1 research outputs found
Creating basis for introducing nonāinvasive prenatal testing in the Estonian public health setting
Objective
The study aimed to validate a wholeāgenome sequencingābased NIPT laboratory method and our recently developed NIPTmer aneuploidy detection software with the potential to integrate the pipeline into prenatal clinical care in Estonia.
Method
In total, 424 maternal blood samples were included. Analysis pipeline involved cellāfree DNA extraction, library preparation and massively parallel sequencing on Illumina platform. Aneuploidies were determined with NIPTmer software, which is based on counting preādefined perāchromosome sets of unique kāmers from sequencing raw data. SeqFF was implemented to estimate cellāfree fetal DNA (cffDNA) fraction.
Results
NIPTmer identified correctly all samples of nonāmosaic trisomy 21 (T21, 15/15), T18 (9/9), T13 (4/4) and monosomy X (4/4) cases, with the 100% sensitivity. However, one mosaic T18 remained undetected. Six falseāpositive (FP) results were observed (FP rate of 1.5%, 6/398), including three for T18 (specificity 99.3%) and three for T13 (specificity 99.3%). The level of cffDNA of <4% was estimated in eight samples, including one sample with T13 and T18. Despite low cffDNA level, these two samples were determined as aneuploid.
Conclusion
We believe that the developed NIPT method can successfully be used as a universal primary screening test in combination with ultrasound scan for the first trimester fetal examination