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Shear MA, Swanson K, Garg R, Jelin AC, Boscardin J, Norton ME, Sparks TN. A systematic review and meta-analysis of cell-free DNA testing for detection of fetal sex chromosome aneuploidy. Prenat Diagn 2023; 43:133-143. [PMID: 36588186 PMCID: PMC10268789 DOI: 10.1002/pd.6298] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/05/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023]
Abstract
OBJECTIVES The aim was to determine the accuracy of cell-free DNA testing (cfDNA) for detecting sex chromosome aneuploidies (SCA) in singleton pregnancies. METHODS A systematic review and meta-analysis was performed to assess cfDNA accuracy for prenatal detection of 45,X, 47,XXY, 47,XXX and 47,XYY. Inclusion was restricted to studies published between January 2010 and December 2021 reporting both cfDNA and confirmatory diagnostic test results. RESULTS For 45,X, the sensitivity was 98.8% (95%CI 94.6%-100%), specificity 99.4% (95%CI 98.7%-99.9%) and positive predictive value (PPV) 14.5% (95%CI 7.0%-43.8%). For 47,XXY, the sensitivity was 100% (95%CI 99.6%-100%), specificity 100% (95%CI 99.9%-100%) and PPV 97.7% (95%CI 78.6%-100%). For 47,XXX, the sensitivity was 100% (95%CI 96.9%-100%), specificity 99.9% (95%CI 99.7%-100%) and PPV 61.6% (95%CI 37.6%-95.4%). For 47,XYY, the sensitivity was 100% (95%CI 91.3%-100%), specificity 100% (95% CI 100%-100%) and PPV 100% (95%CI 76.5%-100%). All four SCAs had estimated negative predictive values (NPV) exceeding 99.99%, though false negatives were reported. CONCLUSIONS This analysis suggests that cfDNA is a reliable screening test for SCA, though both false negatives and false positives were reported. These estimates of test performance are derived from pregnancies at high pretest risk for aneuploidy, limiting the generalisability to average risk pregnancies.
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Affiliation(s)
- Matthew A. Shear
- Department of Obstetrics, Gynecology, & Reproductive Sciences, University of California, San Francisco, California, USA
- Department of Pediatrics, Division of Medical Genetics, University of California, San Francisco, California, USA
| | - Kate Swanson
- Department of Obstetrics, Gynecology, & Reproductive Sciences, University of California, San Francisco, California, USA
- Department of Pediatrics, Division of Medical Genetics, University of California, San Francisco, California, USA
| | - Ria Garg
- Department of Pediatrics, Division of Medical Genetics, University of California, San Francisco, California, USA
| | - Angie C. Jelin
- Department of Gynecology and Obstetrics, The Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - John Boscardin
- Department of Medicine, University of California, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
| | - Mary E. Norton
- Department of Obstetrics, Gynecology, & Reproductive Sciences, University of California, San Francisco, California, USA
- Department of Pediatrics, Division of Medical Genetics, University of California, San Francisco, California, USA
- Institute of Human Genetics, University of California, San Francisco, California, USA
- Center for Maternal Fetal Precision Medicine, University of California, San Francisco, California, USA
| | - Teresa N. Sparks
- Department of Obstetrics, Gynecology, & Reproductive Sciences, University of California, San Francisco, California, USA
- Institute of Human Genetics, University of California, San Francisco, California, USA
- Center for Maternal Fetal Precision Medicine, University of California, San Francisco, California, USA
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2
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Forgacova N, Gazdarica J, Budis J, Kucharik M, Sekelska M, Szemes T. Non-intuitive trends of fetal fraction development related to gestational age and fetal gender, and their practical implications for non-invasive prenatal testing. Mol Cell Probes 2022; 66:101870. [PMID: 36283502 DOI: 10.1016/j.mcp.2022.101870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/04/2022] [Accepted: 10/19/2022] [Indexed: 11/12/2022]
Abstract
Discovery of fetal cell-free DNA fragments in maternal blood revolutionized prenatal diagnostics. Although non-invasive prenatal testing (NIPT) is already a matured screening test with high specificity and sensitivity, the accurate estimation of the proportion of fetal fragments, called fetal fraction, is crucial to avoid false-negative results. In this study, we collected 6999 samples from women undergoing NIPT testing with a single male fetus to demonstrate the influence of fetal fraction by the maternal and fetal characteristics. We show several fetal fraction discrepancies that contradict the generally presented conventional view. At first, the fetal fraction is not consistently rising with the maturity of the fetus due to a drop in 15 weeks of maturation. Secondly, the male samples have a lower fetal fraction than female fetuses, arguably due to the smaller gonosomal chromosomes. Finally, we discuss not only the possible reasons why this inconsistency exists but we also outline why these differences have not yet been identified and published. We demonstrate two non-intuitive trends to better comprehend the fetal fraction development and more precise selection of patients with sufficient fetal fraction for accurate testing.
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Affiliation(s)
- Natalia Forgacova
- Comenius University Science Park, Bratislava, 841 04, Slovakia; Faculty of Natural Sciences, Comenius University, Bratislava, 841 04, Slovakia.
| | - Juraj Gazdarica
- Faculty of Natural Sciences, Comenius University, Bratislava, 841 04, Slovakia; Geneton Ltd., Bratislava, 841 04, Slovakia; Slovak Centre of Scientific and Technical Information, Bratislava, 811 04, Slovakia
| | - Jaroslav Budis
- Comenius University Science Park, Bratislava, 841 04, Slovakia; Geneton Ltd., Bratislava, 841 04, Slovakia; Slovak Centre of Scientific and Technical Information, Bratislava, 811 04, Slovakia
| | - Marcel Kucharik
- Comenius University Science Park, Bratislava, 841 04, Slovakia; Geneton Ltd., Bratislava, 841 04, Slovakia
| | - Martina Sekelska
- TrisomyTest Ltd., Bratislava, 841 04, Slovakia; Medirex Group Academy, Bratislava, 821 04, Slovakia
| | - Tomas Szemes
- Comenius University Science Park, Bratislava, 841 04, Slovakia; Faculty of Natural Sciences, Comenius University, Bratislava, 841 04, Slovakia; Geneton Ltd., Bratislava, 841 04, Slovakia
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3
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Mascarenhas M, Jeve Y, Polanski L, Sharpe A, Yasmin E, Bhandari HM. Management of recurrent implantation failure: British Fertility Society policy and practice guideline. HUM FERTIL 2022; 25:813-837. [PMID: 33820476 DOI: 10.1080/14647273.2021.1905886] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Recurrent implantation failure (RIF) is defined as the absence of a positive pregnancy test after three consecutive transfers of good quality embryos. There remains significant variation in clinical practice in the management of RIF. This British Fertility Society (BFS) Policy and Practice guideline analyses the evidence for investigations and therapies that are employed in RIF and provides recommendations for clinical practice and for further research. Evidence for investigations of sperm and egg quality, uterine and adnexal factors, immunological factors and thrombophilia, endocrine conditions and genetic factors and for associated therapies have been evaluated. This guideline has been devised to assist reproductive medicine specialists and patients in making shared decisions concerning management of RIF. Finally, suggestions for research towards improving understanding and management of RIF have also been provided.
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Affiliation(s)
- Mariano Mascarenhas
- Leeds Fertility, Leeds Teaching Hospitals NHS Trust, Leeds, UK.,Glasgow Centre for Reproductive Medicine, The Fertility Partnership, Glasgow, UK
| | - Yadava Jeve
- Birmingham Women's Fertility Centre, Birmingham Women's Hospital, Birmingham, UK
| | - Lukasz Polanski
- Assisted Conception Unit, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Abigail Sharpe
- Leeds Fertility, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Ephia Yasmin
- Department of Women's Health, University College London Hospitals, London, UK
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4
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Demko Z, Prigmore B, Benn P. A Critical Evaluation of Validation and Clinical Experience Studies in Non-Invasive Prenatal Testing for Trisomies 21, 18, and 13 and Monosomy X. J Clin Med 2022; 11:jcm11164760. [PMID: 36012999 PMCID: PMC9410356 DOI: 10.3390/jcm11164760] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/28/2022] [Accepted: 08/11/2022] [Indexed: 11/25/2022] Open
Abstract
Non-invasive prenatal testing (NIPT) for trisomies 21, 18, 13 and monosomy X is widely utilized with massively parallel shotgun sequencing (MPSS), digital analysis of selected regions (DANSR), and single nucleotide polymorphism (SNP) analyses being the most widely reported methods. We searched the literature to find all NIPT clinical validation and clinical experience studies between January 2011 and January 2022. Meta-analyses were performed using bivariate random-effects and univariate regression models for estimating summary performance measures across studies. Bivariate meta-regression was performed to explore the influence of testing method and study design. Subgroup and sensitivity analyses evaluated factors that may have led to heterogeneity. Based on 55 validation studies, the detection rate (DR) was significantly higher for retrospective studies, while the false positive rate (FPR) was significantly lower for prospective studies. Comparing the performance of NIPT methods for trisomies 21, 18, and 13 combined, the SNP method had a higher DR and lower FPR than other methods, significantly so for MPSS, though not for DANSR. The performance of the different methods in the 84 clinical experience studies was consistent with validation studies. Clinical positive predictive values of all NIPT methods improved over the last decade. We conclude that all NIPT methods are highly effective for fetal aneuploidy screening, with performance differences across methodologies.
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Affiliation(s)
| | | | - Peter Benn
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06030, USA
- Correspondence:
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5
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Sadeghi S, Rahaie M, Ostad-Hasanzadeh B. Nanostructures in non-invasive prenatal genetic screening. Biomed Eng Lett 2022; 12:3-18. [PMID: 35186357 PMCID: PMC8825889 DOI: 10.1007/s13534-021-00208-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/22/2021] [Accepted: 10/02/2021] [Indexed: 11/24/2022] Open
Abstract
Prenatal screening is an important issue during pregnancy to ensure fetal and maternal health, as well as preventing the birth of a defective fetus and further problems such as extra costs for the family and society. The methods for the screening have progressed to non-invasive approaches over the recent years. Limitations of common standard screening tests, including invasive sampling, high risk of abortion and a big delay in result preparation have led to the introduction of new rapid and non-invasive approaches for screening. Non-invasive prenatal screening includes a wide range of procedures, including fetal cell-free DNA analysis, proteome, RNAs and other fetal biomarkers in maternal serum. These biomarkers require less invasive sampling than usual methods such as chorionic villus sampling, amniocentesis or cordocentesis. Advanced strategies including the development of nanobiosensors and the use of special nanoparticles have provided optimization and development of NIPS tests, which leads to more accurate, specific and sensitive screening tests, rapid and more reliable results and low cost, as well. This review discusses the specifications and limitations of current non-invasive prenatal screening tests and introduces a novel collection of detection methods reported studies on nanoparticles' aided detection. It can open a new prospect for further studies and effective investigations in prenatal screening field.
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Affiliation(s)
- Samira Sadeghi
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, 14399-57131 Tehran, Iran
| | - Mahdi Rahaie
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, 14399-57131 Tehran, Iran
| | - Bita Ostad-Hasanzadeh
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, 14399-57131 Tehran, Iran
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6
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Wang JW, Lyu YN, Qiao B, Li Y, Zhang Y, Dhanyamraju PK, Bamme Y, Yu MD, Yang D, Tong YQ. Cell-free fetal DNA testing and its correlation with prenatal indications. BMC Pregnancy Childbirth 2021; 21:585. [PMID: 34429082 PMCID: PMC8385810 DOI: 10.1186/s12884-021-04044-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 08/03/2021] [Indexed: 01/16/2023] Open
Abstract
Background The prenatal test of cell-free fetal DNA (cffDNA) is also known as noninvasive prenatal testing (NIPT) with high sensitivity and specificity. This study is to evaluate the performance of NIPT and its clinical relevance with various clinical indications. Methods A retrospective analysis was conducted on 14,316 pregnant women with prenatal indications, including advanced maternal age (≥35 years), maternal serum screening abnormalities, the thickened nuchal translucency (≥2.5 mm) and other ultrasound abnormalities, twin pregnancy/IVF-ET pregnancy, etc. The whole-genome sequencing (WGS) of maternal plasma cffDNA was employed in this study. Results A total of 189 (1.32%) positive NIPT cases were identified, and 113/189 (59.79%)cases were confirmed by invasive prenatal testing. Abnormal serological screening (53.14%) was the most common indication, followed by elderly pregnancy (23.02%). The positive prediction value for T21, T18, T13, sex chromosome abnormalities, other autosomal aneuploidy abnormalities, and CNV abnormalities were 91.84, 68.75,37.50, 66.67, 14.29, and 6.45%, respectively. The positive rate and the true positive rate of nuchal translucency (NT) thickening were the highest (4.17 and 3.33%), followed by the voluntary requirement group (3.49 and 1.90%) in the various prenatal screening indications. The cffDNA concentration was linearly correlated with gestational age (≥10 weeks) and the positive NIPT group’s Z-score values. Conclusions whole-genome sequencing of cffDNA has extremely high sensitivity and specificity for T21, high sensitivity for T18, sex chromosome abnormalities, and T13. It also provides evidence for other abnormal chromosomal karyotypes (CNV and non-21/18/13 autosomal aneuploidy abnormalities). The cffDNA concentration is closely related to the gestational age and determines the specificity of NIPT. Our results highlight NIPT’s clinical significance, which is an effective prenatal screening tool for high-quality care of pregnancy. The whole-genome sequencing of cell-free fetal DNA from maternal plasma is an effective prenatal screening tool for pregnancies with various prenatal indications. The concentration of cffDNA was linear with gestational age and the Z-score values of the positive NIPT group. NIPT has a significant positive predictive value for pregnancies with prenatal indications.
