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Liu Y, Hao S, Guo X, Fan L, Qiao Z, Wang Y, Wang X, Man J, Wang L, Wei X, Peng H, Peng Z, Sun Y, Song L. Accuracy and depth evaluation of clinical low pass genome sequencing in the detection of mosaic aneuploidies and CNVs. BMC Med Genomics 2023; 16:294. [PMID: 37978521 PMCID: PMC10656965 DOI: 10.1186/s12920-023-01703-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 10/14/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Low-pass genome sequencing (LP GS) has shown distinct advantages over traditional methods for the detection of mosaicism. However, no study has systematically evaluated the accuracy of LP GS in the detection of mosaic aneuploidies and copy number variants (CNVs) in prenatal diagnosis. Moreover, the influence of sequencing depth on mosaicism detection of LP GS has not been fully evaluated. METHODS To evaluate the accuracy of LP GS in the detection of mosaic aneuploidies and mosaic CNVs, 27 samples with known aneuploidies and CNVs and 1 negative female sample were used to generate 6 simulated samples and 21 virtual samples, each sample contained 9 different mosaic levels. Mosaic levels were simulated by pooling reads or DNA from each positive sample and the negative sample according to a series of percentages (ranging from 3 to 40%). Then, the influence of sequencing depth on LP GS in the detection of mosaic aneuploidies and CNVs was evaluated by downsampling. RESULTS To evaluate the accuracy of LP GS in the detection of mosaic aneuploidies and CNVs, a comparative analysis of mosaic levels was performed using 6 simulated samples and 21 virtual samples with 35 M million (M) uniquely aligned high-quality reads (UAHRs). For mosaic levels > 30%, the average difference (detected mosaic levels vs. theoretical mosaic levels) of 6 mosaic CNVs in simulated samples was 4.0%, and the average difference (detected mosaic levels vs. mosaic levels of Y chromosome) of 6 mosaic aneuploidies and 15 mosaic CNVs in virtual samples was 2.7%. Furthermore, LP GS had a higher detection rate and accuracy for the detection of mosaic aneuploidies and CNVs of larger sizes, especially mosaic aneuploidies. For depth evaluation, the results of LP GS in downsampling samples were compared with those of LP GS using 35 M UAHRs. The detection sensitivity of LP GS for 6 mosaic aneuploidies and 15 mosaic CNVs in virtual samples increased with UAHR. For mosaic levels > 30%, the total detection sensitivity reached a plateau at 30 M UAHRs. With 30 M UAHRs, the total detection sensitivity was 99.2% for virtual samples. CONCLUSIONS We demonstrated the accuracy of LP GS in mosaicism detection using simulated data and virtual samples, respectively. Thirty M UAHRs (single-end 35 bp) were optimal for LP GS in the detection of mosaic aneuploidies and most mosaic CNVs larger than 1.48 Mb (Megabases) with mosaic levels > 30%. These results could provide a reference for laboratories that perform clinical LP GS in the detection of mosaic aneuploidies and CNVs.
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Affiliation(s)
- Yanqiu Liu
- Jiangxi Maternal and Child Health Hospital Affiliated to Nanchang Medical College, Nanchang, 33000, Jiangxi, China
| | - Shengju Hao
- Medical Genetics Center, Gansu Provincial Clinical Research Center for Birth Defects and Rare Diseases, Gansu Provincial Maternity and Child-care Hospital, Lanzhou, 730050, China
| | - Xueqin Guo
- Clin Lab, BGI Genomics, Wuhan, 430074, China
| | - Linlin Fan
- Clin Lab, BGI Genomics, Tianjin, 300308, China
| | | | | | - Xiaoli Wang
- Clin Lab, BGI Genomics, Shenzhen, 518083, China
| | - Jianfen Man
- Clin Lab, BGI Genomics, Wuhan, 430074, China
| | - Lina Wang
- Clin Lab, BGI Genomics, Wuhan, 430074, China
| | | | | | | | - Yan Sun
- BGI Genomics, Shenzhen, 518083, China.
| | - Lijie Song
- Clin Lab, BGI Genomics, Tianjin, 300308, China.
- DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, 2800, Denmark.
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He Y, Guo L, Zheng L, Ren C, Wang T, Lu J. Clinical and molecular cytogenetic findings and pregnancy outcomes of fetuses with isochromosome Y. Mol Cytogenet 2022; 15:32. [PMID: 35927742 PMCID: PMC9351221 DOI: 10.1186/s13039-022-00611-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/21/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The mosaic forms and clinical phenotypes of fetuses with isochromosome Y are difficult to predict. Therefore, we summarized the cases of nine fetuses with isochromosome Y identified in prenatal diagnosis with a combination of molecular cytogenetic techniques, providing clinical evidence for prenatal genetic counseling. METHODS The prenatal diagnosis and pregnancy outcomes of nine fetuses with isochromosome Y were obtained by a retrospective analysis. Isochromosome Y was identified prenatally by different approaches, such as conventional karyotyping, chromosomal microarray analysis (CMA), quantitative fluorescent polymerase chain reaction (QF-PCR) and fluorescence in situ hybridization (FISH). RESULTS Seven idic(Y) fetuses and two i(Y) fetuses were identified. One fetus was complete for i(Y)(p10), and the rest with 45,X had mosaic forms. A break and fusion locus was identified in Yp11.3 in one fetus, in Yq11.22 in six fetuses and in Yp10 in two fetuses. The CMA results suggested that different deletions and duplications were found on the Y chromosome. The deletion fragments ranged from 4.7 Mb to the entire Y chromosome, and the duplication fragments ranged from 10.4 to 18.0 Mb. QF-PCR analysis suggested that the AZF region was intact in one fetus, four fetuses had AZFb+c+d deletion, one fetus had AZFa+b+c+d deletion, and one fetus had AZFc+d deletion. Finally, four healthy male neonates were delivered successfully, but the parents of the remaining five fetuses, including three healthy and two unhealthy fetuses, chose to terminate their pregnancies. CONCLUSION The fetus and neonate phenotype of prenatally detected isochromosome Y usually is that of a normally developed male, ascertained in the absence of other indicators of a fetal structural anomaly. Our study provides clinical reference materials for risk assessment and permits better prenatally counseling and preparation of parents facing the birth of isochromosome Y fetuses.
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Affiliation(s)
- Yiqun He
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, 521-523 Xingnan Road, Guangzhou, 511442, Guangdong, China
| | - Li Guo
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, 521-523 Xingnan Road, Guangzhou, 511442, Guangdong, China
| | - Laiping Zheng
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, 521-523 Xingnan Road, Guangzhou, 511442, Guangdong, China
| | - Congmian Ren
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, 521-523 Xingnan Road, Guangzhou, 511442, Guangdong, China
| | - Ting Wang
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, 521-523 Xingnan Road, Guangzhou, 511442, Guangdong, China
| | - Jian Lu
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, 521-523 Xingnan Road, Guangzhou, 511442, Guangdong, China.
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Ahmed SF, Alimusina M, Batista RL, Domenice S, Lisboa Gomes N, McGowan R, Patjamontri S, Mendonca BB. The Use of Genetics for Reaching a Diagnosis in XY DSD. Sex Dev 2022; 16:207-224. [DOI: 10.1159/000524881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/03/2022] [Indexed: 11/19/2022] Open
Abstract
Reaching a firm diagnosis is vital for the long-term management of a patient with a difference or disorder of sex development (DSD). This is especially the case in XY DSD where the diagnostic yield is particularly low. Molecular genetic technology is playing an increasingly important role in the diagnostic process, and it is highly likely that it will be used more often at an earlier stage in the diagnostic process. In many cases of DSD, the clinical utility of molecular genetics is unequivocally clear, but in many other cases there is a need for careful exploration of the benefit of genetic diagnosis through long-term monitoring of these cases. Furthermore, the incorporation of molecular genetics into the diagnostic process requires a careful appreciation of the strengths and weaknesses of the evolving technology, and the interpretation of the results requires a clear understanding of the wide range of conditions that are associated with DSD.
