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Ma L, Li Y, Li L, Wu H, Liu Y, Yang X, Lin A. A high Z-score might increase the positive predictive value of cell-free noninvasive prenatal testing for singleton-pregnant women. J Matern Fetal Neonatal Med 2023; 36:2233662. [PMID: 37433666 DOI: 10.1080/14767058.2023.2233662] [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: 03/09/2023] [Revised: 05/19/2023] [Accepted: 07/01/2023] [Indexed: 07/13/2023]
Abstract
OBJECTIVE To explore the positive predictive value (PPV) in noninvasive prenatal testing (NIPT)-positive cases and analyze the effect of the Z-score intervals on PPV performance. METHODS In this retrospective study, 26,667 pregnant women underwent NIPT from November 2014 to August 2022, of which 169 were NIPT-positive cases. NIPT-positive cases were divided into three groups according to the Z-score: 3 ≤ Z < 6, 6 ≤ Z < 10, and Z ≥ 10. RESULTS The PPVs of NIPT were 91.26% (94/103) for trisomy (T) 21, 80.65% (25/31) for T18, and 36.84% (7/19) for T13. The PPVs for the 3 ≤ Z < 6, 6 ≤ Z < 10, and Z ≥ 10 groups were 50%, 84.62%, and 87.95%, respectively. A higher PPV was found in the NIPT results when the Z-score was larger, with significant differences. The PPVs for T21/T18/T13 were 71.43%/42.86%/25% for 3 ≤ Z < 6, 90.32%/85.71%/57.14% for 6 ≤ Z < 10, and 93.85%/100%/25% for Z ≥ 10. For T21, T18, and T13, the correlations between the Z-score and fetal fraction concentration in true positives were r = 0.85, r = 0.59, and r = 0.71 (all p < .001), respectively. CONCLUSION Z-score is associated with the PPV performance of NIPT in fetal T13, T18, and T21. The possibility of false positives caused by placental chimerism should be considered when determining whether high Z-values lead to high PPVs.
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Affiliation(s)
- Li Ma
- Center for Laboratory Diagnosis, Yantai Yuhuangding Hospital Affiliated to Medical College of Qingdao University, Yantai, Shandong, P.R. China
| | - Yulan Li
- Center for Laboratory Diagnosis, Yantai Yuhuangding Hospital Affiliated to Medical College of Qingdao University, Yantai, Shandong, P.R. China
| | - Lei Li
- Department of Obstetrics, Yantai Yuhuangding Hospital Affiliated to Medical College of Qingdao University, Yantai, Shandong, P.R. China
| | - Hong Wu
- Center for Laboratory Diagnosis, Yantai Yuhuangding Hospital Affiliated to Medical College of Qingdao University, Yantai, Shandong, P.R. China
| | - Yongming Liu
- Center for Laboratory Diagnosis, Yantai Yuhuangding Hospital Affiliated to Medical College of Qingdao University, Yantai, Shandong, P.R. China
| | - Xin Yang
- Center for Laboratory Diagnosis, Yantai Yuhuangding Hospital Affiliated to Medical College of Qingdao University, Yantai, Shandong, P.R. China
| | - Aimin Lin
- Department of Gynaecology, Yantai Yuhuangding Hospital Affiliated to Medical College of Qingdao University, Yantai, Shandong, P.R. China
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Meller C, Aiello H, Otaño L. Noninvasive prenatal testing as first tier-aneuplody screening: the role of ultrasound in the post-test counseling of positive results. J Matern Fetal Neonatal Med 2022; 35:10599-10600. [PMID: 36273848 DOI: 10.1080/14767058.2022.2139174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Cesar Meller
- Fetal Medicine Unit, Department of Obstetrics and Gynecology, Hospital Italiano de Buenos Aires, Instituto Universitario Hospital Italiano, Buenos Aires, Argentina
| | - Horacio Aiello
- Fetal Medicine Unit, Department of Obstetrics and Gynecology, Hospital Italiano de Buenos Aires, Instituto Universitario Hospital Italiano, Buenos Aires, Argentina
| | - Lucas Otaño
- Fetal Medicine Unit, Department of Obstetrics and Gynecology, Hospital Italiano de Buenos Aires, Instituto Universitario Hospital Italiano, Buenos Aires, Argentina
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White K, Batey A, Schmid M. Observed and Modeled Positive Predictive Values Using Cell-free DNA Testing for Fetal Trisomy in a Clinical Laboratory Population. Fetal Diagn Ther 2021; 48:134-139. [PMID: 33472191 DOI: 10.1159/000512501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/22/2020] [Indexed: 11/19/2022]
Abstract
INTRODUCTION The objective of this study was to explore different approaches to communicating the positive predictive value (PPV) of cell-free DNA screening for fetal trisomy. METHODS PPV was established for 4 maternal age-groups (<30, 30-34, 35-39, and >39 years) from clinical laboratory data and compared to the modeled PPV from an online calculator. In women under 35, PPV was compared between 2 subsets, high risk and low risk, classified based on the diagnosis codes that were provided to the laboratory. RESULTS In 503 high-probability trisomy 21 results, the observed PPVs in the 4 age-groups were 97.0% (<30), 98.9% (30-34), 99.5% (35-39), and 96.3% (>39), all higher than those from the calculator, which ranged from 53 to 95%. Likewise, PPVs were 77.4-97.0% observed versus 16-78% modeled in 131 trisomy 18 cases and 30.4-80.0% observed versus 6-61% modeled in 80 trisomy 13 cases. In women under 35, PPV for the trisomies combined was 90.4% in the higher-risk group compared to 79.7% in the lower-risk group. CONCLUSION Modeling PPV based on maternal age will provide an underestimate in a clinical population. Although the PPV is higher for the samples with higher-risk diagnosis codes, the information that accompanies clinical samples is too general to model PPV for a specific patient.
