Development of a single nucleotide polymorphism barcode to genotype Plasmodium vivax infections.

PLoS Neglected Tropical Diseases
Mary Lynn BanieckiPardis C Sabeti

Abstract

Plasmodium vivax, one of the five species of Plasmodium parasites that cause human malaria, is responsible for 25-40% of malaria cases worldwide. Malaria global elimination efforts will benefit from accurate and effective genotyping tools that will provide insight into the population genetics and diversity of this parasite. The recent sequencing of P. vivax isolates from South America, Africa, and Asia presents a new opportunity by uncovering thousands of novel single nucleotide polymorphisms (SNPs). Genotyping a selection of these SNPs provides a robust, low-cost method of identifying parasite infections through their unique genetic signature or barcode. Based on our experience in generating a SNP barcode for P. falciparum using High Resolution Melting (HRM), we have developed a similar tool for P. vivax. We selected globally polymorphic SNPs from available P. vivax genome sequence data that were located in putatively selectively neutral sites (i.e., intergenic, intronic, or 4-fold degenerate coding). From these candidate SNPs we defined a barcode consisting of 42 SNPs. We analyzed the performance of the 42-SNP barcode on 87 P. vivax clinical samples from parasite populations in South America (Brazil, French Guiana), Africa (E...Continue Reading

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Methods Mentioned

BETA
genotyping
PCR
blood draw
PCA

Software Mentioned

Eigensoft
ViiA
SmartPCA
HRM
PrimerDesign
BLAST
LightScanner
COIL
Eco Real - Time PCR System
Genome Analysis Toolkit ( GATK ) Unified Genotyper

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