An optimized microarray platform for assaying genomic variation in Plasmodium falciparum field populations

Genome Biology

Volumn 12, Issue 4, 2011, Pages

  Tan, John C ^a   Miller, Becky A ^a   Tan, Asako ^a   Patel, Jigar J ^a,b   Cheeseman, Ian H ^c   Anderson, Tim J C ^c   Manske, Magnus ^d   Maslen, Gareth ^d   Kwiatkowski, Dominic P ^d   Ferdig, Michael T ^a,e  

^a UNIVERSITY OF NOTRE DAME   (United States)

^b Roche NimbleGen Inc   (United States)

^c SOUTHWEST FOUNDATION FOR BIOMEDICAL RESEARCH   (United States)

^d WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^e 100 Galvin Life Sciences ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; COPY NUMBER VARIATION; DNA CONTAMINATION; EXON; GENETIC VARIABILITY; GENOTYPE; HUMAN; INTRON; MICROARRAY ANALYSIS; MOLECULAR PROBE; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMODIUM FALCIPARUM; REPRODUCIBILITY; SINGLE NUCLEOTIDE POLYMORPHISM; VALIDITY; ANIMAL; DNA MICROARRAY; GENETICS; GENOTYPING TECHNIQUE; METHODOLOGY;

PLASMODIUM FALCIPARUM;

ANIMALS; DNA CONTAMINATION; DNA COPY NUMBER VARIATIONS; GENOTYPING TECHNIQUES; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLASMODIUM FALCIPARUM; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 79953757647     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2011-12-4-r35     Document Type: Article

References (43)

