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Katrachouras A, Kontos H, Konis K, Skentou C, Makrydimas G. Early Non-Invasive Prenatal Testing at 6-9 Weeks of Gestation. Genes (Basel) 2024; 15:895. [PMID: 39062674 PMCID: PMC11275238 DOI: 10.3390/genes15070895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/03/2024] [Accepted: 07/04/2024] [Indexed: 07/28/2024] Open
Abstract
Non-invasive prenatal testing (NIPT) is usually performed beyond 10 weeks of gestation, because earlier in pregnancy, the fetal fraction is low, resulting in failure to obtain reliable results. This study aimed to evaluate the clinical performance of NIPT earlier in pregnancy using a method for cell-free DNA (cfDNA) analysis that eliminates the need for polymerase chain reaction (PCR), DNA sequencing, or microarrays (Vanadis® system, PerkinElmer, Waltham, MA, USA). Cell-free DNA was extracted from the maternal plasma of 30 singleton pregnancies at 6-9 weeks of gestation (group 1) and at 11-14 weeks of gestation of the same patients (group 2). The mean crown-rump length (CRL) and gestational age in group A was 16.12 mm and that in group B was 61.45 mm. In group A, results were obtained in all, but one, cases (97%). From the remaining pregnancies, one miscarried at 8 weeks and, therefore, the follow-up NIPT at 12 weeks could not be performed. The fetal sex was diagnosed correctly in the 28 cases that had a successful early test, and the results were in accordance with the examination at 12 weeks. There were no cases of aneuploidies and disomy was diagnosed correctly in all. The "Vanadis" prenatal NIPT assay can successfully be used early during the first trimester at 6-9 weeks of gestation (early NIPT) to identify the fetal sex. Further studies are needed to explore the diagnostic potential for aneuploidies.
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Affiliation(s)
- Alexandros Katrachouras
- Obstetrics and Gynecology, University Hospital of Ioannina, 455 00 Ioannina, Greece; (A.K.); (C.S.)
| | - Harry Kontos
- Department of Molecular Genetics, Genomedica S.A., 185 37 Piraeus, Greece;
| | - Kyriacos Konis
- Obstetrics and Gynecology, General Hospital of Arta, 471 00 Arta, Greece;
| | - Chara Skentou
- Obstetrics and Gynecology, University Hospital of Ioannina, 455 00 Ioannina, Greece; (A.K.); (C.S.)
| | - George Makrydimas
- Obstetrics and Gynecology, University Hospital of Ioannina, 455 00 Ioannina, Greece; (A.K.); (C.S.)
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Vivanti AJ, Maestroni C, Benachi A, Conotte S, Geipel A, Kagan KO, Borrell A, El Kenz H, Costa JM, Jani JC. Cell-free DNA screening for common autosomal trisomies using rolling-circle replication in twin pregnancies. Prenat Diagn 2024; 44:953-958. [PMID: 38801227 DOI: 10.1002/pd.6615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 05/09/2024] [Accepted: 05/14/2024] [Indexed: 05/29/2024]
Abstract
OBJECTIVE To evaluate the performance of prenatal screening for common autosomal trisomies in twin pregnancies through the use of rolling-circle replication (RCR)-cfDNA as a first-tier test. METHOD Prospective multicenter study. Women who underwent prenatal screening for trisomy (T) 21, 18 and 13 between January 2019 and March 2022 in twin pregnancies were included. Patients were included in two centers. The primary endpoint was the rate of no-call results in women who received prenatal screening for common autosomal trisomies by RCR-cfDNA at the first attempt, compared to that in prospectively collected samples from 16,382 singleton pregnancies. The secondary endpoints were the performance indices of the RCR-cfDNA. RESULTS 862 twin pregnancies underwent screening for T21, T18 and T13 by RCR-cfDNA testing at 10-33 weeks' gestation. The RCR-cfDNA tests provided a no-call result from the first sample obtained from the patients in 107 (0.7%) singleton and 17 (2.0%) twin pregnancies. Multivariable regression analysis demonstrated that significant independent predictors of test failure were twin pregnancy and in vitro fertilization conception. All cases of T21 (n = 20/862; 2.3%), T18 (n = 4/862; 0.5%) and T13 (n = 1/862; 0.1%) were correctly detected by RCR-cfDNA (respectively, 20, 4 and 1 cases). Sensitivity was 100% (95% CI, 83.1%-100%), 100% (95% CI 39.8%-100%) and 100% (95% CI 2.5%-100%) for T21, T18 and T13, respectively, in twin pregnancies. CONCLUSION The RCR-cfDNA test appears to have good accuracy with a low rate of no-call results in a cohort of twin pregnancies for the detection of the most frequent autosomal trisomies.
