Genome-wide analysis of cfDNA fragmentation patterns and nucleosome positioning in dual enzyme-digested NIPT quality control materials (DENQCMs) and maternal plasma

The genome-wide analysis of cfDNA fragmentation patterns in DENQCMs and maternal plasma was performed by deep sequencing using Illumina Novaseq to confirm their biological characteristics. We first performed deep whole genome sequencing of the cfDNA extracted from DENQCMs and maternal plasma cfDNA. Then we analyzed the sequencing data and compared various characteristics of cfDNA fragmentation patterns, such as dinucleotide composition, nucleosome protection length, and nucleosome occupancy based on a windowed protection score (WPS), to the submitter-provided processed data from a healthy individual IH01 (GEO accession GSM1833276). cfDNA profiles of 2 samples were generated by deep sequencing using Illumina NovaSeq.