151
|
Wald NJ, Bestwick JP. Performance of antenatal reflex DNA screening for Down's syndrome. J Med Screen 2015; 22:168-74. [PMID: 25882667 DOI: 10.1177/0969141315581005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 03/17/2015] [Indexed: 11/16/2022]
Abstract
OBJECTIVE Maternal plasma DNA analysis has a high but imperfect antenatal Down's syndrome screening performance. We aimed to determine the effect of combining DNA testing with current tests. METHODS In our modelled screening protocol, women provide two samples, one serum sample for a Combined test, and a plasma sample for a possible DNA test. Women with a Combined test risk above a specified level have a DNA test using the plasma sample without the need to recall them for another sample and counselling (ie. in a reflex manner). Women with a failed DNA test after a second attempt using a fresh plasma sample have an Integrated test. Screening performance was estimated according to the proportion of women reflexed to DNA testing and compared with universal DNA testing. RESULTS Reflexing 10% of women to a DNA test yields a 91% detection rate (DR) for a 0.025% false-positive rate (FPR) and no failed tests, compared with a 98% DR, 0.2% FPR and a 2.5% test failure rate with universal DNA testing (94% for 0.046% if 20% reflexed). DNA test failure rate has little influence on screening performance CONCLUSION Reflex DNA testing substantially reduces the FPR with a relatively small loss in detection compared with universal DNA testing, and reduces patient anxiety by avoiding the recall of women for DNA testing.
Collapse
Affiliation(s)
- Nicholas J Wald
- Wolfson Institute of Preventive Medicine, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ
| | - Jonathan P Bestwick
- Wolfson Institute of Preventive Medicine, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ
| |
Collapse
|
152
|
Allyse M, Sayres LC, Goodspeed T, Michie M, Cho MK. "Don't Want No Risk and Don't Want No Problems": Public Understandings of the Risks and Benefits of Non-Invasive Prenatal Testing in the United States. AJOB Empir Bioeth 2015; 6:5-20. [PMID: 25932463 DOI: 10.1080/23294515.2014.994722] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND The recent availability of new non-invasive prenatal genetic tests for fetal aneuploidy has raised questions concerning whether and how these new tests will be integrated into prenatal medical care. Among the many factors to be considered are public understandings and preferences about prenatal testing mechanisms and the prospect of fetal aneuploidy. METHODS To address these issues, we conducted a nation-wide mixed-method survey of 2,960 adults in the United States to explore justifications for choices among prenatal testing mechanisms. Open responses were qualitatively coded and grouped by theme. RESULTS Respondents cited accuracy, followed by cost, as the most significant aspects of prenatal testing. Acceptance of testing was predicated on differing valuations of knowledge and on personal and religious beliefs. Trust in the medical establishment, attitudes towards risk, and beliefs about health and illness were also considered relevant. CONCLUSIONS Although a significant portion of the sample population valued the additional accuracy provided by the new non-invasive tests, they nevertheless expressed concerns over high costs. Furthermore, participants continued to express reservations about the value of prenatal genetic information per se, regardless of how it was obtained.
Collapse
Affiliation(s)
- Megan Allyse
- Institute for Health and Aging, University of California San Francisco
| | | | | | - Marsha Michie
- Institute for Health and Aging, University of California San Francisco
| | - Mildred K Cho
- Stanford Center for Biomedical Ethics and Department of Pediatrics, Stanford Medical School
| |
Collapse
|
153
|
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.
Collapse
Affiliation(s)
- M M Gil
- Harris Birthright Research Centre for Fetal Medicine, King's College Hospital, London, UK
| | | | | | | | | |
Collapse
|
154
|
Cuckle H, Benn P, Pergament E. Cell-free DNA screening for fetal aneuploidy as a clinical service. Clin Biochem 2015; 48:932-41. [PMID: 25732593 DOI: 10.1016/j.clinbiochem.2015.02.011] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 01/19/2015] [Accepted: 02/12/2015] [Indexed: 12/25/2022]
Abstract
Non-invasive prenatal testing (NIPT) through the analysis of cell free (cf)DNA is revolutionizing prenatal screening for fetal aneuploidy. Current methods used in clinical practice include shotgun massively parallel sequencing (s-MPS); targeted (t-MPS); and an approach that takes advantage of single nucleotide polymorphism (SNP) differences between mother and fetus. Efficacy of cfDNA testing for the common autosomal trisomies far exceeds that of conventional screening. Depending on the methodology used, reasons for discordancy between cfDNA results and fetal karyotype can include true fetal mosaicism, confined placental mosaicism, presence of a maternal karyotype abnormality, insufficient counting due to low fetal fraction, and a vanishing twin. Among the possible cfDNA strategies a Primary test has the highest performance but is expensive, while a Contingent cfDNA test can achieve high performance at a relatively low cost. Practicalities to be considered in the provision of testing include pretest counseling about the scope and accuracy of the testing, the interpretation of results when there is a low fetal fraction and follow-up studies for positive test results. The role of first trimester nuchal translucency measurement and conventional biochemical testing needs to be reassessed in the context of the use of cfDNA.
Collapse
Affiliation(s)
- Howard Cuckle
- Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY 10032, USA.
| | - Peter Benn
- Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, CT 06030, USA
| | | |
Collapse
|
155
|
Gil MM, Akolekar R, Quezada MS, Bregant B, Nicolaides KH. Analysis of cell-free DNA in maternal blood in screening for aneuploidies: meta-analysis. Fetal Diagn Ther 2015; 35:156-73. [PMID: 24513694 DOI: 10.1159/000358326] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 12/26/2013] [Indexed: 11/19/2022]
Abstract
OBJECTIVE To review clinical validation or implementation studies of maternal blood cell-free (cf) DNA analysis in screening for aneuploidies and to explore the potential use of this method in clinical practice. METHODS Searches of PubMed and MEDLINE were performed to identify all peer-reviewed articles on cfDNA testing in screening for aneuploidies between 2011, when the first such study was published, and 20 December 2013. RESULTS Weighted pooled detection rates (DR) and false-positive rates (FPR) in singleton pregnancies were 99.0% (95% CI 98.2–99.6) and 0.08% (95% CI0.03–0.14), respectively, for trisomy 21; 96.8% (95% CI 94.5–98.4) and 0.15% (95% CI 0.08–0.25) for trisomy 18; 92.1% (95% CI 85.9–96.7) and 0.20% (95% CI 0.04–0.46) for trisomy 13; 88.6% (95% CI 83.0–93.1) and 0.12% (95% CI 0.05–0.24) for monosomy X, and 93.8% (95% CI 85.9–98.7) and 0.12% (95% CI 0.02–0.28) for sex chromosome aneuploidies other than monosomy X. For twin pregnancies, the DR was 94.4% (95% 74.2–99.0) and the FPR was 0% (95% CI 0.00–1.84) for trisomy 21. CONCLUSION An analysis of cfDNA in maternal blood provides effective screening for trisomies.
Collapse
|
156
|
Abstract
Rapid progress in genomic medicine in recent years has made it possible to diagnose subtle genetic abnormalities in a clinical setting on routine basis. This has allowed for detailed genotype-phenotype correlations and the identification of the genetic basis of many congenital anomalies. In addition to the availability of chromosomal microarray analysis, exome and whole-genome sequencing on pre- and postnatal samples of cell-free DNA has revolutionized the field of prenatal diagnosis. Incorporation of these technologies in perinatal pathology is bound to play a major role in coming years. In this communication, we briefly present the current experience with use of classical chromosome analysis, fluorescence in situ hybridization, and microarray testing, development of whole-genome analysis by next-generation sequencing technology, offer a detailed review of the history and current status of non-invasive prenatal testing using cell-free DNA, and discuss the advents of these new genomic technologies in perinatal medicine.
