Clinical experience of genome-wide non-invasive prenatal testing as a first-tier screening test in a cohort of 59,771 pregnancies

Abstract

Objective Genome-wide non-invasive prenatal testing (GW-NIPT) for prenatal screening has been widely implemented. However, the related clinical data is still insufficient. Here, we evaluated the clinical performance of GW-NIPT as a first-tier screening test for detecting fetal aneuploidy and copy number variation (CNV). Methods The study included 59,877 pregnant women who underwent GW-NIPT at Shenzhen Baoan Women’s and Children’s Hospital, China, from November 2017 to May 2021. NIPT was performed on the BGISEQ-500 platform. Fetal karyotype analysis, chromosomal microarray analysis (CMA) and fluorescence in situ hybridization were used for invasive diagnostic procedures, and postnatal outcomes were collected. Results Among 59,877 pregnant women who underwent GW-NIPT, 59,771 were successfully tested. Of these, 499 (0.83%) were identified with 504 high-risk fetal chromosomal abnormalities, including 5 cases each carrying two distinct abnormalities. Follow-up analysis demonstrated that GW-NIPT sensitivity exceeded 97% for fetal aneuploidies and was 63.6% for CNV (≥5 Mb). The positive predictive values for T21, T18, T13, sex chromosome aneuploidy, rare autosomal aneuploidy, and CNV (≥5 Mb) were calculated as 83.1%, 25.8%, 10.3%, 51.9%, 2.0%, and 33.9%, respectively. For confirmed fetal mosaicism, the detection rate of NIPT was 70.6%, which was consistent with that of CMA (70.6%). Conclusions GW-NIPT has high sensitivity in screening fetal aneuploidy and moderate clinical utility in detecting CNV and fetal mosaicism, demonstrating that GW-NIPT holds significant application value in current and future prenatal screening procedures.