%) with an uncertain significance. From a diagnostic point of view, it is desirable to limit uncertain test results as secondary test findings. Therefore, we recommend a more targeted assay, such as e.g. QF-PCR, as a replacement of the STC and to provide parents the autonomy to choose between karyotyping and QF-PCR.
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Affiliation(s)
- Angelique Ja Kooper
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands.
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Langlois S, Duncan A, Wilson RD, Audibert F, Brock JA, Carroll J, Cartier L, Désilets VA, Gagnon A, Johnson JA, Langlois S, Murphy-Kaulbeck L, Okun N, Pastuck M, Langlois S, Chitayat D, DeBie I, Demczuk S, Désilets VA, Duncan A, Geraghty MT, Marcadier J, Nelson TN, Siu V, Skidmore D. Use of a DNA Method, QF-PCR, in the Prenatal Diagnosis of Fetal Aneuploidies. JOURNAL OF OBSTETRICS AND GYNAECOLOGY CANADA 2011; 33:955-960. [DOI: 10.1016/s1701-2163(16)35022-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Li X, Quigg RJ, Zhou J, Gu W, Nagesh Rao P, Reed EF. Clinical utility of microarrays: current status, existing challenges and future outlook. Curr Genomics 2011; 9:466-74. [PMID: 19506735 PMCID: PMC2691672 DOI: 10.2174/138920208786241199] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2008] [Revised: 08/11/2008] [Accepted: 08/14/2008] [Indexed: 12/22/2022] Open
Abstract
Microarray-based clinical tests have become powerful tools in the diagnosis and treatment of diseases. In contrast to traditional DNA-based tests that largely focus on single genes associated with rare conditions, microarray-based tests are ideal for the study of diseases with underlying complex genetic causes. Several microarray based tests have been translated into clinical practice such as MammaPrint and AmpliChip CYP450. Additional cancer-related microarray-based tests are either in the process of FDA review or under active development, including Tissue of Tumor Origin and AmpliChip p53. All diagnostic microarray testing is ordered by physicians and tested by a Clinical Laboratories Improvement Amendment-certified (CLIA) reference laboratory. Recently, companies offering consumer based microarray testing have emerged. Individuals can order tests online and service providers deliver the results directly to the clients via a password-protected secure website. Navigenics, 23andMe and deCODE Genetics represent pioneering companies in this field. Although the progress of these microarray-based tests is extremely encouraging with the potential to revolutionize the recognition and treatment of common diseases, these tests are still in their infancy and face technical, clinical and marketing challenges. In this article, we review microarray-based tests which are currently approved or under review by the FDA, as well as the consumer-based testing. We also provide a summary of the challenges and strategic solutions in the development and clinical use of the microarray-based tests. Finally, we present a brief outlook for the future of microarray-based clinical applications.
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Affiliation(s)
- Xinmin Li
- Clinical Microarray Core, Department of Pathology & Laboratory Medicine, University of California at Los Angeles, 1000 Veteran Ave., Los Angeles, CA 90095, USA
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36
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LeBron C, Pal P, Brait M, Dasgupta S, Guerrero-Preston R, Looijenga LH, Kowalski J, Netto G, Hoque MO. Genome-wide analysis of genetic alterations in testicular primary seminoma using high resolution single nucleotide polymorphism arrays. Genomics 2011; 97:341-9. [DOI: 10.1016/j.ygeno.2011.02.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Revised: 01/11/2011] [Accepted: 02/25/2011] [Indexed: 11/26/2022]
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Faas BHW, Cirigliano V, Bui TH. Rapid methods for targeted prenatal diagnosis of common chromosome aneuploidies. Semin Fetal Neonatal Med 2011; 16:81-7. [PMID: 21316319 DOI: 10.1016/j.siny.2011.01.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Improvements in non-invasive screening methods for trisomy 21 (Down syndrome) and other aneuploidies during the first and second trimester of pregnancy have radically changed the indications for prenatal diagnosis over the last decade. Consequently, there was a need for rapid tests for the detection of common chromosome aneuploidies resulting in the development of molecular methods for the rapid, targeted detection of (an)euploidies of the chromosomes 13, 18, 21 and the sex chromosomes. The analysis of large series of prenatal samples has shown that such tests can detect the great majority of chromosome abnormalities in prenatal diagnosis. This resulted in lively discussions on whether conventional karyotyping should remain the standard method for the majority of prenatal cases or can be replaced by rapid tests only. This review gives an overview of different aspects of the three most common tests for rapid, targeted prenatal detection of (an)euploidies, i.e. interphase fluorescence in-situ hybridisation (iFISH), quantitative fluorescent polymerase chain reaction (QF-PCR) and multiplex ligation-dependent probe amplification (MLPA).
