A cloud-based bioinformatic and analytic infrastructure for the Expanded Program on Immunization Consortium

Abstract

The overarching goal of the Expanded Program for Immunization Consortium - Human Immunology Project Consortium (EPIC-HIPC) is to identify and characterize vaccine-induced neonatal responses and define biomarkers that may predict immunogenicity. Key to this effort is the establishment of the Data Management Core (DMC) to provide reliable clinical data and bioinformatic infrastructure for centralized curation, storage, and analysis of multiple deidentified ‘omics datasets. The DMC established a cloud-based platform to track, store, and share data according to set standards using Amazon Web Services (AWS). In our clinical core sites, biosamples collected and shipped across sites are tracked using ItemTracker via AWS Elastic Compute Cloud while their associated clinical data are captured using Research Electronic Data Capture software. Multi-omic datasets are stored in access-regulated Amazon Simple Storage Service (S3) for file version control. All data must complete quality control (QC) processes by the site generating said data, which is then exported to the DMC for quality assurance (QA). Data integration is performed using RStudio Server Pro which directly imports the data files from Amazon S3 via a controlled computing environment. The DMC deposits finalized datasets onto public repositories to be shared openly upon publication. Completion of our goal will provide the resources, planning, and scientific expertise to make this discovery platform possible. Robust DMC operations will allow rapid sharing of integrative results across the entire team. Maintenance of standards and public deposition of high quality ‘omics data will further advance scientific progress for the benefit of vaccine development and public health.