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Affiliation(s)
- Jing-Wei Wang
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, 99 Ziyang Road of Wuchang District, Wuhan, 430060, China
| | - Yong-Nan Lyu
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, 99 Ziyang Road of Wuchang District, Wuhan, 430060, China
| | - Bin Qiao
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, 99 Ziyang Road of Wuchang District, Wuhan, 430060, China
| | - Yan Li
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, 99 Ziyang Road of Wuchang District, Wuhan, 430060, China
| | - Yan Zhang
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, 99 Ziyang Road of Wuchang District, Wuhan, 430060, China
| | - Pavan Kumar Dhanyamraju
- Pennsylvania State University College of Medicine and Hershey Medical center, Hershey, PA, 17033, USA
| | - Yevgeniya Bamme
- Pennsylvania State University College of Medicine and Hershey Medical center, Hershey, PA, 17033, USA
| | - Michael D Yu
- Jefferson University Hospital, 1025 Walnut St, Philadelphia, PA19107, USA
| | - Dongqin Yang
- Department of Digestive Diseases, Huashan Hospital, Fudan University, 12 Middle Wulumuqi Road, Shanghai, 200040, China.
| | - Yong-Qing Tong
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, 99 Ziyang Road of Wuchang District, Wuhan, 430060, China.
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7
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Gou L, Fang Y, Wang N, Zhang M, Liu T, Wang Y, Hu S, Zhang Y, Wu Q, Wang Y, Suo F, Gu M. Clinical management of pregnancies with positive screening results for rare autosomal aneuploidies at a single center. J Int Med Res 2021; 48:300060520966877. [PMID: 33167762 PMCID: PMC7658522 DOI: 10.1177/0300060520966877] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Objective To review our experiences on clinical management of pregnancies with positive noninvasive prenatal testing (NIPT) results for rare autosomal aneuploidies (RAAs) at a single center. Methods We performed a retrospective study and reviewed data from 18,016 pregnancies undergoing NIPT at a single center in China from March 2017 to February 2020. Depending on the patient’s choice, women with positive screening results for RAAs underwent chromosomal microarray analysis for invasive prenatal diagnosis. Results Thirty-three positive cases for RAAs were identified, with a positive screening rate of 0.18%. The most common RAA was trisomy 7 (33.3%), while trisomies for other chromosomes were less frequent. Monosomies involving chromosomes 16, 14, and 22 were observed. Twenty-eight cases of RAAs underwent invasive diagnosis. Abnormal pregnancy outcomes were observed in four cases, including true fetal mosaicism (n=1), partial uniparental disomy (n=1), miscarriage (n=1), and structural anomalies on ultrasound (n=1). Conclusions RAAs at NIPT might be associated with fetal uniparental disomy, mosaic aneuploidy, and poor pregnancy outcomes, but most positive cases have normal pregnancy outcomes. For RAAs, genetic counseling on the potential risks of abnormal NIPT results, as well as on benefits and limitations of invasive prenatal diagnosis, might help guide clinical management.
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Affiliation(s)
- Lingshan Gou
- Center for Genetic Medicine, Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yuan Fang
- Center for Genetic Medicine, Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Na Wang
- DAAN Gene Co., Ltd. of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Man Zhang
- Zhejiang Biosan Biochemical Technologies Co., Ltd., Hangzhou, Zhejiang, China
| | - Tianya Liu
- Department of Pharmacy, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yi Wang
- Center for Genetic Medicine, Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Shunan Hu
- Office of Scientific Research & Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan Province, China
| | - Yan Zhang
- Center for Genetic Medicine, Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Qin Wu
- Zhejiang Biosan Biochemical Technologies Co., Ltd., Hangzhou, Zhejiang, China
| | - Yifan Wang
- Department of Ultrasound, Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Feng Suo
- Center for Genetic Medicine, Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Maosheng Gu
- Center for Genetic Medicine, Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, Jiangsu, China
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8
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Gou L, Suo F, Wang Y, Wang N, Wu Q, Hu S, Wang P, Gu L, Zhang M, Wang C, Zhang Y, Yin X, Zhang P, Xu J, Wang X, Gu M. Clinical value for the detection of fetal chromosomal deletions/duplications by noninvasive prenatal testing in clinical practice. Mol Genet Genomic Med 2021; 9:e1687. [PMID: 33951332 PMCID: PMC8222853 DOI: 10.1002/mgg3.1687] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 03/04/2021] [Accepted: 03/23/2021] [Indexed: 01/13/2023] Open
Abstract
Objective This study was to report the experiences on the clinical value of noninvasive prenatal testing (NIPT) for the screening of fetal chromosomal deletions/duplications. Methods We performed a retrospective analysis of a cohort of 20,439 pregnancies undergoing NIPT from March 2017 to September 2020 at a single center. Patients with positive NIPT results for fetal chromosomal deletions or duplications had options of invasive diagnostic testing or no further testing. The data were complied from all cases with positive NIPT results for chromosomal deletions/duplications. The positive predictive value (PPV) was calculated from tabulated data. Results In this cohort, positive NIPT results for fetal chromosomal deletions/duplications were found in 60 pregnant women. Of the positive samples, further invasive testing was performed in 39 cases, in which 9 cases were found to be true positive. The overall PPV for chromosomal deletions/duplications was 23.1%. In addition, fetal structural anomaly was found by ultrasound examination in three cases, in which the chromosomal deletions/duplications of three cases were not verified. Moreover, an unexpected pathogenic 8p23.3 deletion was identified by invasive testing in 1 fetus with a false positive NIPT screen for 3q27.3q29 duplication. Conclusions In summary, positive NIPT results of chromosomal deletions/duplications were not uncommon in clinical practice, whereas the PPV for the testing was low. Hence, potential risks and high percentage of false positives for these abnormal NIPT results might be informed to pregnant women before the choice made of invasive testing.
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Affiliation(s)
- Lingshan Gou
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Feng Suo
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Yi Wang
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Na Wang
- Department of Technology, Suzhou Beikang Medical Device Co. Ltd., Suzhou, China
| | - Qin Wu
- Zhejiang Biosan Biochemical Technologies Co. Ltd., Hangzhou, China
| | - Shunan Hu
- Office of Scientific Research & Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Peng Wang
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Lize Gu
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Man Zhang
- Zhejiang Biosan Biochemical Technologies Co. Ltd., Hangzhou, China
| | - Chuanxia Wang
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Yan Zhang
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Xin Yin
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Peng Zhang
- Shenzhen Longgang Institute of Stomatology, Shenzhen Longgang E.N.T. Hospital, Shenzhen, China
| | - Jian Xu
- Shenzhen Longgang Institute of Stomatology, Shenzhen Longgang E.N.T. Hospital, Shenzhen, China
| | - Xingqi Wang
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, China
| | - Maosheng Gu
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
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Deng C, Cheung SW, Liu H. Noninvasive prenatal screening for fetal sex chromosome aneuploidies. Expert Rev Mol Diagn 2021; 21:405-415. [PMID: 33787433 DOI: 10.1080/14737159.2021.1911651] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
INTRODUCTION Sex chromosome aneuploidies (SCAs) are among the most common chromosome abnormalities observed in humans. Manifestations include low fertility, infertility, delayed language development, and dysfunction in motor development. Noninvasive prenatal screening (NIPS) based on cell-free fetal DNA from the peripheral blood of pregnant women is increasingly used for the screening of fetal chromosome abnormalities, including screening for fetal gender and fetal sex chromosome aneuploidy. A systematic review of the literature about NIPS for SCAs is needed. AREAS COVERED This review evaluated a vast array of published studies focusing on the clinical significance, detection methods, performance of NIPS for SCAs, and the management of positive SCA results following screening with the aim of facilitating a comprehensive and systematic understanding of NIPS for SCAs. EXPERT COMMENTARY Looking forward, NIPS is expected to become the primary screening test for common aneuploidies as well as other chromosome abnormalities, including some micro-deletions and micro-duplications, with the potential to transition from a screening test to a prenatal diagnosis method. Ultimately, the goal is to provide a safe and accurate method for increasing early diagnosis to improve long-term outcomes for the SCA patients and families by well- informed health care providers.
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Affiliation(s)
- Cechuan Deng
- Medical Genetics Department/Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Hongqian Liu
- Medical Genetics Department/Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
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10
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Soukkhaphone B, Lindsay C, Langlois S, Little J, Rousseau F, Reinharz D. Non-invasive prenatal testing for the prenatal screening of sex chromosome aneuploidies: A systematic review and meta-analysis of diagnostic test accuracy studies. Mol Genet Genomic Med 2021; 9:e1654. [PMID: 33755350 PMCID: PMC8172189 DOI: 10.1002/mgg3.1654] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 10/31/2020] [Accepted: 02/19/2021] [Indexed: 12/19/2022] Open
Abstract
Background There is little evidence on the performance of non‐invasive prenatal testing (NIPT) for the detection of fetal sex chromosomal imbalances. In this review, we aimed to appraise and synthesize the literature on the performance of NIPT for the prenatal detection of fetal sex chromosome aneuploidies. Methods We performed our literature search in PubMed, Embase, Cochrane Library, Web of Science, and CADTH. Study selection and data extraction were performed by two reviewers independently. There were no restrictions on the study population. Meta‐analyses were performed with “R” software. Pooled sensitivities and specificities with their 95% CI were estimated using a random‐effects model. Heterogeneity between studies was assessed by a Q test. Results Based on 11 studies in high prior risk pregnancies, including 116 affected fetuses in aggregate, Massively Parallel Shotgun Sequencing (MPSS) had a sensitivity of 93.9% (95% CI 84.1%, 97.8%) and a specificity of 99.6% (95% CI 98.7%, 99.9%) for the detection of 45,X. Based on four studies in high‐risk pregnancies, with 83 affected fetuses in aggregate, Targeted Massively Parallel Sequencing (TMPS) had a sensitivity of 83.2% (95% CI 49.6%, 96.2%) and specificity was 99.8% (95% CI 98.3%, 100%) for the detection of 45,X. In mixed‐risk pregnancies, the sensitivity of TMPS for the detection of 45,X was 90.9% (2 studies; 95% CI 70%, 97.7%) and specificity 99.9% (2 studies; 95% CI 99.4%, 100%); MPSS data were not available in such pregnancies. Based on smaller numbers of studies, and small numbers of affected fetuses in either high‐risk or mixed‐risk pregnancies (using either MPSS or TMPS), the sensitivities and specificities were equal to or greater than 76.2% for 47,XXX, 47,XXY and 47, XYY. The test failures for SCAs were 0.2% (95% CI 0%, 13.6%) for MPSS and 5.6% (95% CI 3.7%, 8.4%) for TMPS. Conclusion High‐quality studies are still desirable in order to estimate the performance of NIPT for the detection of sex chromosome imbalances.
