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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 is distributed across the genome.The location of the 42 SNPs is illustrated on the 14 chromosomes of the P. vivax genome. SNPs are colored by their average minor allele frequency (AMAF) among the populations tested; 17 SNPs had AMAF ≥ 0.3, 18 SNPs had 0.3 > AMAF ≥ 0.2, and 7 SNPs had 0.2 > AMAF > 0.1 (S7 Table). Putative centromere locations are indicated by the pinched location on the perimeter of each chromosome [16].
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pntd.0003539.g003: The 42-SNP barcode is distributed across the genome.The location of the 42 SNPs is illustrated on the 14 chromosomes of the P. vivax genome. SNPs are colored by their average minor allele frequency (AMAF) among the populations tested; 17 SNPs had AMAF ≥ 0.3, 18 SNPs had 0.3 > AMAF ≥ 0.2, and 7 SNPs had 0.2 > AMAF > 0.1 (S7 Table). Putative centromere locations are indicated by the pinched location on the perimeter of each chromosome [16].

Mentions: The 42 SNPs span all 14 chromosomes of the P. vivax genome, and each SNP is highly informative across four distinct geographic populations: Brazil, Sri Lanka, Ethiopia, and French Guiana. The SNPs captured high degrees of diversity, with the AMAF value for each SNP > 0.1 (Fig. 3, and S7 Table). Moreover, the SNPs were independently informative (S2 Fig). We did not expect SNPs to be in LD since the closest pair of SNPs is 21,237 bp apart (SNPs 5 and 6), which is beyond the map distance over which we typically see significant LD in Plasmodium populations [37,38]. Using the r2 statistic to measure LD (which examines allele correlation from 0 to 1), we found that all SNP pairs had r2 < 0.53 in each. None of the r2 values were significantly different from the background LD levels after multiple comparison corrections.


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 is distributed across the genome.The location of the 42 SNPs is illustrated on the 14 chromosomes of the P. vivax genome. SNPs are colored by their average minor allele frequency (AMAF) among the populations tested; 17 SNPs had AMAF ≥ 0.3, 18 SNPs had 0.3 > AMAF ≥ 0.2, and 7 SNPs had 0.2 > AMAF > 0.1 (S7 Table). Putative centromere locations are indicated by the pinched location on the perimeter of each chromosome [16].
© Copyright Policy
Related In: Results  -  Collection

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

pntd.0003539.g003: The 42-SNP barcode is distributed across the genome.The location of the 42 SNPs is illustrated on the 14 chromosomes of the P. vivax genome. SNPs are colored by their average minor allele frequency (AMAF) among the populations tested; 17 SNPs had AMAF ≥ 0.3, 18 SNPs had 0.3 > AMAF ≥ 0.2, and 7 SNPs had 0.2 > AMAF > 0.1 (S7 Table). Putative centromere locations are indicated by the pinched location on the perimeter of each chromosome [16].
Mentions: The 42 SNPs span all 14 chromosomes of the P. vivax genome, and each SNP is highly informative across four distinct geographic populations: Brazil, Sri Lanka, Ethiopia, and French Guiana. The SNPs captured high degrees of diversity, with the AMAF value for each SNP > 0.1 (Fig. 3, and S7 Table). Moreover, the SNPs were independently informative (S2 Fig). We did not expect SNPs to be in LD since the closest pair of SNPs is 21,237 bp apart (SNPs 5 and 6), which is beyond the map distance over which we typically see significant LD in Plasmodium populations [37,38]. Using the r2 statistic to measure LD (which examines allele correlation from 0 to 1), we found that all SNP pairs had r2 < 0.53 in each. None of the r2 values were significantly different from the background LD levels after multiple comparison corrections.

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