Genomic profiling: CDNA arrays and oligoarrays

Methods in Molecular Biology

Volumn 823, Issue , 2012, Pages 89-105

  Gorreta, Francesco ^a   Carbone, Walter ^b   Barzaghi, Dagania ^c  

^a Genetics and Biomarkers Exploratory Medicine   (Italy)

^b Merck Serono   (Italy)

^c Medestea Research and Production SrI   (Italy)

Author keywords

cDNA; DNA methylation; Genomics; Hybridization; miRNA; Oligoarray; PCR RNA

Indexed keywords

ARTICLE; COMPARATIVE GENOMIC HYBRIDIZATION; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENOMICS; HUMAN; METHODOLOGY; QUALITY CONTROL; REPRODUCIBILITY; SINGLE NUCLEOTIDE POLYMORPHISM; STANDARD;

COMPARATIVE GENOMIC HYBRIDIZATION; GENE EXPRESSION PROFILING; GENOMICS; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; QUALITY CONTROL; REPRODUCIBILITY OF RESULTS;

EID: 82355171042     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-60327-216-2_7     Document Type: Article

References (61)

1. Southern, E., Mir, K., and Shchepinov, M. (1999) Molecular interactions on microarrays. Nat Genet 21, 5-9. (Pubitemid 29031484)
2. Ramsay, G. (1998) DNA chips: state-of-the art. Nat Biotechnol 16, 40-4. (Pubitemid 28035946)
3. Marshall, A., and Hodgson, J. (1998) DNA chips: an array of possibilities. Nat Biotechnol 16, 27-31. (Pubitemid 28035944)
4. Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., et al. (2001) The sequence of the human genome. Science 291, 1304-51. (Pubitemid 32173090)
5. Phimister, B. (1999) Going global. Nature Genetics 21, 1. (Pubitemid 29031481)
6. Lockhart, D. J., and Winzeler, E. A. (2000) Genomics, gene expression and DNA arrays. Nature 405, 827-36. (Pubitemid 30407861)
7. Baldwin, D., Crane, V., and Rice, D. (1999) A comparison of gel-based, nylon fi lter and microarray techniques to detect differential RNA expression in plants. Curr Opin Plant Biol 2, 96-103. (Pubitemid 29181909)
8. Smith, D. R., Quinlan, A. R., Peckham, H. E., Makowsky, K., Tao, W., et al. (2008) Rapid whole-genome mutational profi ling using nextgeneration sequencing technologies. Genome Res 18, 1638-42.
9. Quail, M. A., Kozarewa, I., Smith, F., Scally, A., Stephens, P. J., et al. (2008) A large genome center's improvements to the Illumina sequencing system. Nat Methods 5, 1005-10.
10. Mardis, E. R. (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9, 387-402.
11. Mardis, E. R. (2008) The impact of next-generation sequencing technology on genetics. Trends Genet 24, 133-41.
12. Kozarewa, I., Ning, Z., Quail, M. A., Sanders, M. J., Berriman, M., et al. (2009) Amplifi cationfree Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat Methods 6, 291-5.
13. Bentley, D. R. (2006) Whole-genome resequencing. Curr Opin Genet Dev 16, 545-52.
14. Rouillard, J. M., Zuker, M., and Gulari, E. (2003) OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach. Nucleic Acids Res 31, 3057-62. (Pubitemid 37441764)
15. Hegde, P., Qi, R., Abernathy, K., Gay, C., Dharap, S., et al. (2000) A concise guide to cDNA microarray analysis. Biotechniques 29, 548-50, 52-4, 56 passim.
16. Holloway, A. J., van Laar, R. K., Tothill, R. W., and Bowtell, D. D. (2002) Options available -from start to fi nish - for obtaining data from DNA microarrays II. Nat Genet 32 Suppl, 481-9. (Pubitemid 35435150)
17. Barbulovic-Nad, I., Lucente, M., Sun, Y., Zhang, M., Wheeler, A. R., et al. (2006) Biomicroarray fabrication techniques - a review. Crit Rev Biotechnol 26, 237-59.
18. Grainger, D. W., Greef, C. H., Gong, P., and Lochhead, M. J. (2007) Current microarray surface chemistries. Methods Mol Biol 381, 37-57. (Pubitemid 350189883)
19. Fodor, S. P., Read, J. L., Pirrung, M. C., Stryer, L., Lu, A. T., et al. (1991) Light-directed, spatially addressable parallel chemical synthesis. Science 251, 767-73. (Pubitemid 21926165)
20. Barrett, M. T., Scheffer, A., Ben-Dor, A., Sampas, N., Lipson, D., et al. (2004) Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA. Proc Natl Acad Sci USA 101, 17765-70. (Pubitemid 40051961)