Collapse
Affiliation(s)
- David G. Peters
- Department of Obstetrics, Gynecology, and Reproductive Sciences,
University of Pittsburgh, Pittsburgh, PA 15213,Magee-Womens Research Institute, University of Pittsburgh,
Pittsburgh, PA 15213
| | - Svetlana A. Yatsenko
- Department of Obstetrics, Gynecology, and Reproductive Sciences,
University of Pittsburgh, Pittsburgh, PA 15213,Department of Pathology, University of Pittsburgh, Pittsburgh, PA
15213
| | - Urvashi Surti
- Department of Obstetrics, Gynecology, and Reproductive Sciences,
University of Pittsburgh, Pittsburgh, PA 15213,Department of Pathology, University of Pittsburgh, Pittsburgh, PA
15213,Magee-Womens Research Institute, University of Pittsburgh,
Pittsburgh, PA 15213,Department of Human Genetics, University of Pittsburgh, Pittsburgh,
PA 15213
| | - Aleksandar Rajkovic
- Department of Obstetrics, Gynecology, and Reproductive Sciences,
University of Pittsburgh, Pittsburgh, PA 15213,Department of Pathology, University of Pittsburgh, Pittsburgh, PA
15213,Magee-Womens Research Institute, University of Pittsburgh,
Pittsburgh, PA 15213,Department of Human Genetics, University of Pittsburgh, Pittsburgh,
PA 15213
| |
Collapse
|
157
|
Wong AI, Lo YD. Noninvasive fetal genomic, methylomic, and transcriptomic analyses using maternal plasma and clinical implications. Trends Mol Med 2015; 21:98-108. [DOI: 10.1016/j.molmed.2014.12.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 12/12/2014] [Accepted: 12/18/2014] [Indexed: 01/01/2023]
|
158
|
Allyse M, Minear MA, Berson E, Sridhar S, Rote M, Hung A, Chandrasekharan S. Non-invasive prenatal testing: a review of international implementation and challenges. Int J Womens Health 2015; 7:113-26. [PMID: 25653560 PMCID: PMC4303457 DOI: 10.2147/ijwh.s67124] [Citation(s) in RCA: 207] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Noninvasive prenatal genetic testing (NIPT) is an advance in the detection of fetal chromosomal aneuploidies that analyzes cell-free fetal DNA in the blood of a pregnant woman. Since its introduction to clinical practice in Hong Kong in 2011, NIPT has quickly spread across the globe. While many professional societies currently recommend that NIPT be used as a screening method, not a diagnostic test, its high sensitivity (true positive rate) and specificity (true negative rate) make it an attractive alternative to the serum screens and invasive tests currently in use. Professional societies also recommend that NIPT be accompanied by genetic counseling so that families can make informed reproductive choices. If NIPT becomes more widely adopted, States will have to implement regulation and oversight to ensure it fits into existing legal frameworks, with particular attention to returning fetal sex information in areas where sex-based abortions are prevalent. Although there are additional challenges for NIPT uptake in the developing world, including the lack of health care professionals and infrastructure, the use of NIPT in low-resource settings could potentially reduce the need for skilled clinicians who perform invasive testing. Future advances in NIPT technology promise to expand the range of conditions that can be detected, including single gene disorders. With these advances come questions of how to handle incidental findings and variants of unknown significance. Moving forward, it is essential that all stakeholders have a voice in crafting policies to ensure the ethical and equitable use of NIPT across the world.
Collapse
Affiliation(s)
- Megan Allyse
- Institute for Health and Aging, University of California San Francisco, San Francisco, California, USA
| | | | - Elisa Berson
- Trinity College of Arts and Sciences, Duke University, Durham, NC, USA
| | - Shilpa Sridhar
- Trinity College of Arts and Sciences, Duke University, Durham, NC, USA
| | - Margaret Rote
- Trinity College of Arts and Sciences, Duke University, Durham, NC, USA
| | - Anthony Hung
- Trinity College of Arts and Sciences, Duke University, Durham, NC, USA
| | | |
Collapse
|
159
|
Palomaki GE, Kloza EM, Lambert-Messerlian GM, van den Boom D, Ehrich M, Deciu C, Bombard AT, Haddow JE. Circulating cell free DNA testing: are some test failures informative? Prenat Diagn 2015; 35:289-93. [DOI: 10.1002/pd.4541] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 11/25/2014] [Accepted: 11/26/2014] [Indexed: 12/26/2022]
Affiliation(s)
- G. E. Palomaki
- Department of Pathology and Laboratory Medicine; Women & Infants Hospital; Providence RI USA
- Alpert Medical School; Brown University; Providence RI USA
- Savjani Institute for Health Research; Windham ME USA
| | - E. M. Kloza
- Department of Pathology and Laboratory Medicine; Women & Infants Hospital; Providence RI USA
- Savjani Institute for Health Research; Windham ME USA
| | - G. M. Lambert-Messerlian
- Department of Pathology and Laboratory Medicine; Women & Infants Hospital; Providence RI USA
- Alpert Medical School; Brown University; Providence RI USA
| | | | | | - C. Deciu
- Sequenom Biosciences; San Diego CA USA
| | - A. T. Bombard
- Sequenom, Inc; San Diego CA USA
- Sequenom Biosciences; San Diego CA USA
- ATB: Progenity, Inc.; San Diego CA USA
| | - J. E. Haddow
- Department of Pathology and Laboratory Medicine; Women & Infants Hospital; Providence RI USA
- Alpert Medical School; Brown University; Providence RI USA
- Savjani Institute for Health Research; Windham ME USA
| |
Collapse
|
160
|
Detection of triploid, molar, and vanishing twin pregnancies by a single-nucleotide polymorphism-based noninvasive prenatal test. Am J Obstet Gynecol 2015; 212:79.e1-9. [PMID: 25447960 DOI: 10.1016/j.ajog.2014.10.012] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 08/11/2014] [Accepted: 10/07/2014] [Indexed: 12/11/2022]
Abstract
OBJECTIVE We sought to determine the ability of single-nucleotide polymorphism-based noninvasive prenatal testing (NIPT) to identify triploid, unrecognized twin, and vanishing twin pregnancies. STUDY DESIGN The study included 30,795 consecutive reported clinical cases received for NIPT for fetal whole-chromosome aneuploidies; known multiple gestations were excluded. Cell-free DNA was isolated from maternal blood samples, amplified via 19,488-plex polymerase chain reaction, and sequenced. Sequencing results were analyzed to determine fetal chromosome copy number and to identify the presence of additional fetal haplotypes. RESULTS Additional fetal haplotypes, indicative of fetal triploidy, vanishing twin, or undetected twin pregnancy, were identified in 130 (0.42%) cases. Clinical confirmation (karyotype for singleton pregnancies, ultrasound for multifetal pregnancies) was available for 58.5% (76/130) of cases. Of the 76 cases with confirmation, 42.1% were vanishing twin, 48.7% were viable twin, 5.3% were diandric triploids, and 3.9% were nontriploid pregnancies that lacked evidence of co-twin demise. One pregnancy had other indications suggesting triploidy but lacked karyotype confirmation. Of the 5 vanishing twin cases with a known date of demise, 100% of losses occurred in the first trimester; up to 8 weeks elapsed between loss and detection by NIPT. CONCLUSION This single-nucleotide polymorphism-based NIPT successfully identified vanished twin, previously unrecognized twin, and triploid pregnancies. As vanishing twins are more likely to be aneuploid, and undetected residual cell-free DNA could bias NIPT results, the ability of this method to identify additional fetal haplotypes is expected to result in fewer false-positive calls and prevent incorrect fetal sex calls.
Collapse
|
161
|
|
162
|
Manegold-Brauer G, Hahn S, Lapaire O. What does next-generation sequencing mean for prenatal diagnosis? Biomark Med 2014; 8:499-508. [PMID: 24796613 DOI: 10.2217/bmm.14.18] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The ability to gain genetic information from the fetus in the mother's blood during pregnancy has been a long desired goal of research in prenatal medicine. The detection of fetal DNA in maternal blood, coupled with the development of the powerful techniques of next-generation sequencing finally transferred this analysis into clinical practice. Following the commercial introduction of noninvasive prenatal testing for aneuploidies, there has been a very strong demand, which has fostered an extreme rapid development and improvement of technology. Publications in this field are so numerous so that it is challenging to keep up with the latest state of the art. Here, we describe the current basic concepts of cell-free DNA-based noninvasive prenatal testing, give an overview of the currently commercially available tests and the chromosomal aberrations that can be identified. We also present current and future concepts for the implementation of cell-free DNA testing into clinical care.
Collapse
|
163
|
Abstract
Zusammenfassung
Das Ersttrimesterscreening zur Risikobestimmung für die Trisomien 21, 18 und 13 hat sich in den letzten 15 Jahren in Deutschland etabliert. Die optimale Durchführung setzt die Einhaltung bestimmter Messkriterien beim Ultraschall und bei der biochemischen Analyse voraus sowie die Benutzung evaluierter Risikoberechnungsprogramme wie dem Berechnungsprogramm PRC der Fetal Medicine Foundation Deutschland (FMF-D). Durch die neue Version des Berechnungsprogramms PRC konnten die Trisomie-21-, -18- und -13-Detektionsraten erhöht werden bei gleichzeitiger Senkung der Falsch-positiv-Raten, was einen großen Fortschritt verglichen mit der mütterlichen Altersindikation darstellt.
Durch die Analyse der zellfreien fetalen DNA aus dem mütterlichen Plasma können seit 2 Jahren aber wesentlich bessere Screeningvorhersagen getroffen werden. Über 99 % aller Trisomie-21-Schwangerschaften können mit dieser Methodik als Risikogruppe beschrieben werden. Die Falsch-positiv-Rate liegt unter 1 %. Durch diese Methode ist ein Paradigmenwechsel in der Pränataldiagnostik zu erwarten.
Collapse
Affiliation(s)
- Bernd Eiben
- Aff1 amedes genetics amedes Institut Labormedizin und Klinische Genetik Rhein/Ruhr 45127 Essen Deutschland
| | - Ralf Glaubitz
- Aff2 amedes genetics Hannover Georgstr. 50 Hannover Deutschland
| | - Karl Oliver Kagan
- Aff3 grid.411544.1 0000000101968249 Universitätsfrauenklinik Tübingen Calwerstr. 7 72076 Tübingen Deutschland
| |
Collapse
|
164
|
Sonek JD, Cuckle HS. What will be the role of first-trimester ultrasound if cell-free DNA screening for aneuploidy becomes routine? ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2014; 44:621-630. [PMID: 25449114 DOI: 10.1002/uog.14692] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Affiliation(s)
- J D Sonek
- Department of Obstetrics and Gynecology, Wright State University, Dayton, OH, USA
| | | |
Collapse
|
165
|
Wagner AJ, Mitchell ME, Tomita-Mitchell A. Use of cell-free fetal DNA in maternal plasma for noninvasive prenatal screening. Clin Perinatol 2014; 41:957-66. [PMID: 25459783 DOI: 10.1016/j.clp.2014.08.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Noninvasive prenatal testing (NIPT) using cell-free fetal (cfDNA) offers potential as a screening tool for fetal anomalies. All pregnant women should be offered prenatal screening and diagnostic testing based on current guidelines. Adoption of NIPT in high-risk pregnancies suggests a change in the standard of care for genetic screening; there are advantages to an accurate test with results available early in pregnancy. This accuracy decreases the overall number of invasive tests needed for diagnosis, subjecting fewer pregnancies to the risks of invasive procedures. Women undergoing NIPT need informed consent before testing and accurate, sensitive counseling after results are available.
