A general SNP-based molecular barcode for Plasmodium falciparum identification and tracking

Malaria Journal - Tập 7 Số 1 - 2008
Rachel F. Daniels1, Sarah K. Volkman2, Danny A. Milner3, Nira Mahesh2, Daniel E. Neafsey1, Daniel J. Park1, David Rosen2, Elaine Angelino4, Pardis C. Sabeti1, Dyann F. Wirth2, Roger C. Wiegand1
1Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
2Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, USA
3School for Health Studies, Simmons College, Boston, Massachusetts, USA
4Systems Biology Program, Harvard University, Cambridge, Massachusetts, USA

Tóm tắt

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.

Từ khóa


Tài liệu tham khảo

Global Fund to Fight AIDS, Tuberculosis and Malaria: The global malaria situation: current tools for prevention and control. [http://ftp.who.int/gb/archive/pdf_files/WHA55/ea55id6.pdf]

Su XFM, Huang Y, Huynh CQ, Liu A, You J, Wootton JC, Wellems TE: A genetic map and recombination parameters of the human malaria parasite Plasmodium falciparum. Science. 1999, 286 (5443): 1351-1353. 10.1126/science.286.5443.1351.

Viriyakosol SSN, Petcharapirat C, Petcharapirat P, Jarra W, Thaithong S, Brown KN, Snounou G: Genotyping of Plasmodium falciparum isolates by the polymerase chain reaction and potential uses in epidemiological studies. Bull World Health Organ. 1995, 73 (1): 85-95.

Dent AE, Yohn CT, Zimmerman PA, Vulule J, Kazura JW, Moormann AM: A polymerase chain reaction/ligase detection reaction fluorescent microsphere assay to determine Plasmodium falciparum MSP-119 haplotypes. Am J Trop Med Hyg. 2007, 77 (2): 250-255.

Collins WJ, Greenhouse B, Rosenthal PJ, Dorsey G: The use of genotyping in antimalarial clinical trials: a systematic review of published studies from 1995–2005. Malar J. 2006, 5: 122-10.1186/1475-2875-5-122.

Takala SL, Smith DL, Stine OC, Coulibaly D, Thera MA, Doumbo OK, Plowe CV: A high-throughput method for quantifying alleles and haplotypes of the malaria vaccine candidate Plasmodium falciparum merozoite surface protein-1 19 kDa. Malar J. 2006, 5: 31-10.1186/1475-2875-5-31.

Kwiek JJ, Alker AP, Wenink EC, Chaponda M, Kalilani LV, Meshnick SR: Estimating true antimalarial efficacy by heteroduplex tracking assay in patients with complex Plasmodium falciparum infections. Antimicrob Agents Chemother. 2007, 51 (2): 521-527. 10.1128/AAC.00902-06.

Anderson TJ, Su XZ, Bockarie M, Lagog M, Day KP: Twelve microsatellite markers for characterization of Plasmodium falciparum from finger-prick blood samples. Parasitology. 1999, 119 (Pt 2): 113-125. 10.1017/S0031182099004552.

Greenhouse B, Myrick A, Dokomajilar C, Woo JM, Carlson EJ, Rosenthal PJ, Dorsey G: VALIDATION OF MICROSATELLITE MARKERS FOR USE IN GENOTYPING POLYCLONAL PLASMODIUM FALCIPARUM INFECTIONS. Am J Trop Med Hyg. 2006, 75 (5): 836-842.

Volkman SK, Sabeti PC, DeCaprio D, Neafsey DE, Schaffner SF, Milner DA, Daily JP, Sarr O, Ndiaye D, Ndir O, Mboup S, Duraisingh MT, Lukens A, Derr A, Stange-Thomann N, Waggoner S, Onofrio R, Ziaugra L, Mauceli E, Gnerre S, Jaffe DB, Zainoun J, Wiegand RC, Birren BW, Hartl DL, Galagan JE, Lander ES, Wirth DF: A genome-wide map of diversity in Plasmodium falciparum. Nat Genet. 2007, 39 (1): 113-119. 10.1038/ng1930.

Mu J, Awadalla P, Duan J, McGee KM, Keebler J, Seydel K, McVean GA, Su XZ: Genome-wide variation and identification of vaccine targets in the Plasmodium falciparum genome. Nat Genet. 2007, 39 (1): 126-130. 10.1038/ng1924.

Jeffares DC, Pain A, Berry A, Cox AV, Stalker J, Ingle CE, Thomas A, Quail MA, Siebenthall K, Uhlemann AC, Kyes S, Krishna S, Newbold C, Dermitzakis ET, Berriman M: Genome variation and evolution of the malaria parasite Plasmodium falciparum. Nat Genet. 2007, 39 (1): 120-125. 10.1038/ng1931.

Daly MJ, Rioux JD, Schaffner SF, Hudson TJ, Lander ES: High-resolution haplotype structure in the human genome. Nat Genet. 2001, 29 (2): 229-232. 10.1038/ng1001-229.

Thông tin
Thông tin xuất bản

Malaria Journal

Tập 7 Số 1

Thông tin tác giả