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Affiliation(s)
- Karen White
- Ariosa Diagnostics Inc., Roche Sequencing Solutions Inc., San Jose, California, USA,
| | - Annette Batey
- Ariosa Diagnostics Inc., Roche Sequencing Solutions Inc., San Jose, California, USA
| | - Maximilian Schmid
- Ariosa Diagnostics Inc., Roche Sequencing Solutions Inc., San Jose, California, USA
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Guseh SH. Noninvasive prenatal testing: from aneuploidy to single genes. Hum Genet 2019; 139:1141-1148. [PMID: 31555907 DOI: 10.1007/s00439-019-02061-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 09/04/2019] [Indexed: 12/16/2022]
Abstract
Noninvasive prenatal testing has undergone rapid advances in the last few years. Although researchers have long known about circulating pregnancy-based cell-free fragments of DNA in maternal plasma, it was the introduction of massively parallel sequencing that allowed noninvasive prenatal testing to become a widely used clinical test. This review will begin with an in-depth analysis of the use of noninvasive prenatal testing for aneuploidy, including common causes for inaccurate and/or discordant results. It will also review the ongoing expansion of noninvasive prenatal testing to include copy number variants and select single-gene disorders. Finally, integrated throughout the review is a comparison of noninvasive prenatal testing to more traditional screening methods along with some medical and ethical implications of the widespread use of this new technology.
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Affiliation(s)
- Stephanie H Guseh
- Division of Maternal-Fetal Medicine, Obstetrics and Gynecology, Harvard Medical School, Brigham and Women's Hospital, 75 Francis St, Boston, MA, USA.
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Affiliation(s)
- Wolfgang Holzgreve
- MD, FRCOG, FACOG, MBA, Professor of Obstetrics and Gynecology, Medical Director and CEO, University Medical Center Bonn, Sigmund-Freud-Strasse 25, 53105 Bonn, Germany, Tel.: +49 228.287-10900, Fax: +49 228.287-90 10900, Mobile: +49 151.58 233 667, E-mail:
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Ranzini AC, Hyman F, Jamaer E, van Mieghem T. Aberrant Right Subclavian Artery: Correlation Between Fetal and Neonatal Abnormalities and Abnormal Genetic Screening or Testing. JOURNAL OF ULTRASOUND IN MEDICINE : OFFICIAL JOURNAL OF THE AMERICAN INSTITUTE OF ULTRASOUND IN MEDICINE 2017; 36:785-790. [PMID: 28072476 DOI: 10.7863/ultra.16.05028] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 07/08/2016] [Indexed: 06/06/2023]
Abstract
OBJECTIVES To determine whether fetuses with an isolated aberrant course of the right subclavian artery (ARSA) have increased risk for chromosomal abnormalities, including trisomy 21 or 22q11 deletion. METHODS We performed a retrospective chart review of all fetuses with antenatally diagnosed ARSA. Data were collected from fetal anatomic surveys, fetal echocardiograms, noninvasive trisomy 21 screening programs, invasive genetic studies, and neonatal records. RESULTS Seventy-nine fetuses with ARSA were identified at 20.3 ± 3.8 weeks' gestation. Forty-eight fetuses underwent chromosomal evaluation. Of those, seven had trisomy 21. Four other fetuses had unusual karyotype abnormalities. All fetuses with genetic anomalies had additional aberrant ultrasound findings. There were three spontaneous fetal deaths (trisomy 21-2 and Wolf-Hirshhorn-1). Nine pregnancies were terminated because of abnormalities and one died as a result of hypoplastic left heart syndrome. No neonate was found or suspected to have 22q11.2 deletion. The ARSA was isolated in 43 fetuses; all had unremarkable neonatal outcomes, and none were readmitted within 6 months after discharge. CONCLUSIONS As an apparently isolated finding, ARSA is benign and not associated with trisomy 21 or 22q11.2 deletion. The finding of ARSA, however, warrants a detailed fetal ultrasound. All fetuses with ARSA and genetic anomalies had additional ultrasound findings.
