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Volumn 9, Issue 3, 2015, Pages

Development of a Single Nucleotide Polymorphism Barcode to Genotype Plasmodium vivax Infections

(20)  Baniecki, Mary Lynn a   Faust, Aubrey L b   Schaffner, Stephen F a   Park, Daniel J a   Galinsky, Kevin c   Daniels, Rachel F b   Hamilton, Elizabeth c   Ferreira, Marcelo U d   Karunaweera, Nadira D e   Serre, David f   Zimmerman, Peter A g   Sá, Juliana M h   Wellems, Thomas E h   Musset, Lise i   Legrand, Eric i   Melnikov, Alexandre a   Neafsey, Daniel E a   Volkman, Sarah K a,c,j   Wirth, Dyann F a,c   Sabeti, Pardis C a,b,c  


Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; GENETIC MARKER; PROTOZOAL DNA;

EID: 84928785540     PISSN: 19352727     EISSN: 19352735     Source Type: Journal    
DOI: 10.1371/journal.pntd.0003539     Document Type: Article
Times cited : (73)

References (45)
  • 1
    • 84870381414 scopus 로고    scopus 로고
    • The global public health significance of Plasmodium vivax
    • Battle KE, Gething PW, Elyazar IR, Moyes CL, Sinka ME, et al. (2012) The global public health significance of Plasmodium vivax. Adv Parasitol 80: 1–111. doi: 10.1016/B978-0-12-397900-1.00001-3 23199486
    • (2012) Adv Parasitol , vol.80 , pp. 1-111
    • Battle, K.E.1    Gething, P.W.2    Elyazar, I.R.3    Moyes, C.L.4    Sinka, M.E.5
  • 3
    • 84878183958 scopus 로고    scopus 로고
    • 1912–2012: a century of research on Plasmodium vivax in vitro culture
    • Noulin F, Borlon C, Van Den Abbeele J, D’Alessandro U, Erhart A, (2013) 1912–2012: a century of research on Plasmodium vivax in vitro culture. Trends Parasitol 29: 286–294. doi: 10.1016/j.pt.2013.03.012 23623759
    • (2013) Trends Parasitol , vol.29 , pp. 286-294
    • Noulin, F.1    Borlon, C.2    Van Den Abbeele, J.3    D’Alessandro, U.4    Erhart, A.5
  • 5
    • 84906768748 scopus 로고    scopus 로고
    • Emerging Plasmodium vivax resistance to chloroquine in South America: an overview
    • Goncalves LA, Cravo P, Ferreira MU, (2014) Emerging Plasmodium vivax resistance to chloroquine in South America: an overview. Mem Inst Oswaldo Cruz 0.
    • (2014) Mem Inst Oswaldo Cruz , vol.0
    • Goncalves, L.A.1    Cravo, P.2    Ferreira, M.U.3
  • 6
    • 84925486068 scopus 로고    scopus 로고
    • Is Plasmodium vivax Malaria a Severe Malaria?: A Systematic Review and Meta-Analysis
    • Naing C, Whittaker MA, Nyunt Wai V, Mak JW, (2014) Is Plasmodium vivax Malaria a Severe Malaria?: A Systematic Review and Meta-Analysis. PLoS Negl Trop Dis 8: e3071. doi: 10.1371/journal.pntd.0003071 25121491
    • (2014) PLoS Negl Trop Dis , vol.8 , pp. 3071
    • Naing, C.1    Whittaker, M.A.2    Nyunt Wai, V.3    Mak, J.W.4
  • 7
    • 84895924033 scopus 로고    scopus 로고
    • On the road to eliminate malaria in Sri Lanka: lessons from history, challenges, gaps in knowledge and research needs
    • Karunaweera ND, Galappaththy GN, Wirth DF, (2014) On the road to eliminate malaria in Sri Lanka: lessons from history, challenges, gaps in knowledge and research needs. Malar J 13: 59. doi: 10.1186/1475-2875-13-59 24548783
    • (2014) Malar J , vol.13 , pp. 59
    • Karunaweera, N.D.1    Galappaththy, G.N.2    Wirth, D.F.3
  • 8
    • 33646586069 scopus 로고    scopus 로고
