A comparison of oligonucleotide and cDNA-based microarray systems

Physiological Genomics

Volumn 16, Issue , 2004, Pages 361-370

  Mah, Nancy ^a   Thelin, Anders ^b   Lu, Tim ^a   Nikolaus, Susanna ^a   Kühbacher, Tanja ^a   Gurbuz, Yesim ^a   Eickhoff, Holger ^c   Klöppel, Günther ^a   Lehrach, Hans ^c   Mellgård, Björn ^b   Costello, Christine M ^a   Schreiber, Stefan ^a  

^a UNIVERSITY OF KIEL   (Germany)

^b ASTRAZENECA R AND D   (Sweden)

^c MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

Author keywords

Commercial oligonucleotide based microarray system; Cross platform screening; Expression screening platform; Noncommercial clone based microarray system

Indexed keywords

COMPLEMENTARY DNA; OLIGONUCLEOTIDE; RNA; MESSENGER RNA;

ADULT; AGED; ALU SEQUENCE; ARTICLE; CLINICAL ARTICLE; COMPARATIVE STUDY; CONTROLLED STUDY; DNA MICROARRAY; FEMALE; GENE EXPRESSION; GENE SEQUENCE; HUMAN; HUMAN TISSUE; MALE; MOLECULAR CLONING; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PUBLICATION; TECHNOLOGY; BIOPSY; COLON; GENE EXPRESSION PROFILING; GENETICS; INSTRUMENTATION; INTESTINE MUCOSA; METABOLISM; METHODOLOGY; MIDDLE AGED; REPRODUCIBILITY;

AGED; ALU ELEMENTS; BIOPSY; COLON; DNA, COMPLEMENTARY; FEMALE; GENE EXPRESSION PROFILING; HUMANS; INTESTINAL MUCOSA; MALE; MIDDLE AGED; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OLIGONUCLEOTIDES; REPRODUCIBILITY OF RESULTS; RNA, MESSENGER;

EID: 12144286757     PISSN: 15312267     EISSN: None     Source Type: Journal    
DOI: 10.1152/physiolgenomics.00080.2003     Document Type: Article

References (25)

1. Beer DG, Kardia SL, Huang CC, Giordano TJ, Levin AM, Misek DE, Lin L, Chen G, Gharib TG, Thomas DG, Lizyness ML, Kuick R, Hayasaka S, Taylor JM, Iannettoni MD, Orringer MB, and Hanash S. Gene-expression profiles predict survival of patients with lung adenocarcinoma. Nat Med 8: 816-824, 2002.
2. Eickhoff H, Schuchhardt J, Ivanov I, Meier-Ewert S, O'Brien J, Malik A, Tandon N, Wolski EW, Rohlfs E, Nyarsik L, Reinhardt R, Nietfeld W, and Lehrach H. Tissue gene expression analysis using arrayed normalized cDNA libraries. Genome Res 10: 1230-1240, 2000.
3. Feinberg AP and Vogelstein B. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal Biochem 132: 6-13, 1983.
4. Geschwind DH. Sharing gene expression data: an array of options. Nat Rev Neurosci 2: 435-438, 2001.
5. Gress TM, Hoheisel JD, Lennon GG, Zehetner G, and Lehrach H. Hybridization fingerprinting of high-density cDNA-library arrays with cDNA pools derived from whole tissues. Mamm Genome 3: 609-619, 1992.
6. Halgren RG, Fielden MR, Fong CJ, and Zacharewski TR. Assessment of clone identity and sequence fidelity for 1189 IMAGE cDNA clones. Nucleic Acids Res 29: 582-588, 2001.
7. Jordan B. Historical background and anticipated developments. Ann NY Acad Sci 975: 24-32, 2002.
8. Kane MD, Jatkoe TA, Stumpf CR, Lu J, Thomas JD, and Madore SJ. Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. Nucleic Acids Res 28: 4552-4557, 2000.
9. Kuo WP, Jenssen TK, Butte AJ, Ohno-Machado L, and Kohane IS. Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics 18: 405-412, 2002.
10. Lennon GG and Lehrach H. Hybridization analyses of arrayed cDNA libraries. Trends Genet 7: 314-317, 1991.
11. McDonald MJ and Rosbash M. Microarray analysis and organization of circadian gene expression in Drosophila. Cell 107: 567-578, 2001.
12. McGall G, Labadie J, Brock P, Wallraff G, Nguyen T, and Hinsberg W. Light-directed synthesis of high-density oligonucleotide arrays using semiconductor photoresists. Proc Natl Acad Sci USA 93: 13555-13560, 1996.
13. Middleton FA, Mirnics K, Pierri JN, Lewis DA, and Levitt P. Gene expression profiling reveals alterations of specific metabolic pathways in schizophrenia. J Neurosci 22: 2718-2729, 2002.
14. Nielsen TO, West RB, Linn SC, Alter O, Knowling MA, O'Connell JX, Zhu S, Fero M, Sherlock G, Pollack JR, Brown PO, Botstein D, and van de Rijn M. Molecular characterisation of soft tissue tumours: a gene expression study. Lancet 359: 1301-1307, 2002.
15. Ohki R, Yamamoto K, Mano H, Lee RT, Ikeda U, and Shimada K. Identification of mechanically induced genes in human monocytic cells by DNA microarrays. J Hypertens 20: 685-691, 2002.
16. Okamoto T, Suzuki T, and Yamamoto N. Microarray fabrication with covalent attachment of DNA using bubble jet technology. Nat Biotechnol 18: 438-441, 2000.
17. Rhodes DR, Barrette TR, Rubin MA, Ghosh D, and Chinnaiyan AM. Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer. Cancer Res 62: 4427-4433, 2002.
18. Schena M, Shalon D, Davis RW, and Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467-470, 1995.
19. Sokal RR and Rohlf FJ. Biometry: the Principles and Practice of Statistics in Biological Research. New York: Freeman, 1995.
20. Stillman BA and Tonkinson JL. Expression microarray hybridization kinetics depend on length of the immobilized DNA but are independent of immobilization substrate. Anal Biochem 295: 149-157, 2001.
21. Stoeckert CJ, Causton HC, and Ball CA. Microarray databases: standards and ontologies. Nat Genet 32, Suppl 2: 469-473, 2002.
22. Taylor E, Cogdell D, Coombes K, Hu L, Ramdas L, Tabor A, Hamilton S, and Zhang W. Sequence verification as quality-control step for production of cDNA microarrays. Biotechniques 31: 62-65, 2001.
23. van't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AA, Mao M, Peterse HL, van der Kooy K, Marton MJ, Witteveen AT, Schreiber GJ, Kerkhoven RM, Roberts C, Linsley PS, Bernards R, and Friend SH. Gene expression profiling predicts clinical outcome of breast cancer. Nature 415: 530-536, 2002.
24. Yoshimoto H, Saltsman K, Gasch AP, Li HX, Ogawa N, Botstein D, Brown PO, and Cyert MS. Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae. J Biol Chem 277: 31079-31088, 2002.
25. Yuen T, Wurmbach E, Pfeffer RL, Ebersole BJ, and Sealfon SC. Accuracy and calibration of commercial oligonucleotide and custom cDNA microarrays. Nucleic Acids Res 30: e48, 2002.