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Affiliation(s)
- Alexandre J Vivanti
- Department of Obstetrics and Gynecology, Antoine Béclère Hospital, Paris Saclay University, AP-HP, Clamart, France
| | - Camille Maestroni
- Department of Obstetrics and Gynecology, Antoine Béclère Hospital, Paris Saclay University, AP-HP, Clamart, France
| | - Alexandra Benachi
- Department of Obstetrics and Gynecology, Antoine Béclère Hospital, Paris Saclay University, AP-HP, Clamart, France
| | - Stéphanie Conotte
- Department of Blood Transfusion, University Hospital Brugmann, Brussels, Belgium
| | - Annegret Geipel
- Department of Obstetrics and Prenatal Medicine, University Hospital of Bonn, Bonn, Germany
| | | | - Antoni Borrell
- BCNatal-Hospital Clinic Barcelona, Universitat de Barcelona, Barcelona, Spain
| | - Hanane El Kenz
- Department of Blood Transfusion, University Hospital Brugmann, Brussels, Belgium
| | | | - Jacques C Jani
- Department of Obstetrics and Gynecology, University Hospital Brugmann, Université Libre de Bruxelles, Brussels, Belgium
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Benn P, Cuckle H. Overview of Noninvasive Prenatal Testing (NIPT) for the Detection of Fetal Chromosome Abnormalities; Differences in Laboratory Methods and Scope of Testing. Clin Obstet Gynecol 2023; 66:536-556. [PMID: 37650667 DOI: 10.1097/grf.0000000000000803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Although nearly all noninvasive prenatal testing is currently based on analyzing circulating maternal cell-free DNA, the technical methods usedvary considerably. We review the different methods. Based on validation trials and clinical experience, there are mostly relatively small differences in screening performance for trisomies 21, 18, and 13 in singleton pregnancies. Recent reports show low no-call rates for all methods, diminishing its importance when choosing a laboratory. However, method can be an important consideration for twin pregnancies, screening for sex chromosome abnormalities, microdeletion syndromes, triploidy, molar pregnancies, rare autosomal trisomies, and segmental imbalances, and detecting maternal chromosome abnormalities.
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Affiliation(s)
- Peter Benn
- Department of Obstetrics and Gynecology, University of Connecticut Health Center, Farmington, Connecticut
| | - Howard Cuckle
- Department of Obstetrics and Gynecology, Faculty of Medicine, Tel Aviv University, Israel
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Saidel ML, Ananth U, Rose D, Farrell C. Non-Invasive prenatal testing with rolling circle amplification: Real-world clinical experience in a non-molecular laboratory. J Clin Lab Anal 2023; 37:e24870. [PMID: 36972484 PMCID: PMC10156098 DOI: 10.1002/jcla.24870] [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: 10/03/2022] [Revised: 02/17/2023] [Accepted: 03/08/2023] [Indexed: 03/29/2023] Open
Abstract
BACKGROUND Non-invasive prenatal testing (NIPT) using cell-free DNA (cfDNA) circulating in maternal blood provides a sensitive and specific screening technique for common fetal aneuploidies, but the high cost and workflow complexity of conventional methodologies limit its widespread implementation. A unique rolling circle amplification methodology reduces cost and complexity, providing a promising alternative for increased global accessibility as a first-tier test. METHODS In this clinical study, 8160 pregnant women were screened on the Vanadis system for trisomies 13, 18, and 21, and positive results were compared to clinical outcomes where available. RESULTS The Vanadis system yielded a 0.07% no-call rate, a 98% overall sensitivity, and a specificity of over 99% based on available outcomes. CONCLUSION The Vanadis system provided a sensitive, specific, and cost-effective cfDNA assay for trisomies 13, 18, and 21, with good performance characteristics and low no-call rate, and it eliminated the need for either next-generation sequencing or polymerase chain reaction amplification.
