The application of NIPT using combinatorial probe-anchor synthesis to identify sex chromosomal aneuploidies (SCAs) in a cohort of 570 pregnancies.

Background: Non-invasive prenatal testing (NIPT) as alternative screening method had been proven to have very high sensitivity and specificity for detecting common aneuploidies such as T21, T18, and T13, with low false positive and false negative rates. Unfortunately, recent studies suggested that the NIPT achieved lower accuracy in sex chromosomal aneuploidies (SCAs) detection than autosomal aneuploidies detection. BGISEQ-500 powered by Combinatorial Probe-Anchor Synthesis (CPAS) and DNA Nanoballs (DNBs) technology that combined linear amplification and rolling circle replication to reduce the error rate while enhancing the signal. Therefore, NIPT based on CPAS might be a good method for SCAs screening in routine clinical practice. In the study, we intended to evaluate the clinical utility of NIPT based on CPAS on screening for fetal SCAs.

Results: A total of 570 pregnant women were included in the retrospective study. Maternal blood samples were collected for NIPT; amniocentesis was performed on all pregnant women. NIPT was carried out by BGISEQ-500 sequencing platform based on CPAS. Karyotype analysis of amniotic cells was performed by standard G-banding techniques. 43 out of the total 570 pregnant women tested by NIPT showed fetal SCAs (19 of 45,X, 12 of 47,XXY, 10 of 47,XXX, and 2 of 47,XYY). The following amniocentesis confirmed that 26 cases were true positive (7 of true positive 45,X, 9 of true positive 47,XXY, 9 of true positive 47,XXX as well as 1 of 47,XYY) and the positive predictive value (PPV) for fetal SCAs was 60.47%. In addition, the PPV of advanced maternal age group (67.74%) was higher than the other indications group (45.45%) or serological screening high-risk /critical-risk group (0%).

Conclusions: NIPT based on CPAS could be a potential method for SCAs screening. However, it still had high false positive rates, especially for 45,X. The pregnant women with fetal SCAs detected by NIPT, especially those with non-age-related prenatal diagnostic indications, should be advised to accept invasive prenatal karyotype analysis.