Enabling precision medicine in neonatology, an integrated repository for preterm birth research

Abstract

Preterm birth, or the delivery of an infant prior to 37 weeks of gestation, is a significant cause of infant morbidity and mortality. In the last decade, the advent and continued development of molecular profiling technologies has enabled researchers to generate vast amount of ‘omics’ data, which together with integrative computational approaches, can help refine the current knowledge about disease mechanisms, diagnostics, and therapeutics. Here we describe the March of Dimes’ Database for Preterm Birth Research (http://www.immport.org/resources/mod), a unique resource that contains a variety of ‘omics’ datasets related to preterm birth. The database is open publicly, and as of January 2018, links 13 molecular studies with data across tens of thousands of patients from 6 measurement modalities. The data in the repository are highly diverse and include genomic, transcriptomic, immunological, and microbiome data. Relevant datasets are augmented with additional molecular characterizations of almost 25,000 biological samples from public databases. We believe our data-sharing efforts will lead to enhanced research collaborations and coordination accelerating the overall pace of discovery in preterm birth research.

Multiomics Characterization of Preterm Birth in Low- and Middle-Income Countries

“…In the present study, the predictive accuracy for PTB was augmented by combining various omics data sets, which was consistent with previous studies suggesting that PTB was a condition manifesting within multiple biological systems . Observed differences between cohorts also highlighted that the causes of PTB may be associated with varying environmental and socioeconomic factors .…”

“…In the present study, the predictive accuracy for PTB was augmented by combining various omics data sets, which was consistent with previous studies suggesting that PTB was a condition manifesting within multiple biological systems. 18 , 49 , 50 , 51 , 52 Observed differences between cohorts also highlighted that the causes of PTB may be associated with varying environmental and socioeconomic factors. 53 From a biological standpoint, examination of individual components of the multiomics model emphasized the role of inflammation in the pathobiological features of PTB.…”

Microbiome Preterm Birth DREAM Challenge: Crowdsourcing Machine Learning Approaches to Advance Preterm Birth Research

“…The training dataset was constructed by aggregating and processing vaginal microbiome data from the public domain leveraging resources including dbGAP 37 as well as MOD Database for Preterm Birth Research 38 . The final dataset included data from nine studies, representing 3,578 samples from 1,268 individuals.…”

“…The following vaginal microbiome studies were identified by leveraging the March of Dimes Preterm Birth database 38 , the NCBI Sequence Read Archive 55 , the European Nucleotide Archive 56 , and the database of Genotypes and Phenotypes (dbGaP) 37 . Sequence data and associated metadata for the DiGiulio et al 27 cohort were downloaded from ImmPort 57 , under Study SDY465 in May 2016.…”

“…Sequence data and associated metadata for Study SDY465 were downloaded from ImmPort 57 via the March of Dimes Preterm Birth database 38 . Sequence data and associated metadata for BioProjects PRJNA242473, PRJNA294119, PRJNA393472, and PRJNA430482 were downloaded from the NCBI Sequence Read Archive 55 .…”