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Affiliation(s)
| | - Carmen Lindsay
- CHU de Québec-Université Laval Research Center, Quebec City, QC, Canada
| | | | | | - Francois Rousseau
- Laval University, Quebec City, QC, Canada.,Hôpital Saint-François d'Assise, Quebec, QC, Canada
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11
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Vuorenlehto L, Hinnelä K, Äyräs O, Ulander VM, Louhiala P, Kaijomaa M. Women's experiences of counselling in cases of a screen-positive prenatal screening result. PLoS One 2021; 16:e0247164. [PMID: 33690660 PMCID: PMC7946296 DOI: 10.1371/journal.pone.0247164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/02/2021] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE To study women's apprehensions, understanding and experiences of counselling concerning a screen-positive result in screening for fetal chromosomal defects. METHODS A questionnaire study including different steps of the prenatal screening process was carried out in Helsinki University Hospital. Women's experiences concerning counselling immediately after a screen-positive result and during further examinations in the Fetal Medicine Unit (FMU) were analyzed. RESULTS 143 women filled in the questionnaire. Less than half of the women considered the primary counselling after a screen-positive result to be explicit (43.9%) and sufficient (43.1%). In the FMU, 88.3% and 89.8% of women were satisfied with the explicitness and sufficiency of counselling. Most women (75%) experienced worry before further examinations but less than half (45%) had considered their personal values concerning diagnostic tests. Half (50.5%) of women expected the worry to continue even if diagnostic tests turn out normal. Most (81%) women were aware that diagnostic tests are voluntary and were confident (85.3%) with their decision to participate. CONCLUSIONS After a screen-positive result, women have unanswered questions, experience anxiety and confusion. The possibility of an abnormal screening result is not seriously considered beforehand. To enable an informed consent for prenatal screening, improvements in prescreening counselling during the first visits of antenatal care need to be made.
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Affiliation(s)
- Leena Vuorenlehto
- Department of Obstetrics and Gynecology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
- * E-mail:
| | - Kaisa Hinnelä
- Department of Obstetrics and Gynecology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Outi Äyräs
- Department of Obstetrics and Gynecology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Veli-Matti Ulander
- Department of Obstetrics and Gynecology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Pekka Louhiala
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Marja Kaijomaa
- Department of Obstetrics and Gynecology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
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12
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A retrospective analysis the clinic data and follow-up of non-invasive prenatal test in detection of fetal chromosomal aneuploidy in more than 40,000 cases in a single prenatal diagnosis center. Eur J Med Genet 2020; 63:104001. [PMID: 32622960 DOI: 10.1016/j.ejmg.2020.104001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/22/2020] [Accepted: 06/28/2020] [Indexed: 01/07/2023]
Abstract
OBJECTIVE To evaluate the efficacy of non-invasive prenatal test (NIPT) in the detection of chromosomal aneuploidy according to the follow-up information from a single prenatal diagnosis center. METHODS A total of 40,311 cases were retrospectively reviewed. The screening was performed using a BGI protocol, pre-test and post-test genetic counseling was provided, and the pregnancy outcomes were recorded. The results of NIPT and clinical follow-up data were analyzed together with the pregnancy outcomes, confirmatory testing results, and ultrasound findings. RESULTS Of the 40,311cases were includes in the study, successful follow-up was conducted in 468 (1.16%) cases with high risk, 225 (0.56%) cases with rare autosomal trisomy (RAT) and copy number variation (CNV). 39,572 (98.17%) cases with low risk and 623 (1.57%) cases of which were confirmed with adverse pregnancy outcomes. 46 (0.1%) cases with failed tests. Among them, 398 (84.7%) cases with high-risk results chose invasive testing, revealing 198 true positive cases. In cases with RAT and CNV results, 189 cases underwent invasive testing, revealing 5 cases RAT and 4 pathogenic CNVs. CONCLUSIONS NIPT appears to be effective in detecting the fetal chromosomal aneuploidies T21, T18 and SCAs, but it exist false positive/negative cases, unconfirmed high-risk cfDNA results, and the high false positive rate in cases with RAT and CNV results implied the limitations of this screening method. Our study showed the importance to associate cfDNA screening results with clinical follow-up data and provided information that may help with result interpretation, genetic counseling and the decision making in clinic.
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Lv W, Linpeng S, Li Z, Liang D, Jia Z, Meng D, Cram DS, Zhu H, Teng Y, Yin A, Wu L. Noninvasive prenatal diagnosis for pregnancies at risk for β-thalassaemia: a retrospective study. BJOG 2020; 128:448-457. [PMID: 32363759 DOI: 10.1111/1471-0528.16295] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/16/2020] [Indexed: 01/08/2023]
Abstract
OBJECTIVE To evaluate the clinical feasibility of noninvasive prenatal diagnosis (NIPD) for β-thalassaemia using circulating single molecule amplification and re-sequencing technology (cSMART). DESIGN Through carrier screening, 102 pregnant Chinese couples carrying pathogenic HBB gene variants were recruited to the study. Pregnancies were managed using traditional invasive prenatal diagnosis (IPD). Retrospectively, we evaluated the archived pregnancy plasma DNA by NIPD to evaluate the performance of our cSMART assay for fetal genotyping. SETTING Chinese prenatal diagnostic centres specialising in thalassaemia testing. POPULATION Chinese carrier couples at high genetic risk for β-thalassaemia. METHODS Fetal cell sampling was performed by amniocentesis and HBB genotypes were determined by reverse dot blot. NIPD was performed by a newly designed HBB cSMART assay and fetal genotypes were called by measuring the allelic ratios in the maternal cell-free DNA. MAIN OUTCOME MEASURES Concordance of HBB fetal genotyping between IPD and NIPD and the sensitivity and specificity of NIPD. RESULTS Invasive prenatal diagnosis identified 29 affected homozygotes or compound heterozygotes, 54 heterozygotes and 19 normal homozygotes. Compared with IPD results, 99 of 102 fetuses (97%) were correctly genotyped by our NIPD assay. Two of three discordant samples were false positives and the other sample involved an incorrect call of a heterozygote carrier as a homozygote normal. Overall, the sensitivity and specificity of our NIPD assay was 100% (95% CI 88.06-100.00%) and 97.26% (95% CI 90.45-99.67%), respectively. CONCLUSIONS This study demonstrates that our cSMART-based NIPD assay for β-thalassaemia has potential clinical utility as an alternative to IPD for pregnant HBB carrier couples. TWEETABLE ABSTRACT A new noninvasive test for pregnancies at risk for β-thalassaemia.
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Affiliation(s)
- W Lv
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.,Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
| | - S Linpeng
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Z Li
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - D Liang
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.,Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
| | - Z Jia
- Prenatal Diagnosis Centre of Hunan Province, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan, China
| | - D Meng
- Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi Zhuang Autonomous Region, China
| | - D S Cram
- Berry Genomics Corporation, Beijing, China
| | - H Zhu
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Y Teng
- Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
| | - A Yin
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - L Wu
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
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14
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Xue Y, Zhao G, Li H, Zhang Q, Lu J, Yu B, Wang T. Non-invasive prenatal testing to detect chromosome aneuploidies in 57,204 pregnancies. Mol Cytogenet 2019; 12:29. [PMID: 31249627 PMCID: PMC6584990 DOI: 10.1186/s13039-019-0441-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 06/06/2019] [Indexed: 01/06/2023] Open
Abstract
Background Non-invasive prenatal testing (NIPT) has been widely used to detect common fetal chromosome aneuploidies, such as trisomy 13, 18, and 21 (T13, T18, and T21), and has expanded to sex chromosome aneuploidies (SCAs) during recent years, but few studies have reported NIPT detection of rare fetal chromosome aneuploidies (RCAs). In this study, we evaluated the clinical practical performance of NIPT to analyze all 24 chromosome aneuploidies among 57,204 pregnancies in the Suzhou area of China. Methods This was a retrospective analysis of prospectively collected NIPT data from two next-generation sequencing (NGS) platforms (Illumina and Proton) obtained from The Affiliated Suzhou Hospital of Nanjing Medical University. NIPT results were validated by karyotyping or clinical follow-up. Results NIPT using the Illumina platform identified 586 positive cases; fetal karyotyping and follow-up results validated 178 T21 cases, 49 T18 cases, 4 T13 cases, and 52 SCAs. On the Proton platform, 270 cases were positive during NIPT. Follow-up confirmed 85 T21 cases, 17 T18 cases, 4 T13 cases, 28 SCAs, and 1 fetal chromosome 22 aneuploidy case as true positives. There were 5 false-negative results, including 4 T21 and 1 T18 cases. The NGS platforms showed similar sensitivities and positive predictive values (PPVs) in detecting T21, T18, T13 and SCAs (p > 0.01). However, the Proton platform showed better specificity in detecting 45, X and the Illumina platform had better specificity in detecting T13 (p < 0.01). The major factor contributing to NIPT false-positives on the Illumina platform was false SCAs cases (65.11%). Maternal chromosome aneuploidies, maternal cancers, and confined placental mosaicism caused discordant results between fetal karyotyping and NIPT. Conclusion NIPT with NGS showed good performance for detecting T13, T18, and T21. The Proton platform had better performance for detecting SCAs, but the NIPT accuracy rate for detecting RCAs was insufficient.
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Affiliation(s)
- Ying Xue
- 1The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, 215000 Jiangsu Province China.,2Suzhou Municipal Hospital, Suzhou, 215000 Jiangsu China
| | - Guodong Zhao
- 3Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan, 215300 Jiangsu China
| | - Hong Li
- 1The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, 215000 Jiangsu Province China.,2Suzhou Municipal Hospital, Suzhou, 215000 Jiangsu China
| | - Qin Zhang
- 1The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, 215000 Jiangsu Province China.,2Suzhou Municipal Hospital, Suzhou, 215000 Jiangsu China
| | - Jiafeng Lu
- 1The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, 215000 Jiangsu Province China.,2Suzhou Municipal Hospital, Suzhou, 215000 Jiangsu China
| | - Bin Yu
- 4Changzhou Maternity and Child Health Care Hospital affiliated to Nanjing Medical University, Changzhou, Jiangsu Province, 213003 China
| | - Ting Wang
- 1The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, 215000 Jiangsu Province China.,2Suzhou Municipal Hospital, Suzhou, 215000 Jiangsu China
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15
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Hu P, Liang D, Chen Y, Lin Y, Qiao F, Li H, Wang T, Peng C, Luo D, Liu H, Xu Z. An enrichment method to increase cell-free fetal DNA fraction and significantly reduce false negatives and test failures for non-invasive prenatal screening: a feasibility study. J Transl Med 2019; 17:124. [PMID: 30975179 PMCID: PMC6460836 DOI: 10.1186/s12967-019-1871-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 04/03/2019] [Indexed: 12/18/2022] Open
Abstract
Background Noninvasive prenatal screening (NIPS) based on cell-free fetal DNA (cffDNA) has rapidly been applied into clinic. However, the reliability of this method largely depends on the concentration of cffDNA in the maternal plasma. The chance of test failure results or false negative results would increase when cffDNA fraction is low. In this study, we set out to develop a method to enrich the cffDNA for NIPS based on the size difference between cell-free DNA (cfDNA) of fetal origin and maternal origin, and to evaluate whether the new NIPS method can improve the test quality. Methods We utilized 10,000 previous NIPS data to optimize a size-selection strategy for enrichment. Then, we retrospectively performed our new NIPS method with cffDNA enrichment on the 1415 NIPS samples, including 1404 routine cases and 11 false negative cases, and compared the results to the original NIPS results. Results The 10,000 NIPS data revealed the fetal fraction in short cfDNA fragments (< 160 bp) is significantly higher. By using our new NIPS strategy on the 1404 routine cases, the fetal fraction increased from 11.3 ± 4.2 to 22.6 ± 6.6%, and the new method performed a significant decrease of test-failure rate (0.1% vs 0.7%, P < 0.01). Moreover, in 45.5% (5/11) of the false negative cases, fetal trisomies were successfully detected by our new NIPS method. Conclusions We developed an effective method to enrich cffDNA for NIPS, which shows an increased success rate and a reduced chance of false negative comparing to the ordinary NIPS method. Electronic supplementary material The online version of this article (10.1186/s12967-019-1871-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ping Hu
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Dong Liang
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Yangyi Chen
- CapitalBio Technology Inc., Beijing, 101111, China.,CapitalBio Genomics Co., Ltd., Dongguan, 523808, China.,CapitalBio MedLab, Beijing, 102206, China
| | - Ying Lin
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Fengchang Qiao
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Hang Li
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Ting Wang
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, 215000, Jiangsu, China
| | - Chunfang Peng
- CapitalBio Technology Inc., Beijing, 101111, China.,CapitalBio Genomics Co., Ltd., Dongguan, 523808, China.,CapitalBio MedLab, Beijing, 102206, China
| | - Donghong Luo
- CapitalBio Technology Inc., Beijing, 101111, China.,CapitalBio Genomics Co., Ltd., Dongguan, 523808, China.,CapitalBio MedLab, Beijing, 102206, China
| | - Hailiang Liu
- CapitalBio Technology Inc., Beijing, 101111, China. .,CapitalBio Genomics Co., Ltd., Dongguan, 523808, China. .,CapitalBio MedLab, Beijing, 102206, China.
| | - Zhengfeng Xu
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China.