Collapse
Affiliation(s)
- Amy J Wagner
- Division of Pediatric Surgery, Department of Surgery, Medical College of Wisconsin, 999 North 92nd Street, Suite C320, Milwaukee, WI 53226, USA
| | - Michael E Mitchell
- Division of Cardiothoracic Surgery, Department of Surgery, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Aoy Tomita-Mitchell
- Division of Cardiothoracic Surgery, Department of Surgery, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.
| |
Collapse
|
166
|
Benn P. Noninvasive Prenatal Testing Using Cell-free DNA in Maternal Circulation. JOURNAL OF FETAL MEDICINE 2014. [DOI: 10.1007/s40556-014-0021-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
167
|
Clinical experience and follow-up with large scale single-nucleotide polymorphism-based noninvasive prenatal aneuploidy testing. Am J Obstet Gynecol 2014; 211:527.e1-527.e17. [PMID: 25111587 DOI: 10.1016/j.ajog.2014.08.006] [Citation(s) in RCA: 193] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Revised: 06/30/2014] [Accepted: 08/06/2014] [Indexed: 01/27/2023]
Abstract
OBJECTIVE We sought to report on laboratory and clinical experience following 6 months of clinical implementation of a single-nucleotide polymorphism-based noninvasive prenatal aneuploidy test in high- and low-risk women. STUDY DESIGN All samples received from March through September 2013 and drawn ≥9 weeks' gestation were included. Samples that passed quality control were analyzed for trisomy 21, trisomy 18, trisomy 13, and monosomy X. Results were reported as high or low risk for fetal aneuploidy for each interrogated chromosome. Relationships between fetal fraction and gestational age and maternal weight were analyzed. Follow-up on outcome was sought for a subset of high-risk cases. False-negative results were reported voluntarily by providers. Positive predictive value (PPV) was calculated from cases with an available prenatal or postnatal karyotype or clinical evaluation at birth. RESULTS Samples were received from 31,030 patients, 30,705 met study criteria, and 28,739 passed quality-control metrics and received a report detailing aneuploidy risk. Fetal fraction correlated positively with gestational age, and negatively with maternal weight. In all, 507 patients received a high-risk result for any of the 4 tested conditions (324 trisomy 21, 82 trisomy 18, 41 trisomy 13, 61 monosomy X; including 1 double aneuploidy case). Within the 17,885 cases included in follow-up analysis, 356 were high risk, and outcome information revealed 184 (51.7%) true positives, 38 (10.7%) false positives, 19 (5.3%) with ultrasound findings suggestive of aneuploidy, 36 (10.1%) spontaneous abortions without karyotype confirmation, 22 (6.2%) terminations without karyotype confirmation, and 57 (16.0%) lost to follow-up. This yielded an 82.9% PPV for all aneuploidies, and a 90.9% PPV for trisomy 21. The overall PPV for women aged ≥35 years was similar to the PPV for women aged <35 years. Two patients were reported as false negatives. CONCLUSION The data from this large-scale report on clinical application of a commercially available noninvasive prenatal test suggest that the clinical performance of this single-nucleotide polymorphism-based noninvasive prenatal test in a mixed high- and low-risk population is consistent with performance in validation studies.
Collapse
|
168
|
Thung DT, Beulen L, Hehir-Kwa J, Faas BH. Implementation of whole genome massively parallel sequencing for noninvasive prenatal testing in laboratories. Expert Rev Mol Diagn 2014; 15:111-24. [PMID: 25347354 DOI: 10.1586/14737159.2015.973857] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Noninvasive prenatal testing (NIPT) for fetal aneuploidies using cell-free fetal DNA in maternal plasma has revolutionized the field of prenatal care and methods using massively parallel sequencing are now being implemented almost worldwide. Substantial progress has been made from initially testing for (an)euploidies of chromosomes 13, 18 and 21, to testing for sex chromosome (an)euploidies, additional autosomal aneuploidies as well as partial deletions and duplications genome-wide. Although NIPT is associated with significantly reduced risks for the fetus in comparison to existing invasive prenatal diagnostic methods, it presents several implementation challenges. Here, we review key issues potentially influencing NIPT and illustrate them using both data from literature and in-house data.
Collapse
|
169
|
McCullough RM, Almasri EA, Guan X, Geis JA, Hicks SC, Mazloom AR, Deciu C, Oeth P, Bombard AT, Paxton B, Dharajiya N, Saldivar JS. Non-invasive prenatal chromosomal aneuploidy testing--clinical experience: 100,000 clinical samples. PLoS One 2014; 9:e109173. [PMID: 25289665 PMCID: PMC4188614 DOI: 10.1371/journal.pone.0109173] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 09/09/2014] [Indexed: 01/03/2023] Open
Abstract
Objective As the first laboratory to offer massively parallel sequencing-based noninvasive prenatal testing (NIPT) for fetal aneuploidies, Sequenom Laboratories has been able to collect the largest clinical population experience data to date, including >100,000 clinical samples from all 50 U.S. states and 13 other countries. The objective of this study is to give a robust clinical picture of the current laboratory performance of the MaterniT21 PLUS LDT. Study Design The study includes plasma samples collected from patients with high-risk pregnancies in our CLIA–licensed, CAP-accredited laboratory between August 2012 to June 2013. Samples were assessed for trisomies 13, 18, 21 and for the presence of chromosome Y-specific DNA. Sample data and ad hoc outcome information provided by the clinician was compiled and reviewed to determine the characteristics of this patient population, as well as estimate the assay performance in a clinical setting. Results NIPT patients most commonly undergo testing at an average of 15 weeks, 3 days gestation; and average 35.1 years of age. The average turnaround time is 4.54 business days and an overall 1.3% not reportable rate. The positivity rate for Trisomy 21 was 1.51%, followed by 0.45% and 0.21% rate for Trisomies 18 and 13, respectively. NIPT positivity rates are similar to previous large clinical studies of aneuploidy in women of maternal age ≥35 undergoing amniocentesis. In this population 3519 patients had multifetal gestations (3.5%) with 2.61% yielding a positive NIPT result. Conclusion NIPT has been commercially offered for just over 2 years and the clinical use by patients and clinicians has increased significantly. The risks associated with invasive testing have been substantially reduced by providing another assessment of aneuploidy status in high-risk patients. The accuracy and NIPT assay positivity rate are as predicted by clinical validations and the test demonstrates improvement in the current standard of care.
Collapse
Affiliation(s)
- Ron M. McCullough
- Clinical Science, Sequenom Laboratories, San Diego, California, United States of America
- * E-mail:
| | - Eyad A. Almasri
- Clinical Science, Sequenom Laboratories, San Diego, California, United States of America
| | - Xiaojun Guan
- Clinical Science, Sequenom Laboratories, San Diego, California, United States of America
| | - Jennifer A. Geis
- Clinical Science, Sequenom Laboratories, San Diego, California, United States of America
| | - Susan C. Hicks
- Clinical Science, Sequenom Laboratories, San Diego, California, United States of America
| | - Amin R. Mazloom
- Clinical Science, Sequenom Laboratories, San Diego, California, United States of America
| | - Cosmin Deciu
- Clinical Science, Sequenom Laboratories, San Diego, California, United States of America
| | - Paul Oeth
- Clinical Science, Sequenom Laboratories, San Diego, California, United States of America
| | - Allan T. Bombard
- Clinical Science, Sequenom Laboratories, San Diego, California, United States of America
| | - Bill Paxton
- Clinical Science, Sequenom Laboratories, San Diego, California, United States of America
| | - Nilesh Dharajiya
- Clinical Science, Sequenom Laboratories, San Diego, California, United States of America
| | | |
Collapse
|
170
|
Porreco RP, Garite TJ, Maurel K, Marusiak B, Ehrich M, van den Boom D, Deciu C, Bombard A. Noninvasive prenatal screening for fetal trisomies 21, 18, 13 and the common sex chromosome aneuploidies from maternal blood using massively parallel genomic sequencing of DNA. Am J Obstet Gynecol 2014; 211:365.e1-12. [PMID: 24657131 DOI: 10.1016/j.ajog.2014.03.042] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Revised: 03/06/2014] [Accepted: 03/17/2014] [Indexed: 12/11/2022]
Abstract
OBJECTIVE The objective of this study was to validate the clinical performance of massively parallel genomic sequencing of cell-free deoxyribonucleic acid contained in specimens from pregnant women at high risk for fetal aneuploidy to test fetuses for trisomies 21, 18, and 13; fetal sex; and the common sex chromosome aneuploidies (45, X; 47, XXX; 47, XXY; 47, XYY). STUDY DESIGN This was a prospective multicenter observational study of pregnant women at high risk for fetal aneuploidy who had made the decision to pursue invasive testing for prenatal diagnosis. Massively parallel single-read multiplexed sequencing of cell-free deoxyribonucleic acid was performed in maternal blood for aneuploidy detection. Data analysis was completed using sequence reads unique to the chromosomes of interest. RESULTS A total of 3430 patients were analyzed for demographic characteristics and medical history. There were 137 fetuses with trisomy 21, 39 with trisomy 18, and 16 with trisomy 13 for a prevalence rate of the common autosomal trisomies of 5.8%. There were no false-negative results for trisomy 21, 3 for trisomy 18, and 2 for trisomy 13; all 3 false-positive results were for trisomy 21. The positive predictive values for trisomies 18 and 13 were 100% and 97.9% for trisomy 21. A total of 8.6% of the pregnancies were 21 weeks or beyond; there were no aneuploid fetuses in this group. All 15 of the common sex chromosome aneuploidies in this population were identified, although there were 11 false-positive results for 45,X. Taken together, the positive predictive value for the sex chromosome aneuploidies was 48.4% and the negative predictive value was 100%. CONCLUSION Our prospective study demonstrates that noninvasive prenatal analysis of cell-free deoxyribonucleic acid from maternal plasma is an accurate advanced screening test with extremely high sensitivity and specificity for trisomy 21 (>99%) but with less sensitivity for trisomies 18 and 13. Despite high sensitivity, there was modest positive predictive value for the small number of common sex chromosome aneuploidies because of their very low prevalence rate.