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Shi WH, Jiang ZR, Zhou ZY, Ye MJ, Qin NX, Huang HF, Chen SC, Xu CM. Different Strategies of Preimplantation Genetic Testing for Aneuploidies in Women of Advanced Maternal Age: A Systematic Review and Meta-Analysis. J Clin Med 2021; 10:jcm10173895. [PMID: 34501345 PMCID: PMC8432243 DOI: 10.3390/jcm10173895] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/12/2021] [Accepted: 08/24/2021] [Indexed: 11/16/2022] Open
Abstract
Background: Preimplantation genetic testing for aneuploidies (PGT-A) is widely used in women of advanced maternal age (AMA). However, the effectiveness remains controversial. Method: We conducted a comprehensive literature review comparing outcomes of IVF with or without PGT-A in women of AMA in PubMed, Embase, and the Cochrane Central Register of Controlled Trials in January 2021. All included trials met the criteria that constituted a randomized controlled trial for PGT-A involving women of AMA (≥35 years). Reviews, conference abstracts, and observational studies were excluded. The primary outcome was the live birth rate in included random control trials (RCTs). Results: Nine randomized controlled trials met our inclusion criteria. For techniques of genetic analysis, three trials (270 events) performed with comprehensive chromosomal screening showed that the live birth rate was significantly higher in the women randomized to IVF/ICSI with PGT-A (RR = 1.30, 95% CI 1.03–1.65), which was not observed in six trials used with FISH as well as all nine trials. For different stages of embryo biopsy, only the subgroup of blastocyst biopsy showed a higher live birth rate in women with PGT-A (RR = 1.36, 95% CI 1.04–1.79). Conclusion: The application of comprehensive chromosome screening showed a beneficial effect of PGT-A in women of AMA compared with FISH. Moreover, blastocyst biopsy seemed to be associated with a better outcome than polar body biopsy and cleavage-stage biopsy.
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Affiliation(s)
- Wei-Hui Shi
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, 910 Hengshan Road, Shanghai 200030, China; (W.-H.S.); (Z.-Y.Z.); (M.-J.Y.); (H.-F.H.)
- Shanghai Key Laboratory of Embryo Original Diseases, 145 Guangyuan Road, Shanghai 200030, China
| | - Zi-Ru Jiang
- Obstetrics and Gynecology Hospital, Fudan University, 566 Fangxie Road, Shanghai 200011, China;
| | - Zhi-Yang Zhou
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, 910 Hengshan Road, Shanghai 200030, China; (W.-H.S.); (Z.-Y.Z.); (M.-J.Y.); (H.-F.H.)
- Shanghai Key Laboratory of Embryo Original Diseases, 145 Guangyuan Road, Shanghai 200030, China
| | - Mu-Jin Ye
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, 910 Hengshan Road, Shanghai 200030, China; (W.-H.S.); (Z.-Y.Z.); (M.-J.Y.); (H.-F.H.)
- Shanghai Key Laboratory of Embryo Original Diseases, 145 Guangyuan Road, Shanghai 200030, China
| | - Ning-Xin Qin
- Department of Assisted Reproductive Medicine, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai 200030, China;
| | - He-Feng Huang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, 910 Hengshan Road, Shanghai 200030, China; (W.-H.S.); (Z.-Y.Z.); (M.-J.Y.); (H.-F.H.)
- Shanghai Key Laboratory of Embryo Original Diseases, 145 Guangyuan Road, Shanghai 200030, China
- Obstetrics and Gynecology Hospital, Fudan University, 566 Fangxie Road, Shanghai 200011, China;
| | - Song-Chang Chen
- Shanghai Key Laboratory of Embryo Original Diseases, 145 Guangyuan Road, Shanghai 200030, China
- Obstetrics and Gynecology Hospital, Fudan University, 566 Fangxie Road, Shanghai 200011, China;
- Correspondence: (S.-C.C.); (C.-M.X.); Tel.: +86-21-33189900 (S.-C.C.); +86-21-64073897 (C.-M.X.)
| | - Chen-Ming Xu
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, 910 Hengshan Road, Shanghai 200030, China; (W.-H.S.); (Z.-Y.Z.); (M.-J.Y.); (H.-F.H.)