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16
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Hu H, Wang L, Wu J, Zhou P, Fu J, Sun J, Cai W, Liu H, Yang Y. Noninvasive prenatal testing for chromosome aneuploidies and subchromosomal microdeletions/microduplications in a cohort of 8141 single pregnancies. Hum Genomics 2019; 13:14. [PMID: 30871627 PMCID: PMC6419401 DOI: 10.1186/s40246-019-0198-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 02/26/2019] [Indexed: 12/28/2022] Open
Abstract
Background Noninvasive prenatal testing (NIPT) for fetal aneuploidies by scanning cell-free fetal DNA in maternal plasma is rapidly becoming a first-tier aneuploidy screening test in clinical practices. With the development of whole-genome sequencing technology, small subchromosomal deletions and duplications that could not be detected by conventional karyotyping are now able to be detected with NIPT technology. Methods In the present study, we examined 8141 single pregnancies with NIPT to calculate the positive predictive values of each of the chromosome aneuploidies and the subchromosomal microdeletions and microduplications. Results We confirmed that the positive predictive values (PPV) for trisomy 13, trisomy 18, trisomy 21, and sex chromosome aneuploidy were 14.28%, 60%, 80%, and 45.83%, respectively. At the same time, we also found 51 (0.63%) positive cases for chromosomal microdeletions or microduplications but only 13 (36.11%) true-positive cases. These results indicate that NIPT for trisomy 21 detection had the highest accuracy, while accuracy was low for chromosomal microdeletion and microduplications. Conclusions Therefore, it is very important to improve the specificity, accuracy, and sensitivity of NIPT technology for the detection of subchromosomal microdeletions and microduplications.
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Affiliation(s)
- Hua Hu
- Second Affiliated Hospital, Army Military Medical University, Chongqing, 400037, China
| | - Li Wang
- Second Affiliated Hospital, Army Military Medical University, Chongqing, 400037, China
| | - Jiayan Wu
- Second Affiliated Hospital, Army Military Medical University, Chongqing, 400037, China
| | - Peng Zhou
- Second Affiliated Hospital, Army Military Medical University, Chongqing, 400037, China
| | - Jingli Fu
- Second Affiliated Hospital, Army Military Medical University, Chongqing, 400037, China
| | - Jiuchen Sun
- Second Affiliated Hospital, Army Military Medical University, Chongqing, 400037, China
| | - Weiyi Cai
- CapitalBio Technology Inc., Beijing, 101111, China
| | - Hailiang Liu
- CapitalBio Technology Inc., Beijing, 101111, China.
| | - Ying Yang
- Second Affiliated Hospital, Army Military Medical University, Chongqing, 400037, China.
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17
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Palomaki GE, Kloza EM. Prenatal cell-free DNA screening test failures: a systematic review of failure rates, risks of Down syndrome, and impact of repeat testing. Genet Med 2018; 20:1312-1323. [PMID: 30514979 DOI: 10.1038/gim.2018.22] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/19/2018] [Indexed: 01/12/2023] Open
Abstract
PURPOSE We systematically reviewed the published literature on test failure rates for the sequencing of cell-free DNA (cfDNA) in maternal plasma to identify Down syndrome. METHODS We searched peer-reviewed English publications with diagnostic results on all pregnancies that provided test failure rates. Data on the odds of failure in Down syndrome and euploid pregnancies and the impact of repeat testing were extracted. Random-effects modeling was then used to identify moderators that could explain variability. RESULTS Thirty articles satisfied the inclusion criteria for overall failure rates. Study location (Western and Asian with initial testing, and Western with repeat testing) were significant moderators with failure rates of 3.3, 0.6, and 1.2%, respectively (P = 0.001). The odds ratio for Down syndrome in successful versus failed tests was 0.98 (95% confidence interval: 0.62-1.55, I2 = 0%). Repeat testing from 14 large clinical cohort studies found that 83% (range: 52-100%) of failures were repeated, with 79% (range: 46-97%) being successful. CONCLUSION Lower failure rates in Asian studies may be related to not routinely measuring the fetal fraction and to fewer obese women. Repeat cfDNA testing is effective in providing reliable results after initial failures. Protocols for primary cfDNA screening should focus on Down syndrome, with less common and more structurally abnormal trisomy 18 and 13 pregnancies treated as adjuncts.
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Affiliation(s)
- Glenn E Palomaki
- Department of Pathology and Laboratory Medicine, Women and Infants Hospital, Providence, Rhode Island, USA. .,Department of Pathology and Laboratory Medicine, Alpert Medical School at Brown University, Providence, Rhode Island, USA.
| | - Edward M Kloza
- Department of Pathology and Laboratory Medicine, Women and Infants Hospital, Providence, Rhode Island, USA
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18
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Hill M, Barrett A, Choolani M, Lewis C, Fisher J, Chitty LS. Has noninvasive prenatal testing impacted termination of pregnancy and live birth rates of infants with Down syndrome? Prenat Diagn 2017; 37:1281-1290. [PMID: 29111614 PMCID: PMC5767768 DOI: 10.1002/pd.5182] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Revised: 10/25/2017] [Accepted: 10/29/2017] [Indexed: 12/14/2022]
Abstract
BACKGROUND Implementation of noninvasive prenatal testing (NIPT) as a highly accurate aneuploidy screening test has raised questions around whether the high uptake may result in more terminations of pregnancies and fewer births of children with Down syndrome (DS). AIM The aim of the study was to investigate the impact of NIPT on termination and live birth rates for DS. METHODS Literature reporting pregnancy outcomes following NIPT was reviewed. Termination rates were calculated for women with a high-risk NIPT result for DS. Two audits of pregnancy outcomes where NIPT indicated DS were conducted in the United Kingdom and Singapore. RESULTS Fourteen studies from the United States, Asia, Europe, and the United Kingdom were included in the review. Live births of children with DS were reported in 8 studies. Termination rates following NIPT were unchanged or decreased when compared to termination rates prior to the introduction of NIPT. Audits found 15 of 43 women in the United Kingdom and 2 of 6 in Singapore continued pregnancies following a high-risk NIPT result. CONCLUSIONS Termination rates following the detection of DS by NIPT are unchanged or decreased compared to historical termination rates. Impact on live birth rates may be minimal in settings where termination rates fall. Population-based studies are required to determine the true impact.
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Affiliation(s)
- Melissa Hill
- Genetics and Genomic MedicineUCL Great Ormond Street Institute of Child HealthLondonUK
- North East Thames Regional Genetics ServiceGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK
| | - Angela Barrett
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of MedicineNational University of SingaporeSingapore
| | - Mahesh Choolani
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of MedicineNational University of SingaporeSingapore
| | - Celine Lewis
- Genetics and Genomic MedicineUCL Great Ormond Street Institute of Child HealthLondonUK
- North East Thames Regional Genetics ServiceGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK
| | | | - Lyn S. Chitty
- Genetics and Genomic MedicineUCL Great Ormond Street Institute of Child HealthLondonUK
- North East Thames Regional Genetics ServiceGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK
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Badeau M, Lindsay C, Blais J, Nshimyumukiza L, Takwoingi Y, Langlois S, Légaré F, Giguère Y, Turgeon AF, Witteman W, Rousseau F. Genomics-based non-invasive prenatal testing for detection of fetal chromosomal aneuploidy in pregnant women. Cochrane Database Syst Rev 2017; 11:CD011767. [PMID: 29125628 PMCID: PMC6486016 DOI: 10.1002/14651858.cd011767.pub2] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Common fetal aneuploidies include Down syndrome (trisomy 21 or T21), Edward syndrome (trisomy 18 or T18), Patau syndrome (trisomy 13 or T13), Turner syndrome (45,X), Klinefelter syndrome (47,XXY), Triple X syndrome (47,XXX) and 47,XYY syndrome (47,XYY). Prenatal screening for fetal aneuploidies is standard care in many countries, but current biochemical and ultrasound tests have high false negative and false positive rates. The discovery of fetal circulating cell-free DNA (ccfDNA) in maternal blood offers the potential for genomics-based non-invasive prenatal testing (gNIPT) as a more accurate screening method. Two approaches used for gNIPT are massively parallel shotgun sequencing (MPSS) and targeted massively parallel sequencing (TMPS). OBJECTIVES To evaluate and compare the diagnostic accuracy of MPSS and TMPS for gNIPT as a first-tier test in unselected populations of pregnant women undergoing aneuploidy screening or as a second-tier test in pregnant women considered to be high risk after first-tier screening for common fetal aneuploidies. The gNIPT results were confirmed by a reference standard such as fetal karyotype or neonatal clinical examination. SEARCH METHODS We searched 13 databases (including MEDLINE, Embase and Web of Science) from 1 January 2007 to 12 July 2016 without any language, search filter or publication type restrictions. We also screened reference lists of relevant full-text articles, websites of private prenatal diagnosis companies and conference abstracts. SELECTION CRITERIA Studies could include pregnant women of any age, ethnicity and gestational age with singleton or multifetal pregnancy. The women must have had a screening test for fetal aneuploidy by MPSS or TMPS and a reference standard such as fetal karyotype or medical records from birth. DATA COLLECTION AND ANALYSIS Two review authors independently carried out study selection, data extraction and quality assessment (using the QUADAS-2 tool). Where possible, hierarchical models or simpler alternatives were used for meta-analysis. MAIN RESULTS Sixty-five studies of 86,139 pregnant women (3141 aneuploids and 82,998 euploids) were included. No study was judged to be at low risk of bias across the four domains of the QUADAS-2 tool but applicability concerns were generally low. Of the 65 studies, 42 enrolled pregnant women at high risk, five recruited an unselected population and 18 recruited cohorts with a mix of prior risk of fetal aneuploidy. Among the 65 studies, 44 evaluated MPSS and 21 evaluated TMPS; of these, five studies also compared gNIPT with a traditional screening test (biochemical, ultrasound or both). Forty-six out of 65 studies (71%) reported gNIPT assay failure rate, which ranged between 0% and 25% for MPSS, and between 0.8% and 7.5% for TMPS.In the population of unselected pregnant women, MPSS was evaluated by only one study; the study assessed T21, T18 and T13. TMPS was assessed for T21 in four studies involving unselected cohorts; three of the studies also assessed T18 and 13. In pooled analyses (88 T21 cases, 22 T18 cases, eight T13 cases and 20,649 unaffected pregnancies (non T21, T18 and T13)), the clinical sensitivity (95% confidence interval (CI)) of TMPS was 99.2% (78.2% to 100%), 90.9% (70.0% to 97.7%) and 65.1% (9.16% to 97.2%) for T21, T18 and T13, respectively. The corresponding clinical specificity was above 99.9% for T21, T18 and T13.In high-risk populations, MPSS was assessed for T21, T18, T13 and 45,X in 30, 28, 20 and 12 studies, respectively. In pooled analyses (1048 T21 cases, 332 T18 cases, 128 T13 cases and 15,797 unaffected pregnancies), the clinical sensitivity (95% confidence interval (CI)) of MPSS was 99.7% (98.0% to 100%), 97.8% (92.5% to 99.4%), 95.8% (86.1% to 98.9%) and 91.7% (78.3% to 97.1%) for T21, T18, T13 and 45,X, respectively. The corresponding clinical specificities (95% CI) were 99.9% (99.8% to 100%), 99.9% (99.8% to 100%), 99.8% (99.8% to 99.9%) and 99.6% (98.9% to 99.8%). In this risk group, TMPS was assessed for T21, T18, T13 and 45,X in six, five, two and four studies. In pooled analyses (246 T21 cases, 112 T18 cases, 20 T13 cases and 4282 unaffected pregnancies), the clinical sensitivity (95% CI) of TMPS was 99.2% (96.8% to 99.8%), 98.2% (93.1% to 99.6%), 100% (83.9% to 100%) and 92.4% (84.1% to 96.5%) for T21, T18, T13 and 45,X respectively. The clinical specificities were above 100% for T21, T18 and T13 and 99.8% (98.3% to 100%) for 45,X. Indirect comparisons of MPSS and TMPS for T21, T18 and 45,X showed no statistical difference in clinical sensitivity, clinical specificity or both. Due to limited data, comparative meta-analysis of MPSS and TMPS was not possible for T13.We were unable to perform meta-analyses of gNIPT for 47,XXX, 47,XXY and 47,XYY because there were very few or no studies in one or more risk groups. AUTHORS' CONCLUSIONS These results show that MPSS and TMPS perform similarly in terms of clinical sensitivity and specificity for the detection of fetal T31, T18, T13 and sex chromosome aneuploidy (SCA). However, no study compared the two approaches head-to-head in the same cohort of patients. The accuracy of gNIPT as a prenatal screening test has been mainly evaluated as a second-tier screening test to identify pregnancies at very low risk of fetal aneuploidies (T21, T18 and T13), thus avoiding invasive procedures. Genomics-based non-invasive prenatal testing methods appear to be sensitive and highly specific for detection of fetal trisomies 21, 18 and 13 in high-risk populations. There is paucity of data on the accuracy of gNIPT as a first-tier aneuploidy screening test in a population of unselected pregnant women. With respect to the replacement of invasive tests, the performance of gNIPT observed in this review is not sufficient to replace current invasive diagnostic tests.We conclude that given the current data on the performance of gNIPT, invasive fetal karyotyping is still the required diagnostic approach to confirm the presence of a chromosomal abnormality prior to making irreversible decisions relative to the pregnancy outcome. However, most of the gNIPT studies were prone to bias, especially in terms of the selection of participants.
