A primer on the current state of microarray technologies

Methods in Molecular Biology

Volumn 802, Issue , 2012, Pages 3-17

  Trachtenberg, Alexander J ^a   Robert, Jae Hyung ^b   Abdalla, Azza E ^c   Fraser, Andrew ^d   He, Steven Y ^e   Lacy, Jessica N ^a   Rivas Morello, Chiara ^a   Truong, Allison ^f   Hardiman, Gary ^d   Ohno Machado, Lucila ^g   Liu, Fang ^h,i   Hovig, Eivind ^h   Kuo, Winston Patrick ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

^b HARVARD SCHOOL OF DENTAL MEDICINE   (United States)

^c UNIVERSITY OF SOUTH CAROLINA   (United States)

^d BETH ISRAEL DEACONESS MEDICAL CENTER   (United States)

^e UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^f UNIVERSITY OF CALIFORNIA   (United States)

^g UNIVERSITY OF CALIFORNIA   (United States)

^h OSLO UNIVERSITY HOSPITAL   (Norway)

ⁱ PubGene AS   (Norway)

Author keywords

Cross platform; Gene expression; High throughput; Microarrays; One dye; QRT PCR; Two dye

Indexed keywords

FLUORESCENT DYE; PRIMER DNA;

ARTICLE; DNA MICROARRAY; EQUIPMENT DESIGN; GENE EXPRESSION PROFILING; HUMAN; INSTRUMENTATION; METHODOLOGY; NUCLEIC ACID DATABASE;

DATABASES, NUCLEIC ACID; DNA PRIMERS; EQUIPMENT DESIGN; FLUORESCENT DYES; GENE EXPRESSION PROFILING; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 84555190035     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-400-1_1     Document Type: Article

References (41)

