Quality Assurance and Standardization of Cell-Free DNA-Based Prenatal Testing Laboratory Procedures

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.

Download Full-text

An online tool for fetal fraction prediction based on direct size distribution analysis of maternal cell-free DNA

BioTechniques ◽

10.2144/btn-2020-0143 ◽

2020 ◽

Author(s):

Luca Bedon ◽

Josef Vuch ◽

Simeone Dal Monego ◽

Germana Meroni ◽

Vanna Pecile ◽

...

Keyword(s):

Size Distribution ◽

Prenatal Testing ◽

Distribution Analysis ◽

Blood Draw ◽

Noninvasive Prenatal Testing ◽

Cell Free Dna ◽

Maternal Cell ◽

Fetal Dna ◽

Free Dna ◽

Fetal Fraction

The discovery of circulating fetal DNA in the plasma of pregnant women has greatly promoted advances in noninvasive prenatal testing. Screening performance is enhanced with higher fetal fraction and analysis of samples whose fetal DNA fraction is lower than 4% are unreliable. Although current approaches to fetal fraction measurement are accurate, most of them are expensive and time consuming. Here we present a simple and cost-effective solution that provides a quick and reasonably accurate fetal fraction by directly evaluating the size distribution of circulating DNA fragments in the extracted maternal cell-free DNA. The presented approach could be useful in the presequencing stage of noninvasive prenatal testing to evaluate whether the sample is suitable for the test or a repeat blood draw is recommended.

Download Full-text

OC01.03: State‐wide performance of traditional and cell‐free DNA‐based prenatal testing pathways: the Victorian Perinatal Record Linkage (PeRL) study

Ultrasound in Obstetrics and Gynecology ◽

10.1002/uog.20426 ◽

2019 ◽

Vol 54 (S1) ◽

pp. 1-2 ◽

Cited By ~ 1

Author(s):

L. Hui ◽

A. Lindquist ◽

A. Poulton ◽

E. Kluckow ◽

B. Hutchinson ◽

...

Keyword(s):

Record Linkage ◽

Prenatal Testing ◽

Cell Free Dna ◽

Free Dna

Download Full-text

Noninvasive prenatal testing from cell-free DNA

Canadian Medical Association Journal ◽

10.1503/cmaj.131551 ◽

2014 ◽

Vol 186 (12) ◽

pp. 934-934

Author(s):

C. M. Armour ◽

S. M. Nikkel

Keyword(s):

Prenatal Testing ◽

Noninvasive Prenatal Testing ◽

Cell Free Dna ◽

Free Dna

Download Full-text

Cell-Free DNA Analysis of Targeted Genomic Regions in Maternal Plasma for Non-Invasive Prenatal Testing of Trisomy 21, Trisomy 18, Trisomy 13, and Fetal Sex

Clinical Chemistry ◽

10.1373/clinchem.2015.252502 ◽

2016 ◽

Vol 62 (6) ◽

pp. 848-855 ◽

Cited By ~ 29

Author(s):

George Koumbaris ◽

Elena Kypri ◽

Kyriakos Tsangaras ◽

Achilleas Achilleos ◽

Petros Mina ◽

...

Keyword(s):

Trisomy 21 ◽

Dna Analysis ◽

Prenatal Testing ◽

Cost Effective ◽

Maternal Plasma ◽

Trisomy 13 ◽

Cell Free Dna ◽

Free Dna ◽

Genomic Regions ◽

Fetal Fraction

Abstract BACKGROUND There is great need for the development of highly accurate cost effective technologies that could facilitate the widespread adoption of noninvasive prenatal testing (NIPT). METHODS We developed an assay based on the targeted analysis of cell-free DNA for the detection of fetal aneuploidies of chromosomes 21, 18, and 13. This method enabled the capture and analysis of selected genomic regions of interest. An advanced fetal fraction estimation and aneuploidy determination algorithm was also developed. This assay allowed for accurate counting and assessment of chromosomal regions of interest. The analytical performance of the assay was evaluated in a blind study of 631 samples derived from pregnancies of at least 10 weeks of gestation that had also undergone invasive testing. RESULTS Our blind study exhibited 100% diagnostic sensitivity and specificity and correctly classified 52/52 (95% CI, 93.2%–100%) cases of trisomy 21, 16/16 (95% CI, 79.4%–100%) cases of trisomy 18, 5/5 (95% CI, 47.8%–100%) cases of trisomy 13, and 538/538 (95% CI, 99.3%–100%) normal cases. The test also correctly identified fetal sex in all cases (95% CI, 99.4%–100%). One sample failed prespecified assay quality control criteria, and 19 samples were nonreportable because of low fetal fraction. CONCLUSIONS The extent to which free fetal DNA testing can be applied as a universal screening tool for trisomy 21, 18, and 13 depends mainly on assay accuracy and cost. Cell-free DNA analysis of targeted genomic regions in maternal plasma enables accurate and cost-effective noninvasive fetal aneuploidy detection, which is critical for widespread adoption of NIPT.

Download Full-text