| Title: |
Towards an open analysis ecosystem for Plasmodium genomic epidemiology |
| Authors: |
Ruybal-Pesántez, Shazia; Amaya-Romero, Jorge; Bérubé, Sophie; Brazeau, Nicholas; Diop, Mouhamadou Fadel; Hathaway, Nicholas; Hendry, Jason; Mccann, Kirsty; Murie, Kathryn; Murphy, Maxwell; Niaré, Karamoko; Phelan, Jody; Schaffner, Stephen; Simkin, Alfred; Taylor, Aimee; Greenhouse, Bryan; Wesolowski, Amy; Verity, Robert |
| Contributors: |
Imperial College London; Universidad San Francisco de Quito (USFQ); Harvard T.H. Chan School of Public Health; University of Florida Gainesville (UF); Duke University Medical Center; London School of Hygiene and Tropical Medicine Fajara, Gambia; London School of Hygiene and Tropical Medicine (LSHTM); University of Massachusetts System (UMASS); Max Planck Institute for Infection Biology (MPIIB); Max-Planck-Gesellschaft; Deakin University Melbourne Burwood; University of California San Francisco (UC San Francisco); University of California (UC); Brown University; Broad Institute of MIT and Harvard (BROAD INSTITUTE); Harvard Medical School Boston (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital Boston; Institut Pasteur Paris (IP); Université Paris Cité (UPCité); Johns Hopkins Bloomberg School of Public Health Baltimore; Johns Hopkins University Baltimore (JHU); This work was funded in part by the Bill and Melinda Gates Foundation (INV-031273 to RV; INV-053763 to BG, AW, RV) and NIH/NIAID (U01AI184646 to BG, AW, RV; K24AI144048 to BG). SR-P and RV acknowledge funding from the MRC Centre for Global Infectious Disease Analysis (reference MR/X020258/1), funded by the UK Medical Research Council (MRC). This UK funded award is carried out in the frame of the Global Health EDCTP3 Joint Undertaking. ART is funded by the European Union (project number 101110393).; European Project: 101110393,HORIZON-MSCA-2022-PF-01,HORIZON-MSCA-2022-PF-01,PvRecur(2023) |
| Source: |
https://pasteur.hal.science/pasteur-05266791 ; 2025. |
| Publisher Information: |
CCSD |
| Publication Year: |
2025 |
| Subject Terms: |
[SDV]Life Sciences [q-bio] |
| Description: |
International audience ; Major advances in Plasmodium sequencing approaches, bioinformatic pipelines, and data analysis tools have provided valuable insights into malaria epidemiology from parasite genomic data. However, translating genetic data into actionable information for decision-makers remains a challenge. Significant barriers limit the integration of these advances into a functional data analysis ecosystem that produces standardized, interpretable results for use by national malaria control programs. The Plasmodium Genomic Epidemiology (PlasmoGenEpi) network convened 18 subject matter experts across 15 institutions at the R eproducibility, A ccessibility, D ocumentation, and I nteroperability S tandards H ackathon in 20 23 (RADISH23) to identify available analysis tools, evaluate software standards, improve documentation, and outline workflows. Eight use cases for genomic data were identified, and a subset were developed into analysis workflows in terms of a series of connected functionalities. Software tools were then mapped against functionalities to outline a modular approach to data analysis for these use cases. In addition to outlining workflows, a set of objective criteria were developed for evaluating software standards. Forty Plasmodium genomic analysis tools were identified, of which 22 were prioritized for software standards evaluation. Additional tutorials were developed for 10 tools in the form of reproducible code applied to shared datasets. These resources are available on PGEforge ( mrc- ide.github.io/PGEforge ), a new community resource that serves as a central, open repository for current and future resources for malaria genomic data analysis. |
| Document Type: |
report |
| Language: |
English |
| Relation: |
info:eu-repo/semantics/altIdentifier/pmid/40236429; info:eu-repo/grantAgreement//101110393/EU/Using Plasmodium vivax genetic data to estimate the cause of recurrent vivax malaria/PvRecur; MEDRXIV: 2025.04.01.25325032; PUBMED: 40236429; PUBMEDCENTRAL: PMC11998834 |
| DOI: |
10.1101/2025.04.01.25325032 |
| Availability: |
https://pasteur.hal.science/pasteur-05266791; https://pasteur.hal.science/pasteur-05266791v1/document; https://pasteur.hal.science/pasteur-05266791v1/file/2025.04.01.25325032v1.full.pdf; https://doi.org/10.1101/2025.04.01.25325032 |
| Rights: |
http://creativecommons.org/licenses/by/ ; info:eu-repo/semantics/OpenAccess |
| Accession Number: |
edsbas.B85CBB03 |
| Database: |
BASE |