21. Pokholok, D. K., Harbison, C. T., Levine, S., Cole, M., Hannett, N. M., et al. (2005) Genome-wide map of nucleosome acetylation and methylation in yeast. Cell 122, 517-27. (Pubitemid 41191151)
22. Nielsen, H. B., and Knudsen, S. (2002) Avoiding cross hybridization by choosing nonredundant targets on cDNA arrays. Bioinformatics 18, 321-2. (Pubitemid 34183111)
23. Taylor, E., Cogdell, D., Coombes, K., Hu, L., Ramdas, L., et al. (2001) Sequence verifi cation as quality-control step for production of cDNA microarrays. Biotechniques 31, 62-5. (Pubitemid 32645911)
24. Hager, J. (2006) Making and using spotted DNA microarrays in an academic core laboratory. Methods Enzymol 410, 135-68. (Pubitemid 44287004)
25. Veer, L. J., and De Jong, D. (2002) The microarray way to tailored cancer treatment. Nat Med 8, 13-4. (Pubitemid 34101712)
26. VanGuilder, H. D., Vrana, K. E., and Freeman, W. M. (2008) Twenty-fi ve years of quantitative PCR for gene expression analysis. Biotechniques 44, 619-26. (Pubitemid 351656280)
27. Udvardi, M. K., Czechowski, T., and Scheible, W. R. (2008) Eleven golden rules of quantitative RT-PCR. Plant Cell 20, 1736-7. (Pubitemid 352844528)
28. Logan, J., Edwards, K., and Saunders, N. (2009) Real-Time PCR: Currnet Technology and Applications, Caister Academic Press, Norwich, UK.
29. Van Gelder, R. N., von Zastrow, M. E., Yool, A., Dement, W. C., Barchas, J. D., et al. (1990) Amplifi ed RNA synthesized from limited quantities of heterogeneous cDNA. Proc Natl Acad Sci USA 87, 1663-7.
30. Lee, N. H., and Saeed, A. I. (2007) Microarrays: an overview. Methods Mol Biol 353, 265-300. (Pubitemid 350183282)
31. Gorreta, F., Barzaghi, D., VanMeter, A. J., Chandhoke, V., and Del Giacco, L. (2004) Development of a new reference standard for microarray experiments. Biotechniques 36, 1002-9. (Pubitemid 38747364)
32. Kim, H., Zhao, B., Snesrud, E. C., Haas, B. J., Town, C. D., et al. (2002) Use of RNA and genomic DNA references for inferred comparisons in DNA microarray analyses. Biotechniques 33, 924-30. (Pubitemid 35168078)
33. Sterrenburg, E., Turk, R., Boer, J. M., van Ommen, G. B., and den Dunnen, J. T. (2002) A common reference for cDNA microarray hybridizations. Nucleic Acids Res 30, e116.
34. Li, C., Li, M., Long, J. R., Cai, Q., and Zheng, W. (2008) Evaluating cost effi ciency of SNP chips in genome-wide association studies. Genet Epidemiol 32, 387-95.
35. Li, M., Li, C., and Guan, W. (2008) Evaluation of coverage variation of SNP chips for genomewide association studies. Eur J Hum Genet 16, 635-43. (Pubitemid 351594131)
36. Barrett, J. C., and Cardon, L. R. (2006) Evaluating coverage of genome-wide association studies. Nat Genet 38, 659-62. (Pubitemid 43927307)
37. Baumbusch, L. O., Aaroe, J., Johansen, F. E., Hicks, J., Sun, H., et al. (2008) Comparison of the Agilent, ROMA/NimbleGen and Illumina platforms for classifi cation of copy number alterations in human breast tumors. BMC Genomics 9, 379.
38. Brennan, C., Zhang, Y., Leo, C., Feng, B., Cauwels, C., et al. (2004) High-resolution global profi ling of genomic alterations with long oligonucleotide microarray. Cancer Res 64, 4744-8. (Pubitemid 38924516)
39. Ylstra, B., van den Ijssel, P., Carvalho, B., Brakenhoff, R. H., and Meijer, G. A. (2006) BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH). Nucleic Acids Res 34, 445-50. (Pubitemid 43240234)
40. Dong, L. M., Brennan, P., Karami, S., Hung, R. J., Menashe, I., et al. (2009) An analysis of growth, differentiation and apoptosis genes with risk of renal cancer. PLoS One 4, e4895.
41. Hornberger, J., Cosler, L. E., and Lyman, G. H. (2005) Economic analysis of targeting chemotherapy using a 21-gene RT-PCR assay in lymph-node-negative, estrogen-receptor-positive, early-stage breast cancer. Am J Manag Care 11, 313-24. (Pubitemid 40646936)
