A generic approach for the design of whole-genome oligoarrays, validated for genomotyping, deletion mapping and gene expression analysis on Staphylococcus aureaus

BMC Genomics

Volumn 6, Issue , 2005, Pages

  Charbonnier, Yvan ^a,b   Gettler, Brian ^a,b   François, Patrice ^a   Bento, Manuela ^a   Renzoni, Adriana ^a   Vaudaux, Pierre ^a   Schlegel, Werner ^b   Schrenzel, Jacques ^a  

^a GENEVA UNIVERSITY HOSPITALS   (Switzerland)

^b UNIVERSITY OF GENEVA   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; OLIGONUCLEOTIDE;

ARTICLE; BACTERIAL STRAIN; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; DNA MICROARRAY; ESCHERICHIA COLI; FILTRATION; GENE DELETION; GENE EXPRESSION PROFILING; GENE LIBRARY; GENE MAPPING; GENE TARGETING; GENETIC ALGORITHM; GENETIC ANALYSIS; GENETIC CONSERVATION; GENETIC DATABASE; GENETIC SELECTION; GENETIC VARIABILITY; GENOTYPE; MICROBIAL GENETICS; MOLECULAR BIOLOGY; NONHUMAN; NUCLEOTIDE SEQUENCE; OLIGONUCLEOTIDE PROBE; PREDICTION; PROCESS DESIGN; PROTEIN BINDING; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; STAPHYLOCOCCUS AUREUS; THERMODYNAMICS; TRANSCRIPTION REGULATION; ALGORITHM; BACTERIAL GENOME; BIOLOGICAL MODEL; BIOLOGY; CHEMISTRY; CLUSTER ANALYSIS; COMPUTER PROGRAM; DNA PROBE; GENE EXPRESSION; GENETIC TRANSCRIPTION; GENETICS; GENOME; GENOMICS; METHODOLOGY; NUCLEIC ACID HYBRIDIZATION; POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; PROKARYOTA; STAPHYLOCOCCUS; STAPHYLOCOCCUS AUREUS;

ALGORITHMS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DNA PROBES; GENE DELETION; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENOME; GENOME, BACTERIAL; GENOMICS; MODELS, GENETIC; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OLIGONUCLEOTIDE PROBES; OLIGONUCLEOTIDES; POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SOFTWARE; STAPHYLOCOCCUS AUREUS; THERMODYNAMICS; TRANSCRIPTION, GENETIC;

EID: 25444518699     PISSN: 14712164     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-6-95     Document Type: Article

References (42)