1. Gentleman RC, Carey VJ, Bates DM et al (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5:R80.
2. Kulesh DA, Clive DR, Zarlenga DS et al (1987) Identification of interferon-modulated proliferation-related cDNA sequences. Proc Natl Acad Sci U S A 84: 8453-8457.
3. Kuo WP, Liu F, Trimarchi J et al (2006) A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies. Nat Biotechnol 24:832-840. (Pubitemid 44086625)
4. Fodor SP, Read JL, Pirrung MC et al (1991) Light-directed, spatially addressable parallel chemical synthesis. Science 251:767-773. (Pubitemid 21926165)
5. Lausted C, Dahl T, Warren C et al (2004) POSaM: a fast, flexible, open-source, inkjet oligonucleotide synthesizer and microarrayer. Genome Biol 5:R58.
6. Baum M, Bielau S, Rittner N et al (2003) Validation of a novel, fully integrated and flexible microarray benchtop facility for gene expression profiling. Nucleic Acids Res 31: e151.
7. Ruano JM, Benoit VV, Aitchison JS et al (2000) Flame hydrolysis deposition of glass on silicon for the integration of optical and microfluidic devices. Anal Chem 72: 1093-1097. (Pubitemid 30127421)
8. Benoit V, Steel A, Torres M et al (2001) Evaluation of three-dimensional microchannel glass biochips for multiplexed nucleic acid fluorescence hybridization assays. Anal Chem 73:2412-2420. (Pubitemid 32880638)
9. Hokaiwado N, Asamoto M, Tsujimura K et al (2004) Rapid analysis of gene expression changes caused by liver carcinogens and chemopreventive agents using a newly developed three-dimensional microarray system. Cancer Sci 95: 123-130. (Pubitemid 38404312)
10. Fare TL, Coffey EM, Dai H, et al (2003) Effects of atmospheric ozone on microarray data quality. Anal Chem 75:4672-4675. (Pubitemid 37082262)
11. Quinn MC, Wilson DJ, Young F et al (2009) The chemiluminescence based Ziplex automated workstation focus array reproduces ovarian cancer Affymetrix GeneChip expression profiles. J Transl Med 7:55.
12. Gunderson KL, Kruglyak S, Graige MS et al (2004) Decoding randomly ordered DNA arrays. Genome Res 14:870-877. (Pubitemid 38660504)
13. Bond GL, Hu W, Levine A (2005) A single nucleotide polymorphism in the MDM2 gene: from a molecular and cellular explanation to clinical effect. Cancer Res 65:5481-5484. (Pubitemid 40911143)
14. Guilford P, Hopkins J, Harraway J et al (1998) E-cadherin germline mutations in familial gastric cancer. Nature 392:402-405. (Pubitemid 28168738)
15. Imyanitov EN (2009) Gene polymorphisms, apoptotic capacity and cancer risk. Hum Genet 125:239-246.
16. Lindblad-Toh K, Tanenbaum DM, Daly MJ et al (2000) Loss-of-heterozygosity analysis of small-cell lung carcinomas using singlenucleotide polymorphism arrays. Nat Biotechnol 18:1001-1005. (Pubitemid 32977384)
17. Reddy EP (1983) Nucleotide sequence analysis of the T24 human bladder carcinoma oncogene. Science 220:1061-1063. (Pubitemid 13090147)
18. Tuna M, Knuutila S, Mills GB (2009) Uniparental disomy in cancer. Trends Mol Med 15:120-128.
19. Mockler TC, Chan S, Sundaresan A et al (2005) Applications of DNA tiling arrays for whole-genome analysis. Genomics 85:1-15. (Pubitemid 39655686)
20. Nonne N, Ameyar-Zazoua M, Souidi M et al (2010) Tandem affinity purification of miRNA target mRNAs (TAP-Tar). Nucleic Acids Res 38:e20.
21. Wheeler DL, Church DM, Lash AE et al (2001) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 29:11-16. (Pubitemid 32054396)
22. Brazma A, Parkinson H, Sarkans U et al (2003) ArrayExpress-a public repository for microarray gene expression data at the EBI. Nucleic Acids Res 31:68-71. (Pubitemid 36150335)
23. Brooksbank C, Camon E, Harris MA et al (2003) The European Bioinformatics Institute's data resources. Nucleic Acids Res 31:43-50. (Pubitemid 36150330)
24. Ball CA, Sherlock G, Parkinson H et al (2002) Standards for microarray data. Science 298:539.
25. Ikeo K, Ishi-i J, Tamura Tet al (2003) CIBEX: center for information biology gene expression database. C R Biol 326:1079-1082. (Pubitemid 38016464)
26. Brazma A, Hingamp P, Quackenbush J et al (2001) Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 29:365-371. (Pubitemid 34326681)
27. Kuo WP, Jenssen TK, Butte AJ et al (2002) Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics 18: 405-412. (Pubitemid 34284941)
28. Mecham BH, Klus GT, Strovel J et al (2004) Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements. Nucleic Acids Res 32:e74.
29. Carter SL, Eklund AC, Mecham BH et al (2005) Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements. BMC Bioinformatics 6:107.
30. Bammler T, Beyer RP, Bhattacharya S et al (2005) Standardizing global gene expression analysis between laboratories and across platforms. Nat Methods 2: 351-356.
31. Larkin JE, Frank BC, Gavras H et al (2005) Independence and reproducibility across microarray platforms. NatMethods 2:337-344.
32. Wang H, He X, Band M et al (2005) A study of inter-lab and inter-platform agreement of DNA microarray data. BMC Genomics 6:71.
33. Zhu B, Ping G, Shinohara Y et al (2005) Comparison of gene expression measurements from cDNA and 60-mer oligonucleotide microarrays. Genomics 85:657-665. (Pubitemid 40693354)
34. Barnes M, Freudenberg J, Thompson S et al (2005) Experimental comparison and crossvalidation of the Affymetrix and Illumina gene expression analysis platforms. Nucleic Acids Res 33:5914-5923. (Pubitemid 41742611)
35. Sherlock G (2005) Of fish and chips. Nat Methods 2:329-330. (Pubitemid 41130975)
36. Casciano DA, Woodcock J (2006) Empowering microarrays in the regulatory setting. Nat Biotechnol 24:1103. (Pubitemid 44359719)
37. Shi L, Reid LH, Jones WD et al (2006) The MicroArray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 24:1151-1161. (Pubitemid 44359727)
38. Geiss GK, Bumgarner RE, Birditt B et al (2008) Direct multiplexed measurement of gene expression with color-coded probe pairs. Nat Biotechnol 26:317-325. (Pubitemid 351355126)
39. Spurgeon SL, Jones RC, Ramakrishnan R (2008) High throughput gene expression measurement with real time PCR in a microfluidic dynamic array. PLoS One 3:e1662.
40. Robertson G, Hirst M, Bainbridge M et al (2007) Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 4:651-657. (Pubitemid 47202477)
41. Park PJ (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 10:669-680.