- Shanghai Key Laboratory of Embryo Original Diseases, 145 Guangyuan Road, Shanghai 200030, China
- Obstetrics and Gynecology Hospital, Fudan University, 566 Fangxie Road, Shanghai 200011, China;
- Correspondence: (S.-C.C.); (C.-M.X.); Tel.: +86-21-33189900 (S.-C.C.); +86-21-64073897 (C.-M.X.)
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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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6
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Liu Y, Guo L, Chen H, Lu J, Hu J, Li X, Li X, Wang T, Li F, Yin A. Discrepancy of QF-PCR, CMA and karyotyping on a de novo case of mosaic isodicentric Y chromosomes. Mol Cytogenet 2019; 12:1. [PMID: 30647775 PMCID: PMC6327517 DOI: 10.1186/s13039-018-0413-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/17/2018] [Indexed: 12/19/2022] Open
Abstract
Background Isodicentric chromosomes are the most frequent structural aberrations of human Y chromosome, and usually present in mosaicism with a 45, X cell line. Several cytogenetic techniques have been used for diagnosing of uncommon abnormal sex chromosome abnormalities in prenatal cases. Case presentation A 26-year-old healthy woman was referred to our centre at 24 weeks of gestation age. Ultrasound examination indicated she was pregnant with imbalanced development of twins. Amniocentesis was referred to the patient for further genetic analyses. Quantitative Fluorescent Polymerase Chain Reaction (QF-PCR) indicated the existence of an extra Y chromosome or a structurally abnormal Y chromosome in primary amniotic cells. Chromosome microarray (CMA) analysis based on Comparative Genomic Hybridization (aCGH) platform was performed and identified a 10.1 Mb deletion on Y chromosome in 8-days cultured amniotic cells. Combined with the data of QF-PCR and aCGH, karyotyping and fluorescence in situ hybridization (FISH) revealed a mosaic cell line of 45,X[27]/46,X, idic(Y)(q11.22) [14] in fetus.The karyotyping analysis of cord blood sample was consistent with amniotic cells. The parental karyotypes were normal, which indicated this mosaic case of isodicentric Y (idicY) chromosomes of the fetus was a de novo case. Conclusion Several approaches have been used for the detection of numerical and structural chromosomal alterations of on prenatal cases. Our report supported the essential role of incorporating multiple genetic techniques in prenatal diagnosing and genetic counseling of potential complex sex chromosomal rearrangements.
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Affiliation(s)
- Yuan Liu
- 1Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China.,2Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China
| | - Li Guo
- 1Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China.,2Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China
| | - Hanbiao Chen
- 1Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China.,2Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China
| | - Jian Lu
- 1Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China.,2Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China
| | - Jingjing Hu
- 1Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China.,2Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China
| | - Xianzheng Li
- 1Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China.,2Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China
| | - Xing Li
- 2Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China
| | - Ting Wang
- 1Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China.,2Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China
| | - Fengzhen Li
- 1Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China.,2Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China
| | - Aihua Yin
- 1Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China.,2Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China
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Mann K, Petek E, Pertl B. Prenatal Detection of Chromosome Aneuploidy by Quantitative Fluorescence PCR. Methods Mol Biol 2019; 1885:139-160. [PMID: 30506196 DOI: 10.1007/978-1-4939-8889-1_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Autosomal chromosome aneuploid pregnancies that survive to term, namely, trisomies 13, 18, and 21, account for 89% of chromosome abnormalities with a severe phenotype identified in prenatal samples. They are traditionally detected by full karyotype analysis of cultured cells. The average reporting time for a prenatal karyotype analysis is approximately 14 days, and in recent years, there has been increasing demand for more rapid prenatal results with respect to the common chromosome aneuploidies, to relieve maternal anxiety and facilitate options in pregnancy. The rapid tests that have been developed negate the requirement for cultured cells, instead directly testing cells from the amniotic fluid or chorionic villus sample, with the aim of generating results within 48 h of sample receipt. Interphase fluorescence in situ hybridization is the method of choice in some genetic laboratories, usually because the expertise and equipment are readily available. However, a quantitative fluorescence (QF)-PCR-based approach is now widely used and reported as a clinical diagnostic service in many studies. It may be used as a stand-alone test or as an adjunct test to full karyotype or array CGH analysis, which scan for other chromosome abnormalities not detected by the QF-PCR assay.
