Performance of cell-free DNA sequencing-based non-invasive prenatal testing:  experience on 36,456 singleton and multiple pregnancies

Abstract Background This paper describes the clinical practice and performance of cell-free DNA sequencing-based non-invasive prenatal testing (NIPT) as a screening method for fetal trisomy 21, 18, and 13 (T21, T18, and T13) and sex chromosome aneuploidies (SCA) in a general Italian pregnancy population. Methods The AMES-accredited laboratory offers NIPT in maternal blood as a screening test for fetal T21, T18, T13 and SCA. Samples were sequenced on a NextSeq 550 (Illumina) using the VeriSeq NIPT Solution v1 assay. Results A retrospective analysis was performed on 36,456 consecutive maternal blood samples, including 35,650 singleton pregnancies, 800 twin pregnancies, and 6 triplet pregnancies. Samples were tested between April 2017 and September 2019. The cohort included 46% elevated-risk and 54% low-risk patients. A result indicative of a classic trisomy was found in 356 (1%) of singleton or twin samples: 254 T21, 69 T18, and 33 T13. In addition, 145 results (0.4%) were indicative of a SCA. Of the combined 501 screen-positive cases, 484 had confirmatory diagnostic testing. NIPT results were confirmed in 99.2% (247/249) of T21 cases, 91.2% (62/68) of T18 cases, 84.4% (27/32) of T13 cases, and 86.7% (117/135) of SCA cases. In the 35,955 cases reported as unaffected by a classic trisomy or SCA, no false negative cases were reported. Assuming that false negative results would be reported, the sensitivity of NIPT was 100.00% for T21 (95% Cl 98.47–100.0), T18 (95% Cl 94.17–100.0), and T13 (95% Cl 87.54–100.0). The specificities were 99.99% (95% Cl 99.98–100.0), 99.98% (95% Cl 99.96–100.0), 99.99% (95% Cl 99.97–100.0), and 99.95% (95% Cl 99.92–99.97) for T21, T18, T13, and SCA, respectively. Conclusion This retrospective analysis of a large cohort of consecutive patients who had whole-genome sequencing-based NIPT for classic trisomies and SCA shows excellent detection rates and low false positive rates.

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Performance of Cell-Free DNA Sequencing-Based Non-invasive Prenatal Testing: Our Experience on 36456 both Singleton and Multiple Pregnancies.

10.21203/rs.3.rs-144192/v1 ◽

2021 ◽

Author(s):

Marco La Verde ◽

Luigia De Falco ◽

Annalaura Torella ◽

Giovanni Savarese ◽

Pasquale Saverese ◽

...

Keyword(s):

Dna Sequencing ◽

Retrospective Analysis ◽

False Negative ◽

Screening Method ◽

Prenatal Testing ◽

Maternal Blood ◽

Noninvasive Prenatal Testing ◽

Cell Free Dna ◽

Detection Rates ◽

Free Dna

Abstract Background: To describe the clinical practice and performance of cell-free DNA sequencing-based noninvasive prenatal testing as a screening method for detecting trisomy 21, 18, and 13 (T21, T18, and T13, respectively), as well as sex chromosome aneuploidy (SCA), in a general Italian pregnancy population.Methods: The AMES-accredited laboratory offers noninvasive prenatal testing in maternal blood as a clinical screening test for foetal T21, T18, T13 and SCA. Samples were sequenced on a NextSeq 550 (Illumina) using the VeriSeq NIPT Solution v1 assay.Results: A retrospective analysis was performed on a cohort of 36456 consecutive maternal blood samples, including 35650 singleton pregnancies, 800 twin pregnancies, and 6 triplet pregnancies, which were tested between April 2017 and September 2019. The cohort included 46% elevated-risk and 54% low-risk patients. Genetic and/or clinical outcomes were available in 36000 cases (98.7%). In the overall cohort, 356 (1%) results were indicative of classic trisomy: 254 T21, 69 T18, and 33 T13. In addition, 145 results (0.4%) were indicative of SCA. Of the combined 501 screen-positive cases, 484 had confirmatory diagnostic testing results available: 99.2% (247/249) of T21 cases, 91.2% (62/68) of T18 cases, 84.4% (27/32) of T13 cases, and 86.7% (117/135) of SCA cases were confirmed. Follow-up data were available for 98.8% of the 35955 cases reported as unaffected by trisomy or SCA. No false negative cases were reported. The sensitivity of NIPT was 100.00% for T21 (95% Cl 98.47-100.0), T18 (95% Cl 94.17-100.0), T13 (95% Cl 87.54-100.0) and SCA (95% Cl 96.62-100.0). The specificities were 99.99% (95% Cl 99.98-100.0), 99.98% (95% Cl 99.96-100.0), 99.99% (95% Cl 99.97-100.0), and 99.95% (95% Cl 99.92-99.97) for T21, T18, T13, and SCA, respectively.Conclusion: This retrospective analysis of a large cohort of consecutive patients who had whole-genome sequencing-based NIPT for classic trisomies and SCA showed excellent detection rates and low false positive rates.