Collapse
Affiliation(s)
- Richard P Porreco
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Presbyterian/St Luke's Medical Center, Obstetrix Medical Group of Colorado, Denver, CO.
| | - Thomas J Garite
- University of California, Irvine, Orange, CA, and Pediatrix/Obstetrix Medical Group, Inc, Sunrise, FL/Perigen Inc, Princeton, NJ
| | | | | | | | | | | | | |
Collapse
|
171
|
Korostelev S, Totchiev G, Kanivets I, Gnetetskaya V. Association of non-invasive prenatal testing and chromosomal microarray analysis for prenatal diagnostics. Gynecol Endocrinol 2014; 30 Suppl 1:13-6. [PMID: 25200820 DOI: 10.3109/09513590.2014.945770] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The purposes of this study is to examine possibility to use combination of non-invasive prenatal testing (NIPT) and chromosomal microarray analysis (CMA) for prenatal diagnostics and their advantages between combined first-trimester screen with confirmation by karyotyping of CVS or amniocytes. A total of 1968 pregnant women, in this study, have undergone prenatal screening and/or diagnostic tests. NIPT is more suitable and efficient for the detection of aneuploidy. However, this test has limitations for detection deletions/duplications. Use of CMA for confirmation of some NIPT findings or as first test for women with ultrasound abnormalities can detect small imbalances in chromosomes. Combination of NIPT and CMA allows a higher prenatal detection of chromosomal abnormalities.
Collapse
MESH Headings
- Adult
- Algorithms
- Chromosome Aberrations/embryology
- Chromosomes, Human, Pair 13/genetics
- Chromosomes, Human, Pair 18/genetics
- Chromosomes, Human, Pair 21/genetics
- Chromosomes, Human, X/genetics
- Chromosomes, Human, Y/genetics
- Female
- Humans
- Microarray Analysis/methods
- Polymorphism, Single Nucleotide/genetics
- Pregnancy
- Prenatal Diagnosis/methods
Collapse
Affiliation(s)
- S Korostelev
- First Moscow Medical University , Moscow , Russia
| | | | | | | |
Collapse
|
172
|
Ayres AC, Whitty JA, Ellwood DA. A cost-effectiveness analysis comparing different strategies to implement noninvasive prenatal testing into a Down syndrome screening program. Aust N Z J Obstet Gynaecol 2014; 54:412-7. [PMID: 25196262 DOI: 10.1111/ajo.12223] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Accepted: 04/28/2014] [Indexed: 12/13/2022]
Abstract
BACKGROUND Currently, noninvasive prenatal testing (NIPT) is only recommended in high-risk women following conventional Down syndrome (DS) screening, and it has not yet been included in the Australian DS screening program. AIMS To evaluate the cost-effectiveness of different strategies of NIPT for DS screening in comparison with current practice. METHODS A decision-analytic approach modelled a theoretical cohort of 300,000 singleton pregnancies. The strategies compared were the following: current practice, NIPT as a second-tier investigation, NIPT only in women >35 years, NIPT only in women >40 years and NIPT for all women. The direct costs (low and high estimates) were derived using both health system costs and patient out-of-pocket expenses. The number of DS cases detected and procedure-related losses (PRL) were compared between strategies. The incremental cost per case detected was the primary measure of cost-effectiveness. RESULTS Universal NIPT costs an additional $134,636,832 compared with current practice, but detects 123 more DS cases (at an incremental cost of $1,094,608 per case) and avoids 90 PRL. NIPT for women >40 years was the most cost-effective strategy, costing an incremental $81,199 per additional DS case detected and avoiding 95 PRL. CONCLUSIONS The cost of NIPT needs to decrease significantly if it is to replace current practice on a purely cost-effectiveness basis. However, it may be beneficial to use NIPT as first-line screening in selected high-risk patients. Further evaluation is needed to consider the longer-term costs and benefits of screening.
Collapse
Affiliation(s)
- Alice C Ayres
- School of Medicine, Gold Coast Campus, Griffith University, Gold Coast, Queensland, Australia
| | | | | |
Collapse
|
173
|
Comas C, Echevarria M, Rodríguez MA, Prats P, Rodríguez I, Serra B. Initial experience with non-invasive prenatal testing of cell-free DNA for major chromosomal anomalies in a clinical setting. J Matern Fetal Neonatal Med 2014; 28:1196-201. [PMID: 25048745 DOI: 10.3109/14767058.2014.947579] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
OBJECTIVE To evaluate non-invasive prenatal testing (NIPT) of cell-free DNA (cfDNA) as a screening method for major chromosomal anomalies (CA) in a clinical setting. METHODS From January to December 2013, Panorama™ test or Harmony™ prenatal test were offered as advanced NIPT, in addition to first-trimester combined screening in singleton pregnancies. RESULTS The cohort included 333 pregnant women with a mean maternal age (MA) of 37 years who underwent testing at a mean gestational age of 14.6 weeks. Eighty-four percent were low-risk pregnancies. Results were provided in 97.3% of patients at a mean reporting time of 12.9 calendar days. Repeat sampling was performed in six cases and results were obtained in five of them. No results were provided in four cases. Four cases of Down syndrome were detected and there was one discordant result of Turner syndrome. We found no statistical differences between commercial tests except in reporting time, fetal fraction and MA. The cfDNA fraction was statistically associated with test type, maternal weight, BMI and log βhCG levels. CONCLUSIONS NIPT has the potential to be a highly effective screening method for major CA in a clinical setting.
Collapse
Affiliation(s)
- Carmina Comas
- a Fetal Medicine Unit, Department of Obstetrics and Gynecology , Hospital Universitari Quirón Dexeus , Barcelona , Spain
| | | | | | | | | | | |
Collapse
|
174
|
Pergament E, Cuckle H, Zimmermann B, Banjevic M, Sigurjonsson S, Ryan A, Hall MP, Dodd M, Lacroute P, Stosic M, Chopra N, Hunkapiller N, Prosen DE, McAdoo S, Demko Z, Siddiqui A, Hill M, Rabinowitz M. Single-nucleotide polymorphism-based noninvasive prenatal screening in a high-risk and low-risk cohort. Obstet Gynecol 2014; 124:210-218. [PMID: 25004354 PMCID: PMC4144440 DOI: 10.1097/aog.0000000000000363] [Citation(s) in RCA: 213] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
OBJECTIVE To estimate performance of a single-nucleotide polymorphism-based noninvasive prenatal screen for fetal aneuploidy in high-risk and low-risk populations on single venopuncture. METHODS One thousand sixty-four maternal blood samples from 7 weeks of gestation and beyond were included; 1,051 were within specifications and 518 (49.3%) were low risk. Cell-free DNA was amplified, sequenced, and analyzed using the Next-generation Aneuploidy Test Using SNPs algorithm. Samples were called as trisomies 21, 18, 13, or monosomy X, or euploid, and male or female. RESULTS Nine hundred sixty-six samples (91.9%) successfully generated a cell-free DNA result. Among these, sensitivity was 100% for trisomy 21 (58/58, confidence interval [CI] 93.8-100%), trisomy 13 (12/12, CI 73.5-100%), and fetal sex (358/358 female, CI 99.0-100%; 418/418 male, CI 99.1-100%), 96.0% for trisomy 18 (24/25, CI 79.7-99.9%), and 90% for monosomy X (9/10, CI 55.5-99.8%). Specificity for trisomies 21 and 13 was 100% (905/905, CI 99.6-100%; and 953/953, CI 99.6-100%, respectively) and for trisomy 18 and monosomy X was 99.9% (938/939, CI 99.4-100%; and 953/954, CI 99.4-100%, respectively). However, 16% (20/125) of aneuploid samples did not return a result; 50% (10/20) had a fetal fraction below the 1.5th percentile of euploid pregnancies. Aneuploidy rate was significantly higher in these samples (P<.001, odds ratio 9.2, CI 4.4-19.0). Sensitivity and specificity did not differ in low-risk and high-risk populations. CONCLUSIONS This noninvasive prenatal screen performed with high sensitivity and specificity in high-risk and low-risk cohorts. Aneuploid samples were significantly more likely to not return a result; the number of aneuploidy samples was especially increased among samples with low fetal fraction. This underscores the importance of redraws or, in rare cases, invasive procedures based on low fetal fraction. LEVEL OF EVIDENCE II.
