[1] The Affymetrix GeneChip® Platform: An Overview

Methods in Enzymology

Volumn 410, Issue , 2006, Pages 3-28

  Dalma Weiszhausz, Dennise D ^a   Warrington, Janet ^a   Tanimoto, Eugene Y ^a   Miyada, C Garrett ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

ACUTE GRANULOCYTIC LEUKEMIA; ACUTE LYMPHOBLASTIC LEUKEMIA; CANCER RESEARCH; CHROMATIN IMMUNOPRECIPITATION; COMPUTER PROGRAM; DATA ANALYSIS; DNA MICROARRAY; FLUORESCENCE ANALYSIS; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENOME ANALYSIS; GENOTYPE; HETEROZYGOSITY LOSS; HUMAN; IMAGE ANALYSIS; LUNG CANCER; NONHUMAN; NUCLEIC ACID AMPLIFICATION; NUCLEIC ACID HYBRIDIZATION; NUCLEIC ACID PROBE; NUCLEOTIDE METABOLISM; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REPRODUCIBILITY; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; ANIMAL; INSTRUMENTATION; METHODOLOGY;

ANIMALS; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 33747822629     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(06)10001-4     Document Type: Review

References (45)

1. Affymetrix Technical Note. Guide to Probe Logarithmic Intensity Error (PLIER) Estimation (2005). http://www.affymetrix.com
2. Apidianakis Y., Mindrinos M.N., Xiao W., Lau G.W., Baldini R.L., Davis R.W., and Rahme L.G. Profiling early infection responses: Pseudomonas aeruginosa eludes host defenses by suppressing antimicrobial peptide gene expression. Proc. Natl. Acad. Sci. USA 102 (2005) 2573-2578
3. Armstrong S.A., Staunton J.E., Silverman L.B., Pieters R., den Boer M.L., Minden M.D., Sallan S.E., Lander E.S., Golub T.R., and Korsmeyer S.J. MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia. Nat. Genet. 30 (2002) 41-47
4. Boerma M., van der Wees C.G., Vrieling H., Svensson J.P., Wondergem J., van der Laarse A., Mullenders L.H., and van Zeeland A.A. Microarray analysis of gene expression profiles of cardiac myocytes and fibroblasts after mechanical stress, ionising or ultraviolet radiation. BMC Genom. 6 (2005) 6
5. Cawley S., Bekiranov S., Ng H.H., Kapranov P., Sekinger E.A., Kampa D., Piccolboni A., Sementchenko V., Cheng J., Williams A.J., Wheeler R., Wong B., Drenkow J., Yamanaka M., Patel S., Brubaker S., Tammana H., Helt G., Struhl K., and Gingeras T.R. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116 (2004) 499-509
6. Comer J.E., Galindo C.L., Chopra A.K., and Peterson J.W. GeneChip analyses of global transcriptional responses of murine macrophages to the lethal toxin of Bacillus anthracis. Infect. Immun. 73 (2005) 1879-1885
7. Cutler D.J., Zwick M.E., Carrasquillo M.M., Yohn C.T., Tobin K.P., Kashuk C., Mathews D.J., Shah N.A., Eichler E.E., Warrington J.A., and Chakravarti A. High-throughput variation detection and genotyping using microarrays. Genome Res. 11 (2001) 1913-1925
8. Davletova S., Rizhsky L., Liang H., Shengqiang Z., Oliver D.J., Coutu J., Shulaev V., Schlauch K., and Mittler R. Cytosolic ascorbate peroxidase 1 is a central component of the reactive oxygen gene network of Arabidopsis. Plant Cell 17 (2005) 268-281
9. Di X., Matsuzaki H., Webster T.A., Hubbell E., Liu G., Dong S., Bartell D., Huang J., Chiles R., Yang G., Shen M.M., Kulp D., Kennedy G.C., Mei R., Jones K.W., and Cawley S. Dynamic model based algorithms for screening and genotyping over 100 K SNPs on oligonucleotide microarrays. Bioinformatics 21 (2005) 1958-1963