    • Microsatellite variation, repeat array length, and population history of Plasmodium vivax
    • Imwong M, Sudimack D, Pukrittayakamee S, Osorio L, Carlton JM, et al. (2006) Microsatellite variation, repeat array length, and population history of Plasmodium vivax. Mol Biol Evol 23: 1016–1018. 16507919
    • (2006) Mol Biol Evol , vol.23 , pp. 1016-1018
    • Imwong, M.1    Sudimack, D.2    Pukrittayakamee, S.3    Osorio, L.4    Carlton, J.M.5
  • 10
    • 40649121266 scopus 로고    scopus 로고
    • Extensive microsatellite diversity in the human malaria parasite Plasmodium vivax
    • Karunaweera ND, Ferreira MU, Munasinghe A, Barnwell JW, Collins WE, et al. (2008) Extensive microsatellite diversity in the human malaria parasite Plasmodium vivax. Gene 410: 105–112. doi: 10.1016/j.gene.2007.11.022 18226474
    • (2008) Gene , vol.410 , pp. 105-112
    • Karunaweera, N.D.1    Ferreira, M.U.2    Munasinghe, A.3    Barnwell, J.W.4    Collins, W.E.5
  • 11
  • 12
    • 44649085711 scopus 로고    scopus 로고
    • Local adaptation and vector-mediated population structure in Plasmodium vivax malaria
    • Joy DA, Gonzalez-Ceron L, Carlton JM, Gueye A, Fay M, et al. (2008) Local adaptation and vector-mediated population structure in Plasmodium vivax malaria. Mol Biol Evol 25: 1245–1252. doi: 10.1093/molbev/msn073 18385220
    • (2008) Mol Biol Evol , vol.25 , pp. 1245-1252
    • Joy, D.A.1    Gonzalez-Ceron, L.2    Carlton, J.M.3    Gueye, A.4    Fay, M.5
  • 13
    • 77449132489 scopus 로고    scopus 로고
    • High complexity of Plasmodium vivax infections in symptomatic patients from a rural community in central Vietnam detected by microsatellite genotyping
    • Van den Eede P, Erhart A, Van der Auwera G, Van Overmeir C, Thang ND, et al. (2010) High complexity of Plasmodium vivax infections in symptomatic patients from a rural community in central Vietnam detected by microsatellite genotyping. Am J Trop Med Hyg 82: 223–227. doi: 10.4269/ajtmh.2010.09-0458 20133996
    • (2010) Am J Trop Med Hyg , vol.82 , pp. 223-227
    • Van den Eede, P.1    Erhart, A.2    Van der Auwera, G.3    Van Overmeir, C.4    Thang, N.D.5
  • 14
    • 84889827637 scopus 로고    scopus 로고
    • A call to arms: on refining Plasmodium vivax microsatellite marker panels for comparing global diversity
    • Sutton PL, (2013) A call to arms: on refining Plasmodium vivax microsatellite marker panels for comparing global diversity. Malar J 12: 447. doi: 10.1186/1475-2875-12-447 24330329
    • (2013) Malar J , vol.12 , pp. 447
    • Sutton, P.L.1
  • 15
    • 77949787771 scopus 로고    scopus 로고
    • A comparison of SNPs and microsatellites as linkage mapping markers: lessons from the zebra finch (Taeniopygia guttata)
    • Ball AD, Stapley J, Dawson DA, Birkhead TR, Burke T, et al. (2010) A comparison of SNPs and microsatellites as linkage mapping markers: lessons from the zebra finch (Taeniopygia guttata). BMC Genomics 11: 218. doi: 10.1186/1471-2164-11-218 20359323
    • (2010) BMC Genomics , vol.11 , pp. 218
    • Ball, A.D.1    Stapley, J.2    Dawson, D.A.3    Birkhead, T.R.4    Burke, T.5
  • 16
    • 53649104458 scopus 로고    scopus 로고
    • Comparative genomics of the neglected human malaria parasite Plasmodium vivax