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Affiliation(s)
- Matthew L Saidel
- Women's Health USA and Medical Director, Women's Health Connecticut, Rocky Hill, Connecticut, USA
| | - Uma Ananth
- Umagen LLC, Shrewsbury, Massachusetts, USA
| | - Donna Rose
- Women's Health Connecticut Laboratory, Rocky Hill, Connecticut, USA
| | - Cara Farrell
- Ancillary Growth Women's Health Connecticut, Rocky Hill, Connecticut, USA
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Tian M, Feng L, Li J, Zhang R. Focus on the frontier issue: progress in noninvasive prenatal screening for fetal trisomy from clinical perspectives. Crit Rev Clin Lab Sci 2023; 60:248-269. [PMID: 36647189 DOI: 10.1080/10408363.2022.2162843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The discovery of cell-free fetal DNA (cffDNA) in maternal blood and the rapid development of massively parallel sequencing have revolutionized prenatal testing from invasive to noninvasive. Noninvasive prenatal screening (NIPS) based on cffDNA enables the detection of fetal trisomy through sequencing, comparison, and bioassays. Its accuracy is better than that of traditional screening methods, and it is the most advanced clinical application of high-throughput sequencing technologies. However, the existing sequencing methods are limited by high costs and complex sequencing procedures. These limitations restrict the availability of NIPS for pregnant women. Many amplification methods have been developed to overcome the limitations of sequencing methods. The rapid development of non-sequencing methods has not been accompanied by reviews to summarize them. In this review, we initially describe the detection principles for sequencing-based NIPS. We summarize the rapidly evolving amplification technologies, focusing on the need to reduce costs and simplify the procedures. To ensure that the testing systems are feasible and that the testing processes are reliable, we expand our vision to the clinic. We evaluate the clinical validity of NIPS in terms of sensitivity, specificity, and positive predictive value. Finally, we summarize the application guidelines and discuss the corresponding quality control methods for NIPS. In addition to cffDNA, extracellular vesicle DNA, RNA, protein/peptide, and fetal cells can also be detected as biomarkers of NIPS. With the development of prenatal testing, NIPS has become increasingly important. Notably, NIPS is a screening test instead of a diagnostic test. The testing methods and procedures used in the NIPS process require standardization.
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Affiliation(s)
- Meng Tian
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P. R. China.,Peking University Fifth School of Clinical Medicine, Beijing, P. R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
| | - Lei Feng
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P. R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P. R. China.,Peking University Fifth School of Clinical Medicine, Beijing, P. R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China
| | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P. R. China.,Peking University Fifth School of Clinical Medicine, Beijing, P. R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China
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Palomaki GE, Eklund EE, Kloza EM, Lambert-Messerlian GM. Assessment of a Simplified Cell-Free DNA Method for Prenatal Down Syndrome Screening. Clin Chem 2022; 68:1449-1458. [DOI: 10.1093/clinchem/hvac131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/06/2022] [Indexed: 11/13/2022]
Abstract
Abstract
Background
Prenatal screening for common trisomies via cell-free (cfDNA) is usually implemented by technologies utilizing massively parallel sequencing, stringent environmental controls, complex bioinformatics, and molecular expertise. An alternative and less complex methodology utilizes rolling circle amplification (RCA). Further evaluation of its performance and related requirements are warranted.