1. WHO World Malaria Report 2009 2009, Geneva: World Health Organization, WHO.
2. Enserink M. Malaria's drug miracle in danger. Science 2010, 328:844-846. 10.1126/science.328.5980.844, 20466917.
3. Fidock DA, Nomura T, Talley AK, Cooper RA, Dzekunov SM, Ferdig MT, Ursos LM, Sidhu AB, Naude B, Deitsch KW, Su XZ, Wootton JC, Roepe PD, Wellems TE. Mutations in the P. falciparum digestive vacuole transmembrane protein PfCRT and evidence for their role in chloroquine resistance. Mol Cell 2000, 6:861-871. 10.1016/S1097-2765(05)00077-8, 2944663, 11090624.
4. Wellems TE, Walker-Jonah A, Panton LJ. Genetic mapping of the chloroquine-resistance locus on Plasmodium falciparum chromosome 7. Proc Natl Acad Sci USA 1991, 88:3382-3386. 10.1073/pnas.88.8.3382, 51451, 1673031.
5. Lozovsky ER, Chookajorn T, Brown KM, Imwong M, Shaw PJ, Kamchonwongpaisan S, Neafsey DE, Weinreich DM, Hartl DL. Stepwise acquisition of pyrimethamine resistance in the malaria parasite. Proc Natl Acad Sci USA 2009, 106:12025-12030. 10.1073/pnas.0905922106, 2715478, 19587242.
6. Mita T. Origins and spread of pfdhfr mutant alleles in Plasmodium falciparum. Acta Trop 2010, 114:166-170. 10.1016/j.actatropica.2009.07.008, 19607799.
7. Plowe CV, Cortese JF, Djimde A, Nwanyanwu OC, Watkins WM, Winstanley PA, Estrada-Franco JG, Mollinedo RE, Avila JC, Cespedes JL, Carter D, Doumbo OK. Mutations in Plasmodium falciparum dihydrofolate reductase and dihydropteroate synthase and epidemiologic patterns of pyrimethamine-sulfadoxine use and resistance. J Infect Dis 1997, 176:1590-1596. 10.1086/514159, 9395372.
8. Triglia T, Menting JG, Wilson C, Cowman AF. Mutations in dihydropteroate synthase are responsible for sulfone and sulfonamide resistance in Plasmodium falciparum. Proc Natl Acad Sci USA 1997, 94:13944-13949. 10.1073/pnas.94.25.13944, 28412, 9391132.
9. Barnes DA, Foote SJ, Galatis D, Kemp DJ, Cowman AF. Selection for high-level chloroquine resistance results in deamplification of the pfmdr1 gene and increased sensitivity to mefloquine in Plasmodium falciparum. EMBO J 1992, 11:3067-3075. 556790, 1353446.
10. Cowman AF, Galatis D, Thompson JK. Selection for mefloquine resistance in Plasmodium falciparum is linked to amplification of the pfmdr1 gene and cross-resistance to halofantrine and quinine. Proc Natl Acad Sci USA 1994, 91:1143-1147. 10.1073/pnas.91.3.1143, 521470, 8302844.
11. Sidhu AB, Uhlemann AC, Valderramos SG, Valderramos JC, Krishna S, Fidock DA. Decreasing pfmdr1 copy number in plasmodium falciparum malaria heightens susceptibility to mefloquine, lumefantrine, halofantrine, quinine, and artemisinin. J Infect Dis 2006, 194:528-535. 10.1086/507115, 2978021, 16845638.
12. Kidgell C, Volkman SK, Daily J, Borevitz JO, Plouffe D, Zhou Y, Johnson JR, Le Roch K, Sarr O, Ndir O, Mboup S, Batalov S, Wirth DF, Winzeler EA. A systematic map of genetic variation in Plasmodium falciparum. PLoS Pathog 2006, 2:e57. 10.1371/journal.ppat.0020057, 1480597, 16789840.
13. Nair S, Miller B, Barends M, Jaidee A, Patel J, Mayxay M, Newton P, Nosten F, Ferdig MT, Anderson TJ. Adaptive copy number evolution in malaria parasites. PLoS Genet 2008, 4:e1000243. 10.1371/journal.pgen.1000243, 2570623, 18974876.
14. Hayton K, Su XZ. Drug resistance and genetic mapping in Plasmodium falciparum. Curr Genet 2008, 54:223-239. 10.1007/s00294-008-0214-x, 18802698.
15. Carret CK, Horrocks P, Konfortov B, Winzeler E, Qureshi M, Newbold C, Ivens A. Microarray-based comparative genomic analyses of the human malaria parasite Plasmodium falciparum using Affymetrix arrays. Mol Biochem Parasitol 2005, 144:177-186. 10.1016/j.molbiopara.2005.08.010, 16174539.
16. Cheeseman IH, Gomez-Escobar N, Carret CK, Ivens A, Stewart LB, Tetteh KK, Conway DJ. Gene copy number variation throughout the Plasmodium falciparum genome. BMC Genomics 2009, 10:353. 10.1186/1471-2164-10-353, 2732925, 19653891.
17. Ribacke U, Mok BW, Wirta V, Normark J, Lundeberg J, Kironde F, Egwang TG, Nilsson P, Wahlgren M. Genome wide gene amplifications and deletions in Plasmodium falciparum. Mol Biochem Parasitol 2007, 155:33-44. 10.1016/j.molbiopara.2007.05.005, 17599553.
18. 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, 39:120-125. 10.1038/ng1931, 2663918, 17159978.
19. 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, 39:126-130. 10.1038/ng1924, 17159981.
20. 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, 39:113-119. 10.1038/ng1930, 17159979.
21. Dharia NV, Sidhu AB, Cassera MB, Westenberger SJ, Bopp SE, Eastman RT, Plouffe D, Batalov S, Park DJ, Volkman SK, Wirth DF, Zhou Y, Fidock DA, Winzeler EA. Use of high-density tiling microarrays to identify mutations globally and elucidate mechanisms of drug resistance in Plasmodium falciparum. Genome Biol 2009, 10:R21. 10.1186/gb-2009-10-2-r21, 2688282, 19216790.
22. Jiang H, Yi M, Mu J, Zhang L, Ivens A, Klimczak LJ, Huyen Y, Stephens RM, Su XZ. Detection of genome-wide polymorphisms in the AT-rich Plasmodium falciparum genome using a high-density microarray. BMC Genomics 2008, 9:398. 10.1186/1471-2164-9-398, 2543026, 18724869.
23. Tan JC, Patel JJ, Tan A, Blain JC, Albert TJ, Lobo NF, Ferdig MT. Optimizing comparative genomic hybridization probes for genotyping and SNP detection in Plasmodium falciparum. Genomics 2009, 93:543-550. 10.1016/j.ygeno.2009.02.007, 19285129.