    • Carlton JM, Adams JH, Silva JC, Bidwell SL, Lorenzi H, et al. (2008) Comparative genomics of the neglected human malaria parasite Plasmodium vivax. Nature 455: 757–763. doi: 10.1038/nature07327 18843361
    • (2008) Nature , vol.455 , pp. 757-763
    • Carlton, J.M.1    Adams, J.H.2    Silva, J.C.3    Bidwell, S.L.4    Lorenzi, H.5
  • 17
    • 84873170038 scopus 로고    scopus 로고
    • Genomics, population genetics and evolutionary history of Plasmodium vivax
    • Carlton JM, Das A, Escalante AA, (2013) Genomics, population genetics and evolutionary history of Plasmodium vivax. Adv Parasitol 81: 203–222. doi: 10.1016/B978-0-12-407826-0.00005-9 23384624
    • (2013) Adv Parasitol , vol.81 , pp. 203-222
    • Carlton, J.M.1    Das, A.2    Escalante, A.A.3
  • 18
    • 84862492581 scopus 로고    scopus 로고
    • Whole genome sequencing analysis of Plasmodium vivax using whole genome capture
    • Bright AT, Tewhey R, Abeles S, Chuquiyauri R, Llanos-Cuentas A, et al. (2012) Whole genome sequencing analysis of Plasmodium vivax using whole genome capture. BMC Genomics 13: 262. doi: 10.1186/1471-2164-13-262 22721170
    • (2012) BMC Genomics , vol.13 , pp. 262
    • Bright, A.T.1    Tewhey, R.2    Abeles, S.3    Chuquiyauri, R.4    Llanos-Cuentas, A.5
  • 19
    • 84866918014 scopus 로고    scopus 로고
    • Whole genome sequencing of field isolates provides robust characterization of genetic diversity in Plasmodium vivax
    • Chan ER, Menard D, David PH, Ratsimbasoa A, Kim S, et al. (2012) Whole genome sequencing of field isolates provides robust characterization of genetic diversity in Plasmodium vivax. PLoS Negl Trop Dis 6: e1811. doi: 10.1371/journal.pntd.0001811 22970335
    • (2012) PLoS Negl Trop Dis , vol.6 , pp. 1811
    • Chan, E.R.1    Menard, D.2    David, P.H.3    Ratsimbasoa, A.4    Kim, S.5
  • 20
    • 84865681782 scopus 로고    scopus 로고
    • The malaria parasite Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparum
    • Neafsey DE, Galinsky K, Jiang RH, Young L, Sykes SM, et al. (2012) The malaria parasite Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparum. Nat Genet 44: 1046–1050. doi: 10.1038/ng.2373 22863733
    • (2012) Nat Genet , vol.44 , pp. 1046-1050
    • Neafsey, D.E.1    Galinsky, K.2    Jiang, R.H.3    Young, L.4    Sykes, S.M.5
  • 21
    • 84902504071 scopus 로고    scopus 로고
    • A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains
    • Preston MD, Campino S, Assefa SA, Echeverry DF, Ocholla H, et al. (2014) A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains. Nat Commun 5: 4052. doi: 10.1038/ncomms5052 24923250
    • (2014) Nat Commun , vol.5 , pp. 4052
    • Preston, M.D.1    Campino, S.2    Assefa, S.A.3    Echeverry, D.F.4    Ocholla, H.5
  • 22
    • 56349168406 scopus 로고    scopus 로고
    • A general SNP-based molecular barcode for Plasmodium falciparum identification and tracking
    • Daniels R, Volkman SK, Milner DA, Mahesh N, Neafsey DE, et al. (2008) A general SNP-based molecular barcode for Plasmodium falciparum identification and tracking. Malar J 7: 223. doi: 10.1186/1475-2875-7-223 18959790
    • (2008) Malar J , vol.7 , pp. 223
    • Daniels, R.1    Volkman, S.K.2    Milner, D.A.3    Mahesh, N.4    Neafsey, D.E.5
  • 23
    • 84861157365 scopus 로고    scopus 로고
