Selection and Utility of Single Nucleotide Polymorphism Markers to Reveal Fine-Scale Population Structure in Human Malaria Parasite Plasmodium falciparum

Abstract

Single nucleotide polymorphisms (SNPs) have been shown to be useful in revealing population structure with continental-and regional-scale samples. In epidemiological study, a careful selection of SNPs to track disease spread in local communities would provide an important addition to traditional disease surveillance. This study used SNPs and microsatellites to examine population structure of Plasmodium falciparum at fine-scale in malaria-endemic areas of Western Kenya. A set of high performance (HP) SNPs were selected from a large SNP panel based on BELS ranking, FST values and minor allele frequency criteria. The discriminative power and assignment accuracy of different SNP panels including nonsynonymous SNPs, silent SNPs, previously published barcode SNPs, and the HP SNPs were evaluated together with microsatellites. Among all SNP panels, HP SNPs showed the highest level of differentiation and self-assignment accuracy on average among sites. Clear distinction was observed between the northern and southern P. falciparum samples, whereas samples from the south were least diverged from one another. These results were comparable to those by microsatellites. Nonsynonymous, silent, and barcode SNPs all showed similar levels of genetic variability to one another and weaker structure than the HP SNPs. We described here the procedure of selecting a set of HP SNPs from a large panel of SNPs that resolve population structure of P. falciparum between the northern and southern regions of Western Kenya. Future work is needed to determine if this procedure can result in SNPs panels capable of tracing Plasmodium spread at finer geographical scales.

Genome-wide analysis of 10664 SARS-CoV-2 genomes to identify virus strains in 73 countries based on single nucleotide polymorphism

“…Hence, SNPs play a vital role in tracking virus strains and variations. Analysis of SNP was carried out in ( Lo et al, 2018 ) as well where they suggested a change in the samples of Plasmodium falciparum between the northern and southern regions of Western Kenya; the samples from the southern part showed lesser divergence from each other. Furthermore, clustering has been used by many studies ( Sevilla-Reyes et al, 2013 , Fischer et al, 2018 , Hahn et al, 2020 ) to understand genetic characteristics for a large set of genomes.…”

Distinguishing gene flow between malaria parasite populations

“…The properties of various estimators of F ST have been studied extensively and there is a rich and longstanding literature on IBD [ 15 ]. However, there is currently only limited guidance on the size [ 5 ] and type [ 16 ] of genetic data needed for measuring gene flow between malaria parasite populations, and none specific to the questions of ranking and classification. Most studies of this kind use genetic data of widely varying sizes and types, including both whole genome sequence data and SNP ‘barcode’ data (typically consisting of 24- to 100-SNPs [ 17 , 18 ]), limiting generalizability and comparability between studies.…”

Effects of the MTOR and AKT1 genes polymorphisms on papillary thyroid cancer development

“…Single nucleotide polymorphisms (SNPs) are the popular subjects in the population studies, because of their high frequencies, low cost, and ease of evaluation and analysis methods 18 . MTOR gene, located on the long arm of human chromosome 1 (1q36.2), consists of 3,434 genetic polymorphisms.…”

“…16,17 Single nucleotide polymorphisms (SNPs) are the popular subjects in the population studies, because of their high frequencies, low cost, and ease of evaluation and analysis methods. 18 MTOR gene, located on the long arm of human chromosome 1 (1q36.2), consists of 3,434 genetic polymorphisms. rs2295080 (T > G) in the promoter region and rs2536 T > C in the 3 0 -untranslated region (3 0 UTR) of MTOR gene are well-evaluated SNPs of this gene.…”