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Affiliation(s)
- Brigitte H W Faas
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
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38
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Maya I, Davidov B, Gershovitz L, Zalzstein Y, Taub E, Coppinger J, Shaffer LG, Shohat M. Diagnostic utility of array-based comparative genomic hybridization (aCGH) in a prenatal setting. Prenat Diagn 2011; 30:1131-7. [PMID: 20925131 DOI: 10.1002/pd.2626] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
OBJECTIVE Array-based comparative genomic hybridization (aCGH) is a new technique for detecting submicroscopic deletions and duplications. There is limited information regarding its use in the prenatal setting. Here, we present our experience of 269 prenatal aCGHs between 2006 and 2009. METHOD The indications for testing were fetal anomalies on ultrasound (U/S), advanced maternal age (AMA), family history of a disorder of unknown etiology, parental concern, abnormal routine karyotype and abnormal serum biochemical screening for common fetal aneuploidies. RESULTS Of 15 cases with a known abnormal karyotype, 11 had a normal aCGH. This enabled us to reassure the families and the pregnancies were continued. The remaining four showed an abnormal aCGH, confirming the chromosomes were unbalanced, and were terminated. Of 254 cases with a normal karyotype, 3 had an abnormal aCGH and were terminated. Overall, new clinically relevant results were detected by aCGH in 18 cases, providing additional information for prenatal genetic counseling and risk assessment. CONCLUSION Our results suggest that prenatal aCGH should be offered particularly in cases with abnormal U/S. We found the rate of detecting an abnormality by aCGH in low-risk pregnancies was 1:84, but larger studies will be needed to expand our knowledge and validate our conclusions.
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Affiliation(s)
- Idit Maya
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel.
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Konialis C, Hagnefelt B, Sevastidou S, Karapanou S, Pispili K, Markaki A, Pangalos C. Uncovering recurrent microdeletion syndromes and subtelomeric deletions/duplications through non-selective application of a MLPA-based extended prenatal panel in routine prenatal diagnosis. Prenat Diagn 2011; 31:571-7. [DOI: 10.1002/pd.2750] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2010] [Revised: 12/27/2010] [Accepted: 12/30/2010] [Indexed: 11/09/2022]
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40
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Rapid aneuploidy diagnosis by multiplex ligation-dependent probe amplification and array comparative genomic hybridization in pregnancy with major congenital malformations. Taiwan J Obstet Gynecol 2011; 50:85-94. [DOI: 10.1016/j.tjog.2010.05.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2010] [Indexed: 12/18/2022] Open
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41
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Bui TH, Vetro A, Zuffardi O, Shaffer LG. Current controversies in prenatal diagnosis 3: is conventional chromosome analysis necessary in the post-array CGH era? Prenat Diagn 2011; 31:235-43. [PMID: 21374637 DOI: 10.1002/pd.2722] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Accepted: 01/09/2011] [Indexed: 01/20/2023]
Affiliation(s)
- The-Hung Bui
- The Karolinska Institute, Center For Molecular Medicine & Surgery, Karolinska University Hospital, Stockholm, Sweden
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42
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Prospective validation of quantitative fluorescent polymerase chain reaction for rapid detection of common aneuploidies. Genet Med 2011; 13:140-7. [DOI: 10.1097/gim.0b013e3182036763] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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43
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Gross SJ, Bajaj K, Garry D, Klugman S, Karpel BM, Roe AM, Wagner BJ, Zhan J, Apfelroth SD, Schreiber-Agus N. Rapid and novel prenatal molecular assay for detecting aneuploidies and microdeletion syndromes. Prenat Diagn 2011; 31:259-66. [PMID: 21207408 DOI: 10.1002/pd.2674] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2010] [Revised: 10/22/2010] [Accepted: 10/24/2010] [Indexed: 11/12/2022]
Abstract
OBJECTIVES To develop a targeted aneuploidy and microdeletion detection platform for use in the prenatal setting, to assess the integrity of the platform with a robust validation system, and to prospectively determine the performance of the platform under routine clinical conditions. METHODS To generate proxies for the various disorders assessed by the assay for analytical validation purposes, cells from ten microdeletion syndromes as well as from common aneuploidies were spiked into cleared amniotic fluid. Genomic DNA was isolated, labeled, and hybridized to microbeads that have been coupled to DNA derived from Bacterial Artificial Chromosome (BAC) from the relevant regions targeted by the array. Beads were read using a flow cytometric multiplex bead array detection system. In the prospective part of the study, 104 amniotic fluid samples were collected and analyzed. RESULTS All microdeletion syndromes and aneuploidies were validated in a blinded fashion. In the prospective study, the total number of readable samples was 101 of 104 (97%). All sample results were confirmed independently. CONCLUSION The bead array approach is a rapid and reliable test for detecting aneuploidies and microdeletions. This assay has the potential to provide the benefit of expanded molecular cytogenetic testing to pregnant women undergoing invasive prenatal diagnosis. This approach may be especially useful in parts of the world where cytogenetic personnel and facilities may be limited.