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Affiliation(s)
- Kathy Mann
- Viapath Analytics, Guy's Hospital, London, UK.
| | - Erwin Petek
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
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Lilley M, Hume S, Karpoff N, Maire G, Taylor S, Tomaszewski R, Yoshimoto M, Christian S. Assessing the cost of implementing the 2011 Society of Obstetricians and Gynecologists of Canada and Canadian College of Medical Genetics practice guidelines on the detection of fetal aneuploidies. Prenat Diagn 2017; 37:916-923. [DOI: 10.1002/pd.5112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 06/27/2017] [Accepted: 07/05/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Margaret Lilley
- Department of Medical Genetics; University of Alberta; Edmonton Alberta Canada
| | - Stacey Hume
- Department of Medical Genetics; University of Alberta; Edmonton Alberta Canada
| | - Nina Karpoff
- Department of Medical Genetics; University of Alberta; Edmonton Alberta Canada
| | - Georges Maire
- Department of Medical Genetics; University of Alberta; Edmonton Alberta Canada
| | - Sherry Taylor
- Department of Medical Genetics; University of Alberta; Edmonton Alberta Canada
| | - Robert Tomaszewski
- Department of Medical Genetics; University of Alberta; Edmonton Alberta Canada
| | - Maisa Yoshimoto
- Department of Medical Genetics; University of Alberta; Edmonton Alberta Canada
| | - Susan Christian
- Department of Medical Genetics; University of Alberta; Edmonton Alberta Canada
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de Moraes RW, de Carvalho MHB, de Amorim-Filho AG, Francisco RPV, Romão RM, Levi JE, Zugaib M. Validation of QF-PCR for prenatal diagnoses in a Brazilian population. Clinics (Sao Paulo) 2017; 72:400-404. [PMID: 28792998 PMCID: PMC5525164 DOI: 10.6061/clinics/2017(07)02] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 02/14/2017] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVES: Quantitative fluorescence polymerase chain reaction (QF-PCR) is a rapid and reliable method for screening aneuploidies, but in Brazil, it is not used in public services. We investigated the accuracy of QF-PCR for the prenatal recognition of common aneuploidies and compared these results with cytogenetic results in our laboratory. METHOD: A ChromoQuant QF-PCR kit containing 24 primer pairs targeting loci on chromosomes 21, 13, 18, X and Y was employed to identify aneuploidies of the referred chromosomes. RESULTS: A total of 162 amniotic fluid samples analyzed using multiplex QF-PCR were compared with karyotyping analysis. The QF-PCR results were consistent with the results of cytogenetic analysis in 95.4% of all samples. CONCLUSION: QF-PCR was demonstrated to be efficient and reliable for prenatal aneuploidy screening. This study suggests that QF-PCR can be used as a rapid diagnostic method. However, rearrangements and some mosaic samples cannot be detected with this test; thus, those exceptions must undergo cytogenetic analysis.