    • Rapid, field-deployable method for genotyping and discovery of single-nucleotide polymorphisms associated with drug resistance in Plasmodium falciparum
    • Daniels R, Ndiaye D, Wall M, McKinney J, Sene PD, et al. (2012) Rapid, field-deployable method for genotyping and discovery of single-nucleotide polymorphisms associated with drug resistance in Plasmodium falciparum. Antimicrob Agents Chemother 56: 2976–2986. doi: 10.1128/AAC.05737-11 22430961
    • (2012) Antimicrob Agents Chemother , vol.56 , pp. 2976-2986
    • Daniels, R.1    Ndiaye, D.2    Wall, M.3    McKinney, J.4    Sene, P.D.5
  • 24
    • 77952449084 scopus 로고    scopus 로고
    • Rapid identification of chloroquine and atovaquone drug resistance in Plasmodium falciparum using high-resolution melt polymerase chain reaction
    • Gan LS, Loh JP, (2010) Rapid identification of chloroquine and atovaquone drug resistance in Plasmodium falciparum using high-resolution melt polymerase chain reaction. Malar J 9: 134. doi: 10.1186/1475-2875-9-134 20487570
    • (2010) Malar J , vol.9 , pp. 134
    • Gan, L.S.1    Loh, J.P.2
  • 25
    • 84875952747 scopus 로고    scopus 로고
    • Genetic surveillance detects both clonal and epidemic transmission of malaria following enhanced intervention in Senegal
    • Daniels R, Chang HH, Sene PD, Park DC, Neafsey DE, et al. (2013) Genetic surveillance detects both clonal and epidemic transmission of malaria following enhanced intervention in Senegal. PLoS One 8: e60780. doi: 10.1371/journal.pone.0060780 23593309
    • (2013) PLoS One , vol.8 , pp. 60780
    • Daniels, R.1    Chang, H.H.2    Sene, P.D.3    Park, D.C.4    Neafsey, D.E.5
  • 27
    • 3042651880 scopus 로고    scopus 로고
    • Genotyping of single-nucleotide polymorphisms by high-resolution melting of small amplicons
    • Liew M, Pryor R, Palais R, Meadows C, Erali M, et al. (2004) Genotyping of single-nucleotide polymorphisms by high-resolution melting of small amplicons. Clin Chem 50: 1156–1164. 15229148
    • (2004) Clin Chem , vol.50 , pp. 1156-1164
    • Liew, M.1    Pryor, R.2    Palais, R.3    Meadows, C.4    Erali, M.5
  • 28
    • 34250658870 scopus 로고    scopus 로고
    • High-resolution DNA melting analysis for simple and efficient molecular diagnostics
    • Reed GH, Kent JO, Wittwer CT, (2007) High-resolution DNA melting analysis for simple and efficient molecular diagnostics. Pharmacogenomics 8: 597–608. 17559349
    • (2007) Pharmacogenomics , vol.8 , pp. 597-608
    • Reed, G.H.1    Kent, J.O.2    Wittwer, C.T.3
  • 29
    • 79955483667 scopus 로고    scopus 로고
    • A framework for variation discovery and genotyping using next-generation DNA sequencing data
    • DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, et al. (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43: 491–498. doi: 10.1038/ng.806 21478889
    • (2011) Nat Genet , vol.43 , pp. 491-498
    • DePristo, M.A.1    Banks, E.2    Poplin, R.3    Garimella, K.V.4    Maguire, J.R.5
  • 30
    • 78650552144 scopus 로고    scopus 로고
    • Whole-genome sequencing and microarray analysis of ex vivo Plasmodium vivax reveal selective pressure on putative drug resistance genes
