First-trimester multi-modal cell-free DNA analysis for prediction of preterm and term preeclampsia

BACKGROUND: Preeclampsia, which is a leading cause of maternal and perinatal mortality and morbidity, represents a biologically heterogeneous syndrome. First-trimester screening with the Fetal Medicine Foundation (FMF) competing-risks model for preterm preeclampsia enables earlier identification of at-risk pregnancies, allowing risk reduction through aspirin prophylaxis, but depends on Doppler velocimetry and biochemical measurements that limit scalability and offer limited discrimination for term disease. A unified, molecular first-trimester test capable of stratifying risk across the full clinical spectrum of preeclampsia has not been established. OBJECTIVE: To determine whether multi-modal, tissue-resolved analysis of first-trimester circulating cell-free DNA (cfDNA), obtained during routine noninvasive prenatal testing (NIPT), enables early prediction of both preterm and term preeclampsia. STUDY DESIGN: This nested case-control study included 125 singleton pregnancies sampled at 11 to 14 weeks' gestation after quality control (48 controls, 30 preterm preeclampsia, 47 term preeclampsia). For 80 pregnancies, matched placental villi and maternal buffy coat samples were available to derive tissue reference profiles. Plasma cfDNA underwent multi-modal sequencing using Oxford Nanopore Technologies, enabling tissue-resolved analysis of fragmentomic and epigenetic signatures. Separate ensemble machine-learning classifiers were developed to capture distinct disease pathways for preterm (