Clinical performance of DNA-based prenatal screening using single-nucleotide polymorphisms approach in Thai women with singleton pregnancy

Abstract

© 2020 The Authors. Molecular Genetics & Genomic Medicine published by Wiley Periodicals, Inc. Background: To review the performance of noninvasive prenatal screening (NIPS) using targeted single-nucleotide polymorphisms (SNPs) approach in mixed-risk Thai women. Methods: Retrospective analysis of data for detection of trisomy 21 (T21), 18 (T18), 13 (T13), monosomy X (XO), other sex chromosome aneuploidies (SCA), and triploidy/vanishing twins (VT) from a single commercial laboratory. Results: Mean (±SD) gestational age and maternal weight were 13.2 (±2.1) weeks and 125.7 (±22.4) pounds, respectively (n = 8,572). From 462/8,572 (5.4%) no-calls; 1/462 (0.2%) was uninformative SNPs, and 1/462 chose amniocentesis. Redraw settled 323/460 (70%) samples with low fetal fraction (FF); and 8,434/8,572 (98.4%) were finally reportable, with 131 high risks (1.6%). The median (min-max) FF of reportable (n = 8,434) and unreportable samples (n = 137) samples were 10.5% (2.6–37.9) and 3.8% (1–14.1), respectively (p <.05). Fetal karyotypes were available in 106/131 (80.9%) and 52/138 (37.7%) high risk and repeated no-calls, respectively. The positive predictive values (PPVs) for T21 (n = 47), T18 (n = 15), T13 (n = 7), XO (n = 8), other SCA (n = 7), and triploidy/VT were 94%, 100%, 58.3%, 66.7%, 70%, and 57.1%, respectively. None of repeated no-calls had aneuploidies. Conclusion: SNP-based NIPS has high PPVs for T21 and T18. Although the proprietary SNPs library is not population-specific, uninformative SNPs are uncommon.