A general SNP-based molecular barcode for Plasmodium falciparum identification and tracking
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...
| Main Authors: | , , , , , , , , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | en_US |
| Published: |
BioMed Central Ltd.
2009
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| Online Access: | http://hdl.handle.net/1721.1/49467 |
| _version_ | 1811092005663539200 |
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| author | Daniels, Rachel F. Volkman, Sarah K. Milner, Danny A. Mahesh, Nira Neafsey, Daniel E. Park, Daniel J. Rosen, David Angelino, Elaine Sabeti, Pardis C. Wirth, Dyann F. Wiegand, Roger C. |
| author2 | Broad Institute of MIT and Harvard |
| author_facet | Broad Institute of MIT and Harvard Daniels, Rachel F. Volkman, Sarah K. Milner, Danny A. Mahesh, Nira Neafsey, Daniel E. Park, Daniel J. Rosen, David Angelino, Elaine Sabeti, Pardis C. Wirth, Dyann F. Wiegand, Roger C. |
| author_sort | Daniels, Rachel F. |
| collection | MIT |
| description | 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. |
| first_indexed | 2024-09-23T15:11:08Z |
| format | Article |
| id | mit-1721.1/49467 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T15:11:08Z |
| publishDate | 2009 |
| publisher | BioMed Central Ltd. |
| record_format | dspace |
| spelling | mit-1721.1/494672022-09-29T13:14:58Z A general SNP-based molecular barcode for Plasmodium falciparum identification and tracking Daniels, Rachel F. Volkman, Sarah K. Milner, Danny A. Mahesh, Nira Neafsey, Daniel E. Park, Daniel J. Rosen, David Angelino, Elaine Sabeti, Pardis C. Wirth, Dyann F. Wiegand, Roger C. Broad Institute of MIT and Harvard Daniels, Rachel F. Daniels, Rachel F. Neafsey, Daniel E. Park, Daniel J. Sabeti, Pardis C. Wiegand, Roger C. 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. 2009-10-19T13:35:20Z 2009-10-19T13:35:20Z 2008-10 2008-04 Article http://purl.org/eprint/type/JournalArticle 1475-2875 http://hdl.handle.net/1721.1/49467 Daniels, Rachel et al. “A general SNP-based molecular barcode for Plasmodium falciparum identification and tracking.” Malaria Journal 7.1 (2008): 223. 18959790 en_US http://dx.doi.org/10.1186/1475-2875-7-223 Malaria Journal Creative Commons Attribution http://creativecommons.org/licenses/by/2.0 application/pdf BioMed Central Ltd. Publisher |
| spellingShingle | Daniels, Rachel F. Volkman, Sarah K. Milner, Danny A. Mahesh, Nira Neafsey, Daniel E. Park, Daniel J. Rosen, David Angelino, Elaine Sabeti, Pardis C. Wirth, Dyann F. Wiegand, Roger C. A general SNP-based molecular barcode for Plasmodium falciparum identification and tracking |
| title | 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_short | 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 |
| url | http://hdl.handle.net/1721.1/49467 |
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