Collapse
|
175
|
Bruno DL, Ganesamoorthy D, Thorne NP, Ling L, Bahlo M, Forrest S, Veenendaal M, Katerelos M, Skene A, Ierino FL, Power DA, Slater HR. Use of Copy Number Deletion Polymorphisms to Assess DNA Chimerism. Clin Chem 2014; 60:1105-14. [DOI: 10.1373/clinchem.2013.216077] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Abstract
BACKGROUND
We describe a novel approach that harnesses the ubiquity of copy number deletion polymorphisms in human genomes to definitively detect and quantify chimeric DNA in clinical samples. Unlike other molecular approaches to chimerism analysis, the copy number deletion (CND) method targets genomic loci (>50 base pairs in length) that are wholly absent from wild-type (i.e., self) background DNA sequences in a sex-independent manner.
METHODS
Bespoke quantitative PCR (qPCR) CND assays were developed and validated using a series of DNA standards and chimeric plasma DNA samples collected from 2 allogeneic kidney transplant recipients and 12 pregnant women. Assay performance and informativeness were assessed using appropriate statistical methods.
RESULTS
The CND qPCR assays showed high sensitivity, precision, and reliability for linear quantification of DNA chimerism down to 16 genomic equivalents (i.e., 106 pg). Fetal fraction (%) in 12 singleton male pregnancies was calculated using the CND qPCR approach, which showed closer agreement with single-nucleotide polymorphism–based massively parallel sequencing than the SRY (sex determining region Y) (Y chromosome) qPCR assay. The latter consistently underestimated the fetal fraction relative to the other methods. We also were able to measure biological changes in plasma nonself DNA concentrations in 2 renal transplant recipients.
CONCLUSIONS
The CND qPCR technique is suitable for measurement of chimerism for monitoring of rejection in allogeneic organ transplantation and quantification of the cell-free fetal DNA fraction in maternal plasma samples used for noninvasive prenatal genetic testing.
Collapse
Affiliation(s)
- Damien L Bruno
- Murdoch Childrens Research Institute, Melbourne, VIC, Australia
| | - Devika Ganesamoorthy
- Murdoch Childrens Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Natalie P Thorne
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Ling Ling
- Murdoch Childrens Research Institute, Melbourne, VIC, Australia
| | - Melanie Bahlo
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Mathematics and Statistics, University of Melbourne, Melbourne, VIC, Australia
| | - Sue Forrest
- The Australian Genome Research Facility, Parkville, VIC, Australia
| | | | - Marina Katerelos
- Department of Nephrology, Austin Health, Melbourne, VIC, Australia
| | - Alison Skene
- Department of Anatomical Pathology, Austin Hospital, Melbourne, VIC, Australia
| | - Frank L Ierino
- Department of Nephrology, Austin Health, Melbourne, VIC, Australia
| | - David A Power
- Department of Nephrology, Austin Health, Melbourne, VIC, Australia
| | - Howard R Slater
- Murdoch Childrens Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| |
Collapse
|
176
|
A commentary on comparison of the performance of Ion Torrent chips in noninvasive prenatal trisomy detection. J Hum Genet 2014; 59:421-2. [PMID: 24990312 DOI: 10.1038/jhg.2014.56] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
177
|
Verweij EJ, de Boer MA, Oepkes D. Non-invasive prenatal testing for trisomy 13: more harm than good? ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2014; 44:112-114. [PMID: 24753041 DOI: 10.1002/uog.13388] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 04/07/2014] [Accepted: 04/11/2014] [Indexed: 06/03/2023]
Abstract
A 35-year-old primigravida, pregnant after in-vitro fertilization, was seen because of a trisomy 13/trisomy 18 (T13/T18) risk of 1:55, based on the result of her first-trimester combined test. She elected for non-invasive prenatal testing (NIPT) at 14 + 5 weeks' gestation, which was positive for T13. After counseling, the patient elected to undergo amniocentesis. Quantitative fluorescence polymerase chain reaction (QF-PCR) showed no signs of trisomy, and full karyotyping confirmed a normal 46,XY result. Analysis of the published literature on NIPT for T13 gives an overall detection rate of 91.6%, with a false-positive rate of 0.097%. Based on this detection rate, hypothetical calculations show that the positive predictive value is highly dependent on the prevalence of the disease, resulting in an unfavorable balance between benefit and harm in a general population.
Collapse
Affiliation(s)
- E J Verweij
- Leiden University Medical Center, Department of Obstetrics, Leiden, The Netherlands
| | | | | |
Collapse
|
178
|
Traver S, Assou S, Scalici E, Haouzi D, Al-Edani T, Belloc S, Hamamah S. Cell-free nucleic acids as non-invasive biomarkers of gynecological cancers, ovarian, endometrial and obstetric disorders and fetal aneuploidy. Hum Reprod Update 2014; 20:905-23. [PMID: 24973359 DOI: 10.1093/humupd/dmu031] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Proper folliculogenesis is fundamental to obtain a competent oocyte that, once fertilized, can support the acquisition of embryo developmental competence and pregnancy. MicroRNAs (miRNAs) are crucial regulators of folliculogenesis, which are expressed in the cumulus-oocyte complex and in granulosa cells and some can also be found in the bloodstream. These circulating miRNAs are intensively studied and used as diagnostic/prognostic markers of many diseases, including gynecological and pregnancy disorders. In addition, serum contains small amounts of cell-free DNA (cfDNA), presumably resulting from the release of genetic material from apoptotic/necrotic cells. The quantification of nucleic acids in serum samples could be used as a diagnostic tool for female infertility. METHODS An overview of the published literature on miRNAs, and particularly on the use of circulating miRNAs and cfDNA as non-invasive biomarkers of gynecological diseases, was performed (up to January 2014). RESULTS In the past decade, cell-free nucleic acids have been studied for potential use as biomarkers in many diseases, particularly in gynecological cancers, ovarian and endometrial disorders, as well as in pregnancy-related pathologies and fetal aneuploidy. The data strongly suggest that the concentration of cell-free nucleic acids in serum from IVF patients or in embryo culture medium could be related to the ovarian hormone status and embryo quality, respectively, and be used as a non-invasive biomarker of IVF outcome. CONCLUSIONS The profiling of circulating nucleic acids, such as miRNAs and cfDNA, opens new perspectives for the diagnosis/prognosis of ovarian disorders and for the prediction of IVF outcomes, namely (embryo quality and pregnancy).
Collapse
Affiliation(s)
- S Traver
- CHU Montpellier, Institute for Research in Biotherapy, Hôpital Saint-Eloi, INSERM U1040, Montpellier, France
| | - S Assou
- CHU Montpellier, Institute for Research in Biotherapy, Hôpital Saint-Eloi, INSERM U1040, Montpellier, France Université Montpellier 1, UFR de Médecine, Montpellier, France
| | - E Scalici
- CHU Montpellier, Institute for Research in Biotherapy, Hôpital Saint-Eloi, INSERM U1040, Montpellier, France Université Montpellier 1, UFR de Médecine, Montpellier, France
| | - D Haouzi
- CHU Montpellier, Institute for Research in Biotherapy, Hôpital Saint-Eloi, INSERM U1040, Montpellier, France
| | - T Al-Edani
- CHU Montpellier, Institute for Research in Biotherapy, Hôpital Saint-Eloi, INSERM U1040, Montpellier, France Université Montpellier 1, UFR de Médecine, Montpellier, France
| | - S Belloc
- Eylau-Unilabs Laboratory, Paris, France
| | - S Hamamah
- CHU Montpellier, Institute for Research in Biotherapy, Hôpital Saint-Eloi, INSERM U1040, Montpellier, France Université Montpellier 1, UFR de Médecine, Montpellier, France ART-PGD Department, Hôpital Arnaud de Villeneuve, CHU Montpellier, Montpellier, France
| |
Collapse
|
179
|
Attitudes towards non-invasive prenatal testing for aneuploidy among US adults of reproductive age. J Perinatol 2014; 34:429-34. [PMID: 24603453 PMCID: PMC4399855 DOI: 10.1038/jp.2014.30] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Revised: 01/19/2014] [Accepted: 01/27/2014] [Indexed: 12/11/2022]
Abstract
OBJECTIVE To determine how adults in the United States view non-invasive prenatal testing using cell-free fetal DNA (cffDNA testing) in order to help estimate uptake. STUDY DESIGN A national sample of 1861 US-based adults was surveyed using a validated online survey instrument. The survey was administered by a commercial survey research company. Respondents were randomized to receive a survey about prenatal testing for trisomy 13 and 18 or trisomy 21. Participants were asked to select among testing modalities, including cffDNA testing, and rank the features of testing that they considered most important to decision making. RESULT There was substantive interest in the use of cffDNA testing rather than traditional screening mechanisms, with a minority of respondents reporting that they would support the use of both methods in combination. The lower rates of false-negative and false-positive test results and the ability to use the test earlier in the pregnancy were the most highly rated benefits of cffDNA testing. Participants expressed strong support for diagnostic confirmation via invasive testing after a positive result from either screening or cffDNA testing. However, almost one-third of participants reported that they would not endorse the use of either invasive or non-invasive prenatal testing. CONCLUSION There appears to be support for uptake of non-invasive prenatal tests. Clinical guidelines should therefore go forward in providing guidance on how to integrate non-invasive methods into the current standard of care. However, our findings indicate that even when accuracy, which is rated by patients as the most important aspect of prenatal testing, is significantly improved over existing screening methods and testing is offered non-invasively, the number of individuals who reported that they would decline any testing remained the same. Attention should therefore be directed at ensuring that the right of informed refusal of prenatal testing is not impacted by new, non-invasive methods.