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Affiliation(s)
- Mylène Badeau
- CHU de Québec ‐ Université LavalPopulation Health and Optimal Health Practices Research Axis45 Rue LeclercQuébec CityQCCanadaG1L 3L5
| | - Carmen Lindsay
- CHU de Québec ‐ Université LavalPopulation Health and Optimal Health Practices Research Axis45 Rue LeclercQuébec CityQCCanadaG1L 3L5
| | - Jonatan Blais
- CHAU‐Hôtel‐Dieu de LévisDepartment of Medical Biology143 Rue WolfeLévisQCCanadaG6V 3Z1
- Faculty of Medicine, Université LavalDepartment of Molecular Biology, Medical Biochemistry and PathologyQuebec CityQuebecCanada
| | - Leon Nshimyumukiza
- University of AlbertaSchool of Public Health8303 112 StreetEdmontonAlbertaCanadaT6G 2T4
| | - Yemisi Takwoingi
- University of BirminghamInstitute of Applied Health ResearchEdgbastonBirminghamUKB15 2TT
| | - Sylvie Langlois
- University of British ColumbiaDepartment of Medical Genetics, Faculty of MedicineC234, 4500 Oak StreetVancouverBCCanadaV6H 3N1
| | - France Légaré
- CHU de Québec ‐ Université LavalPopulation Health and Optimal Health Practices Research Axis45 Rue LeclercQuébec CityQCCanadaG1L 3L5
| | - Yves Giguère
- CHU de Québec ‐ Université LavalReproductive, Mother and Child Health Research Axis10, rue de l'Espinay, A2‐226Québec CityQCCanadaG1L 3L5
- Faculty of Medicine, Université LavalDepartment of Molecular Biology, Medical Biochemistry and Pathology10, rue de l'EspinayQuébec CityQcCanadaG1L 3L5
| | - Alexis F Turgeon
- CHU de Québec ‐ Université Laval, Université LavalDepartment of Anesthesiology and Critical Care Medicine, Division of Critical Care Medicine, and Population Health and Optimal Health Practices Research Unit, CHU de Québec ‐ Université Laval Research Center1401, 18eme rueQuebec CityQCCanadaG1J 1Z4
- CHU de Québec Research Center, Université LavalPopulation Health and Optimal Health Practices Research Axis1401, 18eme rueQuébec CityQuébecCanadaG1J 1Z4
| | - William Witteman
- CHU de Québec ‐ Université LavalPopulation Health and Optimal Health Practices Research Axis45 Rue LeclercQuébec CityQCCanadaG1L 3L5
| | - François Rousseau
- Faculty of Medicine, Université LavalDepartment of Molecular Biology, Medical Biochemistry and Pathology10, rue de l'EspinayQuébec CityQcCanadaG1L 3L5
- CHU de Québec Research Center, Université LavalPopulation Health and Optimal Health Practices Research Axis1401, 18eme rueQuébec CityQuébecCanadaG1J 1Z4
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Gil MM, Accurti V, Santacruz B, Plana MN, Nicolaides KH. Analysis of cell-free DNA in maternal blood in screening for aneuploidies: updated meta-analysis. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2017; 50:302-314. [PMID: 28397325 DOI: 10.1002/uog.17484] [Citation(s) in RCA: 407] [Impact Index Per Article: 58.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 03/28/2017] [Accepted: 04/03/2017] [Indexed: 06/07/2023]
Abstract
OBJECTIVES To review clinical validation or implementation studies of maternal blood cell-free (cf) DNA analysis and define the performance of screening for fetal trisomies 21, 18 and 13 and sex chromosome aneuploidies (SCA). METHODS Searches of PubMed, EMBASE and The Cochrane Library were performed to identify all peer-reviewed articles on cfDNA testing in screening for aneuploidies between January 2011, when the first such study was published, and 31 December 2016. The inclusion criteria were peer-reviewed study reporting on clinical validation or implementation of maternal cfDNA testing in screening for aneuploidies, in which data on pregnancy outcome were provided for more than 85% of the study population. We excluded case-control studies, proof-of-principle articles and studies in which the laboratory scientists carrying out the tests were aware of fetal karyotype or pregnancy outcome. Pooled detection rates (DRs) and false-positive rates (FPRs) were calculated using bivariate random-effects regression models. RESULTS In total, 35 relevant studies were identified and these were used for the meta-analysis on the performance of cfDNA testing in screening for aneuploidies. These studies reported cfDNA results in relation to fetal karyotype from invasive testing or clinical outcome. In the combined total of 1963 cases of trisomy 21 and 223 932 non-trisomy 21 singleton pregnancies, the weighted pooled DR and FPR were 99.7% (95% CI, 99.1-99.9%) and 0.04% (95% CI, 0.02-0.07%), respectively. In a total of 563 cases of trisomy 18 and 222 013 non-trisomy 18 singleton pregnancies, the weighted pooled DR and FPR were 97.9% (95% CI, 94.9-99.1%) and 0.04% (95% CI, 0.03-0.07%), respectively. In a total of 119 cases of trisomy 13 and 212 883 non-trisomy 13 singleton pregnancies, the weighted pooled DR and FPR were 99.0% (95% CI, 65.8-100%) and 0.04% (95% CI, 0.02-0.07%), respectively. In a total of 36 cases of monosomy X and 7676 unaffected singleton pregnancies, the weighted pooled DR and FPR were 95.8% (95% CI, 70.3-99.5%) and 0.14% (95% CI, 0.05-0.38%), respectively. In a combined total of 17 cases of SCA other than monosomy X and 5400 unaffected singleton pregnancies, the weighted pooled DR and FPR were 100% (95% CI, 83.6-100%) and 0.004% (95% CI, 0.0-0.08%), respectively. For twin pregnancies, in a total of 24 cases of trisomy 21 and 1111 non-trisomy 21 cases, the DR was 100% (95% CI, 95.2-100%) and FPR was 0.0% (95% CI, 0.0-0.003%), respectively. CONCLUSIONS Screening by analysis of cfDNA in maternal blood in singleton pregnancies could detect > 99% of fetuses with trisomy 21, 98% of trisomy 18 and 99% of trisomy 13 at a combined FPR of 0.13%. The number of reported cases of SCA is too small for accurate assessment of performance of screening. In twin pregnancies, performance of screening for trisomy 21 is encouraging but the number of cases reported is small. Copyright © 2017 ISUOG. Published by John Wiley & Sons Ltd.
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Affiliation(s)
- M M Gil
- Fetal Medicine Research Institute, King's College Hospital, London, UK
- Obstetrics and Gynecology Department, Torrejon University Hospital, Torrejon de Ardoz, Madrid, Spain
- Obstetrics and Gynecology Department, Universidad Francisco de Vitoria, Pozuelo de Alarcón, Madrid, Spain
| | - V Accurti
- Fetal Medicine Research Institute, King's College Hospital, London, UK
| | - B Santacruz
- Obstetrics and Gynecology Department, Torrejon University Hospital, Torrejon de Ardoz, Madrid, Spain
| | - M N Plana
- Clinical Biostatistics Unit, Ramón y Cajal Hospital (IRYCIS), CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - K H Nicolaides
- Fetal Medicine Research Institute, King's College Hospital, London, UK
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Jin J, Yang J, Chen Y, Huang J. Systematic review and meta-analysis of non-invasive prenatal DNA testing for trisomy 21: implications for implementation in China. Prenat Diagn 2017; 37:864-873. [PMID: 28686807 DOI: 10.1002/pd.5111] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 05/20/2017] [Accepted: 07/03/2017] [Indexed: 12/27/2022]
Abstract
OBJECTIVES To systematically review clinical validation studies of massive parallel sequencing (MPS) technology in prenatal screening for trisomy 21 and to explore the potential implementation strategies in China compared with those in developing countries. METHODS Searches of the Cochrane Library, Medline, EMBASE, Web of Science, Biosis Previews, and three major Chinese databases were performed to identify all the peer-reviewed articles published between 1 January 2011 and 15 October 2016. We also reviewed and discussed the potential challenges and risks in the future promotion of MPS technology in China compared with those in developing countries. RESULTS The weighted pooled sensitivity and specificity of MPS technology for the prenatal detection of trisomy 21 were 99.7% (95% CI 98.3-99.9%) and 100.0% (95% CI 99.9-100.0%), respectively, based on a meta-analysis of 44 included studies. An additional meta-analysis was conducted based on the 25 included studies that were performed in medical/genetic sequencing institutions in mainland China, showing a weighted pooled sensitivity and specificity of MPS technology as 99.5% (95% CI 98.7-99.8%) and 100% (95% CI 99.9-100%), respectively. CONCLUSION MPS technology offers effective screening performance for trisomy 21 but should be cautiously promoted due to its clinical limitations and challenges that stem from the ethics and business aspects. © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Jiajie Jin
- School of Public Health, Fudan University, Shanghai, China.,Key Laboratory of Health Technology Assessment, National Health and Family Planning Committee (Fudan University), Shanghai, China
| | - Junwen Yang
- School of Public Health, Fudan University, Shanghai, China.,Key Laboratory of Health Technology Assessment, National Health and Family Planning Committee (Fudan University), Shanghai, China
| | - Yingyao Chen
- School of Public Health, Fudan University, Shanghai, China.,Key Laboratory of Health Technology Assessment, National Health and Family Planning Committee (Fudan University), Shanghai, China
| | - Jiayan Huang
- School of Public Health, Fudan University, Shanghai, China.,Key Laboratory of Health Technology Assessment, National Health and Family Planning Committee (Fudan University), Shanghai, China
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Yu B, Lu BY, Zhang B, Zhang XQ, Chen YP, Zhou Q, Jiang J, Wang HY. Overall evaluation of the clinical value of prenatal screening for fetal-free DNA in maternal blood. Medicine (Baltimore) 2017; 96:e7114. [PMID: 28682865 PMCID: PMC5502138 DOI: 10.1097/md.0000000000007114] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
OBJECTIVE To explore the clinical value of prenatal screening for fetal-free DNA in maternal blood. METHODS A total of 10,275 maternal blood samples were collected from October 2012 to May 2016 at the prenatal diagnosis center of Changzhou Woman and Children Health Hospital. RESULTS Among 10,275 pregnant women accepted noninvasive prenatal testing (NIPT), 9 cases could not get the results after collected the blood second times. The rate of NIPT failure was 0.09%. Seventy-two cases got the NIPT positive results of trisomy 21/trisomy 18/trisomy 13, and the detection rate, specificity, positive predictive value (PPV), and false positive rate were 98.59%, 99.99%, 97.22%, and 0.02%. The top-3 indications of the study were advanced age women (34.90%), high risk (25.22%), and intermediate risk (19.56%). They all had the satisfactory results of NIPT. Fifty-seven pregnant women had the high risk of fetal sex chromosomal aneuploidies (SCA). After informed consent, 33 cases accepted prenatal diagnosis. Eighteen cases were confirmed as sex chromosome aneuploidies. The PPV was 54.54%. Compared with other SCA, the PPV of Turner syndrome was lower. One case was false negative after followed up. CONCLUSIONS NIPT showed a broad application prospects for prenatal screening and diagnosis of fetal chromosomal diseases. We should deepen mining and analyzing the clinical data, and explore the use of NIPT more reasonably from the perspective of evidence-based medicine.