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Affiliation(s)
- Renata Wendel de Moraes
- Departamento de Ginecologia e Obstetricia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | | | - Antonio Gomes de Amorim-Filho
- Departamento de Ginecologia e Obstetricia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | | | - Renata Moscolini Romão
- Departamento de Ginecologia e Obstetricia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | | | - Marcelo Zugaib
- Departamento de Ginecologia e Obstetricia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
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Donaghue C, Davies N, Ahn JW, Thomas H, Ogilvie CM, Mann K. Efficient and cost-effective genetic analysis of products of conception and fetal tissues using a QF-PCR/array CGH strategy; five years of data. Mol Cytogenet 2017; 10:12. [PMID: 28396697 PMCID: PMC5382376 DOI: 10.1186/s13039-017-0313-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 03/22/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Traditional testing of miscarriage products involved culture of tissue followed by G-banded chromosome analysis; this approach has a high failure rate, is labour intensive and has a resolution of around 10 Mb. G-banded chromosome analysis has been replaced by molecular techniques in some laboratories; we previously introduced a QF-PCR/MLPA testing strategy in 2007. To improve diagnostic yield and efficiency we have now updated our testing strategy to a more comprehensive QF-PCR assay followed by array CGH. Here we describe the results from the last 5 years of service. METHODS Fetal tissue samples and products of conception were tested using QF-PCR which will detect aneuploidy for chromosomes 13, 14, 15, 16, 18, 21, 22, X and Y. Samples that were normal were then tested by aCGH and all imbalance >1Mb and fully penetrant clinically significant imbalance <1Mb was reported. RESULTS QF-PCR analysis identified aneuploidy/triploidy in 25.6% of samples. aCGH analysis detected imbalance in a further 9.6% of samples; this included 1.8% with submicroscopic imbalance and 0.5% of uncertain clinical significance. This approach has a failure rate of 1.4%, compared to 30% for G-banded chromosome analysis. CONCLUSIONS This efficient QF-PCR/aCGH strategy has a lower failure rate and higher diagnostic yield than karyotype or MLPA strategies; both findings are welcome developments for couples with recurrent miscarriage.
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Affiliation(s)
- Celia Donaghue
- Genetics Department, Viapath Analytics, Guy's Hospital, London, SE1 9RT UK
| | - Nada Davies
- Genetics Department, Viapath Analytics, Guy's Hospital, London, SE1 9RT UK
| | - Joo Wook Ahn
- Genetics Department, Guys and St Thomas NHS Foundation Trust, London, SE1 9RT UK
| | - Helen Thomas
- Genetics Department, Viapath Analytics, Guy's Hospital, London, SE1 9RT UK
| | | | - Kathy Mann
- Genetics Department, Viapath Analytics, Guy's Hospital, London, SE1 9RT UK
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ÖZER KAYA Ö, KOÇ A, ÖZDEMİR TR, KIRBIYIK Ö, ÖZYILMAZ B, ÖZEREN M, ÖZTEKİN DC, TANER CE, KUTBAY YB. QF-PCR in invasive prenatal diagnosis: a single-center experience in Turkey. Turk J Med Sci 2017; 47:142-147. [DOI: 10.3906/sag-1511-157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 05/15/2016] [Indexed: 11/03/2022] Open
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Lawin O'Brien A, Dall'Asta A, Tapon D, Mann K, Ahn JW, Ellis R, Ogilvie C, Lees C. Gestation related karyotype, QF-PCR and CGH-array failure rates in diagnostic amniocentesis. Prenat Diagn 2016; 36:708-13. [PMID: 27192044 DOI: 10.1002/pd.4843] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 05/09/2016] [Accepted: 05/14/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Anna Lawin O'Brien
- Centre for Fetal Care; Queen Charlotte's and Chelsea Hospital, Imperial College; London UK
| | - Andrea Dall'Asta
- Centre for Fetal Care; Queen Charlotte's and Chelsea Hospital, Imperial College; London UK
- Department of Obstetrics and Gynaecology; University of Parma; Parma Italy
| | - Dagmar Tapon
- Centre for Fetal Care; Queen Charlotte's and Chelsea Hospital, Imperial College; London UK
| | - Kathy Mann
- Genetics Laboratories, Viapath Analytics; Guys and St Thomas' Hospital Foundation Trust; London UK
| | - Joo Wook Ahn
- Genetics Department; Guys and St Thomas' Hospital Foundation Trust; London UK
| | - Richard Ellis
- North West Thames Regional Genetics Service; London UK
| | - Caroline Ogilvie
- Genetics Department; Guys and St Thomas' Hospital Foundation Trust; London UK
- King's College; London UK
| | - Christoph Lees
- Centre for Fetal Care; Queen Charlotte's and Chelsea Hospital, Imperial College; London UK