Collapse
|
180
|
Emad A, Drouin R. Evaluation of the impact of density gradient centrifugation on fetal cell loss during enrichment from maternal peripheral blood. Prenat Diagn 2014; 34:878-85. [DOI: 10.1002/pd.4387] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 03/08/2014] [Accepted: 04/10/2014] [Indexed: 12/16/2022]
Affiliation(s)
- Ahmed Emad
- Division of Genetics, Department of Pediatrics, Faculty of Medicine and Health Sciences; Université de Sherbrooke; Sherbrooke QC Canada
| | - Régen Drouin
- Division of Genetics, Department of Pediatrics, Faculty of Medicine and Health Sciences; Université de Sherbrooke; Sherbrooke QC Canada
| |
Collapse
|
181
|
O'Leary P, Maxwell S, Murch A, Hendrie D. Prenatal screening for Down syndrome in Australia: costs and benefits of current and novel screening strategies. Aust N Z J Obstet Gynaecol 2014; 53:425-33. [PMID: 24090461 DOI: 10.1111/ajo.12136] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Accepted: 08/12/2013] [Indexed: 01/27/2023]
Abstract
OBJECTIVE To analyse the cost-effectiveness and performance of noninvasive prenatal testing (NIPT) for high-risk pregnancies following first-trimester screening compared with current practice. METHODS A decision tree analysis was used to compare the costs and benefits of current practice of first-trimester screening with a testing pathway incorporating NIPT. We applied the model to 32 478 singleton pregnancies screened between January 2005 and December 2006, adding Medicare rebate data as a measure of public health system costs. The analyses reflect the actual uptake of screening and diagnostic testing and pregnancy outcomes in this cohort. RESULTS The introduction of NIPT would reduce the number of invasive diagnostic procedures and procedure-related fetal losses in high-risk women by 88%. If NIPT was adopted by all women identified as high risk by first-trimester combined screening, up to 7 additional Down syndrome fetuses could be confirmed. The cost per trisomy 21 case confirmed, including NIPT was 9.7% higher ($56,360) than the current prenatal testing strategy ($51,372) at a total cost of $3.91 million compared with $3.57 million over 2 years. CONCLUSION Based on the uptake of screening and diagnostic testing in a retrospective cohort of first-trimester screening in Western Australia, the implementation of NIPT would reduce the number of invasive diagnostic tests and the number of procedure-related fetal losses and increase the cost by 9.7% over two years. Policy planning and guidelines are urgently required to manage the funding and demand for NIPT services in Australia.
Collapse
Affiliation(s)
- Peter O'Leary
- Centre for Population Health Research, Faculty of Health Sciences, Curtin University, Bentley, Western Australia, Australia; School of Pathology and Laboratory Medicine, University of Western Australia, Crawley, Western Australia, Australia; School of Women's and Infants' Health, University of Western Australia, Crawley, Western Australia, Australia
| | | | | | | |
Collapse
|
182
|
Benn P. Non-Invasive Prenatal Testing Using Cell Free DNA in Maternal Plasma: Recent Developments and Future Prospects. J Clin Med 2014; 3:537-65. [PMID: 26237390 PMCID: PMC4449688 DOI: 10.3390/jcm3020537] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 04/11/2014] [Accepted: 04/14/2014] [Indexed: 01/09/2023] Open
Abstract
Recent advances in molecular genetic technologies have facilitated non-invasive prenatal testing (NIPT) through the analysis of cell-free fetal DNA in maternal plasma. NIPT can be used to identify monogenic disorders including the identification of autosomal recessive disorders where the maternally inherited mutation needs to be identified in the presence of an excess of maternal DNA that contains the same mutation. In the future, simultaneous screening for multiple monogenic disorders is anticipated. Several NIPT methods have been developed to screen for trisomy. These have been shown to be effective for fetal trisomy 21, 18 and 13. Although the testing has been extended to sex chromosome aneuploidy, robust estimates of the efficacy are not yet available and maternal mosaicism for gain or loss of an X-chromosome needs to be considered. Using methods based on the analysis of single nucleotide polymorphisms, diandric triploidy can be identified. NIPT is being developed to identify a number of microdeletion syndromes including α-globin gene deletion. NIPT is a profoundly important development in prenatal care that is substantially advancing the individual patient and public health benefits achieved through conventional prenatal screening and diagnosis.
Collapse
Affiliation(s)
- Peter Benn
- Department of Genetics and Developmental Biology, Human Genetics Laboratory, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030-3808, USA.
| |
Collapse
|
183
|
Gregg AR, Van den Veyver IB, Gross SJ, Madankumar R, Rink BD, Norton ME. Noninvasive prenatal screening by next-generation sequencing. Annu Rev Genomics Hum Genet 2014; 15:327-47. [PMID: 24849140 DOI: 10.1146/annurev-genom-090413-025341] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Noninvasive prenatal screening (NIPS) has emerged as a highly accurate method of screening for fetal Down syndrome, with a detection rate and specificity approaching 100%. Challenging the widespread use of this technology are cost and the paradigm shift in counseling that accompanies any emerging technology. The expense of the test is expected to decrease with increased utilization, and well beyond the current NIPS technology, its components (fetal genome measurements, sequencing technology, and bioinformatics) will be utilized alone or in combinations to interrogate the fetal genome. The end goal is simple: to offer patients information early in pregnancy about fetal genomes without incurring procedural risks. This will allow patients an opportunity to make informed reproductive and pregnancy management decisions based on precise fetal genomic information.
Collapse
Affiliation(s)
- Anthony R Gregg
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, University of Florida College of Medicine, Gainesville, Florida 32610;
| | | | | | | | | | | |
Collapse
|
184
|
Hall MP, Hill M, Zimmermann B, Sigurjonsson S, Westemeyer M, Saucier J, Demko Z, Rabinowitz M. Non-invasive prenatal detection of trisomy 13 using a single nucleotide polymorphism- and informatics-based approach. PLoS One 2014; 9:e96677. [PMID: 24805989 PMCID: PMC4013011 DOI: 10.1371/journal.pone.0096677] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 04/11/2014] [Indexed: 01/08/2023] Open
Abstract
Purpose To determine how a single nucleotide polymorphism (SNP)- and informatics-based non-invasive prenatal aneuploidy test performs in detecting trisomy 13. Methods Seventeen trisomy 13 and 51 age-matched euploid samples, randomly selected from a larger cohort, were analyzed. Cell-free DNA was isolated from maternal plasma, amplified in a single multiplex polymerase chain reaction assay that interrogated 19,488 SNPs covering chromosomes 13, 18, 21, X, and Y, and sequenced. Analysis and copy number identification involved a Bayesian-based maximum likelihood statistical method that generated chromosome- and sample-specific calculated accuracies. Results Of the samples that passed a stringent DNA quality threshold (94.1%), the algorithm correctly identified 15/15 trisomy 13 and 49/49 euploid samples, for 320/320 correct copy number calls. Conclusions This informatics- and SNP-based method accurately detects trisomy 13-affected fetuses non-invasively and with high calculated accuracy.
Collapse
Affiliation(s)
- Megan P. Hall
- Department of Research and Development, Natera Inc., San Carlos, California, United States of America
| | - Matthew Hill
- Department of Research and Development, Natera Inc., San Carlos, California, United States of America
| | - Bernhard Zimmermann
- Department of Research and Development, Natera Inc., San Carlos, California, United States of America
| | - Styrmir Sigurjonsson
- Department of Research and Development, Natera Inc., San Carlos, California, United States of America
| | - Margaret Westemeyer
- Department of Genetic Counseling, Natera Inc., San Carlos, California, United States of America
| | - Jennifer Saucier
- Department of Genetic Counseling, Natera Inc., San Carlos, California, United States of America
| | - Zachary Demko
- Department of Genetic Counseling, Natera Inc., San Carlos, California, United States of America
| | - Matthew Rabinowitz
- Department of Research and Development, Natera Inc., San Carlos, California, United States of America
- * E-mail:
| |
Collapse
|
185
|
Benn P, Cuckle H. Theoretical performance of non-invasive prenatal testing for chromosome imbalances using counting of cell-free DNA fragments in maternal plasma. Prenat Diagn 2014; 34:778-83. [PMID: 24676912 DOI: 10.1002/pd.4366] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 02/26/2014] [Accepted: 03/23/2014] [Indexed: 12/16/2022]
Abstract
OBJECTIVE The aim of this study was to calculate the theoretical performance of non-invasive prenatal testing based on counting methods. METHODS The calculations were based on Gaussian distributions of the percent cell-free DNA from selected chromosome regions in affected and normal pregnancies. The means were derived from the relative genomic size of the chromosome region and the fetal fraction. The standard deviations were derived from the bivariate distributions of proportional counts. Depth of sequencing was varied from 50,000,000 to 100,000 and fetal fraction from 20% to 3%. Detection rate was estimated for a fixed 0.13% false-positive rate. RESULTS When either depth or fetal fraction is high, expected Down syndrome screening detection rates are high. However, when fetal fraction is low, deeper sequencing is required to obtain high detection rates. For microdeletion and microduplication screening, deeper sequencing is routinely required to consistently achieve high detection rates. There are small differences in the ability to detect a microdeletion compared with a duplication of the same size. CONCLUSION While the theoretical calculations do not necessarily reflect the performance of currently available non-invasive prenatal testing tests, it confirms that fetal fraction is a key factor. Efficacy can be substantially altered depending on the abnormality under investigation and the depth of sequencing.