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A quantitative cSMART assay for noninvasive prenatal screening of autosomal recessive nonsyndromic hearing loss caused by GJB2 and SLC26A4 mutations. Genet Med 2017; 19:1309-1316. [PMID: 28541280 DOI: 10.1038/gim.2017.54] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 03/27/2017] [Indexed: 12/22/2022] Open
Abstract
PurposeThe aim of this study was to assess the performance of a noninvasive prenatal screening (NIPS) assay for accurate fetal genotyping of pregnancies at genetic risk for autosomal recessive nonsyndromic hearing loss (ARNSHL).MethodsA total of 80 pregnant couples carrying known mutations in either the GJB2 or SLC26A4 genes associated with a risk for ARNSHL were recruited to the study. Fetal amniocyte samples were genotyped by invasive prenatal screening (IPS), whereas the cell-free fetal DNA present in maternal plasma samples was genotyped using a novel NIPS method based on circulating single-molecule amplification and resequencing technology (cSMART).ResultsIPS of the 80 at-risk pregnancies identified 20 normal homozygote, 42 heterozygote, 5 affected homozygote, and 13 affected compound heterozygote fetuses. Benchmarking against IPS, 73 of 80 fetuses (91.3%) were correctly genotyped by the cSMART NIPS assay. A low fetal DNA fraction (<6%) was identified as the main contributing factor in five of seven discordant NIPS results. At fetal DNA fractions >6%, the sensitivity and specificity of the cSMART assay for correctly diagnosing ARNSHL were 100 and 96.5%, respectively.ConclusionBased on key performance indicators, the cSMART NIPS assay has clinical potential as an alternative to traditional IPS of ARNSHL.
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Tartaglia NR, Wilson R, Miller JS, Rafalko J, Cordeiro L, Davis S, Hessl D, Ross J. Autism Spectrum Disorder in Males with Sex Chromosome Aneuploidy: XXY/Klinefelter Syndrome, XYY, and XXYY. J Dev Behav Pediatr 2017; 38:197-207. [PMID: 28333849 PMCID: PMC5423728 DOI: 10.1097/dbp.0000000000000429] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
OBJECTIVE Neurodevelopmental concerns in males with sex chromosome aneuploidy (SCA) (XXY/Klinefelter syndrome, XYY, XXYY) include symptoms seen in autism spectrum disorder (ASD), such as language impairments and social difficulties. We aimed to: (1) evaluate ASD characteristics in research cohorts of SCA males under DSM-IV compared to DSM-5 criteria, and (2) analyze factors associated with ASD diagnoses in SCA. METHODS Evaluation of participants with XXY/KS (n=20), XYY (n=57) and XXYY (n=21) included medical history, cognitive/adaptive testing, Social Communication Questionnaire, Social Responsiveness Scale, Autism Diagnostic Observation Schedule, Autism Diagnostic Interview-Revised, and DSM ASD criteria. Clinical impressions of ASD diagnostic category using the ADOS and DSM-IV criteria were compared to ADOS-2 and DSM-5 criteria. T-tests compared cognitive, adaptive, SES and prenatal vs. postnatal diagnoses between ASD and no ASD groups. RESULTS ASD rates in these research cohorts were 10% in XXY/KS, 38% in XYY, and 52% in XXYY using ADOS-2/DSM-5, and were not statistically different compared to DSM-IV criteria. In XYY and XXYY, the ASD group had lower verbal IQ and adaptive functioning compared to those without ASD. Many children without ASD still showed some social difficulties. CONCLUSION ASD rates in males with SCA are higher than reported for the general population. Males with Y chromosome aneuploidy (XYY and XXYY) were 4.8 times more likely to have a diagnosis of ASD than the XXY/KS group, and 20 times more likely than males in the general population (1 in 42 males, CDC 2010). ASD should be considered when evaluating social difficulties in SCA. Studies of SCA and Y-chromosome genes may provide insight into male predominance in idiopathic ASD.
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Affiliation(s)
- Nicole R Tartaglia
- University of Colorado School of Medicine, Department of Pediatrics
- eXtraordinarY Kids Clinic, Developmental Pediatrics, Children's Hospital Colorado, Aurora, Colorado
| | - Rebecca Wilson
- eXtraordinarY Kids Clinic, Developmental Pediatrics, Children's Hospital Colorado, Aurora, Colorado
| | - Judith S. Miller
- Perelman School of Medicine, University of Pennsylvania, Department of Psychiatry, Philadelphia, Pennsylvania
| | - Jessica Rafalko
- Nemours/DuPont Hospital for Children, Thomas Jefferson University, Department of Pediatrics, Philadelphia, Pennsylvania
| | - Lisa Cordeiro
- University of Colorado School of Medicine, Department of Pediatrics
- eXtraordinarY Kids Clinic, Developmental Pediatrics, Children's Hospital Colorado, Aurora, Colorado
| | - Shanlee Davis
- University of Colorado School of Medicine, Department of Pediatrics
- eXtraordinarY Kids Clinic, Developmental Pediatrics, Children's Hospital Colorado, Aurora, Colorado
| | - David Hessl
- University of California Davis Medical Center, M.I.N.D. Institute, Sacramento, California
- University of California Davis School of Medicine, Department of Psychiatry and Behavioral Sciences
| | - Judith Ross
- Nemours/DuPont Hospital for Children, Thomas Jefferson University, Department of Pediatrics, Philadelphia, Pennsylvania
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25
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Zhang B, Lu BY, Yu B, Zheng FX, Zhou Q, Chen YP, Zhang XQ. Noninvasive prenatal screening for fetal common sex chromosome aneuploidies from maternal blood. J Int Med Res 2017; 45:621-630. [PMID: 28357876 PMCID: PMC5536640 DOI: 10.1177/0300060517695008] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Objective To explore the feasibility of high-throughput massively parallel genomic DNA sequencing technology for the noninvasive prenatal detection of fetal sex chromosome aneuploidies (SCAs). Methods The study enrolled pregnant women who were prepared to undergo noninvasive prenatal testing (NIPT) in the second trimester. Cell-free fetal DNA (cffDNA) was extracted from the mother’s peripheral venous blood and a high-throughput sequencing procedure was undertaken. Patients identified as having pregnancies associated with SCAs were offered prenatal fetal chromosomal karyotyping. Results The study enrolled 10 275 pregnant women who were prepared to undergo NIPT. Of these, 57 pregnant women (0.55%) showed fetal SCA, including 27 with Turner syndrome (45,X), eight with Triple X syndrome (47,XXX), 12 with Klinefelter syndrome (47,XXY) and three with 47,XYY. Thirty-three pregnant women agreed to undergo fetal karyotyping and 18 had results consistent with NIPT, while 15 patients received a normal karyotype result. The overall positive predictive value of NIPT for detecting SCAs was 54.54% (18/33) and for detecting Turner syndrome (45,X) was 29.41% (5/17). Conclusion NIPT can be used to identify fetal SCAs by analysing cffDNA using massively parallel genomic sequencing, although the accuracy needs to be improved particularly for Turner syndrome (45,X).
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Affiliation(s)
- Bin Zhang
- Prenatal Diagnosis Laboratory, Changzhou Woman and Children Health Hospital affiliated with Nanjing Medical University, Changzhou City, Jiangsu Province, China
| | - Bei-Yi Lu
- Prenatal Diagnosis Laboratory, Changzhou Woman and Children Health Hospital affiliated with Nanjing Medical University, Changzhou City, Jiangsu Province, China
| | - Bin Yu
- Prenatal Diagnosis Laboratory, Changzhou Woman and Children Health Hospital affiliated with Nanjing Medical University, Changzhou City, Jiangsu Province, China
| | - Fang-Xiu Zheng
- Prenatal Diagnosis Laboratory, Changzhou Woman and Children Health Hospital affiliated with Nanjing Medical University, Changzhou City, Jiangsu Province, China
| | - Qin Zhou
- Prenatal Diagnosis Laboratory, Changzhou Woman and Children Health Hospital affiliated with Nanjing Medical University, Changzhou City, Jiangsu Province, China
| | - Ying-Ping Chen
- Prenatal Diagnosis Laboratory, Changzhou Woman and Children Health Hospital affiliated with Nanjing Medical University, Changzhou City, Jiangsu Province, China
| | - Xiao-Qing Zhang
- Prenatal Diagnosis Laboratory, Changzhou Woman and Children Health Hospital affiliated with Nanjing Medical University, Changzhou City, Jiangsu Province, China
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Non‐invasive prenatal screening for chromosomal abnormalities using circulating cell-free fetal DNA in maternal plasma: Current applications, limitations and prospects. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2017. [DOI: 10.1016/j.ejmhg.2016.07.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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27
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Chen Y, Liu Y, Wang B, Mao J, Wang T, Ye K, Ye Y, Cram DS, Li H. Development and validation of a fetal genotyping assay with potential for noninvasive prenatal diagnosis of hereditary hearing loss. Prenat Diagn 2016; 36:1233-1241. [PMID: 27862068 DOI: 10.1002/pd.4962] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Revised: 10/24/2016] [Accepted: 11/02/2016] [Indexed: 12/26/2022]
Affiliation(s)
- Ying Chen
- Central Lab; Suzhou Hospital Affiliated to Nanjing Medical University; Suzhou Jiangsu China
- Nanjing Medical University Affiliated Wuxi Maternity and Child Health Care Hospital; Wuxi Jiangsu China
| | - Yiqian Liu
- Berry Genomics Corporation; Beijing China
| | - Benjing Wang
- Gynecology Department; Suzhou Hospital Affiliated to Nanjing Medical University; Suzhou Jiangsu China
| | - Jun Mao
- Central Lab; Suzhou Hospital Affiliated to Nanjing Medical University; Suzhou Jiangsu China
- Obstetrics Department; Suzhou Hospital Affiliated to Nanjing Medical University; Suzhou Jiangsu China
| | - Ting Wang
- Center for Reproduction and Genetics; Suzhou Hospital Affiliated to Nanjing Medical University; Suzhou Jiangsu China
| | - Kan Ye
- Child Health Care Department; Suzhou Hospital Affiliated to Nanjing Medical University; Suzhou Jiangsu China
| | - Yanlin Ye
- Child Health Care Department; Suzhou Hospital Affiliated to Nanjing Medical University; Suzhou Jiangsu China
| | | | - Hong Li
- Center for Reproduction and Genetics; Suzhou Hospital Affiliated to Nanjing Medical University; Suzhou Jiangsu China
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Iwarsson E, Jacobsson B, Dagerhamn J, Davidson T, Bernabé E, Heibert Arnlind M. Analysis of cell-free fetal DNA in maternal blood for detection of trisomy 21, 18 and 13 in a general pregnant population and in a high risk population - a systematic review and meta-analysis. Acta Obstet Gynecol Scand 2016; 96:7-18. [DOI: 10.1111/aogs.13047] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 10/19/2016] [Indexed: 01/09/2023]
Affiliation(s)
- Erik Iwarsson
- Department of Molecular Medicine and Surgery; Clinical Genetics Unit; Karolinska Institute; Karolinska University Hospital; Stockholm Sweden
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology; Sahlgrenska Academy; Gothenburg University; Gothenburg Sweden
- Department of Genetics and Bioinformatics; Area of Health Data and Digitalisation; Institute of Public Health; Oslo Norway
| | - Jessica Dagerhamn
- Swedish Agency for Health Technology Assessment and Assessment of Social Services (SBU); Stockholm Sweden
| | - Thomas Davidson
- Swedish Agency for Health Technology Assessment and Assessment of Social Services (SBU); Stockholm Sweden
- Division of Health Care Analysis; Department of Medical and Health Sciences; Linköping University; Linköping Sweden
| | - Eduardo Bernabé
- Division of Population and Patient Health; King's College London Dental Institute at Guy's; King's College and St Thomas Hospitals; London UK
| | - Marianne Heibert Arnlind
- Swedish Agency for Health Technology Assessment and Assessment of Social Services (SBU); Stockholm Sweden
- Medical Management Center/LIME; Karolinska Institute; Stockholm Sweden
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Mackie FL, Hemming K, Allen S, Morris RK, Kilby MD. The accuracy of cell-free fetal DNA-based non-invasive prenatal testing in singleton pregnancies: a systematic review and bivariate meta-analysis. BJOG 2016; 124:32-46. [DOI: 10.1111/1471-0528.14050] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2016] [Indexed: 12/18/2022]
Affiliation(s)
- FL Mackie
- Centre for Women's & Newborn Health and the Institute of Metabolism and Systems Research; University of Birmingham; Birmingham UK
| | - K Hemming
- Public Health, Epidemiology and Biostatistics; Institute of Applied Health Sciences; University of Birmingham; Birmingham UK
| | - S Allen
- West Midlands Regional Genetics Laboratory; Birmingham Women's Hospital NHS Foundation Trust; Birmingham UK
| | - RK Morris
- Centre for Women's & Newborn Health and the Institute of Metabolism and Systems Research; University of Birmingham; Birmingham UK
- Fetal Medicine Centre; Birmingham Women's Hospital NHS Foundation Trust; Birmingham UK
| | - MD Kilby
- Centre for Women's & Newborn Health and the Institute of Metabolism and Systems Research; University of Birmingham; Birmingham UK
- Fetal Medicine Centre; Birmingham Women's Hospital NHS Foundation Trust; Birmingham UK
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Straver R, Oudejans CBM, Sistermans EA, Reinders MJT. Calculating the fetal fraction for noninvasive prenatal testing based on genome-wide nucleosome profiles. Prenat Diagn 2016; 36:614-21. [PMID: 26996738 PMCID: PMC5111749 DOI: 10.1002/pd.4816] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 02/18/2016] [Accepted: 03/12/2016] [Indexed: 01/06/2023]
Abstract
Objective While large fetal copy number aberrations can generally be detected through sequencing of DNA in maternal blood, the reliability of tests depends on the fraction of DNA that originates from the fetus. Existing methods to determine this fetal fraction require additional work or are limited to male fetuses. We aimed to create a sex‐independent approach without additional work. Methods DNA fragments used for noninvasive prenatal testing are cut only by natural processes; thus, influences on cutting by the packaging of DNA in nucleosomes will be preserved in sequencing. As cuts are expected to be made preferentially in linker regions, the shorter fetal fragments should be enriched for reads starting in nucleosome covered positions. Results We generated genome‐wide nucleosome profiles based on single end sequencing of cell‐free DNA. We found a difference between DNA digestion of fetal cell‐free DNA and maternal cell‐free DNA and used this to calculate the fraction of fetal DNA in maternal plasma for both male and female fetuses. Conclusion Our method facilitates cost‐effective noninvasive prenatal testing, as the fetal DNA fraction can be estimated without the need for expensive paired‐end sequencing or additional tests. The methodology is implemented as a tool, which we called SANEFALCON (Single reAds Nucleosome‐basEd FetAL fraCtiON). It is available for academic and non‐profit purposes under Creative Commons Attribution‐NonCommercial‐ShareAlike 4.0 International Public License. github.com/rstraver/sanefalcon. © 2016 The Authors. Prenatal Diagnosis published by John Wiley & Sons, Ltd. What's Already Known About This Topic?Fetal DNA is found in small and varying amounts in maternal blood, enough to detect fetal aberrations such as Down syndrome through next generation sequencing methods. Fetal DNA is generally shorter, and this is believed to be influenced by nucleosomes.
