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

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.

Non‐invasive cell‐free fetal DNA testing for aneuploidy: multicenter study of 31 515 singleton pregnancies in southeastern China

“…This is not uncommon in China; in previous studies on perinatal outcome following NIPT, around 30% of Chinese pregnant women did not follow up their positive test result with their primary clinician and thus data are commonly lost to follow‐up. Despite this limitation, our findings on the performance of NIPT are in line with previous reports worldwide.…”

Predicting fetoplacental chromosomal mosaicism during non‐invasive prenatal testing

“…NIPT allows the early detection of trisomy 13, 18, and 21 via blood sampling, avoiding the significant risk of invasive procedure-induced miscarriage. 7 Genome-wide random and targeted massively parallel sequencing 6,[8][9][10][11] are the 2 main approaches applied for the detection of common fetal aneuploidies. Both approaches show high sensitivity and specificity for detection of fetal trisomy 21, 18, and 13.…”

Maternal plasma metabolic fingerprint indicative for fetal Down syndrome

“…A novel, non‐invasive diagnostic method is a genetic test for free fetal DNA in maternal peripheral blood. However, despite a lower percentage of false positive results (0.5%), the method remains relatively expensive …”

“…However, despite a lower percentage of false positive results (0.5%), the method remains relatively expensive. [9][10][11][12][13] Despite the fact that a number of tools for the detection of fetal trisomy 21 are available, diagnosis can be improved further. New, noninvasive techniques that would allow for an easy, definitive, and relatively inexpensive diagnosis of fetal trisomy 21 are eagerly awaited.…”