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

Gazdarica, J.1,2,3, Hekel, R.4,5,6, Budis, J.4,6,7, Kucharik, M.4, Duris, F.8, Radvanszky, J.4,9, Turna, J.5,7,9, Szemes, T.4,5,7

1Geneton Ltd., Bratislava 841 04, Slovakia
2Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava 841 04, Slovakia
3Slovak Centre of Scientific and Technical Information, Bratislava 811 04, Slovakia
4Geneton Ltd., Bratislava 841 04, Slovakia
5Slovak Centre of Scientific and Technical Information, Bratislava 811 04, Slovakia
6Comenius University Science Park, Comenius University, Bratislava 841 04, Slovakia
7Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava 841 04, Slovakia

Abstract

Recent advances in massively parallel shotgun sequencing opened up new options for affordable non-invasive prenatal testing (NIPT) for fetus aneuploidy from DNA material extracted from maternal plasma. Tests typically compare chromosomal distributions of a tested sample with a control set of healthy samples with unaffected fetuses. Deviations above certain threshold levels are concluded as positive findings. The main problem with this approach is that the variance of the control set is dependent on the number of sequenced fragments. The higher the amount, the more precise the estimation of actual chromosomal proportions is. Testing a sample with a highly different number of sequenced reads as used in training may thus lead to over- or under-estimation of their variance, and so lead to false predictions. We propose the calculation of a variance for each tested sample adaptively, based on the actual number of its sequenced fragments. We demonstrate how it leads to more stable predictions, mainly in real-world diagnostics with the highly divergent inter-sample coverage.