Pf-HaploAtlas

Pf-HaploAtlas enables exploratory data analysis of genomic variation in Plasmodium falciparum, facilitating spatial and temporal exploration of genes and variants of interest.

Key Features:

• Analysis-ready data catalogues: The app provides analysis-ready data catalogues and visualizations of amino acid haplotypes for all 5102 core P. falciparum genes.
• Spatiotemporal exploration: Pf-HaploAtlas facilitates comprehensive spatial and temporal exploration of genes and variants of interest using data from 16,203 samples from 33 countries spanning 1984 to 2018.
• Data download: Users can download the underlying amino acid haplotype data for further analyses.

Scientific Applications:

• Drug resistance monitoring: Monitoring genomic evolution of Plasmodium falciparum supports decision-making in response to changes in drug resistance.
• Diagnostic surveillance: The tool enables tracking of genetic changes associated with diagnostic test failures.
• Vaccine effectiveness research: Spatiotemporal analysis of gene variants informs studies on vaccine effectiveness.
• Malaria control and research: Exploration of genetic variation data supports efforts in studying and controlling malaria in both public health and academic research contexts.

Methodology:

Pf-HaploAtlas uses MalariaGEN whole genome sequencing databases for Plasmodium parasites and processes data from 16,203 samples across 33 countries collected between 1984 and 2018 to generate amino acid haplotype visualizations.