42. Habel, L. A., Shak, S., Jacobs, M. K., Capra, A., Alexander, C., et al. (2006) A populationbased study of tumor gene expression and risk of breast cancer death among lymph node-negative patients. Breast Cancer Res 8, R25.
43. Paik, S., Shak, S., Tang, G., Kim, C., Baker, J., et al. (2004) A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. N Engl J Med 351, 2817-26. (Pubitemid 40051905)
44. Paik, S., Tang, G., Shak, S., Kim, C., Baker, J., et al. (2006) Gene expression and benefi t of chemotherapy in women with node-negative, estrogen receptor-positive breast cancer. J Clin Oncol 24, 3726-34. (Pubitemid 46622311)
45. Buyse, M., Loi, S., Veer, L., Viale, G., Delorenzi, M., et al. (2006) Validation and clinical utility of a 70-gene prognostic signature for women with node-negative breast cancer. J Natl Cancer Inst 98, 1183-92. (Pubitemid 44390989)
46. Glas, A. M., Floore, A., Delahaye, L. J., Witteveen, A. T., Pover, R. C., et al. (2006) Converting a breast cancer microarray signature into a high-throughput diagnostic test. BMC Genomics 7, 278.
47. van de Vijver, M. J., He, Y. D., Veer, L. J., Dai, H., Hart, A. A., et al. (2002) A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med 347, 1999-2009. (Pubitemid 35461656)
48. Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G., Spellman, P., et al. (2001) Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 29, 365-71. (Pubitemid 34326681)
49. Shi, L., Tong, W., Su, Z., Han, T., Han, J., et al. (2005) Microarray scanner calibration curves: characteristics and implications. BMC Bioinformatics 6 Suppl 2, S11.
50. Shi, L., Reid, L. H., Jones, W. D., Shippy, R., Warrington, J. A., et al. (2006) The MicroArray Quality Control (MAQC) project shows interand intraplatform reproducibility of gene expression measurements. Nat Biotechnol 24, 1151-61. (Pubitemid 44359727)
51. Shi, L., Tong, W., Fang, H., Scherf, U., Han, J., et al. (2005) Cross-platform comparability of microarray technology: intra-platform consistency and appropriate data analysis procedures are essential. BMC Bioinformatics 6 Suppl 2, S12.
52. Patterson, T. A., Lobenhofer, E. K., Fulmer-Smentek, S. B., Collins, P. J., Chu, T. M., et al. (2006) Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project. Nat Biotechnol 24, 1140-50. (Pubitemid 44359726)
53. Goodsaid, F., and Frueh, F. W. (2007) Implementing the U.S. FDA guidance on pharmacogenomic data submissions. Environ Mol Mutagen 48, 354-8. (Pubitemid 47011763)
54. Lee, C., and Roy, M. (2004) Analysis of alternative splicing with microarrays: successes and challenges. Genome Biol 5, 231.
55. Tang, F., Hajkova, P., Barton, S. C., Lao, K., and Surani, M. A. (2006) MicroRNA expression profi ling of single whole embryonic stem cells. Nucleic Acids Res 34, e9.
56. Tang, F., Hajkova, P., Barton, S. C., O'Carroll, D., Lee, C., et al. (2006) 220-plex microRNA expression profi le of a single cell. Nat Protoc 1, 1154-9.
57. Cummins, J. M., He, Y., Leary, R. J., Pagliarini, R., Diaz, L. A., Jr., et al. (2006) The colorectal microRNAome. Proc Natl Acad Sci USA 103, 3687-92. (Pubitemid 43376616)
58. Kathiresan, S., Voight, B. F., Purcell, S., Musunuru, K., Ardissino, D., et al. (2009) Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants. Nat Genet 41, 334-41.
59. Zheng, W., Long, J., Gao, Y. T., Li, C., Zheng, Y., et al. (2009) Genome-wide association study identifi es a new breast cancer susceptibility locus at 6q25.1. Nat Genet 41, 324-8.
60. Collas, P., and Dahl, J. A. (2008) Chop it, ChIP it, check it: the current status of chromatin immunoprecipitation. Front Biosci 13, 929-43. (Pubitemid 351594738)
61. Imbeaud, S., and Auffray, C. (2005) 'The 39 steps' in gene expression profi ling: critical issues and proposed best practices for microarray experiments. Drug Discov Today 10, 1175-82. (Pubitemid 41327774)