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Opinion on a new and Challenging Tool in Prenatal Counseling: Non invasive Prenatal Testing by Fetal Cell-Free DNA in Maternal Blood

Journal of Health & Medical Informatics ◽

10.4172/2157-7420.1000138 ◽

2013 ◽

Vol 4 (4) ◽

Author(s):

Justo Alonso

Keyword(s):

Prenatal Testing ◽

Maternal Blood ◽

Fetal Cell ◽

Prenatal Counseling ◽

Cell Free Dna ◽

Non Invasive ◽

Free Dna

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THE CELL-FREE DNA DETECTION AND ANALYSIS AS THE NEW NON-INVASIVE PRENATAL DIAGNOSTICS OPTION

Facta Universitatis Series Medicine and Biology ◽

10.22190/fumb170227003m ◽

2017 ◽

pp. 006

Author(s):

Maja Milojković ◽

Jelena Milenković

Keyword(s):

Dna Detection ◽

False Negative ◽

Prenatal Testing ◽

Screening Methods ◽

Cell Free Dna ◽

Testing Procedures ◽

Non Invasive ◽

Free Dna ◽

First Choice ◽

Positive Results

Screening procedures for chromosomal abnormalities in fetuses are a standard of care for pregnant women. Ultrasound and maternal serum analysis are traditional prenatal screening methods with detection rates between 75%-95%, and considerable false-negative and false-positive results. Also, both require follow up by invasive diagnostic tests in screen-positive cases, mostly amniocentesis and chorionic villi sampling, which are associated with notable risk of pregnancy loss. One of the innovative non-invasive prenatal testing (NIPT) options is the analysis of cell-free DNA (cfDNA) in plasma, which is detected in maternal circulation in a relatively high concentration. Commercial tests for cfDNA in maternal blood have recently become available. Cell-free DNA detection tests do not separate fetal from maternal DNA but use full cfDNA complement and analyze difference in total amount of sequenced DNA fragments, with the help of sophisticated data analysis software. It seems that cfDNA technology testing is highly accurate and has a very high sensitivity, so the difference compared to routine serum sample screening shows its significant superiority. However, cfDNA positive results still need confirmation by the invasive testing. The cell-free DNA analysis aims to become the first choice NIPT option due to its safety and high accuracy rate. The final goal is to develop the reliable method that could eventually replace invasive prenatal testing procedures.

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Non-Invasive Prenatal Testing Using Cell Free DNA in Maternal Plasma: Recent Developments and Future Prospects

Journal of Clinical Medicine ◽

10.3390/jcm3020537 ◽

2014 ◽

Vol 3 (2) ◽

pp. 537-565 ◽

Cited By ~ 35

Author(s):

Peter Benn

Keyword(s):

Prenatal Testing ◽

Maternal Plasma ◽

Future Prospects ◽

Cell Free Dna ◽

Non Invasive ◽

Free Dna ◽

Recent Developments

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Implementation of cell-free DNA-based non-invasive prenatal testing in a National Health Service Regional Genetics Laboratory

Genetics Research ◽

10.1017/s0016672319000119 ◽

2019 ◽

Vol 101 ◽

Cited By ~ 1

Author(s):

Fiona S. Togneri ◽

Mark D. Kilby ◽

Elizabeth Young ◽

Samantha Court ◽

Denise Williams ◽

...

Keyword(s):

National Health Service ◽

High Risk ◽

Health Service ◽

National Health ◽

Prenatal Testing ◽

Low Risk ◽

Trisomy 13 ◽

Cell Free Dna ◽

Non Invasive ◽

Free Dna

Abstract Background Non-invasive prenatal testing (NIPT) for the detection of foetal aneuploidy through analysis of cell-free DNA (cfDNA) in maternal blood is offered routinely by many healthcare providers across the developed world. This testing has recently been recommended for evaluative implementation in the UK National Health Service (NHS) foetal anomaly screening pathway as a contingent screen following an increased risk of trisomy 21, 18 or 13. In preparation for delivering a national service, we have implemented cfDNA-based NIPT in our Regional Genetics Laboratory. Here, we describe our validation and verification processes and initial experiences of the technology prior to rollout of a national screening service. Methods Data are presented from more than 1000 patients (215 retrospective and 840 prospective) from ‘high- and low-risk pregnancies’ with outcome data following birth or confirmatory invasive prenatal sampling. NIPT was by the Illumina Verifi® test. Results Our data confirm a high-fidelity service with a failure rate of ~0.24% and a high sensitivity and specificity for the detection of foetal trisomy 13, 18 and 21. Secondly, the data show that a significant proportion of patients continue their pregnancies without prenatal invasive testing or intervention after receiving a high-risk cfDNA-based result. A total of 46.5% of patients referred to date were referred for reasons other than high screen risk. Ten percent (76/840 clinical service referrals) of patients were referred with ultrasonographic finding of a foetal structural anomaly, and data analysis indicates high- and low-risk scan indications for NIPT. Conclusions NIPT can be successfully implemented into NHS regional genetics laboratories to provide high-quality services. NHS provision of NIPT in patients with high-risk screen results will allow for a reduction of invasive testing and partially improve equality of access to cfDNA-based NIPT in the pregnant population. Patients at low risk for a classic trisomy or with other clinical indications are likely to continue to access cfDNA-based NIPT as a private test.

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