Characterization of ultra-short plasma cell-free DNA in maternal blood and its potential as a screening marker for pregnancy complications

Abstract

Background Cell-free DNA (cfDNA) in maternal blood is the basis for non-invasive prenatal testing (NIPT). Recently, a new category of cfDNA with a length of 30 to 70 base pairs (bp) has been identified, and its diagnostic potential for cancer has been proposed. However, the characteristics of ultrashort cfDNA in maternal blood during pregnancy have not been determined. This study aimed to investigate the characteristics of ultra-short cfDNA during pregnancy. Methods Ultra-short cfDNA was isolated from the plasma of pregnant and non-pregnant women, and next-generation Sequencing (NGS) libraries were constructed. Deep sequencing and characterization of the features in ultra-short cfDNA in pregnancy were performed. A preeclampsia cohort was included, and high-depth sequencing data identified distinct enriched ultra-short peaks. These features were selected and used to build a diagnostic model in a training cohort, which was subsequently validated in a test cohort. Results Sequencing data revealed that ultra-short cfDNA in maternal blood was enriched in accessible open chromatin regions of blood cells and placental cells. The adoption of a potential G-quadruplex (G4) motif on the antisense was found in a significant proportion of peaks. Distinct features of the ultra-short cfDNA were observed between preeclampsia and healthy controls. The model constructed from these components achieved an area under the curve (AUC) of 0.96 in the training set and 0.86 in the test set. Conclusions Our results provide a characterization of ultra-short cfDNA in maternal blood and an assessment of its potential for the early diagnosis of pregnancy complications.