Development of a single nucleotide polymorphism barcode to genotype Plasmodium vivax infections.
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 di...
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ftdoajarticles:oai:doaj.org/article:61039b73b895415e94caa469820cdeac 2023-05-15T15:12:04+02:00 Development of a single nucleotide polymorphism barcode to genotype Plasmodium vivax infections. Mary Lynn Baniecki Aubrey L Faust Stephen F Schaffner Daniel J Park Kevin Galinsky Rachel F Daniels Elizabeth Hamilton Marcelo U Ferreira Nadira D Karunaweera David Serre Peter A Zimmerman Juliana M Sá Thomas E Wellems Lise Musset Eric Legrand Alexandre Melnikov Daniel E Neafsey Sarah K Volkman Dyann F Wirth Pardis C Sabeti 2015-03-01T00:00:00Z https://doi.org/10.1371/journal.pntd.0003539 https://doaj.org/article/61039b73b895415e94caa469820cdeac EN eng Public Library of Science (PLoS) http://europepmc.org/articles/PMC4362761?pdf=render https://doaj.org/toc/1935-2727 https://doaj.org/toc/1935-2735 1935-2727 1935-2735 doi:10.1371/journal.pntd.0003539 https://doaj.org/article/61039b73b895415e94caa469820cdeac PLoS Neglected Tropical Diseases, Vol 9, Iss 3, p e0003539 (2015) Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 article 2015 ftdoajarticles https://doi.org/10.1371/journal.pntd.0003539 2022-12-31T16:24:59Z 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. Article in Journal/Newspaper Arctic Directory of Open Access Journals: DOAJ Articles Arctic PLOS Neglected Tropical Diseases 9 3 e0003539 |
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Open Polar |
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Directory of Open Access Journals: DOAJ Articles |
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ftdoajarticles |
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English |
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Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
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Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 Mary Lynn Baniecki Aubrey L Faust Stephen F Schaffner Daniel J Park Kevin Galinsky Rachel F Daniels Elizabeth Hamilton Marcelo U Ferreira Nadira D Karunaweera David Serre Peter A Zimmerman Juliana M Sá Thomas E Wellems Lise Musset Eric Legrand Alexandre Melnikov Daniel E Neafsey Sarah K Volkman Dyann F Wirth Pardis C Sabeti Development of a single nucleotide polymorphism barcode to genotype Plasmodium vivax infections. |
topic_facet |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Mary Lynn Baniecki Aubrey L Faust Stephen F Schaffner Daniel J Park Kevin Galinsky Rachel F Daniels Elizabeth Hamilton Marcelo U Ferreira Nadira D Karunaweera David Serre Peter A Zimmerman Juliana M Sá Thomas E Wellems Lise Musset Eric Legrand Alexandre Melnikov Daniel E Neafsey Sarah K Volkman Dyann F Wirth Pardis C Sabeti |
author_facet |
Mary Lynn Baniecki Aubrey L Faust Stephen F Schaffner Daniel J Park Kevin Galinsky Rachel F Daniels Elizabeth Hamilton Marcelo U Ferreira Nadira D Karunaweera David Serre Peter A Zimmerman Juliana M Sá Thomas E Wellems Lise Musset Eric Legrand Alexandre Melnikov Daniel E Neafsey Sarah K Volkman Dyann F Wirth Pardis C Sabeti |
author_sort |
Mary Lynn Baniecki |
title |
Development of a single nucleotide polymorphism barcode to genotype Plasmodium vivax infections. |
title_short |
Development of a single nucleotide polymorphism barcode to genotype Plasmodium vivax infections. |
title_full |
Development of a single nucleotide polymorphism barcode to genotype Plasmodium vivax infections. |
title_fullStr |
Development of a single nucleotide polymorphism barcode to genotype Plasmodium vivax infections. |
title_full_unstemmed |
Development of a single nucleotide polymorphism barcode to genotype Plasmodium vivax infections. |
title_sort |
development of a single nucleotide polymorphism barcode to genotype plasmodium vivax infections. |
publisher |
Public Library of Science (PLoS) |
publishDate |
2015 |
url |
https://doi.org/10.1371/journal.pntd.0003539 https://doaj.org/article/61039b73b895415e94caa469820cdeac |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
PLoS Neglected Tropical Diseases, Vol 9, Iss 3, p e0003539 (2015) |
op_relation |
http://europepmc.org/articles/PMC4362761?pdf=render https://doaj.org/toc/1935-2727 https://doaj.org/toc/1935-2735 1935-2727 1935-2735 doi:10.1371/journal.pntd.0003539 https://doaj.org/article/61039b73b895415e94caa469820cdeac |
op_doi |
https://doi.org/10.1371/journal.pntd.0003539 |
container_title |
PLOS Neglected Tropical Diseases |
container_volume |
9 |
container_issue |
3 |
container_start_page |
e0003539 |
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1766342809645744128 |