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Affiliation(s)
- Susan J Gross
- Department of Obstetrics and Gynecology, North Bronx Healthcare Network, Albert Einstein College of Medicine, Bronx, NY, USA.
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Lichtenbelt K, Knoers N, Schuring-Blom G. From Karyotyping to Array-CGH in Prenatal Diagnosis. Cytogenet Genome Res 2011; 135:241-50. [DOI: 10.1159/000334065] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
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Gekas J, van den Berg DG, Durand A, Vallée M, Wildschut HIJ, Bujold E, Forest JC, Rousseau F, Reinharz D. Rapid testing versus karyotyping in Down's syndrome screening: cost-effectiveness and detection of clinically significant chromosome abnormalities. Eur J Hum Genet 2011; 19:3-9. [PMID: 20842178 PMCID: PMC3039505 DOI: 10.1038/ejhg.2010.138] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Revised: 06/22/2010] [Accepted: 07/09/2010] [Indexed: 11/09/2022] Open
Abstract
In all, 80% of antenatal karyotypes are generated by Down's syndrome screening programmes (DSSP). After a positive screening, women are offered prenatal foetus karyotyping, the gold standard. Reliable molecular methods for rapid aneuploidy diagnosis (RAD: fluorescence in situ hybridization (FISH) and quantitative fluorescence PCR (QF-PCR)) can detect common aneuploidies, and are faster and less expensive than karyotyping.In the UK, RAD is recommended as a standalone approach in DSSP, whereas the US guidelines recommend that RAD be followed up by karyotyping. A cost-effectiveness (CE) analysis of RAD in various DSSP is lacking. There is a debate over the significance of chromosome abnormalities (CA) detected with karyotyping but not using RAD. Our objectives were to compare the CE of RAD versus karyotyping, to evaluate the clinically significant missed CA and to determine the impact of detecting the missed CA. We performed computer simulations to compare six screening options followed by FISH, PCR or karyotyping using a population of 110948 pregnancies. Among the safer screening strategies, the most cost-effective strategy was contingent screening with QF-PCR (CE ratio of $24084 per Down's syndrome (DS) detected). Using karyotyping, the CE ratio increased to $27898. QF-PCR missed only six clinically significant CA of which only one was expected to confer a high risk of an abnormal outcome. The incremental CE ratio (ICER) to find the CA missed by RAD was $66608 per CA. These costs are much higher than those involved for detecting DS cases. As the DSSP are mainly designed for DS detection, it may be relevant to question the additional costs of karyotyping.
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Affiliation(s)
- Jean Gekas
- Centre de Recherche du CHUQ, Service de Génétique Médicale, Unité de Diagnostic Prénatal, Département de Pédiatrie, Université Laval, Québec City, Québec, Canada.
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Comas C, Echevarria M, Carrera M, Serra B. Rapid aneuploidy testing versus traditional karyotyping in amniocentesis for certain referral indications. J Matern Fetal Neonatal Med 2010; 23:949-55. [PMID: 20718579 DOI: 10.3109/14767050903334893] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVE (1) To determine the suitability of replacing full karyotype analysis with quantitative fluorescent polymerase chain reaction (QF-PCR) for prenatal diagnosis in amniotic fluid samples obtained by amniocentesis. (2) To evaluate an indication-based classification of cases at risk of missing clinically relevant chromosomal disorders by QF-PCR. METHODS We reviewed all fetal karyotypes obtained by amniocentesis between January 2004 and December 2008. We compared the cytogenetic findings obtained through conventional karyotype with those that would have been theoretically obtained using QF-PCR. RESULTS Of the 4007 karyotypes obtained, 110 abnormal karyotypes were found (2.8%). Out of these, 30 (27%) were chromosomal abnormalities (CA) which would not have been detected by PCR alone. These included 16 cases (53%) predicted to confer no increased risk, 9 (30%) predicted to have a low risk, and 5 (17%) with an uncertain or high risk of fetal abnormality. A policy of QF-PCR alone would have identified 80 of 85 (94%) clinically significant CA. When QF-PCR shows a normal result, the overall residual risk is 0.75% for any CA and 0.12% for a clinical significant CA. CONCLUSION In our population, a policy of QF-PCR alone would miss 0.12% clinically relevant CA. QF-PCR directed to common aneuploidies can be considered as an economically and clinically acceptable prenatal diagnosis policy, offering full karyotype only for specific indications.
