Selection and evaluation of DNase I hypersensitive sites for prenatal screening of trisomy 21 in the fetus

This study introduces a novel approach for noninvasive prenatal testing (NIPT) of chromosomal abnormalities, based on analysis of epigenetic features in circulating cell-free DNA (cfDNA). The core innovation of our method leverages fundamental differences in chromatin organization between maternal and fetal cells. Specifically, we focused on genomic regions that exhibit open chromatin configuration in maternal blood cells but remain tightly packed in fetal tissues (DNase I hypersensitive sites or DHSs). These epigenetic differences create distinct cfDNA fragmentation signatures that allow selective identification of fetal DNA within the maternal cfDNA pool. The study workflow comprised several key steps: performing genome-wide screening to identify differentially accessible chromatin regions, selecting the most informative markers using a machine learning algorithm, and targeted sequencing of the selected epigenetic markers using molecular barcodes. Subsequently, a LASSO regression model was constructed and validated. As a proof of concept, the study demonstrates the method’s efficacy in identifying trisomy 21 (Down syndrome), though the underlying principles can be readily adapted to other abnormalities. Complementing its robust performance, the technique offers practical advantages in terms of platform compatibility – the same epigenetic markers can be assessed using either next-generation sequencing or simpler, more cost-efficient methods like digital PCR. With further refinement, the approach could be extended to screen for additional aneuploidies (trisomies 13 and 18) and microdeletion syndromes. Therefore, this approach offers new opportunities for developing cost-effective testing systems suitable for widespread routine clinical implementation, combining high diagnostic accuracy with reduced analysis costs.

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