Molecular epidemiology of pregnancy using omics data: advances, success stories, and challenges

Abstract

Multi-omics approaches have been successfully applied to investigate pregnancy and health outcomes at a molecular and genetic level in several studies. As omics technologies advance, research areas are open to study further. Here we discuss overall trends and examples of successfully using omics technologies and techniques (e.g., genomics, proteomics, metabolomics, and metagenomics) to investigate the molecular epidemiology of pregnancy. In addition, we outline omics applications and study characteristics of pregnancy for understanding fundamental biology, causal health, and physiological relationships, risk and prediction modeling, diagnostics, and correlations.

Keywords: Computational biology; Epidemiology; Omics; Pregnancy.

Fig. 1

Current important scientific directions of omics utilization in pregnancy. We processed the abstracts of 428 papers identified in our search of omics and pregnancy and conditions we processed. From 2020 extracted scientific keywords from abstracts that occurred with pregnancy and omics, we show 181 keywords with at least 5 co-occurrences. The co-occurrence link with other keywords is also measured and shown as links between keywords. Colors represent general topics and technology used, for example, blue for animals and green for pregnancy, etc.". The network analysis was performed by VOSviewer [6]. Nodes are keywords that are linked by edges for their co-occurrence. Edges between two keywords in the graph reflect the number of co-occurrences

Fig. 2

Omics advancements featured in Row 1 literature overall, and Row 2 pregnancy investigation. Omics technology usage continues to grow in research studies. The number of publications by year with omics keywords and pregnancy in their abstract extracted from the PubMed database is shown in panel Row 2. The colors in the stacked bar charts show the trends of different specific omic technologies. For example, gas chromatography-mass spectrometry (GC–MS) has always been used in metabolomics. However, the use of liquid chromatography-mass spectrometry (LC–MS) is more common in recent years; for proteomics, mass spectrometry continues to be the dominant technique. This figure was generated with pubSight [8]

Fig. 3

Overview workflow of multi-omics in pregnancy. a, study design is a key feature in a project to collect samples and measure omics to investigate birth development, pregnancy physiology and pathophysiology, and long-term health effect at molecular levels. b, various sample matrices can be collected from individuals (mothers and babies), including breast milk, stool, urine, and blood. c, d, omics technologies such as Next Generation Sequencing (NGS) for genome and metagenome data, and LC–MS for metabolomics and proteomics profiling enable measuring millions of biomarkers of health. e, downstream analysis includes processing data and applying computational approaches to discover patterns that explain molecular dynamics of pregnancy biology, causality, and correlations. This figure is created with BioRender.com