PlasmoSTR

PlasmoSTR performs genome-wide short tandem repeat (STR) typing in Plasmodium falciparum and Plasmodium vivax to support population-level analyses of genetic diversity, population structure, and genomic signatures of selection.

Key Features:

• Genome-wide STR genotyping: Uses HipSTR to genotype STRs from more than 3,000 Plasmodium falciparum and 174 Plasmodium vivax whole-genome sequencing samples.
• High-quality STR loci identification: Applies a multivariable logistic regression model to select high-quality STR loci, yielding 6,768 STRs for P. falciparum and 3,496 STRs for P. vivax.
• Quality control for short-read data: Implements rigorous quality control measures to address noise and variability inherent to STR genotyping from short-read sequencing.
• Population genetics analysis: Enables analysis of genetic diversity, population structure, and genomic signatures of selection with results consistent with genome-wide SNP data while identifying STR-specific signals.
• Integration with SNP genotyping: Integrates high-quality STR data with SNP genotyping results for comparative analyses.

Scientific Applications:

• Understanding genetic diversity: Provides higher-resolution characterization of population structure and genetic variation in P. falciparum and P. vivax compared with SNP-only analyses.
• Studying genomic signatures of selection: Reveals genomic regions under selection in malaria parasites using STR variation.
• Antimalarial drug resistance research: Contributes STR-based insights into genetic variation relevant to the emergence and spread of antimalarial drug resistance.

Methodology:

HipSTR-based genotyping of STRs from >3,000 P. falciparum and 174 P. vivax WGS samples, followed by rigorous quality control and a multivariable logistic regression model to identify high-quality loci, with integration of STR data with SNP genotyping for comparative analyses.