1. Yershov G, Barsky V, Belgovskiy A, Kirillov E, Kreindlin E, Ivanov I, Parinov S, Guschin D, Drobishev A, Dubiley S, Mirzabekov A: DNA analysis and diagnostics on oligonucleotide microchips. Proc Natl Acad Sci U S A 1996, 93:4913-4918.
2. Dubiley S, Kirillov E, Mirzabekov A: Polymorphism analysis and gene detection by minisequencing on an array of gel-immobilized primers. Nucleic Acids Res 1999, 27:e19.
3. Kim CC, Joyce EA, Chan K, Falkow S: Improved analytical methods for microarray-based genome-composition analysis. Genome Biol 2002, 3:RESEARCH0065.
4. Lucchini S, Thompson A, Hinton JC: Microarrays for microbiologists. Microbiology 2001, 147:1403-1414.
5. Eriksson S, Lucchini S, Thompson A, Rhen M, Hinton JC: Unravelling the biology of macrophage infection by gene expression profiling of intracellular Salmonella enterica. Mol Microbiol 2003, 47:103-118.
6. Staudinger BJ, Oberdoerster MA, Lewis PJ, Rosen H: mRNA expression profiles for Escherichia coli ingested by normal and phagocyte oxidase-deficient human neutrophils. J Clin Invest 2002, 110:1151-1163.
7. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, Bloomfield CD, Lander ES: Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 1999, 286:531-537.
8. Array Designer 3.01 http://www premierbiosoft com/dnamicroarray/index html 2004 [http://www.premierbiosoft.com/dnamicroarray/index.html].
9. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
10. Talla E, Tekaia F, Brino L, Dujon B: A novel design of whole-genome microarray probes for Saccharomyces cerevisiae which minimizes cross-hybridization. BMC Genomics 2003, 4:38.
11. Rouillard JM, Herbert CJ, Zuker M: OligoArray: genome-scale oligonucleotide design for microarrays. Bioinformatics 2002, 18:486-487.
12. Wright MA, Church GM: An open-source oligomicroarray standard for human and mouse. Nat Biotechnol 2002, 20:1082-1083.
13. Bozdech Z, Zhu J, Joachimiak MP, Cohen FE, Pulliam B, DeRisi JL: Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. Genome Biol 2003, 4:R9.
14. Nielsen HB, Wernersson R, Knudsen S: Design of oligonucleotides for microarrays and perspectives for design of multitranscriptome arrays. Nucleic Acids Res 2003, 31:3491-3496.
15. Hughes TR, Mao M, Jones AR, Burchard J, Marton MJ, Shannon KW, Ziman M, Meyer MR, Kobayashi S, Dai H, He YD, Stephaniants SB, Cavet G, Walker WL, West A, Coffey E, Shoemaker DD, Stoughton R, Blanchard AP, Friend SH, Linsley PS: Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat Biotechnol 2001, 19:342-347.
16. Kuroda M, Ohta T, Uchiyama I, Baba T, Yuzawa H, Kobayashi I, Cui L, Oguchi A, Aoki K, Nagai Y, Lian J, Ito T, Kanamori M, Matsumaru H, Maruyama A, Murakami H, Hosoyama A, Mizutani-Ui Y, Takahashi NK, Sawano T, Inoue R, Kaito C, Sekimizu K, Hirakawa H, Kuhara S, Goto S, Yabuzaki J, Kanehisa M, Yamashita A, Oshima K, Furuya K, Yoshino C, Shiba T, Hattori M, Ogasawara N, Hayashi H, Hiramatsu K: Whole genome sequencing of meticillin-resistant Staphylococcus aureus. Lancet 2001, 357:1225-1240.
17. Baba T, Takeuchi F, Kuroda M, Yuzawa H, Aoki K, Oguchi A, Nagai Y, Iwama N, Asano K, Naimi T, Kuroda H, Cui L, Yamamoto K, Hiramatsu K: Genome and virulence determinants of high virulence community-acquired MRSA. Lancet 2002, 359:1819-1827.
18. Gill SR: Staphylococcus aureus COL genome. http://www tigr org/tigr-scripts/CMR2/GenomePage3 spl?database=gsa 2004 [http://www.tigr.org/tigr-scripts/CMR2/GenomePage3.spl?database=gsa].
19. Blattner FR, Plunkett G III, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y: The complete genome sequence of Escherichia coli K-12. Science 1997, 277:1453-1474.
20. Cramton SE, Gerke C, Schnell NF, Nichols WW, Gotz F: The intercellular adhesion (ica) locus is present in Staphylococcus aureus and is required for biofilm formation. Infect Immun 1999, 67:5427-5433.
21. Novick RP, Schlievert P, Ruzin A: Pathogenicity and resistance islands of staphylococci. Microbes Infect 2001, 3:585-594.