- Department of Surgery and Cancer; Imperial College London; London UK
- Department of Development and Regeneration; KU Leuven; Belgium
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Van Opstal D, Srebniak MI. Cytogenetic confirmation of a positive NIPT result: evidence-based choice between chorionic villus sampling and amniocentesis depending on chromosome aberration. Expert Rev Mol Diagn 2016; 16:513-20. [DOI: 10.1586/14737159.2016.1152890] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Diane Van Opstal
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
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Muthuswamy S, Bhalla P, Agarwal S, Phadke SR. Performance of QF-PCR in targeted prenatal aneuploidy diagnosis: Indian scenario. Gene 2015; 562:55-61. [PMID: 25724394 DOI: 10.1016/j.gene.2015.02.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Revised: 02/09/2015] [Accepted: 02/13/2015] [Indexed: 10/23/2022]
Abstract
OBJECTIVE Among the rapid aneuploidy detection methods, QF-PCR has now become an alternative tool for prenatal aneuploidy diagnosis concomitant with karyotyping. This method has been validated in many of the western clinics but in India no study was conducted to assess its utility as standalone procedure. The study was designed to answer the question whether QF-PCR can be implemented as a standalone diagnostic method for rapid aneuploidy diagnosis in our present clinical setup? MATERIALS AND METHODS Study was conducted during March 2012 to August 2014 consisting of 270 prenatal samples that underwent for aneuploidy diagnosis. In addition to karyotyping, QF-PCR was also performed on these samples and the results were compared. RESULTS Of 270 samples screened, 262 samples showed euploid genome (125 normal male and 137 normal female). Eight samples were consistent with aneuploidy--four trisomy 21 male sample, 2 trisomy 21 female sample, 1 trisomy 18 samples and 1 Klinefelter sample. The specificity, sensitivity, positive prediction value and negative prediction values were 100% while false positive rate and false negative rate were 0%. CONCLUSION Outcome of this study strongly suggests that QF-PCR can be used as standalone procedure for targeted rapid aneuploidy diagnosis.
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Affiliation(s)
- Srinivasan Muthuswamy
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Poonam Bhalla
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Sarita Agarwal
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India.
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
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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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Crolla JA, Wapner R, Van Lith JMM. Controversies in prenatal diagnosis 3: should everyone undergoing invasive testing have a microarray? Prenat Diagn 2014; 34:18-22. [PMID: 24302430 DOI: 10.1002/pd.4287] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 11/25/2013] [Indexed: 12/23/2022]
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Liang D, Peng Y, Lv W, Deng L, Zhang Y, Li H, Yang P, Zhang J, Song Z, Xu G, Cram DS, Wu L. Copy Number Variation Sequencing for Comprehensive Diagnosis of Chromosome Disease Syndromes. J Mol Diagn 2014; 16:519-526. [DOI: 10.1016/j.jmoldx.2014.05.002] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 04/18/2014] [Accepted: 05/16/2014] [Indexed: 10/25/2022] Open
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Karampetsou E, Morrogh D, Chitty L. Microarray Technology for the Diagnosis of Fetal Chromosomal Aberrations: Which Platform Should We Use? J Clin Med 2014; 3:663-78. [PMID: 26237396 PMCID: PMC4449692 DOI: 10.3390/jcm3020663] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 03/28/2014] [Accepted: 04/01/2014] [Indexed: 12/02/2022] Open
Abstract
The advantage of microarray (array) over conventional karyotype for the diagnosis of fetal pathogenic chromosomal anomalies has prompted the use of microarrays in prenatal diagnostics. In this review we compare the performance of different array platforms (BAC, oligonucleotide CGH, SNP) and designs (targeted, whole genome, whole genome, and targeted, custom) and discuss their advantages and disadvantages in relation to prenatal testing. We also discuss the factors to consider when implementing a microarray testing service for the diagnosis of fetal chromosomal aberrations.
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Affiliation(s)
- Evangelia Karampetsou
- NE Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, 37 Queen Square, London WC1N 3BH, UK.
| | - Deborah Morrogh
- NE Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, 37 Queen Square, London WC1N 3BH, UK.
| | - Lyn Chitty
- UCL Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK.