Methods
At 16 sites, women at 10 to 20 weeks gestation provided informed consent, relevant information, and 2 to 3 blood samples. Samples shipped for testing were processed and stored. Women were enrolled at primary cfDNA screening, or following such screening at referral for diagnostic testing. RCA testing occurred post-enrollment, over 11 months. Diagnostic results and delivery notes determined clinical truth. Detection rates were based on confirmed trisomic pregnancies; false-positive rates were based on unaffected pregnancies from the general population.
Results
Detection rate for the common trisomies was 95.9% (117/122, 95% CI, 90.5%–98.5%); overall false-positive rate was 1.00% (22/2,205, 0.65%–1.51%). Test failure rate after repeat testing was 0.04%. When assay standard deviations were below pre-specified levels, the overall false-positive rate was much lower at 0.30% (P < 0.001). Fetal sex calls were correct for 99.7%. One technician analyzed 560 samples over 2 weeks, a rate of 14 000/year.
Conclusions
Our assessment of this simplified cfDNA-based system for prenatal screening for common trisomies performed in a prenatal screening laboratory is encouraging. Improved detection, low failure rates and rapid reporting can be achieved by collecting 2 samples. Future priorities should include achieving higher run precision using a single collection tube.
Clinicaltrials.gov Registration Number: NCT03087357.
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Affiliation(s)
- Glenn E Palomaki
- Department of Pathology and Laboratory Medicine, Women & Infants Hospital , Providence, RI , USA
- Department of Pathology and Laboratory Medicine, Alpert Medical School at Brown University , Providence, RI , USA
| | - Elizabeth E Eklund
- Department of Pathology and Laboratory Medicine, Women & Infants Hospital , Providence, RI , USA
| | - Edward M Kloza
- Department of Pathology and Laboratory Medicine, Women & Infants Hospital , Providence, RI , USA
| | - Geralyn M Lambert-Messerlian
- Department of Pathology and Laboratory Medicine, Women & Infants Hospital , Providence, RI , USA
- Department of Pathology and Laboratory Medicine, Alpert Medical School at Brown University , Providence, RI , USA
- Department of Obstetrics and Gynecology, Women & Infants Hospital , Providence, RI , USA
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Demko Z, Prigmore B, Benn P. A Critical Evaluation of Validation and Clinical Experience Studies in Non-Invasive Prenatal Testing for Trisomies 21, 18, and 13 and Monosomy X. J Clin Med 2022; 11:jcm11164760. [PMID: 36012999 PMCID: PMC9410356 DOI: 10.3390/jcm11164760] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/28/2022] [Accepted: 08/11/2022] [Indexed: 11/25/2022] Open
Abstract
Non-invasive prenatal testing (NIPT) for trisomies 21, 18, 13 and monosomy X is widely utilized with massively parallel shotgun sequencing (MPSS), digital analysis of selected regions (DANSR), and single nucleotide polymorphism (SNP) analyses being the most widely reported methods. We searched the literature to find all NIPT clinical validation and clinical experience studies between January 2011 and January 2022. Meta-analyses were performed using bivariate random-effects and univariate regression models for estimating summary performance measures across studies. Bivariate meta-regression was performed to explore the influence of testing method and study design. Subgroup and sensitivity analyses evaluated factors that may have led to heterogeneity. Based on 55 validation studies, the detection rate (DR) was significantly higher for retrospective studies, while the false positive rate (FPR) was significantly lower for prospective studies. Comparing the performance of NIPT methods for trisomies 21, 18, and 13 combined, the SNP method had a higher DR and lower FPR than other methods, significantly so for MPSS, though not for DANSR. The performance of the different methods in the 84 clinical experience studies was consistent with validation studies. Clinical positive predictive values of all NIPT methods improved over the last decade. We conclude that all NIPT methods are highly effective for fetal aneuploidy screening, with performance differences across methodologies.
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Affiliation(s)
| | | | - Peter Benn
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06030, USA
- Correspondence:
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