22. Ramakrishnan R, Dorris D, Lublinsky A, Nguyen A, Domanus M, Prokhorova A, Gieser L, Touma E, Lockner R, Tata M, Zhu X, Patterson M, Shippy R, Sendera TJ, Mazumder A: An assessment of Motorola CodeLink microarray performance for gene expression profiling applications. Nucleic Acids Res 2002, 30:e30.
23. 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.
24. Wang D, Coscoy L, Zylberberg M, Avila PC, Boushey HA, Ganem D, DeRisi JL: Microarray-based detection and genotyping of viral pathogens. Proc Natl Acad Sci U S A 2002, 99:15687-15692.
25. Okamoto T, Suzuki T, Yamamoto N: Microarray fabrication with covalent attachment of DNA using bubble jet technology. Nat Biotechnol 2000, 18:438-441.
26. Blanchard AP, Friend SH: Cheap DNA arrays-it's not all smoke and mirrors. Nat Biotechnol 1999, 17:953.
27. Barczak A, Rodriguez MW, Hanspers K, Koth LL, Tai YC, Bolstad BM, Speed TP, Erle DJ: Spotted long oligonucleotide arrays for human gene expression analysis. Genome Res 2003, 13:1775-1785.
28. Kothapalli R, Yoder SJ, Mane S, Loughran TPJ: Microarray results: how accurate are they? BMC Bioinformatics 2002, 3:22.
29. Li J, Pankratz M, Johnson JA: Differential gene expression patterns revealed by oligonucleotide versus long cDNA arrays. Toxicol Sci 2002, 69:383-390.
30. Yang IV, Chen E, Hasseman JP, Liang W, Frank BC, Wang S, Sharov V, Saeed AI, White J, Li J, Lee NH, Yeatman TJ, Quackenbush J: Within the fold: assessing differential expression measures and reproducibility in microarray assays. Genome Biol 2002, 3:research0062.
31. Haas SA, Hild M, Wright AP, Hain T, Talibi D, Vingron M: Genome-scale design of PCR primers and long oligomers for DNA microarrays. Nucleic Acids Res 2003, 31:5576-5581.
32. Quackenbush J: Microarray data normalization and transformation. Nat Genet 2002, 32 Suppl:496-501.
33. Rosenow C, Saxena RM, Durst M, Gingeras TR: Prokaryotic RNA preparation methods useful for high density array analysis: comparison of two approaches. Nucleic Acids Research 2001, 29:U35-U42.
34. Dunman PM, Murphy E, Hanney S, Palacio D, Tucker-Kellogg G, Wu S, Brown EL, Zagurski RJ, Shlaes D, Projan SJ: Transcription Profiling-Based Identification of Staphylococcus aureus Genes Regulated by the agr and/or sarA Loci. J Bacteriol 2001, 183:7341-7353.
35. Tolstrup N, Nielsen PS, Kolberg JG, Frankel AM, Vissing H, Kauppinen S: OligoDesign: Optimal design of LNA (locked nucleic acid) oligonucleotide capture probes for gene expression profiling. Nucleic Acids Res 2003, 31:3758-3762.
36. Rouillard JM, Zuker M, Gulari E: OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach. Nucleic Acids Res 2003, 31:3057-3062.
37. SantaLucia JJ: A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci U S A 1998, 95:1460-1465.
38. Ketomaki K, Hakala H, Kuronen O, Lonnberg H: Hybridization properties of support-bound oligonucleotides: the effect of the site of immobilization on the stability and selectivity of duplex formation. Bioconjug Chem 2003, 14:811-816.
39. Gill SR, Fouts DE, Archer GL, Mongodin EF, Deboy RT, Ravel J, Paulsen IT, Kolonay JF, Brinkac L, Beanan M, Dodson RJ, Daugherty SC, Madupu R, Angiuoli SV, Durkin AS, Haft DH, Vamathevan J, Khouri H, Utterback T, Lee C, Dimitrov G, Jiang L, Qin H, Weidman J, Tran K, Kang K, Hance IR, Nelson KE, Fraser CM: Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain. J Bacteriol 2005, 187:2426-2438.
40. Genomic Research Laboratory http://www genomic ch/software php 2004 [http://www.genomic.ch/software.php].
41. Vaudaux P, Francois P, Bisognano C, Kelley WL, Lew DP, Schrenzel J, Proctor RA, McNamara PJ, Peters G, von Eiff C: Increased expression of clumping factor and fibronectin-binding proteins by hemB mutants of Staphylococcus aureus expressing small colony variant phenotypes. Infect Immun 2002, 70:5428-5437.
42. Talaat AM, Howard ST, Hale W, Lyons R, Garner H, Johnston SA: Genomic DNA standards for gene expression profiling in Mycobacterium tuberculosis. Nucleic Acids Res 2002, 30:e104.