Objective: Non-invasive prenatal testing (NIPT) for fetal aneuploidies has been widely adopted in developed countries. Despite the sharp decrease in the cost of massively parallel sequencing, the technical know-how and skilled personnel are still one of the major limiting factors for applying this technology to NIPT in low-income settings. Here, we present the establishment and validation of our NIPT procedure called triSure for detection of fetal aneuploidies. Methods: We established the triSure algorithm based on the difference in proportion of fetal and maternal fragments from the target chromosome to all chromosomes. Our algorithm was validated using a published data set and an in-house data set obtained from high-risk pregnant women in Vietnam who have undergone amniotic testing. Several other aneuploidy calling methods were also applied to the same data set to benchmark triSure performance. Results: The triSure algorithm showed similar accuracy to size-based method when comparing them using published data set. Using our in-house data set from 130 consecutive samples, we showed that triSure correctly identified the most samples (overall sensitivity and specificity of 0.983 and 0.986, respectively) compared to other methods tested including count-based, sized-based, RAPIDR and NIPTeR. Conclusion: We have demonstrated that our triSure NIPT procedure can be applied to pregnant women in low-income settings such as Vietnam, providing low-risk screening option to reduce the need for invasive diagnostic tests.

What's already known about this topic? The false positive rate of detecting monosomy X by NIPT is higher than that of other autosomal aneuploidies, due in part to maternal mosaic monosomy X. What does this study add? Our triSure method is less sensitive to the confounding effect of maternal DNA than NIPTeR method. By combining z‐scores of chrX from triSure and NIPTeR, we can detect cases of fetal XX (−2.5 < zX by triSure < 2.5) with maternal mosaicism monosomy X (zX by NIPTeR < −2.5), potentially reducing false positive rate of fetal monosomy X.