Early-onset severe preeclampsia (EO-PE) is a distinct and highly consequential form of preeclampsia (PE), presenting significant challenges for early detection. Here, we investigated the fragmentation pattern of plasma cell-free DNA (cfDNA) in EO-PE patients. We uncovered that the nucleotide composition at the 5' end (i.e. ends motif) of plasma cfDNA showed a unique pathological preference in EO-PE pregnancies and gestational-psychology preference in healthy pregnancies. By integrating 91 EO-PE specific motifs into a machine-learning model, we achieved accurate prediction of EO-PE development in early pregnancies. Remarkably, our model demonstrated robust performance in an independent cohort of 74 early pregnancies and 1,241 non-invasive prenatal testing (NIPT) samples with ultra-low sequencing depth. Additionally, we revealed that these PE-specific motif signatures lacked tissue specificity, originating extracellularly, and were associated with the abnormal concentration of DNA fragmentation factor subunit beta (DFFB) in EO-PE patients' plasma. These findings establish the plasma DNA fragmentome as a non-invasive and cost-effective biomarker that can be simultaneously captured during NIPT for early EO-PE detection and provide valuable insights into cfDNA production mechanisms in preeclampsia patients.

The authors have declared no competing interest.

This work was supported by the National Natural Science Foundation of China (Grant No. 82001576), Primary Research & Development Plan of Jiangsu Province (BE2022736), Jiangsu Maternal and Children health care key discipline (FXK202142), National Natural Science Foundation of China (32171441, 32000398), National Key R&D Program of China (2022YFC2502402).

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Our study was approved by the Institutional Review Board of BGI (BGI-IRB 20040-T1) and the Institutional Review Board of Suzhou Municipal Hospital (K-2019-019-K01).

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All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. The key raw data have been deposited onto the China National GeneBank DataBase (CNGBdb) with accession number CNP0003056.

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