A general SNP-based molecular barcode for Plasmodium falciparum identification and tracking
Abstract Background Single nucleotide polymorphism (SNP) genotyping provides the means to develop a practical, rapid, inexpensive assay that will uniquely identify any Plasmodium falciparum parasite using a small amount of DNA. Such an assay could be used to distinguish recrudescence from re-infecti...
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ftdoajarticles:oai:doaj.org/article:1e30b9e179914a1493fab8de998b1d22 2023-05-15T15:14:14+02:00 A general SNP-based molecular barcode for Plasmodium falciparum identification and tracking Rosen David Park Daniel J Neafsey Daniel E Mahesh Nira Milner Danny A Volkman Sarah K Daniels Rachel Angelino Elaine Sabeti Pardis C Wirth Dyann F Wiegand Roger C 2008-10-01T00:00:00Z https://doi.org/10.1186/1475-2875-7-223 https://doaj.org/article/1e30b9e179914a1493fab8de998b1d22 EN eng BMC http://www.malariajournal.com/content/7/1/223 https://doaj.org/toc/1475-2875 doi:10.1186/1475-2875-7-223 1475-2875 https://doaj.org/article/1e30b9e179914a1493fab8de998b1d22 Malaria Journal, Vol 7, Iss 1, p 223 (2008) Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 article 2008 ftdoajarticles https://doi.org/10.1186/1475-2875-7-223 2022-12-30T23:46:23Z Abstract Background Single nucleotide polymorphism (SNP) genotyping provides the means to develop a practical, rapid, inexpensive assay that will uniquely identify any Plasmodium falciparum parasite using a small amount of DNA. Such an assay could be used to distinguish recrudescence from re-infection in drug trials, to monitor the frequency and distribution of specific parasites in a patient population undergoing drug treatment or vaccine challenge, or for tracking samples and determining purity of isolates in the laboratory during culture adaptation and sub-cloning, as well as routine passage. Methods A panel of twenty-four SNP markers has been identified that exhibit a high minor allele frequency (average MAF > 35%), for which robust TaqMan genotyping assays were constructed. All SNPs were identified through whole genome sequencing and MAF was estimated through Affymetrix array-based genotyping of a worldwide collection of parasites. These assays create a "molecular barcode" to uniquely identify a parasite genome. Results Using 24 such markers no two parasites known to be of independent origin have yet been found to have the same allele signature. The TaqMan genotyping assays can be performed on a variety of samples including cultured parasites, frozen whole blood, or whole blood spotted onto filter paper with a success rate > 99%. Less than 5 ng of parasite DNA is needed to complete a panel of 24 markers. The ability of this SNP panel to detect and identify parasites was compared to the standard molecular methods, MSP-1 and MSP-2 typing. Conclusion This work provides a facile field-deployable genotyping tool that can be used without special skills with standard lab equipment, and at reasonable cost that will unambiguously identify and track P. falciparum parasites both from patient samples and in the laboratory. Article in Journal/Newspaper Arctic Directory of Open Access Journals: DOAJ Articles Arctic Malaria Journal 7 1 223 |
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Directory of Open Access Journals: DOAJ Articles |
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English |
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Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 |
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Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 Rosen David Park Daniel J Neafsey Daniel E Mahesh Nira Milner Danny A Volkman Sarah K Daniels Rachel Angelino Elaine Sabeti Pardis C Wirth Dyann F Wiegand Roger C A general SNP-based molecular barcode for Plasmodium falciparum identification and tracking |
topic_facet |
Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 |
description |
Abstract Background Single nucleotide polymorphism (SNP) genotyping provides the means to develop a practical, rapid, inexpensive assay that will uniquely identify any Plasmodium falciparum parasite using a small amount of DNA. Such an assay could be used to distinguish recrudescence from re-infection in drug trials, to monitor the frequency and distribution of specific parasites in a patient population undergoing drug treatment or vaccine challenge, or for tracking samples and determining purity of isolates in the laboratory during culture adaptation and sub-cloning, as well as routine passage. Methods A panel of twenty-four SNP markers has been identified that exhibit a high minor allele frequency (average MAF > 35%), for which robust TaqMan genotyping assays were constructed. All SNPs were identified through whole genome sequencing and MAF was estimated through Affymetrix array-based genotyping of a worldwide collection of parasites. These assays create a "molecular barcode" to uniquely identify a parasite genome. Results Using 24 such markers no two parasites known to be of independent origin have yet been found to have the same allele signature. The TaqMan genotyping assays can be performed on a variety of samples including cultured parasites, frozen whole blood, or whole blood spotted onto filter paper with a success rate > 99%. Less than 5 ng of parasite DNA is needed to complete a panel of 24 markers. The ability of this SNP panel to detect and identify parasites was compared to the standard molecular methods, MSP-1 and MSP-2 typing. Conclusion This work provides a facile field-deployable genotyping tool that can be used without special skills with standard lab equipment, and at reasonable cost that will unambiguously identify and track P. falciparum parasites both from patient samples and in the laboratory. |
format |
Article in Journal/Newspaper |
author |
Rosen David Park Daniel J Neafsey Daniel E Mahesh Nira Milner Danny A Volkman Sarah K Daniels Rachel Angelino Elaine Sabeti Pardis C Wirth Dyann F Wiegand Roger C |
author_facet |
Rosen David Park Daniel J Neafsey Daniel E Mahesh Nira Milner Danny A Volkman Sarah K Daniels Rachel Angelino Elaine Sabeti Pardis C Wirth Dyann F Wiegand Roger C |
author_sort |
Rosen David |
title |
A general SNP-based molecular barcode for Plasmodium falciparum identification and tracking |
title_short |
A general SNP-based molecular barcode for Plasmodium falciparum identification and tracking |
title_full |
A general SNP-based molecular barcode for Plasmodium falciparum identification and tracking |
title_fullStr |
A general SNP-based molecular barcode for Plasmodium falciparum identification and tracking |
title_full_unstemmed |
A general SNP-based molecular barcode for Plasmodium falciparum identification and tracking |
title_sort |
general snp-based molecular barcode for plasmodium falciparum identification and tracking |
publisher |
BMC |
publishDate |
2008 |
url |
https://doi.org/10.1186/1475-2875-7-223 https://doaj.org/article/1e30b9e179914a1493fab8de998b1d22 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
Malaria Journal, Vol 7, Iss 1, p 223 (2008) |
op_relation |
http://www.malariajournal.com/content/7/1/223 https://doaj.org/toc/1475-2875 doi:10.1186/1475-2875-7-223 1475-2875 https://doaj.org/article/1e30b9e179914a1493fab8de998b1d22 |
op_doi |
https://doi.org/10.1186/1475-2875-7-223 |
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Malaria Journal |
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7 |
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1 |
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223 |
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