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Affiliation(s)
- Angela C Ranzini
- Department of Obstetrics and Gynecology, Saint Peter's University Hospital, New Brunswick, New Jersey, USA
| | - Francine Hyman
- Department of Obstetrics and Gynecology, Saint Peter's University Hospital, New Brunswick, New Jersey, USA
| | - Emily Jamaer
- Department of Obstetrics and Gynecology, University Hospitals Leuven, Leuven, Belgium
| | - Tim van Mieghem
- Department of Obstetrics and Gynecology, University Hospitals Leuven, Leuven, Belgium
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Abstract
Screening for fetal aneuploidy in pregnant women using cell-free DNA has increased dramatically since the technology became commercially available in 2011. Since that time, numerous trials have demonstrated high sensitivity and specificity to screen for common aneuploidies in high-risk populations. Studies assessing the performance of these tests in low-risk populations have also demonstrated improved detection rates compared with traditional, serum-based screening strategies. Concurrent with the increased use of this technology has been a decrease in invasive procedures (amniocentesis and chorionic villus sampling). As the technology becomes more widely understood, available, and utilized, challenges regarding its clinical implementation have become apparent. Some of these challenges include test failures, false-positive and false-negative results, limitations in positive predictive value in low-prevalence populations, and potential maternal health implications of abnormal results. In addition, commercial laboratories are expanding screening beyond common aneuploidies to include microdeletion screening and whole genome screening. This review article is intended to provide the practicing obstetrician with a summary of the complexities of cell-free DNA screening and the challenges of implementing it in the clinical setting.
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NIPTRIC: an online tool for clinical interpretation of non-invasive prenatal testing (NIPT) results. Sci Rep 2016; 6:38359. [PMID: 27917919 PMCID: PMC5137038 DOI: 10.1038/srep38359] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 11/09/2016] [Indexed: 12/31/2022] Open
Abstract
To properly interpret the result of a pregnant woman’s non-invasive prenatal test (NIPT), her a priori risk must be taken into account in order to obtain her personalised a posteriori risk (PPR), which more accurately expresses her true likelihood of carrying a foetus with trisomy. Our aim was to develop a tool for laboratories and clinicians to calculate easily the PPR for genome-wide NIPT results, using diploid samples as a control group. The tool takes the a priori risk and Z-score into account. Foetal DNA percentage and coefficient of variation can be given default settings, but actual values should be used if known. We tested the tool on 209 samples from pregnant women undergoing NIPT. For Z-scores < 5, the PPR is considerably higher at a high a priori risk than at a low a priori risk, for NIPT results with the same Z-score, foetal DNA percentage and coefficient of variation. However, the PPR is effectively independent under all conditions for Z-scores above 6. A high PPR for low a priori risks can only be reached at Z-scores > 5. Our online tool can assist clinicians in understanding NIPT results and conveying their true clinical implication to pregnant women, because the PPR is crucial for individual counselling and decision-making.
