Genotyping Malaria Parasite Isolates

We also examined each parasite isolate genome for their genotypes at the 96 SNPs in a genome-wide panel using the Illumina GoldenGate platform as described (Nkhoma et al., 2013 (link)). These SNPs were gleaned from PlasmoDB version 6.2 (www.plasmodb.org) and were chosen if they were highly polymorphic for parasites from the Thai-Burma border, assayable, not in genes encoding surface proteins (e.g., var, rifin, surfin, stevor), transporters or telomeric genes that may be under strong selection, were distributed across all 14 chromosomes and were found to have MAFs between 0.10 and 0.50. No formal linkage or neutrality analysis was reported in regard to the generation of the SNP barcode. The 96-SNP panel was used to analyse genetic diversity and population structure of asymptomatic and clinical isolates from pregnant women and children younger than 5 years old at the Thai-Burma border (N = 1,731) from 2001 to 2010 (Nkhoma et al., 2013 (link)).

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Argyropoulos D.C., Tan M.H., Adobor C., Mensah B., Labbé F., Tiedje K.E., Koram K.A., Ghansah A, & Day K.P. (2023). Performance of SNP barcodes to determine genetic diversity and population structure of Plasmodium falciparum in Africa. Frontiers in Genetics, 14, 1071896.

Publication 2023

GoldenGate platform

14 chromosomes Children Genes Genetic diversity Genome Genotypes Mafs Parasites Polymorphic Pregnant women Surface proteins Telomeric Thai Transporters Younger

Corresponding Organization : University of Melbourne

Other organizations : University of Ghana, Noguchi Memorial Institute for Medical Research, University of Chicago

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Variable analysis

independent variables

Genotypes at the 96 SNPs in a genome-wide panel

dependent variables

Genetic diversity and population structure of asymptomatic and clinical isolates from pregnant women and children younger than 5 years old at the Thai-Burma border

control variables

SNPs were chosen if they were highly polymorphic for parasites from the Thai-Burma border, assayable, not in genes encoding surface proteins (e.g., var, rifin, surfin, stevor), transporters or telomeric genes that may be under strong selection, were distributed across all 14 chromosomes and were found to have MAFs between 0.10 and 0.50.
No formal linkage or neutrality analysis was reported in regard to the generation of the SNP barcode.

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