10. Dinkova T.D., Keiper B.D., Korneeva N.L., Aamodt E.J., and Rhoads R.E. Translation of a small subset of Caenorhabditis elegans mRNAs is dependent on a specific eukaryotic translation initiation factor 4E isoform. Mol. Cell. Biol. 25 (2005) 100-113
11. Fan W., Bubman D., Chadburn A., Harrington Jr. W.J., Cesarman E., and Knowles D.M. Distinct subsets of primary effusion lymphoma can be identified based on their cellular gene expression profile and viral association. J. Virol. 79 (2005) 1244-1251
12. Fodor S.P., Read J.L., Pirrung M.C., Stryer L., Lu A.T., and Solas D. Light-directed, spatially addressable parallel chemical synthesis. Science 251 (1991) 767-773
13. Girardot F., Monnier V., and Tricoire H. Genome wide analysis of common and specific stress responses in adult Drosophila melanogaster. BMC Genom. 5 (2004) 74
14. Gomez-Mena C., de Folter S., Costa M.M., Angenent G.C., and Sablowski R. Transcriptional program controlled by the floral homeotic gene AGAMOUS during early organogenesis. Development 132 (2005) 429-438
15. Hardenbol P., Baner J., Jain M., Nilsson M., Namsaraev E.A., Karlin-Neumann G.A., Fakhrai-Rad H., Ronaghi M., Willis T.D., Landegren U., and Davis R.W. Multiplexed genotyping with sequence-tagged molecular inversion probes. Nat. Biotechnol. 21 (2003) 673-678
16. Hekmat-Scafe D.S., Dang K.N., and Tanouye M.A. Seizure suppression by gain-of-function escargot mutations. Genetics 169 (2005) 1477-1493
17. Huang J., Wei W., Zhang J., Liu G., Bignell G.R., Stratton M.R., Futreal P.A., Wooster R., Jones K.W., and Shapero M.H. Whole genome DNA copy number changes identified by high density oligonucleotide arrays. Hum. Genom. 1 (2004) 287-299
18. Irizarry R.A., Bolstad B.M., Collin F., Cope L.M., Hobbs B., and Speed T.P. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 31 (2003) e15
19. Iwamoto K., Bundo M., and Kato T. Altered expression of mitochondria-related genes in postmortem brains of patients with bipolar disorder or schizophrenia, as revealed by large-scale DNA microarray analysis. Hum. Mol. Genet. 14 (2005) 241-253
20. Janne P.A., Li C., Zhao X., Girard L., Chen T.H., Minna J., Christiani D.C., Johnson B.E., and Meyerson M. High-resolution single-nucleotide polymorphism array and clustering analysis of loss of heterozygosity in human lung cancer cell lines. Oncogene 23 (2004) 2716-2726
21. Jemal A., Murray T., Samuels A., Ghafoor A., Ward E., and Thun M.J. Cancer statistics, 2003. CA Cancer J. Clin. 53 (2003) 5-26
22. Kapranov P., Cawley S.E., Drenkow J., Bekiranov S., Strausberg R.L., Fodor S.P., and Gingeras T.R. Large-scale transcriptional activity in chromosomes 21 and 22. Science 296 (2002) 916-919
23. Kennedy G.C., Matsuzaki H., Dong S., Liu W.M., Huang J., Liu G., Su X., Cao M., Chen W., Zhang J., Liu W., Yang G., Di X., Ryder T., He Z., Surti U., Phillips M.S., Boyce-Jacino M.T., Fodor S.P., and Jones K.W. Large-scale genotyping of complex DNA. Nat. Biotechnol. 21 (2003) 1233-1237
24. Klein R.J., Zeiss C., Chew E.Y., Tsai J.Y., Sackler R.S., Haynes C., Henning A.K., SanGiovanni J.P., Mane S.M., Mayne S.T., Bracken M.B., Ferris F.L., Ott J., Barnstable C., and Hoh J. Complement factor H polymorphism in age-related macular degeneration. Science 308 (2005) 385-389