- University College Hospital NHS Foundation Trust, London NW1 2PG, UK.
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK.
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Jenderny J, Schmidt W, Kochhan L. Chromosome aberrations identified by cytogenetic analysis of the first two clones of cultured amniotic fluid cells compared with QF-PCR results. Cytogenet Genome Res 2014; 142:239-44. [PMID: 24853086 DOI: 10.1159/000362524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2014] [Indexed: 11/19/2022] Open
Abstract
We report on our experience of studying amniotic fluid cells by cytogenetic analysis (CA) of the first 2 clones. We investigated the incidence and types of chromosome aberrations detected by CA of 196 amniocenteses performed on pregnant women at high risk. Of these cases, 178 were analysed by QF-PCR (risk group A). The results were compared with the data obtained by CA of 1,263 amniocenteses carried out in patients with other indications. QF-PCR was used to investigate 1,030 of these cases (risk group B). The combined average turnaround time for a CA result of the first 2 clones in both risk groups was within 9 ± 2 days. The final CA results (≥6 clones) were obtained within 12 ± 4 days. In risk group A, CA was not possible in 2 cases due to cell culture failure. The foetal karyotype was abnormal in 13.8% of the cases by CA of ≥6 clones and in 13.5% of the cases by QF-PCR. Together, CA of ≥6 clones and QF-PCR detected chromosome aberrations in 14.8% of the cases. With the exception of 2 cases of in vitro culture failure and 1 case with low gonosomal mosaicism, CA of the first 2 clones detected all cases with chromosome aberrations. Five cases with clinically significant chromosome aberrations were not detected by QF-PCR. In risk group B, the foetal karyotype was found to be abnormal in 2.2% of the cases by CA of ≥6 clones and in 1.0% of the cases by QF-PCR. Together, CA of ≥6 clones and QF-PCR revealed chromosome aberrations in 2.2% of the cases. With the exception of 1 case with low gonosomal mosaicism, CA of the first 2 clones detected all other cases with chromosome aberrations. The majority of these cases were inherited chromosome aberrations. Eighteen cases with chromosome aberrations were not detected by QF-PCR. Based on our results, CA of ≥6 clones, together with QF-PCR as a first test, should be performed in all prenatal cases with abnormal ultrasound findings. In pregnancies with other indications, CA of the first 2 clones alone is sufficient to identify all clinically significant (and inherited) chromosome aberrations.
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Benn P, Cuckle H, Pergament E. Non-invasive prenatal testing for aneuploidy: current status and future prospects. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2013; 42:15-33. [PMID: 23765643 DOI: 10.1002/uog.12513] [Citation(s) in RCA: 225] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 05/13/2013] [Accepted: 05/14/2013] [Indexed: 05/09/2023]
Abstract
Non-invasive prenatal testing (NIPT) for aneuploidy using cell-free DNA in maternal plasma is revolutionizing prenatal screening and diagnosis. We review NIPT in the context of established screening and invasive technologies, the range of cytogenetic abnormalities detectable, cost, counseling and ethical issues. Current NIPT approaches involve whole-genome sequencing, targeted sequencing and assessment of single nucleotide polymorphism (SNP) differences between mother and fetus. Clinical trials have demonstrated the efficacy of NIPT for Down and Edwards syndromes, and possibly Patau syndrome, in high-risk women. Universal NIPT is not cost-effective, but using NIPT contingently in women found at moderate or high risk by conventional screening is cost-effective. Positive NIPT results must be confirmed using invasive techniques. Established screening, fetal ultrasound and invasive procedures with microarray testing allow the detection of a broad range of additional abnormalities not yet detectable by NIPT. NIPT approaches that take advantage of SNP information potentially allow the identification of parent of origin for imbalances, triploidy, uniparental disomy and consanguinity, and separate evaluation of dizygotic twins. Fetal fraction enrichment, improved sequencing and selected analysis of the most informative sequences should result in tests for additional chromosomal abnormalities. Providing adequate prenatal counseling poses a substantial challenge given the broad range of prenatal testing options now available.
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Affiliation(s)
- P Benn
- Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, CT, USA.
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