Prenatal cell‐free DNA screening for fetal aneuploidy in pregnant women at average or high risk: Results from a large US clinical laboratory

Abstract

Background We evaluated the performance of a cell‐free DNA (cfDNA) prenatal screening assay for trisomies 21, 18, and 13, and sex chromosome aneuploidies (SCAs) among a population of pregnant women that included both those at average and high risk. Methods Specimen collection, cfDNA extraction, massively parallel sequencing, and bioinformatics analysis were conducted per laboratory protocol. Assay results, concordance with pregnancy outcomes, and performance characteristics were evaluated. Results A total 75,658 specimens from 72,176 individual pregnant women were received. Technical reasons accounted for 288 (0.4% of all received samples) tests not performed. In the final analysis cohort ( N = 69,794), 13% of pregnancies were considered at average risk and 87% at high risk. Mean gestational age at specimen collection was 15.1 weeks. Of the 69,794 unique pregnancies, 1,359 (1.9%) had positive test results. Among the results with confirmed outcomes, PPV for trisomies 21, 18, and 13 was 98.1%, 88.2%, and 59.3%, respectively; the PPV was 69.0% for SCAs and 75.0% for microdeletions. Overall, PPV was 87.2%, sensitivity was 97.9%, and specificity was 99.9%. Conclusion This cfDNA prenatal screening assay provides highly accurate discrimination between affected and unaffected pregnancies among a population of pregnant women at average and high risk for fetal genetic abnormalities.

Observed and Modeled Positive Predictive Values Using Cell-free DNA Testing for Fetal Trisomy in a Clinical Laboratory Population

“…Other laboratories performing cell-free DNA testing have reported clinical experience using retrospectively obtained pregnancy outcome information in similarly large series [17][18][19]. The observations in the current study are consistent with these previous reports, showing PPV to be higher for trisomy 21 than trisomies 18 and 13.…”

“…The primary limitation of this study is that it relies on retrospective follow-up and thus does not have complete outcome information. Other laboratories studying clinical experience are similarly challenged and report similar proportions of cases with diagnostic outcome obtained, generally between 30 and 40% [17][18][19]. In each of these studies, the calculation of PPV is based on the concordance observed in cases with outcome information and assumes that the ratio of concordant and discordant cases reported to the laboratory accurately reflects the entire cohort.…”

“…Screening for trisomy 21 using cell-free DNA, also known as noninvasive prenatal testing or noninvasive prenatal screening, offers higher sensitivity and a nearly 100 times lower false positive rate than standard biochemical and ultrasonographic screening [2]. Despite the decades of experience with prenatal screening, there is concern that the high performance of this newer screening test, with sensitivities of well over 90% for trisomy 21, 18, and 13 and specificities of greater than 99.9% [3], contributes to a misperception that cell-free DNA testing is Fetal Diagn Ther 2021;48:134-139 DOI: 10.1159/000512501 diagnostic [4,5]. This has led to calls for healthcare providers to understand and communicate positive predictive value (PPV) [6][7][8].…”

Omics Approaches to Study Formation and Function of Human Placental Syncytiotrophoblast

“…Syncytiotrophoblast is a major source of cfDNA in maternal blood, accounting for 5–10% of total circulating DNA in maternal serum (reviewed in Hahn and Holzgreve, 2002 ; Hudecova et al, 2014 ). DNA sequencing (DNA-seq) of cfDNA has revolutionized non-invasive prenatal diagnostic testing and is widely used to detect de novo mutations and common fetal aneuploidies like trisomy 21 ( Bianchi, 2019 ; Guy et al, 2019 ). Intriguingly, the quantity of cfDNA is fivefold higher in the blood of women with preeclampsia compared to healthy control women ( Lo et al, 1999 ; Rafaeli-Yehudai et al, 2018 ).…”

Cell Free DNA Analysis for Chromosomal Abnormalities among Pregnant Females of Pakistan

“…Plasma sample is used for investigation of circulating DNA segments, which contains both maternal and placental cfDNA, as opposed to the seclusion of entire fetal cells from maternal blood. Fetal fraction which is the amount of placental to total (comprising of maternal and placental) cfDNA, increases as pregnancy progresses [8,9]. cfDNA testing is usually recommended to be carried out from the tenth week of gestation, since the fetal fraction in the maternal circulation reaches the ample amount required for an informative test result.…”