25. Kong S.W., Bodyak N., Yue P., Liu Z., Brown J., Izumo S., and Kang P.M. Genetic expression profiles during physiological and pathological cardiac hypertrophy and heart failure in rats. Physiol. Genom. 21 (2005) 34-42
26. Korenberg J.R. Toward a molecular understanding of Down syndrome. Prog. Clin. Biol. Res. 384 (1993) 87-115
27. Lander E.S., Linton L.M., Birren B., Nusbaum C., Zody M.C., Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W., Funke R., Gage D., Harris K., Heaford A., Howland J., Kann L., Lehoczky J., LeVine R., McEwan P., McKernan K., Meldrim J., Mesirov J.P., Miranda C., Morris W., Naylor J., Raymond C., Rosetti M., Santos R., Sheridan A., Sougnez C., Stange-Thomann N., Stojanovic N., Subramanian A., Wyman D., Rogers J., Sulston J., Ainscough R., Beck S., Bentley D., Burton J., Clee C., Carter N., Coulson A., Deadman R., Deloukas P., Dunham A., Dunham I., Durbin R., French L., Grafham D., Gregory S., Hubbard T., Humphray S., Hunt A., Jones M., Lloyd C., McMurray A., Matthews L., Mercer S., Milne S., Mullikin J.C., Mungall A., Plumb R., Ross M., Shownkeen R., Sims S., Waterston R.H., Wilson R.K., Hillier L.W., McPherson J.D., Marra M.A., Mardis E.R., Fulton L.A., Chinwalla A.T., Pepin K.H., Gish W.R., Chissoe S.L., Wendl M.C., Delehaunty K.D., Miner T.L., Delehaunty A., Kramer J.B., Cook L.L., Fulton R.S., Johnson D.L., Minx P.J., Clifton S.W., Hawkins T., Branscomb E., Predki P., Richardson P., Wenning S., Slezak T., Doggett N., Cheng J.F., Olsen A., Lucas S., Elkin C., Uberbacher E., Frazier M., et al. Initial sequencing and analysis of the human genome. Nature 409 (2001) 860-921
28. Lindblad-Toh K., Tanenbaum D.M., Daly M.J., Winchester E., Lui W.O., Villapakkam A., Stanton S.E., Larsson C., Hudson T.J., Johnson B.E., Lander E.S., and Meyerson M. Loss-of-heterozygosity analysis of small-cell lung carcinomas using single-nucleotide polymorphism arrays. Nat. Biotechnol. 18 (2000) 1001-1005
29. Lipshutz R.J., Morris D., Chee M., Hubbell E., Kozal M.J., Shah N., Shen N., Yang R., and Fodor S.P. Using oligonucleotide probe arrays to access genetic diversity. Biotechniques 19 (1995) 442-447
30. Matsuzaki H., Dong S., Loi H., Di X., Liu G., Hubbell E., Law J., Berntsen T., Chadha M., Hui H., Yang G., Kennedy G.C., Webster T.A., Cawley S., Walsh P.S., Jones K.W., Fodor S.P., and Mei R. Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays. Nat. Methods 1 (2004) 109-111
31. Matsuzaki H., Loi H., Dong S., Tsai Y.Y., Fang J., Law J., Di X., Liu W.M., Yang G., Liu G., Huang J., Kennedy G.C., Ryder T.B., Marcus G.A., Walsh P.S., Shriver M.D., Puck J.M., Jones K.W., and Mei R. Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high-density oligonucleotide array. Genome Res. 14 (2004) 414-425
32. McGall G.H., and Christians F.C. High-density genechip oligonucleotide probe arrays. Adv. Biochem. Eng. Biotechnol. 77 (2002) 21-42
33. Mei R., Hubbell E., Bekiranov S., Mittmann M., Christians F.C., Shen M.-M., Lu G., Fang J., Liu W.-M., Ryder T., Kaplan P., Kulp D., and Webster T.A. Probe selection for high density oligonucleotide arrays. Proc. Natl. Acad. Sci. USA 100 (2003) 11237-11242