    • Dharia NV, Bright AT, Westenberger SJ, Barnes SW, Batalov S, et al. (2010) Whole-genome sequencing and microarray analysis of ex vivo Plasmodium vivax reveal selective pressure on putative drug resistance genes. Proc Natl Acad Sci U S A 107: 20045–20050. doi: 10.1073/pnas.1003776107 21037109
    • (2010) Proc Natl Acad Sci U S A , vol.107 , pp. 20045-20050
    • Dharia, N.V.1    Bright, A.T.2    Westenberger, S.J.3    Barnes, S.W.4    Batalov, S.5
  • 31
    • 73949087294 scopus 로고    scopus 로고
    • Recurrent parasitemias and population dynamics of Plasmodium vivax polymorphisms in rural Amazonia
    • Orjuela-Sanchez P, da Silva NS, da Silva-Nunes M, Ferreira MU, (2009) Recurrent parasitemias and population dynamics of Plasmodium vivax polymorphisms in rural Amazonia. Am J Trop Med Hyg 81: 961–968. doi: 10.4269/ajtmh.2009.09-0337 19996423
    • (2009) Am J Trop Med Hyg , vol.81 , pp. 961-968
    • Orjuela-Sanchez, P.1    da Silva, N.S.2    da Silva-Nunes, M.3    Ferreira, M.U.4
  • 32
    • 77449112648 scopus 로고    scopus 로고
    • Geographic structure of Plasmodium vivax: microsatellite analysis of parasite populations from Sri Lanka, Myanmar, and Ethiopia
    • Gunawardena S, Karunaweera ND, Ferreira MU, Phone-Kyaw M, Pollack RJ, et al. (2010) Geographic structure of Plasmodium vivax: microsatellite analysis of parasite populations from Sri Lanka, Myanmar, and Ethiopia. Am J Trop Med Hyg 82: 235–242. doi: 10.4269/ajtmh.2010.09-0588 20133999
    • (2010) Am J Trop Med Hyg , vol.82 , pp. 235-242
    • Gunawardena, S.1    Karunaweera, N.D.2    Ferreira, M.U.3    Phone-Kyaw, M.4    Pollack, R.J.5
  • 33
    • 85015535086 scopus 로고    scopus 로고
    • Biosciences A (2009) Manual: Applied Biosystems High Resolution Melting. In: Biosciences A, editor.
  • 34
    • 33646226097 scopus 로고
    • Linkage disequilibrium in finite populations
    • Hill WG, Robertson A, (1968) Linkage disequilibrium in finite populations. Theor Appl Genet 38: 226–231. doi: 10.1007/BF01245622 24442307
    • (1968) Theor Appl Genet , vol.38 , pp. 226-231
    • Hill, W.G.1    Robertson, A.2
  • 35
    • 0036957370 scopus 로고    scopus 로고
    • Estimating F-statistics
    • Weir BS, Hill WG, (2002) Estimating F-statistics. Annu Rev Genet 36: 721–750. 12359738
    • (2002) Annu Rev Genet , vol.36 , pp. 721-750
    • Weir, B.S.1    Hill, W.G.2
  • 36
    • 33846006923 scopus 로고    scopus 로고
    • Population structure and eigenanalysis
    • Patterson N, Price AL, Reich D, (2006) Population structure and eigenanalysis. PLoS Genet 2: e190. 17194218
    • (2006) PLoS Genet , vol.2 , pp. 190
    • Patterson, N.1    Price, A.L.2    Reich, D.3
  • 38
    • 58149395271 scopus 로고    scopus 로고
    • Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence
    • Neafsey DE, Schaffner SF, Volkman SK, Park D, Montgomery P, et al. (2008) Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence. Genome Biol 9: R171. doi: 10.1186/gb-2008-9-12-r171 19077304
    • (2008) Genome Biol , vol.9 , pp. 171
    • Neafsey, D.E.1    Schaffner, S.F.2    Volkman, S.K.3    Park, D.4    Montgomery, P.5
  • 39
    • 18344396798 scopus 로고    scopus 로고
    • Comprehensive human genome amplification using multiple displacement amplification
    • Dean FB, Hosono S, Fang L, Wu X, Faruqi AF, et al. (2002) Comprehensive human genome amplification using multiple displacement amplification. Proc Natl Acad Sci U S A 99: 5261–5266. 11959976
