EPPIcenter award featured by NIAID

The NIAID recently called out funding presented to Dr. Bryan Greenhouse, in collaboration with other members of the PlasmoGenEpi network, in support of infectious and immune-mediated disease (IID) research. Titled “Data and Analysis Ecosystem for Eukaryotic Pathogen Targeted Sequencing”, the project focuses on first establishing a robust, standardized storage format for microhaplotypes generated from targeted sequencing data. This will then be used to develop modular and open source end-to-end workflows that integrate tools for common research use cases into a standardized framework.The EPPIcenter is a leader in bringing the tools of genomic epidemiology to bear on malaria transmission, developing molecular biology techniques, data analysis tools, and training local researchers to become experts as quickly as the tools can be developed. 

Fundamental differences in the biology and transmission of malaria parasites render many of the genomic data and analysis tools developed for other organisms (humans, viruses, and bacteria) impossible to use. Using a modular system of targeted amplicon sequencing for eukaryotic pathogens, the Center, its trainees, and the wider community are generating large genomic datasets without agreed upon ways to share or analyze these data. These data and the way they are handled need standardization and robust software for analysis. These tools will be curated and housed in the proposed ecosystem, including tools for interacting with the standardized data format f, and modular software toolkits to conduct downstream analyses (e.g. prevalence of drug resistance in a population). Accessible and vetted workflows will reduce duplication of pipeline development and allow for continuous integration of new tools into the workflows.Standardizing the way analysis is performed will also facilitate more direct comparisons across geographies and epidemiological conditions. 

Advisors and experts in the analysis of genomic data for eukaryotic pathogens will work together to develop the standards that are needed in this field. The ecosystem will then act as a malleable online hub, meeting the needs of research and policy communities and encouraging broader uptake of genomic epidemiology as a public health tool in malaria endemic areas and beyond.

Check us out on the NIAID website here and our collaborative resource development here.