24. Aurrecoechea C, Brestelli J, Brunk BP, Dommer J, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Innamorato F, Iodice J, Kissinger JC, Kraemer E, Li W, Miller JA, Nayak V, Pennington C, Pinney DF, Roos DS, Ross C, Stoeckert CJ, Treatman C, Wang H. PlasmoDB: a functional genomic database for malaria parasites. Nucleic Acids Res 2009, 37:D539-543. 10.1093/nar/gkn814, 2686598, 18957442.
25. Wong CW, Albert TJ, Vega VB, Norton JE, Cutler DJ, Richmond TA, Stanton LW, Liu ET, Miller LD. Tracking the evolution of the SARS coronavirus using high-throughput, high-density resequencing arrays. Genome Res 2004, 14:398-405. 10.1101/gr.2141004, 353227, 14993206.
26. Neafsey DE, Schaffner SF, Volkman SK, Park D, Montgomery P, Milner DA, Lukens A, Rosen D, Daniels R, Houde N, Cortese JF, Tyndall E, Gates C, Stange-Thomann N, Sarr O, Ndiaye D, Ndir O, Mboup S, Ferreira MU, Moraes Sdo L, Dash AP, Chitnis CE, Wiegand RC, Hartl DL, Birren BW, Lander ES, Sabeti PC, Wirth DF. Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence. Genome Biol 2008, 9:R171. 10.1186/gb-2008-9-12-r171, 2646275, 19077304.
27. Mu J, Myers RA, Jiang H, Liu S, Ricklefs S, Waisberg M, Chotivanich K, Wilairatana P, Krudsood S, White NJ, Udomsangpetch R, Cui L, Ho M, Ou F, Li H, Song J, Li G, Wang X, Seila S, Sokunthea S, Socheat D, Sturdevant DE, Porcella SF, Fairhurst RM, Wellems TE, Awadalla P, Su XZ. Plasmodium falciparum genome-wide scans for positive selection, recombination hot spots and resistance to antimalarial drugs. Nat Genet 2010, 42:268-271. 10.1038/ng.528, 2828519, 20101240.
28. Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S, Paulsen IT, James K, Eisen JA, Rutherford K, Salzberg SL, Craig A, Kyes S, Chan MS, Nene V, Shallom SJ, Suh B, Peterson J, Angiuoli S, Pertea M, Allen J, Selengut J, Haft D, Mather MW, Vaidya AB, Martin DM, et al. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 2002, 419:498-511. 10.1038/nature01097, 12368864.
29. Biggs BA, Kemp DJ, Brown GV. Subtelomeric chromosome deletions in field isolates of Plasmodium falciparum and their relationship to loss of cytoadherence in vitro. Proc Natl Acad Sci USA 1989, 86:2428-2432. 10.1073/pnas.86.7.2428, 286926, 2648403.
30. Day KP, Karamalis F, Thompson J, Barnes DA, Peterson C, Brown H, Brown GV, Kemp DJ. Genes necessary for expression of a virulence determinant and for transmission of Plasmodium falciparum are located on a 0.3-megabase region of chromosome 9. Proc Natl Acad Sci USA 1993, 90:8292-8296. 10.1073/pnas.90.17.8292, 47335, 8367496.
31. Gresham D, Curry B, Ward A, Gordon DB, Brizuela L, Kruglyak L, Botstein D. Optimized detection of sequence variation in heterozygous genomes using DNA microarrays with isothermal-melting probes. Proc Natl Acad Sci USA 2010, 107:1482-1487. 10.1073/pnas.0913883107, 2824413, 20080586.
32. Bjornsson HT, Albert TJ, Ladd-Acosta CM, Green RD, Rongione MA, Middle CM, Irizarry RA, Broman KW, Feinberg AP. SNP-specific array-based allele-specific expression analysis. Genome Res 2008, 18:771-779. 10.1101/gr.073254.107, 2336807, 18369178.
33. Chou CC, Chen CH, Lee TT, Peck K. Optimization of probe length and the number of probes per gene for optimal microarray analysis of gene expression. Nucleic Acids Res 2004, 32:e99. 10.1093/nar/gnh099, 484198, 15243142.
34. Letowski J, Brousseau R, Masson L. Designing better probes: effect of probe size, mismatch position and number on hybridization in DNA oligonucleotide microarrays. J Microbiol Methods 2004, 57:269-278. 10.1016/j.mimet.2004.02.002, 15063067.
35. Relogio A, Schwager C, Richter A, Ansorge W, Valcarcel J. Optimization of oligonucleotide-based DNA microarrays. Nucleic Acids Res 2002, 30:e51. 10.1093/nar/30.11.e51, 117213, 12034852.
36. Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, Nair P, Brothman AR, Stallings RL. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 2005, 44:305-319. 10.1002/gcc.20243, 16075461.
37. Nuwaysir EF, Huang W, Albert TJ, Singh J, Nuwaysir K, Pitas A, Richmond T, Gorski T, Berg JP, Ballin J, McCormick M, Norton J, Pollock T, Sumwalt T, Butcher L, Porter D, Molla M, Hall C, Blattner F, Sussman MR, Wallace RL, Cerrina F, Green RD. Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. Genome Res 2002, 12:1749-1755. 10.1101/gr.362402, 187555, 12421762.
38. Singh-Gasson S, Green RD, Yue Y, Nelson C, Blattner F, Sussman MR, Cerrina F. Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nat Biotechnol 1999, 17:974-978. 10.1038/13664, 10504697.
39. MR4/ATCC Methods in Malaria Research 2008, Manassas, Virginia, 5, MR4/ATCC.
40. Trager W, Jensen JB. Human malaria parasites in continuous culture. Science 1976, 193:673-675. 10.1126/science.781840, 781840.
41. Samarakoon U, Regier A, Tan A, Desany BA, Collins B, Tan JC, Emrich SJ, Ferdig MT. High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum. BMC Genomics 2011, 12:116. 10.1186/1471-2164-12-116, 3055840, 21324207.
42. Manske HM, Kwiatkowski DP. SNP-o-matic. Bioinformatics 2009, 25:2434-2435. 10.1093/bioinformatics/btp403, 2735664, 19574284.
43. Nair S, Nash D, Sudimack D, Jaidee A, Barends M, Uhlemann AC, Krishna S, Nosten F, Anderson TJ. Recurrent gene amplification and soft selective sweeps during evolution of multidrug resistance in malaria parasites. Mol Biol Evol 2007, 24:562-573.