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 5261-5266
    • Dean, F.B.1    Hosono, S.2    Fang, L.3    Wu, X.4    Faruqi, A.F.5
  • 40
    • 84891499118 scopus 로고    scopus 로고
    • Population structure and spatio-temporal transmission dynamics of Plasmodium vivax after radical cure treatment in a rural village of the Peruvian Amazon
    • Delgado-Ratto C, Soto-Calle VE, Van den Eede P, Gamboa D, Rosas A, et al. (2014) Population structure and spatio-temporal transmission dynamics of Plasmodium vivax after radical cure treatment in a rural village of the Peruvian Amazon. Malar J 13: 8. doi: 10.1186/1475-2875-13-8 24393454
    • (2014) Malar J , vol.13 , pp. 8
    • Delgado-Ratto, C.1    Soto-Calle, V.E.2    Van den Eede, P.3    Gamboa, D.4    Rosas, A.5
  • 41
    • 77953015403 scopus 로고    scopus 로고
    • Multilocus genotyping reveals high heterogeneity and strong local population structure of the Plasmodium vivax population in the Peruvian Amazon
    • Van den Eede P, Van der Auwera G, Delgado C, Huyse T, Soto-Calle VE, et al. (2010) Multilocus genotyping reveals high heterogeneity and strong local population structure of the Plasmodium vivax population in the Peruvian Amazon. Malar J 9: 151. doi: 10.1186/1475-2875-9-151 20525233
    • (2010) Malar J , vol.9 , pp. 151
    • Van den Eede, P.1    Van der Auwera, G.2    Delgado, C.3    Huyse, T.4    Soto-Calle, V.E.5
  • 42
    • 66149150596 scopus 로고    scopus 로고
    • Analysis of genetic variability of Plasmodium vivax isolates from different Brazilian Amazon areas using tandem repeats
    • Rezende AM, Tarazona-Santos E, Couto AD, Fontes CJ, De Souza JM, et al. (2009) Analysis of genetic variability of Plasmodium vivax isolates from different Brazilian Amazon areas using tandem repeats. Am J Trop Med Hyg 80: 729–733. 19407114
    • (2009) Am J Trop Med Hyg , vol.80 , pp. 729-733
    • Rezende, A.M.1    Tarazona-Santos, E.2    Couto, A.D.3    Fontes, C.J.4    De Souza, J.M.5
  • 43
    • 34249997585 scopus 로고    scopus 로고
    • Contrasting genetic structure in Plasmodium vivax populations from Asia and South America
    • Imwong M, Nair S, Pukrittayakamee S, Sudimack D, Williams JT, et al. (2007) Contrasting genetic structure in Plasmodium vivax populations from Asia and South America. Int J Parasitol 37: 1013–1022. 17442318
    • (2007) Int J Parasitol , vol.37 , pp. 1013-1022
    • Imwong, M.1    Nair, S.2    Pukrittayakamee, S.3    Sudimack, D.4    Williams, J.T.5
  • 45
    • 77954623570 scopus 로고    scopus 로고
    • Single-nucleotide polymorphism, linkage disequilibrium and geographic structure in the malaria parasite Plasmodium vivax: prospects for genome-wide association studies
    • Orjuela-Sanchez P, Karunaweera ND, da Silva-Nunes M, da Silva NS, Scopel KK, et al. (2010) Single-nucleotide polymorphism, linkage disequilibrium and geographic structure in the malaria parasite Plasmodium vivax: prospects for genome-wide association studies. BMC Genet 11: 65. doi: 10.1186/1471-2156-11-65 20626846
    • (2010) BMC Genet , vol.11 , pp. 65
    • Orjuela-Sanchez, P.1    Karunaweera, N.D.2    da Silva-Nunes, M.3    da Silva, N.S.4    Scopel, K.K.5


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