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Evans MI, Wapner RJ, Berkowitz RL. Noninvasive prenatal screening or advanced diagnostic testing: caveat emptor. Am J Obstet Gynecol 2016; 215:298-305. [PMID: 27131582 DOI: 10.1016/j.ajog.2016.04.029] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 03/30/2016] [Accepted: 04/19/2016] [Indexed: 11/30/2022]
Abstract
The past few years have seen extraordinary advances in prenatal genetic practice led by 2 major technological advances; next-generation sequencing of cell-free DNA in the maternal plasma to noninvasively identify fetal chromosome abnormalities, and microarray analysis of chorionic villus sampling and amniotic fluid samples, resulting in increased cytogenetic resolution. Noninvasive prenatal screening of cell-free DNA has demonstrated sensitivity and specificity for trisomy 21 superior to all previous screening approaches with slightly lower performance for other common aneuploidies. These tests have rapidly captured an increasing market share, with substantial reductions in the number of chorionic villus sampling and amniocentesis performed suggesting that physicians and patients regard such screening approaches as an equivalent replacement for diagnostic testing. Simultaneously, many clinical programs have noted significant decreases in patient counseling. In 2012 the Eunice Kennedy Shriver National Institute of Child Health and Human Development funded a blinded comparison of karyotype with the emerging technology of array comparative genomic hybridization showing that in patients with a normal karyotype, 2.5% had a clinically relevant microdeletion or duplication identified. In pregnancies with an ultrasound-detected structural anomaly, 6% had an incremental finding, and of those with a normal scan, 1.6% had a copy number variant. For patients of any age with a normal ultrasound and karyotype, the chance of a pathogenic copy number variant is greater than 1%, similar to the age-related risk of aneuploidy in the fetus of a 38 year old. This risk is 4-fold higher than the risk of trisomy 21 in a woman younger than 30 years and 5- to 10-fold higher than the present accepted risk of a diagnostic procedure. Based on this, we contend that every patient, regardless of her age, be educated about these risks and offered the opportunity to have a diagnostic procedure with array comparative genomic hybridization performed.
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Affiliation(s)
- Mark I Evans
- Comprehensive Genetics PLLC and Department of Obstetrics and Gynecology, New York, NY; Mt Sinai School of Medicine, New York, NY.
| | - Ronald J Wapner
- Columbia University College of Physicians and Surgeons, New York, NY
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Benn P. Posttest risk calculation following positive noninvasive prenatal screening using cell-free DNA in maternal plasma. Am J Obstet Gynecol 2016; 214:676.e1-7. [PMID: 26772793 DOI: 10.1016/j.ajog.2016.01.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 12/31/2015] [Accepted: 01/04/2016] [Indexed: 11/18/2022]
Abstract
Noninvasive prenatal screening (NIPS) for fetal chromosome defects has high sensitivity and specificity but is not fully diagnostic. In response to a desire to provide more information to individual women with positive NIPS results, 2 online calculators have been developed to calculate posttest risk (PTR). Use of these calculators is critically reviewed. There is a mathematically dictated requirement for a precise estimate for the specificity to provide an accurate PTR. This is illustrated by showing that a 0.1% decrease in the value for specificities for trisomies 21, 18, and 13 can reduce the PTR from 79-64% for trisomy 21, 39-27% for trisomy 18, and 21-13% for trisomy 13, respectively. Use of the calculators assumes that sensitivity and specificity are constant for all women receiving the test but there is evidence that discordancy between screening results and true fetal karyotype is more common for older women. Use of an appropriate value for the prior risk is also important and for rare disorders there is considerable uncertainty regarding prevalence. For example, commonly used rates for trisomy 13, monosomy-X, triploidy, and 22q11.2 deletion syndrome can vary by >4-fold and this can translate into large differences in PTR. When screening for rare disorders, it may not be possible to provide a reliable PTR if there is uncertainty over the false-positive rate and/or prevalence. These limitations, per se, do not negate the value of screening for rare conditions. However, counselors need to carefully weigh the validity of PTR before presenting them to patients. Additional epidemiologic and NIPS outcome data are needed.
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Affiliation(s)
- Peter Benn
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT.
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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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Abstract
Genetic carrier screening, prenatal screening for aneuploidy, and prenatal diagnostic testing have expanded dramatically over the past 2 decades. Driven in part by powerful market forces, new complex testing modalities have become available after limited clinical research. The responsibility for offering these tests lies primarily on the obstetrical care provider and has become more burdensome as the number of testing options expands. Genetic testing in pregnancy is optional, and decisions about undergoing tests, as well as follow-up testing, should be informed and based on individual patients' values and needs. Careful pre- and post-test counseling is central to supporting informed decision-making. This article explores three areas of technical expansion in genetic testing: expanded carrier screening, non-invasive prenatal screening for fetal aneuploidies using cell-free DNA, and diagnostic testing using fetal chromosomal microarray testing, and provides insights aimed at enabling the obstetrical practitioner to better support patients considering these tests.
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Affiliation(s)
- Jill Fonda Allen
- Department of Obstetrics and Gynecology, The George Washington University, 2150 Pennsylvania Ave, NW Washington, DC 20037.
| | - Katie Stoll
- Genetic Support Foundation, Olympia, WA; Providence Health & Services, Olympia, WA
| | - Barbara A Bernhardt
- Division of Translational Medicine and Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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Macones GA. Helping providers interpret cell-free fetal DNA testing. Am J Obstet Gynecol 2015; 213:2. [PMID: 26113226 DOI: 10.1016/j.ajog.2015.05.042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 05/19/2015] [Indexed: 01/12/2023]
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