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

Baniecki ML, Faust AL, Schaffner SF, Park DJ, Galinsky K, Daniels RF, Hamilton E, Ferreira MU, Karunaweera ND, Serre D, Zimmerman PA, Sá JM, Wellems TE, Musset L, Legrand E, Melnikov A, Neafsey DE, Volkman SK, Wirth DF, Sabeti PC - PLoS Negl Trop Dis (2015)

Bottom Line: We found that the P. vivax barcode is robust, as it requires only a small quantity of DNA (limit of detection 0.3 ng/μl) to yield reproducible genotype calls, and detects polymorphic genotypes with high sensitivity.Population genetic and statistical analyses show the barcode captures high degrees of population diversity and differentiates geographically distinct populations.Our 42-SNP barcode provides a robust, informative, and standardized genetic marker set that accurately identifies a genomic signature for P. vivax infections.

View Article: PubMed Central - PubMed

Affiliation: Broad Institute, Cambridge, Massachusetts, United States of America.

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 (Ethiopia) and Asia (Sri Lanka). We found that the P. vivax barcode is robust, as it requires only a small quantity of DNA (limit of detection 0.3 ng/μl) to yield reproducible genotype calls, and detects polymorphic genotypes with high sensitivity. The markers are informative across all clinical samples evaluated (average minor allele frequency > 0.1). Population genetic and statistical analyses show the barcode captures high degrees of population diversity and differentiates geographically distinct populations. Our 42-SNP barcode provides a robust, informative, and standardized genetic marker set that accurately identifies a genomic signature for P. vivax infections.

No MeSH data available.


Related in: MedlinePlus

The 42-SNP barcode detects population divergence.(A) 95% confidence intervals for FST values. All FST values reflect statistically significant population divergence (p < 10-5). (B) Population pairs separate in PCA with the first two principal components.
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pntd.0003539.g005: The 42-SNP barcode detects population divergence.(A) 95% confidence intervals for FST values. All FST values reflect statistically significant population divergence (p < 10-5). (B) Population pairs separate in PCA with the first two principal components.

Mentions: We used the median value obtained from bootstrapping of the FST statistic to quantitatively assess pairwise population divergence, and confirmed the separation visually identified by PCA. We found clear population divergence by both FST and PCA for Brazil and Sri Lanka (FST = 0.18; POV = 26), Ethiopia and Sri Lanka (FST = 0.21; POV = 30), French Guiana and Sri Lanka (FST = 0.21; POV = 26), Ethiopia and French Guiana (FST = 0.27; POV = 30), and Ethiopia and Brazil (FST = 0.31; POV = 33) (Fig. 5A). Bootstrapping analysis rejected the hypothesis of a panmictic population in each case (p < 10-5), showing that all the FST values capture statistically significant population divergence. Although separation of the samples from the neighboring countries of Brazil and French Guiana was not visually resolved by the first two principal components in PCA (POV = 21), the FST value was still highly significant (FST = 0.10, p < 10-5) (Fig. 5B).


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

Baniecki ML, Faust AL, Schaffner SF, Park DJ, Galinsky K, Daniels RF, Hamilton E, Ferreira MU, Karunaweera ND, Serre D, Zimmerman PA, Sá JM, Wellems TE, Musset L, Legrand E, Melnikov A, Neafsey DE, Volkman SK, Wirth DF, Sabeti PC - PLoS Negl Trop Dis (2015)

The 42-SNP barcode detects population divergence.(A) 95% confidence intervals for FST values. All FST values reflect statistically significant population divergence (p < 10-5). (B) Population pairs separate in PCA with the first two principal components.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4362761&req=5

pntd.0003539.g005: The 42-SNP barcode detects population divergence.(A) 95% confidence intervals for FST values. All FST values reflect statistically significant population divergence (p < 10-5). (B) Population pairs separate in PCA with the first two principal components.
Mentions: We used the median value obtained from bootstrapping of the FST statistic to quantitatively assess pairwise population divergence, and confirmed the separation visually identified by PCA. We found clear population divergence by both FST and PCA for Brazil and Sri Lanka (FST = 0.18; POV = 26), Ethiopia and Sri Lanka (FST = 0.21; POV = 30), French Guiana and Sri Lanka (FST = 0.21; POV = 26), Ethiopia and French Guiana (FST = 0.27; POV = 30), and Ethiopia and Brazil (FST = 0.31; POV = 33) (Fig. 5A). Bootstrapping analysis rejected the hypothesis of a panmictic population in each case (p < 10-5), showing that all the FST values capture statistically significant population divergence. Although separation of the samples from the neighboring countries of Brazil and French Guiana was not visually resolved by the first two principal components in PCA (POV = 21), the FST value was still highly significant (FST = 0.10, p < 10-5) (Fig. 5B).

Bottom Line: We found that the P. vivax barcode is robust, as it requires only a small quantity of DNA (limit of detection 0.3 ng/μl) to yield reproducible genotype calls, and detects polymorphic genotypes with high sensitivity.Population genetic and statistical analyses show the barcode captures high degrees of population diversity and differentiates geographically distinct populations.Our 42-SNP barcode provides a robust, informative, and standardized genetic marker set that accurately identifies a genomic signature for P. vivax infections.

View Article: PubMed Central - PubMed

Affiliation: Broad Institute, Cambridge, Massachusetts, United States of America.

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 (Ethiopia) and Asia (Sri Lanka). We found that the P. vivax barcode is robust, as it requires only a small quantity of DNA (limit of detection 0.3 ng/μl) to yield reproducible genotype calls, and detects polymorphic genotypes with high sensitivity. The markers are informative across all clinical samples evaluated (average minor allele frequency > 0.1). Population genetic and statistical analyses show the barcode captures high degrees of population diversity and differentiates geographically distinct populations. Our 42-SNP barcode provides a robust, informative, and standardized genetic marker set that accurately identifies a genomic signature for P. vivax infections.

No MeSH data available.


Related in: MedlinePlus