34. Middleton F.A., Pato M.T., Gentile K.L., Morley C.P., Zhao X., Eisener A.F., Brown A., Petryshen T.L., Kirby A.N., Medeiros H., Carvalho C., Macedo A., Dourado A., Coelho I., Valente J., Soares M.J., Ferreira C.P., Lei M., Azevedo M.H., Kennedy J.L., Daly M.J., Sklar P., and Pato C.N. Genomewide linkage analysis of bipolar disorder by use of a high-density single-nucleotide-polymorphism (SNP) genotyping assay: A comparison with microsatellite marker assays and finding of significant linkage to chromosome 6q22. Am. J. Hum. Genet. 74 (2004) 886-897
35. Moore G. Cramming more components onto integrated circuits. Electronics 38 (1965) 114-117
36. Presneau N., Dewar K., Forgetta V., Provencher D., Mes-Masson A.M., and Tonin P.N. Loss of heterozygosity and transcriptome analyses of a 1.2 Mb candidate ovarian cancer tumor suppressor locus region at 17q25.1-q25.2. Mol. Carcinog. 43 (2005) 141-154
37. Puffenberger E.G., Hu-Lince D., Parod J.M., Craig D.W., Dobrin S.E., Conway A.R., Donarum E.A., Strauss K.A., Dunckley T., Cardenas J.F., Melmed K.R., Wright C.A., Liang W., Stafford P., Flynn C.R., Morton D.H., and Stephan D.A. Mapping of sudden infant death with dysgenesis of the testes syndrome (SIDDT) by a SNP genome scan and identification of TSPYL loss of function. Proc. Natl. Acad. Sci. USA 101 (2004) 11689-11694
38. Reinke V., Gil I.S., Ward S., and Kazmer K. Genome-wide germline-enriched and sex-biased expression profiles in Caenorhabditis elegans. Development 131 (2004) 311-323
39. Schadt E.E., Edwards S.W., GuhaThakurta D., Holder D., Ying L., Svetnik V., Leonardson A., Hart K.W., Russell A., Li G., Cavet G., Castle J., McDonagh P., Kan Z., Chen R., Kasarskis A., Margarint M., Caceres R.M., Johnson J.M., Armour C.D., Garrett-Engele P.W., Tsinoremas N.F., and Shoemaker D.D. A comprehensive transcript index of the human genome generated using microarrays and computational approaches. Genome Biol. 5 (2004) R73
40. Sellick G.S., Garrett C., and Houlston R.S. A novel gene for neonatal diabetes maps to chromosome 10p12.1-p13. Diabetes 52 (2003) 2636-2638
41. Steinman L., and Zamvil S. Transcriptional analysis of targets in multiple sclerosis. Nat. Rev. Immunol. 3 (2003) 483-492
42. Van Gelder R.N., von Zastrow M.E., Yool A., Dement W.C., Barchas J.D., and Eberwine J.H. Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc. Natl. Acad. Sci. USA 87 (1990) 1663-1667
43. Wang J., Iwasaki H., Krivtsov A., Febbo P.G., Thorner A.R., Ernst P., Anastasiadou E., Kutok J.L., Kogan S.C., Zinkel S.S., Fisher J.K., Hess J.L., Golub T.R., Armstrong S.A., Akashi K., and Korsmeyer S.J. Conditional MLL-CBP targets GMP and models therapy-related myeloproliferative disease. EMBO J. 24 (2005) 368-381
44. Yeoh E.J., Ross M.E., Shurtleff S.A., Williams W.K., Patel D., Mahfouz R., Behm F.G., Raimondi S.C., Relling M.V., Patel A., Cheng C., Campana D., Wilkins D., Zhou X., Li J., Liu H., Pui C.H., Evans W.E., Naeve C., Wong L., and Downing J.R. Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling. Cancer Cell 1 (2002) 133-143
45. Zhao X., Li C., Paez J.G., Chin K., Janne P.A., Chen T.H., Girard L., Minna J., Christiani D., Leo C., Gray J.W., Sellers W.R., and Meyerson M. An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays. Cancer Res. 64 (2004) 3060-3071