RT Journal Article
SR Electronic
T1 MOIRE: A software package for the estimation of allele frequencies and effective multiplicity of infection from polyallelic data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2023.10.03.560769
DO 10.1101/2023.10.03.560769
A1 Murphy, Maxwell
A1 Greenhouse, Bryan
YR 2024
UL http://biorxiv.org/content/early/2024/08/02/2023.10.03.560769.abstract
AB Motivation Malaria parasite genetic data can provide insight into parasite phenotypes, evolution, and transmission. However, estimating key parameters such as allele frequencies, multiplicity of infection (MOI), and within-host relatedness from genetic data is challenging, particularly in the presence of multiple related coinfecting strains. Existing methods often rely on single nucleotide polymorphism (SNP) data and do not account for within-host relatedness.Results We present MOIRE (Multiplicity Of Infection and allele frequency REcovery), a Bayesian approach to estimate allele frequencies, MOI, and within-host relatedness from genetic data subject to experimental error. MOIRE accommodates both polyallelic and SNP data, making it applicable to diverse genotyping panels. We also introduce a novel metric, the effective MOI (eMOI), which integrates MOI and within-host relatedness, providing a robust and interpretable measure of genetic diversity. Extensive simulations and real-world data from a malaria study in Namibia demonstrate the superior performance of MOIRE over naive estimation methods, accurately estimating MOI up to 7 with moderate sized panels of diverse loci (e.g. microhaplotypes). MOIRE also revealed substantial heterogeneity in population mean MOI and mean relatedness across health districts in Namibia, suggesting detectable differences in transmission dynamics. Notably, eMOI emerges as a portable metric of within-host diversity, facilitating meaningful comparisons across settings when allele frequencies or genotyping panels differ. Compared to existing software, MOIRE enables more comprehensive insights into within-host diversity and population structure.Availability MOIRE is available as an R package at https://eppicenter.github.io/moire/.Contact mm{at}maxmurphy.devSupplementary information Supplementary data are available at Bioinformatics online.Competing Interest StatementThe authors have declared no competing interest.