5: Promoter Footprints Predicting Preterm Birth

Guo Z et al., PLOS Medicine - Large multi-center case-control study shows promoter-region nucleosome footprints in plasma cell-free DNA can predict spontaneous preterm birth. The authors developed PTerm, an 83-gene SVM classifier applied to routine NIPT data, validated across three cohorts. Key terms: cell-free DNA, preterm birth, promoter profiling, NIPT, machine learning. Study Highlights:The study used whole-genome cfDNA sequencing from 2,590 pregnancies across three hospitals to compare promoter (pTSS) read-depths and identify 277 differentially covered genes between preterm and full-term births. Promoter profiling reflected tissue-specific expression and highlighted placenta- and immune-related pathways. A linear SVM classifier (PTerm) with 83 genes achieved AUC 0.878 by LOOCV in training and an overall AUC 0.849 across three validation cohorts. The method is compatible with routine NIPT data without additional tests or cost. Conclusion:Promoter profiling of plasma cfDNA yields a robust, non-invasive classifier (PTerm) for early prediction of preterm birth that can be applied to existing NIPT workflows, though prospective and ethnically diverse validation is needed. QC:This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-04-16. QC Scope:- article metadata and core scientific claims from the narration- excludes analogies, intro/outro, and music QC Summary:- factual score: 10/10- metadata score: 10/10- supported core claims: 6- claims flagged for review: 0- metadata checks passed: 4- metadata issues found: 0 Metadata Audited:- article_doi- article_title- article_journal- license Factual Items Audited:- PTerm is an 83-gene SVM classifier that predicts preterm birth with high accuracy across three validation cohorts (AUC 0.849).- Promoter footprints depth reflects gene expression: higher footprint depth at pTSS indicates decreased expression.- PTerm outperforms BMI and fetal fraction in predicting PTB; BMI/FF alone are around 0.527, while PTerm alone is 0.849 (and integration yields similar).- PTerm can be applied to routine NIPT data with no additional procedures or costs.- Hub genes ESR1, NFKBIA, and ATF3 are among hub genes related to PTB; they support the biology behind the model.- Limitations include Chinese cohort, gestational window 12-28 weeks, lack of placental histology, and generalizability concerns. QC result: Pass.