What Does This Study Add?We obtained nucleosome positions from cell‐free DNA over a combination of low‐coverage samples. Our method shows how fetal fragments are influenced by nucleosomes compared with maternal fragments. We deduced the fetal fraction using the distribution of reads starting around nucleosome positions, independent of the fetal sex.
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Affiliation(s)
- Roy Straver
- Department of Clinical Genetics, VU University Medical Center Amsterdam, Amsterdam, The Netherlands
| | - Cees B M Oudejans
- Department of Clinical Chemistry, VU University Medical Center Amsterdam, Amsterdam, The Netherlands
| | - Erik A Sistermans
- Department of Clinical Genetics, VU University Medical Center Amsterdam, Amsterdam, The Netherlands
| | - Marcel J T Reinders
- Department of Clinical Genetics, VU University Medical Center Amsterdam, Amsterdam, The Netherlands.,Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
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Yaron Y. The implications of non-invasive prenatal testing failures: a review of an under-discussed phenomenon. Prenat Diagn 2016; 36:391-6. [DOI: 10.1002/pd.4804] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 02/08/2016] [Accepted: 02/29/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Yuval Yaron
- Genetic Institute, Tel Aviv Sourasky Medical Center; Tel Aviv University; Tel Aviv Israel
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Poon LC, Dumidrascu‐Diris D, Francisco C, Fantasia I, Nicolaides KH. IONA test for first-trimester detection of trisomies 21, 18 and 13. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2016; 47:184-187. [PMID: 26387684 PMCID: PMC5064725 DOI: 10.1002/uog.15749] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 09/11/2015] [Accepted: 09/13/2015] [Indexed: 06/05/2023]
Abstract
OBJECTIVE To assess the potential performance of screening for fetal trisomies 21, 18 and 13 by cell-free DNA (cfDNA) analysis of maternal blood using the IONA® test. METHODS This was a nested case-control study of cfDNA analysis of maternal plasma using the IONA test. Samples were obtained at 11-13 weeks' gestation, before chorionic villus sampling, from 201 euploid pregnancies, 35 with trisomy 21, four with trisomy 18 and two with trisomy 13. Laboratory personnel were blinded to the fetal karyotype. RESULTS Probability scores for trisomies 21, 18 and 13 were given for 241/242 samples analyzed. No probability score was provided for one (0.5%) euploid pregnancy because of low fetal fraction. In all 35 cases of trisomy 21 the probability score for trisomy 21 was > 95% and the scores for trisomies 18 and 13 were ≤ 0.0001%. In all four cases of trisomy 18, the probability score for trisomy 18 was > 77% and the scores for trisomies 21 and 13 were ≤ 0.0001%. In the two cases of trisomy 13, the probability score for trisomy 13 was > 59% and the scores for trisomies 21 and 18 were ≤ 0.0001%. In the 200 euploid pregnancies with a test result, the probability score was < 0.08% for trisomy 21, < 0.001% for trisomy 18 and < 0.002% for trisomy 13. Therefore, the IONA test detected 100% of all three trisomies, with a false-positive rate of 0%. CONCLUSION The IONA test successfully differentiated all cases of trisomies 21, 18 and 13 from euploid pregnancies.
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Affiliation(s)
- L. C. Poon
- Harris Birthright Research Centre for Fetal MedicineKing's College HospitalLondonUK
| | - D. Dumidrascu‐Diris
- Harris Birthright Research Centre for Fetal MedicineKing's College HospitalLondonUK
| | - C. Francisco
- Harris Birthright Research Centre for Fetal MedicineKing's College HospitalLondonUK
| | - I. Fantasia
- Harris Birthright Research Centre for Fetal MedicineKing's College HospitalLondonUK
| | - K. H. Nicolaides
- Harris Birthright Research Centre for Fetal MedicineKing's College HospitalLondonUK
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Taylor-Phillips S, Freeman K, Geppert J, Agbebiyi A, Uthman OA, Madan J, Clarke A, Quenby S, Clarke A. Accuracy of non-invasive prenatal testing using cell-free DNA for detection of Down, Edwards and Patau syndromes: a systematic review and meta-analysis. BMJ Open 2016; 6:e010002. [PMID: 26781507 PMCID: PMC4735304 DOI: 10.1136/bmjopen-2015-010002] [Citation(s) in RCA: 223] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVE To measure test accuracy of non-invasive prenatal testing (NIPT) for Down, Edwards and Patau syndromes using cell-free fetal DNA and identify factors affecting accuracy. DESIGN Systematic review and meta-analysis of published studies. DATA SOURCES PubMed, Ovid Medline, Ovid Embase and the Cochrane Library published from 1997 to 9 February 2015, followed by weekly autoalerts until 1 April 2015. ELIGIBILITY CRITERIA FOR SELECTING STUDIES English language journal articles describing case-control studies with ≥ 15 trisomy cases or cohort studies with ≥ 50 pregnant women who had been given NIPT and a reference standard. RESULTS 41, 37 and 30 studies of 2012 publications retrieved were included in the review for Down, Edwards and Patau syndromes. Quality appraisal identified high risk of bias in included studies, funnel plots showed evidence of publication bias. Pooled sensitivity was 99.3% (95% CI 98.9% to 99.6%) for Down, 97.4% (95.8% to 98.4%) for Edwards, and 97.4% (86.1% to 99.6%) for Patau syndrome. The pooled specificity was 99.9% (99.9% to 100%) for all three trisomies. In 100,000 pregnancies in the general obstetric population we would expect 417, 89 and 40 cases of Downs, Edwards and Patau syndromes to be detected by NIPT, with 94, 154 and 42 false positive results. Sensitivity was lower in twin than singleton pregnancies, reduced by 9% for Down, 28% for Edwards and 22% for Patau syndrome. Pooled sensitivity was also lower in the first trimester of pregnancy, in studies in the general obstetric population, and in cohort studies with consecutive enrolment. CONCLUSIONS NIPT using cell-free fetal DNA has very high sensitivity and specificity for Down syndrome, with slightly lower sensitivity for Edwards and Patau syndrome. However, it is not 100% accurate and should not be used as a final diagnosis for positive cases. TRIAL REGISTRATION NUMBER CRD42014014947.
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Affiliation(s)
| | - Karoline Freeman
- Warwick Medical School, The University of Warwick, Coventry, West Midlands, UK
| | - Julia Geppert
- Warwick Medical School, The University of Warwick, Coventry, West Midlands, UK
| | - Adeola Agbebiyi
- Warwick Medical School, The University of Warwick, Coventry, West Midlands, UK
| | - Olalekan A Uthman
- Warwick Medical School, The University of Warwick, Coventry, West Midlands, UK
| | - Jason Madan
- Warwick Medical School, The University of Warwick, Coventry, West Midlands, UK
| | - Angus Clarke
- Institute of Cancer & Genetics, Cardiff University School of Medicine, Cardiff, UK
| | - Siobhan Quenby
- Warwick Medical School, The University of Warwick, Coventry, West Midlands, UK
| | - Aileen Clarke
- Warwick Medical School, The University of Warwick, Coventry, West Midlands, UK
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Abstract
Cell-free DNA (cfDNA) testing has recently become indispensable in diagnostic testing and screening. In the prenatal setting, this type of testing is often called noninvasive prenatal testing (NIPT). With a number of techniques, using either next-generation sequencing or single nucleotide polymorphism-based approaches, fetal cfDNA in maternal plasma can be analyzed to screen for rhesus D genotype, common chromosomal aneuploidies, and increasingly for testing other conditions, including monogenic disorders. With regard to screening for common aneuploidies, challenges arise when implementing NIPT in current prenatal settings. Depending on the method used (targeted or nontargeted), chromosomal anomalies other than trisomy 21, 18, or 13 can be detected, either of fetal or maternal origin, also referred to as unsolicited or incidental findings. For various biological reasons, there is a small chance of having either a false-positive or false-negative NIPT result, or no result, also referred to as a "no-call." Both pre- and posttest counseling for NIPT should include discussing potential discrepancies. Since NIPT remains a screening test, a positive NIPT result should be confirmed by invasive diagnostic testing (either by chorionic villus biopsy or by amniocentesis). As the scope of NIPT is widening, professional guidelines need to discuss the ethics of what to offer and how to offer. In this review, we discuss the current biochemical, clinical, and ethical challenges of cfDNA testing in the prenatal setting and its future perspectives including novel applications that target RNA instead of DNA.
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35
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Bevilacqua E, Guizani M, Cos Sanchez T, Jani JC. Concerns with performance of screening for aneuploidy by cell-free DNA analysis of maternal blood in twin pregnancy. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2016; 47:124-125. [PMID: 26148199 DOI: 10.1002/uog.14938] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 06/30/2015] [Accepted: 06/30/2015] [Indexed: 06/04/2023]
Affiliation(s)
- E Bevilacqua
- Department of Obstetrics and Gynecology, University Hospital Brugmann, Université Libre de Bruxelles, Brussels, Belgium
| | - M Guizani
- Department of Obstetrics and Gynecology, University Hospital Brugmann, Université Libre de Bruxelles, Brussels, Belgium
| | - T Cos Sanchez
- Department of Obstetrics and Gynecology, University Hospital Brugmann, Université Libre de Bruxelles, Brussels, Belgium
| | - J C Jani
- Department of Obstetrics and Gynecology, University Hospital Brugmann, Université Libre de Bruxelles, Brussels, Belgium
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36
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Performance of Momguard, a new non-invasive prenatal testing protocol developed in Korea. Obstet Gynecol Sci 2015; 58:340-5. [PMID: 26430657 PMCID: PMC4588837 DOI: 10.5468/ogs.2015.58.5.340] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 05/15/2015] [Accepted: 05/20/2015] [Indexed: 11/25/2022] Open
Abstract
Objective To evaluate the performance of Momguard, non-invasive prenatal test (NIPT) for detecting trisomy (T) 21, T18, T13, and sex-chromosome abnormalities recently developed in Korea. Methods This preliminary study formed part of a large prospective cohort study conducted at Asan Medical Center, Seoul, Korea. Only pregnant women who underwent both NIPT and confirmatory karyotyping were included in this study. NIPT results were compared with those of karyotype analyses. Results Among 93 eligible cases, NIPT results could not be obtained in one case due to a low fetal cell-free DNA fraction. Based on NIPT, eight cases of fetal aneuploidies, including T21 (n=5), T18 (n=2), and T13 (n=1), were identified. For T21 and T18, the sensitivity and specificity of NIPT were both 100%, with a false-positive and false-negative rate of 0% and a positive-predictive value of 100%. One patient classified as having intermediate risk for T13 by NIPT was confirmed to have T13 by karyotyping, and there were no false-negative cases. No cases of sex-chromosome anomalies were detected by NIPT or karyotyping during the study period. Conclusion Momguard is a reliable screening tool for detecting T21 and T18. For T13 and sex-chromosome anomalies, further prospective studies are necessary to confirm its utility.