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Affiliation(s)
- Carmen Comas
- Fetal Medicine Unit, Department of Obstetrics and Gynecology, Institut Universitari Dexeus, Barcelona, Spain.
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Keren B, Schluth-Bolard C, Egea G, Sanlaville D. Nouvelles méthodes d’analyse globale du génome humain. Arch Pediatr 2010; 17:1605-8. [DOI: 10.1016/j.arcped.2010.06.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Revised: 06/10/2010] [Accepted: 06/16/2010] [Indexed: 10/19/2022]
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Badenas C, Rodríguez-Revenga L, Morales C, Mediano C, Plaja A, Pérez-Iribarne MM, Soler A, Clusellas N, Borrell A, Sánchez MÁ, Miró E, Sánchez A, Milà M, Jiménez W. Assessment of QF-PCR as the first approach in prenatal diagnosis. J Mol Diagn 2010; 12:828-34. [PMID: 20889556 DOI: 10.2353/jmoldx.2010.090224] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Quantitative fluorescent PCR (QF-PCR) has been used by many laboratories for prenatal diagnosis of the most common aneuploidies. QF-PCR is rapid, cost-effective, and suitable for automation and can detect most abnormalities diagnosed by conventional karyotyping. Whether QF-PCR should be used alone in most of the samples and in which karyotyping should also be offered is currently a topic of debate. We evaluated and compared the results obtained from 7679 prenatal samples in which conventional karyotype and QF-PCR had been performed, including 1243 chorionic villi and 6436 amniotic fluid samples. Concordant QF-PCR and karyotype results were obtained in 98.75% of the samples. An abnormal karyotype associated with adverse clinical outcome undetected by QF-PCR was found in 0.05% of samples. Therefore, QF-PCR can be used alone in a large number of samples studied in a prenatal laboratory, thereby reducing both the workload in cytogenetic laboratories and parental anxiety when awaiting results.
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Affiliation(s)
- Celia Badenas
- Biochemistry and Molecular Genetics Service, Villarroel 170, Hospital Clínic de Barcelona, 08036 Barcelona, Spain.
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Soucy JF, Lavoie J, Duncan AMV. Locus-specific dual color-probe for the enumeration of chromosome 18 in rapid FISH aneuploidy testing on uncultured amniocytes. Prenat Diagn 2010; 30:811-2. [PMID: 20661896 DOI: 10.1002/pd.2569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Park JH, Woo JH, Shim SH, Yang SJ, Choi YM, Yang KS, Cha DH. Application of a target array comparative genomic hybridization to prenatal diagnosis. BMC MEDICAL GENETICS 2010; 11:102. [PMID: 20576126 PMCID: PMC2909938 DOI: 10.1186/1471-2350-11-102] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Accepted: 06/24/2010] [Indexed: 11/30/2022]
Abstract
Background While conventional G-banded karyotyping still remains a gold standard in prenatal genetic diagnoses, the widespread adoption of array Comparative Genomic Hybridization (array CGH) technology for postnatal genetic diagnoses has led to increasing interest in the use of this same technology for prenatal diagnosis. We have investigated the value of our own designed DNA chip as a prenatal diagnostic tool for detecting submicroscopic deletions/duplications and chromosome aneuploidies. Methods We designed a target bacterial artificial chromosome (BAC)-based aCGH platform (MacArray™ M-chip), which specifically targets submicroscopic deletions/duplications for 26 known genetic syndromes of medical significance observed prenatally. To validate the DNA chip, we obtained genomic DNA from 132 reference materials generated from patients with 22 genetic diseases and 94 clinical amniocentesis samples obtained for karyotyping. Results In the 132 reference materials, all known genomic alterations were successfully identified. In the 94 clinical samples that were also subjected to conventional karyotyping, three cases of balanced chromosomal aberrations were not detected by aCGH. However, we identified eight cases of microdeletions in the Yq11.23 chromosomal region that were not found by conventional karyotyping. This region harbors the DAZ gene, and deletions may lead to non-obstructive spermatogenesis. Conclusions We have successfully designed and applied a BAC-based aCGH platform for prenatal diagnosis. This platform can be used in conjunction with conventional karyotyping and will provide rapid and accurate diagnoses for the targeted genomic regions while eliminating the need to interpret clinically-uncertain genomic regions.
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Affiliation(s)
- Ji Hyeon Park
- Department of Obstetrics and Gynecology, CHA Bundang Medical Center, CHA University, Seongnam-si, Korea
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