cfRNA POP Study

Introduction

This is a website to supplement the following paper by Gong et al. submitted to STM: Elevated levels of circulating Leptin (LEP) and Pappalysin2 (PAPPA2) cell-free RNAs are the hallmarks of pregnancies complicated by preeclampsia combined with fetal growth restriction.

It contains the R and other relevant codes (e.g. bash or graphviz) that were used to process the RNA-seq data and to generate the main and the supplementary figures in the paper.

The aim of this study was to identify cell-free RNA (cfRNA) transcripts circulating in the maternal blood that are predictive of pregnancies in combination of fetal growth restriction (FGR) and preeclampsia (PE).

Figure 1: Schematic diagrams showing the current study design

The maternal blood was drawn at around 12, 20, 28 and 36 weeks of gestational age (wkGA) and 2ml of plasma from each of the blood sample was used to extract RNA. A total of 751 maternal plasma samples from 195 pregnant women (39 cases; 156 non-cases) were collected and samples from a case subject at a given gestational age were analysed in the same batch as the matched controls which were also obtained at the same gestational age.

We divided our cohort into discovery and validation groups. The discovery group consisted of 15 PE with FGR cases resulting in preterm delivery (<37 week of gestational age) and the validation group consisted of 24 PE with FGR resulting in term delivery. Each case was paired with ~4 matched controls hence a total of 60 and 96 healthy control samples, with no overlap, were included in the discovery and the validation group, respectively.

At the discovery stage, cfRNAs that were differentially expressed in cases compared to controls were detected at each of the gestational age group and 11 machine learning (ML) methods (Figure 3.1) were compared to find the best predictive models by controlling the number of predictor mRNAs. The best performing model from the discovery stage was validated across each gestational age group in our internal validation dataset. We also analysed the external validation dataset which reported cfRNAs in plasma samples from women with an established diagnosis of PE.