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37
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Peterson JF, Mikulec K, Grignon JW, Behmaram B, Cruz MO, van Tuinen P. Elucidating discrepant results in a prenatal diagnosis of 48,XXY,+18 (Edwards and Klinefelter syndromes). Am J Med Genet A 2015; 167A:2855-7. [PMID: 26227211 DOI: 10.1002/ajmg.a.37250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 06/26/2015] [Indexed: 01/21/2023]
Affiliation(s)
- Jess F Peterson
- Department of Pathology, Medical College of Wisconsin, Milwaukee, Wisconsin.,Wisconsin Diagnostic Laboratories, Milwaukee, Wisconsin
| | - Kendra Mikulec
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | | | - Behnaz Behmaram
- Department of Pathology, Medical College of Wisconsin, Milwaukee, Wisconsin.,Wisconsin Diagnostic Laboratories, Milwaukee, Wisconsin
| | - Meredith O Cruz
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Peter van Tuinen
- Department of Pathology, Medical College of Wisconsin, Milwaukee, Wisconsin.,Wisconsin Diagnostic Laboratories, Milwaukee, Wisconsin
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38
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Birth of a child with trisomy 9 mosaicism syndrome associated with paternal isodisomy 9: case of a positive noninvasive prenatal test result unconfirmed by invasive prenatal diagnosis. Mol Cytogenet 2015; 8:44. [PMID: 26120364 PMCID: PMC4482096 DOI: 10.1186/s13039-015-0145-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 04/25/2015] [Indexed: 12/31/2022] Open
Abstract
Background Non-invasive prenatal testing (NIPT) is currently used as a frontline screening test to identify fetuses with common aneuploidies. Occasionally, incidental NIPT results are conveyed to the clinician suggestive of fetuses with rare chromosome disease syndromes. We describe a child with trisomy 9 (T9) mosaicism where the prenatal history reported a positive NIPT result for T9 that was unconfirmed by conventional prenatal diagnosis. Methods NIPT was performed by low coverage whole genome plasma DNA sequencing. Karyotyping and fluorescent in situ hybridization (FISH) analysis with chromosome 9p-ter and 9q-ter probes was used to determine the somatic cell level of T9 mosaicism in the fetus and child. Quantitative fluorescent PCR (Q-PCR) of highly polymorphic short tandem repeat (STR) chromosome 9 markers was also performed to investigate the nature of the T9 mosaicism and the parental origin. Results A 22 month old girl presented with severe developmental delay, congenital cerebral dysplasia and congenital heart disease consistent with phenotypes associated with T9 mosaicism syndrome. Review of the prenatal testing history revealed a positive NIPT result for chromosome T9. However, follow up confirmatory karyotyping and FISH analysis of fetal cells returned a normal karyotype. Post-natal studies of somatic cell T9 mosaicism by FISH detected levels of approximately 20 % in blood and buccal cells. Q-PCR STR analysis of family DNA samples suggested that the T9 mosaicism originated by post-zygotic trisomic rescue of a paternal meiotic II chromosome 9 non-disjunction error resulting in the formation of two distinct somatic cell lines in the proband, one with paternal isodisomy 9 and one with T9. Conclusion This study shows that NIPT may also be a useful screening technology to increase prenatal detection rates of rare fetal chromosome disease syndromes.
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40
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Gil MM, Quezada MS, Revello R, Akolekar R, Nicolaides KH. Analysis of cell-free DNA in maternal blood in screening for fetal aneuploidies: updated meta-analysis. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2015; 45:249-266. [PMID: 25639627 DOI: 10.1002/uog.14791] [Citation(s) in RCA: 352] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Accepted: 01/13/2015] [Indexed: 06/04/2023]
Abstract
OBJECTIVE To review clinical validation or implementation studies of maternal blood cell-free (cf) DNA analysis and define the performance of screening for fetal trisomies 21, 18 and 13 and sex chromosome aneuploidies. METHODS Searches of PubMed, EMBASE and The Cochrane Library were performed to identify all peer-reviewed articles on cfDNA testing in screening for aneuploidies between January 2011, when the first such study was published, and 4 January 2015. RESULTS In total, 37 relevant studies were identified and these were used for the meta-analysis on the performance of cfDNA testing in screening for aneuploidies. These studies reported cfDNA results in relation to fetal karyotype from invasive testing or clinical outcome. Weighted pooled detection rates (DR) and false-positive rates (FPR) in singleton pregnancies were 99.2% (95% CI, 98.5-99.6%) and 0.09% (95% CI, 0.05-0.14%), respectively, for trisomy 21, 96.3% (95% CI, 94.3-97.9%) and 0.13% (95% CI, 0.07-0.20) for trisomy 18, 91.0% (95% CI, 85.0-95.6%) and 0.13% (95% CI, 0.05-0.26%) for trisomy 13, 90.3% (95% CI, 85.7-94.2%) and 0.23% (95% CI, 0.14-0.34%) for monosomy X and 93.0% (95% CI, 85.8-97.8%) and 0.14% (95% CI, 0.06-0.24%) for sex chromosome aneuploidies other than monosomy X. For twin pregnancies, the DR for trisomy 21 was 93.7% (95% CI, 83.6-99.2%) and the FPR was 0.23% (95% CI, 0.00-0.92%). CONCLUSION Screening for trisomy 21 by analysis of cfDNA in maternal blood is superior to that of all other traditional methods of screening, with higher DR and lower FPR. The performance of screening for trisomies 18 and 13 and sex chromosome aneuploidies is considerably worse than that for trisomy 21.
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Affiliation(s)
- M M Gil
- Harris Birthright Research Centre for Fetal Medicine, King's College Hospital, London, UK
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41
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Yagel S, Cohen SM, Benacerraf BR, Cuckle H, Kagan KO, Van den Veyver I, Wapner R, Lee W. Noninvasive prenatal testing and fetal sonographic screening: roundtable discussion. JOURNAL OF ULTRASOUND IN MEDICINE : OFFICIAL JOURNAL OF THE AMERICAN INSTITUTE OF ULTRASOUND IN MEDICINE 2015; 34:363-369. [PMID: 25715356 DOI: 10.7863/ultra.34.3.363] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Affiliation(s)
- Simcha Yagel
- From the Baylor College of Medicine/Texas Children's Hospital, Houston, Texas USA (W.L.); Department of Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, Mt Scopus, Jerusalem, Israel (S.Y., S.M.C.); Departments of Radiology and Obstetrics and Gynecology, Brigham and Women's Hospital, and Department of Obstetrics and Gynecology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts USA (B.R.B.); Department of Reproductive Epidemiology, University of Leeds, Leeds, England (H.C.); Department of Obstetrics and Gynecology, University of Tübingen, Tübingen, Germany (K.O.K.); Departments of Obstetrics and Gynecology and Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas USA (I.V.d.V.); and Department of Obstetrics and Gynecology, Columbia University College of Physicians and Surgeons, New York, New York USA (R.W.).
| | - Sarah M Cohen
- From the Baylor College of Medicine/Texas Children's Hospital, Houston, Texas USA (W.L.); Department of Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, Mt Scopus, Jerusalem, Israel (S.Y., S.M.C.); Departments of Radiology and Obstetrics and Gynecology, Brigham and Women's Hospital, and Department of Obstetrics and Gynecology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts USA (B.R.B.); Department of Reproductive Epidemiology, University of Leeds, Leeds, England (H.C.); Department of Obstetrics and Gynecology, University of Tübingen, Tübingen, Germany (K.O.K.); Departments of Obstetrics and Gynecology and Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas USA (I.V.d.V.); and Department of Obstetrics and Gynecology, Columbia University College of Physicians and Surgeons, New York, New York USA (R.W.)
| | - Beryl R Benacerraf
- From the Baylor College of Medicine/Texas Children's Hospital, Houston, Texas USA (W.L.); Department of Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, Mt Scopus, Jerusalem, Israel (S.Y., S.M.C.); Departments of Radiology and Obstetrics and Gynecology, Brigham and Women's Hospital, and Department of Obstetrics and Gynecology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts USA (B.R.B.); Department of Reproductive Epidemiology, University of Leeds, Leeds, England (H.C.); Department of Obstetrics and Gynecology, University of Tübingen, Tübingen, Germany (K.O.K.); Departments of Obstetrics and Gynecology and Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas USA (I.V.d.V.); and Department of Obstetrics and Gynecology, Columbia University College of Physicians and Surgeons, New York, New York USA (R.W.)
| | - Howard Cuckle
- From the Baylor College of Medicine/Texas Children's Hospital, Houston, Texas USA (W.L.); Department of Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, Mt Scopus, Jerusalem, Israel (S.Y., S.M.C.); Departments of Radiology and Obstetrics and Gynecology, Brigham and Women's Hospital, and Department of Obstetrics and Gynecology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts USA (B.R.B.); Department of Reproductive Epidemiology, University of Leeds, Leeds, England (H.C.); Department of Obstetrics and Gynecology, University of Tübingen, Tübingen, Germany (K.O.K.); Departments of Obstetrics and Gynecology and Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas USA (I.V.d.V.); and Department of Obstetrics and Gynecology, Columbia University College of Physicians and Surgeons, New York, New York USA (R.W.)
| | - Karl O Kagan
- From the Baylor College of Medicine/Texas Children's Hospital, Houston, Texas USA (W.L.); Department of Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, Mt Scopus, Jerusalem, Israel (S.Y., S.M.C.); Departments of Radiology and Obstetrics and Gynecology, Brigham and Women's Hospital, and Department of Obstetrics and Gynecology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts USA (B.R.B.); Department of Reproductive Epidemiology, University of Leeds, Leeds, England (H.C.); Department of Obstetrics and Gynecology, University of Tübingen, Tübingen, Germany (K.O.K.); Departments of Obstetrics and Gynecology and Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas USA (I.V.d.V.); and Department of Obstetrics and Gynecology, Columbia University College of Physicians and Surgeons, New York, New York USA (R.W.)
| | - Ignatia Van den Veyver
- From the Baylor College of Medicine/Texas Children's Hospital, Houston, Texas USA (W.L.); Department of Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, Mt Scopus, Jerusalem, Israel (S.Y., S.M.C.); Departments of Radiology and Obstetrics and Gynecology, Brigham and Women's Hospital, and Department of Obstetrics and Gynecology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts USA (B.R.B.); Department of Reproductive Epidemiology, University of Leeds, Leeds, England (H.C.); Department of Obstetrics and Gynecology, University of Tübingen, Tübingen, Germany (K.O.K.); Departments of Obstetrics and Gynecology and Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas USA (I.V.d.V.); and Department of Obstetrics and Gynecology, Columbia University College of Physicians and Surgeons, New York, New York USA (R.W.)
| | - Ron Wapner
- From the Baylor College of Medicine/Texas Children's Hospital, Houston, Texas USA (W.L.); Department of Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, Mt Scopus, Jerusalem, Israel (S.Y., S.M.C.); Departments of Radiology and Obstetrics and Gynecology, Brigham and Women's Hospital, and Department of Obstetrics and Gynecology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts USA (B.R.B.); Department of Reproductive Epidemiology, University of Leeds, Leeds, England (H.C.); Department of Obstetrics and Gynecology, University of Tübingen, Tübingen, Germany (K.O.K.); Departments of Obstetrics and Gynecology and Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas USA (I.V.d.V.); and Department of Obstetrics and Gynecology, Columbia University College of Physicians and Surgeons, New York, New York USA (R.W.)
| | - Wesley Lee
- From the Baylor College of Medicine/Texas Children's Hospital, Houston, Texas USA (W.L.); Department of Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, Mt Scopus, Jerusalem, Israel (S.Y., S.M.C.); Departments of Radiology and Obstetrics and Gynecology, Brigham and Women's Hospital, and Department of Obstetrics and Gynecology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts USA (B.R.B.); Department of Reproductive Epidemiology, University of Leeds, Leeds, England (H.C.); Department of Obstetrics and Gynecology, University of Tübingen, Tübingen, Germany (K.O.K.); Departments of Obstetrics and Gynecology and Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas USA (I.V.d.V.); and Department of Obstetrics and Gynecology, Columbia University College of Physicians and Surgeons, New York, New York USA (R.W.)
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