Collapse
Affiliation(s)
- Peter Benn
- Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, CT, USA
| | | |
Collapse
|
186
|
Buchanan A, Sachs A, Toler T, Tsipis J. NIPT: current utilization and implications for the future of prenatal genetic counseling. Prenat Diagn 2014; 34:850-7. [PMID: 24711206 DOI: 10.1002/pd.4382] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 03/24/2014] [Accepted: 04/03/2014] [Indexed: 12/25/2022]
Abstract
BACKGROUND Non-invasive prenatal testing (NIPT) for select fetal trisomies became clinically available in 2011. When it was introduced, there were no recommendations from the major governing bodies in prenatal genetics regarding its incorporation. PURPOSE We sought to determine how genetic counselors have incorporated NIPT into clinical practice and how NIPT has changed the informed consent process. METHODS We distributed an anonymous, online survey to National Society of Genetic Counselors (NSGC) members in October 2012. RESULTS There were 181 respondents who indicated they incorporated NIPT into their practice with the majority (94.1%) offering it to patients with high risk pregnancies. Of the respondents, 45.1% indicated that there should be a separate informed consent form for NIPT. Respondents indicated that a discussion about NIPT with a patient should highlight that it is a screening test, the detection rate is superior to that of maternal serum screening, it screens for specific conditions, and a positive NIPT result should be confirmed with a diagnostic test. CONCLUSION Following data collection, the American Congress of Obstetricians and Gynecologists, the American College of Medical Genetics, and NSGC released practice guidelines surrounding NIPT. Our results demonstrate that most genetic counselors have been offering NIPT consistent with these guidelines.
Collapse
Affiliation(s)
- Amanda Buchanan
- Brandeis University, Genetic Counseling Program, Waltham, MA, USA; Tufts Medical Center, Division of Maternal-Fetal Medicine, Boston, MA, USA
| | | | | | | |
Collapse
|
187
|
Kantak C, Chang CP, Wong CC, Mahyuddin A, Choolani M, Rahman A. Lab-on-a-chip technology: impacting non-invasive prenatal diagnostics (NIPD) through miniaturisation. LAB ON A CHIP 2014; 14:841-854. [PMID: 24452749 DOI: 10.1039/c3lc50980j] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
This paper aims to provide a concise review of non-invasive prenatal diagnostics (NIPD) to the lab-on-a-chip and microfluidics community. Having a market of over one billion dollars to explore and a plethora of applications, NIPD requires greater attention from microfluidics researchers. In this review, a complete overview of conventional diagnostic procedures including invasive as well as non-invasive (fetal cells and cell-free fetal DNA) types are discussed. Special focus is given to reviewing the recent and past microfluidic approaches to NIPD, as well as various commercial entities in NIPD. This review concludes with future challenges and ethical considerations of the field.
Collapse
Affiliation(s)
- Chaitanya Kantak
- Institute of Microelectronics, Agency for Science Technology and Research, 11 Science Park Road, Singapore Science Park 2, Singapore 117685, Singapore.
| | | | | | | | | | | |
Collapse
|
188
|
Lau TK, Cheung SW, Lo PSS, Pursley AN, Chan MK, Jiang F, Zhang H, Wang W, Jong LFJ, Yuen OKC, Chan HYC, Chan WSK, Choy KW. Non-invasive prenatal testing for fetal chromosomal abnormalities by low-coverage whole-genome sequencing of maternal plasma DNA: review of 1982 consecutive cases in a single center. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2014; 43:254-264. [PMID: 24339153 DOI: 10.1002/uog.13277] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Revised: 12/06/2013] [Accepted: 12/10/2013] [Indexed: 06/03/2023]
Abstract
OBJECTIVE To review the performance of non-invasive prenatal testing (NIPT) by low-coverage whole-genome sequencing of maternal plasma DNA at a single center. METHODS The NIPT result and pregnancy outcome of 1982 consecutive cases were reviewed. NIPT was based on low coverage (0.1×) whole-genome sequencing of maternal plasma DNA. All subjects were contacted for pregnancy and fetal outcome. RESULTS Of the 1982 NIPT tests, a repeat blood sample was required in 23 (1.16%). In one case, a conclusive report could not be issued, probably because of an abnormal vanished twin fetus. NIPT was positive for common trisomies in 29 cases (23 were trisomy 21, four were trisomy 18 and two were trisomy 13); all were confirmed by prenatal karyotyping (specificity=100%). In addition, 11 cases were positive for sex-chromosomal abnormalities (SCA), and nine cases were positive for other aneuploidies or deletion/duplication. Fourteen of these 20 subjects agreed to undergo further investigations, and the abnormality was found to be of fetal origin in seven, confined placental mosaicism (CPM) in four, of maternal origin in two and not confirmed in one. Overall, 85.7% of the NIPT-suspected SCA were of fetal origin, and 66.7% of the other abnormalities were caused by CPM. Two of the six cases suspected or confirmed to have CPM were complicated by early-onset growth restriction requiring delivery before 34 weeks. Fetal outcome of the NIPT-negative cases was ascertained in 1645 (85.15%). Three chromosomal abnormalities were not detected by NIPT, including one case each of a balanced translocation, unbalanced translocation and triploidy. There were no known false negatives involving the common trisomies (sensitivity=100%). CONCLUSIONS Low-coverage whole-genome sequencing of maternal plasma DNA was highly accurate in detecting common trisomies. It also enabled the detection of other aneuploidies and structural chromosomal abnormalities with high positive predictive value.
Collapse
Affiliation(s)
- T K Lau
- Fetal Medicine Centre, Paramount Medical Centre, Hong Kong, China
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
189
|
Petersen OB, Vogel I, Ekelund C, Hyett J, Tabor A. Potential diagnostic consequences of applying non-invasive prenatal testing: population-based study from a country with existing first-trimester screening. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2014; 43:265-271. [PMID: 24375770 DOI: 10.1002/uog.13270] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 11/20/2013] [Accepted: 11/25/2013] [Indexed: 06/03/2023]
Abstract
OBJECTIVES Targeted non-invasive prenatal testing (NIPT) tests for trisomies 21, 18 and 13 and sex chromosome aneuploidies and could be an alternative to traditional karyotyping. The aim of this study was to determine the risk of missing other abnormal karyotypes of probable phenotypic significance by NIPT. METHODS This was a retrospective population-based analysis of all singleton pregnancies booked for combined first-trimester screening (cFTS) in Denmark over a 4-year period. Data concerning maternal demographics, cFTS and prenatal or postnatal karyotypes were collected from the Danish Fetal Medicine database. Karyotypes were classified according to whether the chromosomal anomaly would have been detected by NIPT and whether it was likely to affect phenotype. RESULTS cFTS was completed in 193638 pregnancies. 10205 (5.3%) had cytogenetic or molecular analysis performed. Of these, 1122 (11.0%) had an abnormal karyotype, of which 262 (23.4%) would have been missed by NIPT, but would probably have been clinically significant. The prevalence of such 'atypical abnormal karyotypes' was increased in women above 45 years of age, in pregnancies with increased nuchal translucency (NT) thickness (≥ 3.5 mm), with abnormal levels of free β-human chorionic gonadotropin (<0.2 or ≥ 5.0 multiples of the median (MoM)) or pregnancy-associated plasma protein-A<0.2 MoM. One or more of these factors was present in 3% of women, and the prevalence of atypical abnormal karyotypes in this high-risk cohort was 1.6%. CONCLUSIONS A significant proportion of karyotypic abnormalities will be missed by targeted NIPT. Women of advanced maternal age, or with increased fetal NT or abnormal biochemistry, have a higher risk of having a fetus affected by an atypical abnormal karyotype and need to be counseled accordingly when considering NIPT.
