Innovative method for reducing uninformative calls in non-invasive prenatal testing

Abstract

Motivation. Non-invasive prenatal testing or NIPT is currently among the top researched topic in obstetric care. While the performance of the current state-of-the-art NIPT solutions achieve high sensitivity and specicity, they still struggle with a considerable number of samples that cannot be concluded with certainty. Such uninformative results are often subject to repeated blood sampling and re-analysis, usually after two weeks, and this period may cause a stress to the future mothers as well as increase the overall cost of the test.Results. We propose a supplementary method to traditional z-scores to reduce the number of such uninformative calls. The method is based on a novel analysis of the length prole of circulating cell free DNA which compares the change in such proles when random-based and length-based elimination of some fragments is performed. The proposed method is not as accurate as the standard z-score; however, our results suggest that combination of these two independent methods correctly resolves a substantial portion of healthy samples with an uninformative result. Additionally, we discuss how the proposed method can be used to identify maternal aberrations, thus reducing the risk of false positive and false negative calls.Availability and Implementation.

Combination of Fetal Fraction Estimators Based on Fragment Lengths and Fragment Counts in Non-Invasive Prenatal Testing

“…The length of DNA fragment is another promising attribute for differentiation of DNA fragments, since fetal fragments tend to be shorter than maternal ones (Figure 1). Although the fragment lengths improve prediction of NIPT tests by detection of false positive predictions [20,21,22], their potential for prediction of FF has been understudied. Only a simple length-based metric has been proposed in [23], where the ratio of the number of shorter (100–150 bases) and longer (163–168 bases) fragments has correlated with the FF.…”

The effect of plasma‐activated water in a mouse model of inflammatory bowel disease

“…[ 27 ] All computational analyses were written and executed using the SnakeLines framework (v0.9.2). [ 28,29 ] The functionality of the metagenomic content was investigated by PICRUSt (version 2.3.0) [ 30 ] based on the abundance of corresponding OTUs. Differences in the abundance of bacterial families or KEGG pathways [ 31 ] between groups were analyzed by t‐test with the false detection rate correction.…”