An online tool for fetal fraction prediction based on direct size distribution analysis of maternal cell-free DNA

METHOD SUMMARY Cell-free DNA was extracted from plasma samples from pregnant women, concentrated and then analyzed using microchip-based capillary electrophoresis. Cell-free DNA from the same cohort was processed with a CE-approved kit to achieve a postsequencing fetal fraction determination. Sample records were used to investigate the correlation between electrophoresis data and the reference fetal fraction. We created a prediction model and an online tool to estimate the cell-free fetal DNA fraction starting from the major peak height and fetal fragment ratio. The discovery of circulating fetal DNA in the plasma of pregnant women has greatly promoted advances in noninvasive prenatal testing. Screening performance is enhanced with higher fetal fraction and analysis of samples whose fetal DNA fraction is lower than 4% are unreliable. Although current approaches to fetal fraction measurement are accurate, most of them are expensive and time consuming. Here we present a simple and cost-effective solution that provides a quick and reasonably accurate fetal fraction by directly evaluating the size distribution of circulating DNA fragments in the extracted maternal cell-free DNA. The presented approach could be useful in the presequencing stage of noninvasive prenatal testing to evaluate whether the sample is suitable for the test or a repeat blood draw is recommended.