Collapse
Affiliation(s)
- O B Petersen
- Fetal Medicine Unit, Department of Obstetrics, Aarhus University Hospital, Aarhus, Denmark
| | | | | | | | | |
Collapse
|
190
|
Haymon L, Simi E, Moyer K, Aufox S, Ouyang DW. Clinical implementation of noninvasive prenatal testing among maternal fetal medicine specialists. Prenat Diagn 2014; 34:416-23. [DOI: 10.1002/pd.4301] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 11/15/2013] [Accepted: 12/12/2013] [Indexed: 12/26/2022]
Affiliation(s)
- Lori Haymon
- Center for Genetic Medicine Graduate Program in Genetic Counseling; Northwestern University Feinberg School of Medicine; Chicago USA
| | - Eve Simi
- Division of Maternal-Fetal Medicine; NorthShore University HealthSystem; Evanston USA
| | - Kelly Moyer
- Loyola University Medical Center; Maywood USA
| | - Sharon Aufox
- Center for Genetic Medicine Graduate Program in Genetic Counseling; Northwestern University Feinberg School of Medicine; Chicago USA
| | - David W. Ouyang
- Division of Maternal-Fetal Medicine; NorthShore University HealthSystem; Evanston USA
| |
Collapse
|
191
|
Odibo AO, Ghidini A. Role of the second-trimester ‘genetic sonogram’ for Down syndrome screen in the era of first-trimester screening and noninvasive prenatal testing. Prenat Diagn 2014; 34:511-7. [DOI: 10.1002/pd.4329] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 12/24/2013] [Accepted: 01/12/2014] [Indexed: 12/22/2022]
Affiliation(s)
- Anthony O. Odibo
- Department of Obstetrics and Gynecology; Washington University School of Medicine; St. Louis MO USA
| | | |
Collapse
|
192
|
A Case of False Negative NIPT for Down Syndrome-Lessons Learned. Case Rep Genet 2014; 2014:823504. [PMID: 24649382 PMCID: PMC3932282 DOI: 10.1155/2014/823504] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 12/25/2013] [Indexed: 12/16/2022] Open
Abstract
Down syndrome or trisomy 21 is the most common cause of prenatal chromosome abnormalities with approximately 50% of all reported chromosome conditions. With the successful introduction of noninvasive prenatal testing (NIPT) for Down syndrome into routine prenatal care, it is important to understand the risks, benefits, and limitations in order to guide patients in making an informed decision. Herein, we describe the first published case report of a patient whose fetus tested “negative” for Trisomy 21 by NIPT but was diagnosed postnatally with trisomy 21. We present the importance of proper pretest and posttest genetic counseling to ensure prenatal patients are able to make informed decisions and are educated appropriately about NIPT.
Collapse
|
193
|
Twiss P, Hill M, Daley R, Chitty LS. Non-invasive prenatal testing for Down syndrome. Semin Fetal Neonatal Med 2014; 19:9-14. [PMID: 24210903 DOI: 10.1016/j.siny.2013.10.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Prenatal screening and diagnosis of Down syndrome and other major aneuploidies may be transformed following the identification of cell-free fetal DNA in maternal plasma at the end of the last millennium. Next generation sequencing has enabled the development of tests that accurately predict the presence of fetal trisomies by analysis of cell-free DNA in maternal blood from as early as 10 weeks of gestation. These tests are now widely available in the commercial sector but are yet to be implemented in publicly led health services. In this article we discuss the technical, social, and ethical challenges that these new tests bring.
Collapse
Affiliation(s)
- Philip Twiss
- NE Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, 37 Queen Square, London WC1N 3BH, UK
| | - Melissa Hill
- NE Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, 37 Queen Square, London WC1N 3BH, UK
| | - Rebecca Daley
- NE Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, 37 Queen Square, London WC1N 3BH, UK
| | - Lyn S Chitty
- NE Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, 37 Queen Square, London WC1N 3BH, UK; UCL Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK.
| |
Collapse
|
194
|
Daley R, Hill M, Lewis C, Chitty L. Non-invasive prenatal testing for Down's syndrome—Where are we now? ACTA ACUST UNITED AC 2014. [DOI: 10.12968/bjom.2014.22.2.85] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Rebecca Daley
- Research Midwife, Great Ormond Street Hospital for Children NHS Foundation Trust; University College London Hospital NHS Foundation Trust
| | - Melissa Hill
- RAPID Project Coordinator, Great Ormond Street Hospital for Children NHS Foundation Trust
| | - Celine Lewis
- Research Psychologist, Great Ormond Street Hospital for Children NHS Foundation Trust; UCL Institute of Child Health
| | - Lyn Chitty
- Professor, Genetics and Fetal Medicine Great Ormond Street Hospital for Children NHS Foundation Trust; UCL Institute of Child Health
| |
Collapse
|
195
|
Investigating and correcting plasma DNA sequencing coverage bias to enhance aneuploidy discovery. PLoS One 2014; 9:e86993. [PMID: 24489824 PMCID: PMC3906086 DOI: 10.1371/journal.pone.0086993] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 12/16/2013] [Indexed: 12/11/2022] Open
Abstract
Pregnant women carry a mixture of cell-free DNA fragments from self and fetus (non-self) in their circulation. In recent years multiple independent studies have demonstrated the ability to detect fetal trisomies such as trisomy 21, the cause of Down syndrome, by Next-Generation Sequencing of maternal plasma. The current clinical tests based on this approach show very high sensitivity and specificity, although as yet they have not become the standard diagnostic test. Here we describe improvements to the analysis of the sequencing data by reducing GC bias and better handling of the genomic repeats. We show substantial improvements in the sensitivity of the standard trisomy 21 statistical tests, which we measure by artificially reducing read coverage. We also explore the bias stemming from the natural cleavage of plasma DNA by examining DNA motifs and position specific base distributions. We propose a model to correct this fragmentation bias and observe that incorporating this bias does not lead to any further improvements in the detection of fetal trisomy. The improved bias corrections that we demonstrate in this work can be readily adopted into existing fetal trisomy detection protocols and should also lead to improvements in sub-chromosomal copy number variation detection.
Collapse
|
196
|
Agarwal A, Sayres LC, Cho MK, Cook-Deegan R, Chandrasekharan S. Commercial landscape of noninvasive prenatal testing in the United States. Prenat Diagn 2014; 33:521-31. [PMID: 23686656 DOI: 10.1002/pd.4101] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Cell-free fetal DNA-based noninvasive prenatal testing (NIPT) could significantly change the paradigm of prenatal testing and screening. Intellectual property (IP) and commercialization promise to be important components of the emerging debate about clinical implementation of these technologies. We have assembled information about types of testing, prices, turnaround times, and reimbursement of recently launched commercial tests in the United States from the trade press, news articles, and scientific, legal, and business publications. We also describe the patenting and licensing landscape of technologies underlying these tests and ongoing patent litigation in the United States. Finally, we discuss how IP issues may affect clinical translation of NIPT and their potential implications for stakeholders. Fetal medicine professionals (clinicians and researchers), genetic counselors, insurers, regulators, test developers, and patients may be able to use this information to make informed decisions about clinical implementation of current and emerging noninvasive prenatal tests.
Collapse
|
197
|
Yang JI. Clinical application of non-invasive prenatal testing using cell free fetal DNA. JOURNAL OF THE KOREAN MEDICAL ASSOCIATION 2014. [DOI: 10.5124/jkma.2014.57.9.771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Jeong In Yang
- Department of Obstetrics and Gynecology, Ajou University School of Medicine, Suwon, Korea
| |
Collapse
|
198
|
Gratacós E, Nicolaides K. Clinical Perspective of Cell-Free DNA Testing for Fetal Aneuploidies. Fetal Diagn Ther 2014; 35:151-5. [DOI: 10.1159/000362940] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Cell-free DNA testing in maternal blood provides the most effective method of screening for trisomy 21, with a reported detection rate of 99% and a false positive rate of less than 0.1%. After many years of research, this method is now commercially available and is carried out in an increasing number of patients, and there is an expanding number of conditions that can be screened for. However, the application of these methods in clinical practice requires a careful analysis. Current first-trimester screening strategies are based on a complex combination of tests, aiming at detecting fetal defects and predicting the risk of main pregnancy complications. It is therefore necessary to define the optimal way of combining cell-free DNA testing with current first-trimester screening methods. In this concise review we describe the basis of cell-free DNA testing and discuss the potential approaches for its implementation in combination with current tests in the first trimester.
Collapse
|
199
|
Cell-free fetal DNA in maternal blood – an update of the method and clinical practice. REV ROMANA MED LAB 2014. [DOI: 10.2478/rrlm-2014-0045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
200
|
Benn P, Chapman AR, Erickson K, DeFrancesco MS, Wilkins-Haug L, Egan JFX, Schulkin J. Obstetricians and gynecologists' practice and opinions of expanded carrier testing and noninvasive prenatal testing. Prenat Diagn 2013; 34:145-52. [DOI: 10.1002/pd.4272] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 10/21/2013] [Accepted: 11/01/2013] [Indexed: 12/20/2022]
Affiliation(s)
- Peter Benn
- Department of Genetics and Developmental Biology; University of Connecticut Health Center; Farmington CT USA
| | - Audrey R. Chapman
- Department of Community Medicine and Healthcare; University of Connecticut School of Medicine; Farmington CT USA
| | | | - Mark S. DeFrancesco
- Women's Health Connecticut; Avon CT USA
- Department of Obstetrics and Gynecology; University of Connecticut Health Center; Farmington CT USA
| | - Louise Wilkins-Haug
- Department of Obstetrics and Gynecology; Brigham and Women's Hospital; Boston MA USA
- Department of Obstetrics and Gynecology; Harvard Medical School; Boston MA USA
| | - James F. X. Egan
- Department of Obstetrics and Gynecology; University of Connecticut Health Center; Farmington CT USA
| | - Jay Schulkin
- American Congress of Obstetricians and Gynecologists; Washington DC USA
| |
Collapse
|