Introduction to miRNA profiling technologies and cross-platform comparison

Methods in Molecular Biology

Volumn 822, Issue , 2012, Pages 19-31

  Aldridge, Sarah ^a   Hadfield, James ^a  

^a CANCER RESEARCH UK CAMBRIDGE RESEARCH INSTITUTE   (United Kingdom)

Author keywords

Comparison; In situ hybridisation; Microarray; MicroRNA; Reverse transcription quantitative PCR; Sequencing

Indexed keywords

MICRORNA;

ANIMAL; ARTICLE; GENE EXPRESSION PROFILING; GENETICS; HUMAN; METHODOLOGY; MICROARRAY ANALYSIS; SEQUENCE ANALYSIS;

ANIMALS; GENE EXPRESSION PROFILING; HUMANS; MICROARRAY ANALYSIS; MICRORNAS; SEQUENCE ANALYSIS, RNA;

EID: 84855964620     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-427-8_2     Document Type: Article

References (59)

1. Volinia, S., Galasso, M., Costinean, S., Tagliavini, L., Gamberoni, G., Drusco, A., et al. (2010). Reprogramming of miRNA networks in cancer and leukemia. Genome Res 20, 589-99.
2. Lin, P-Y., Yu, S-L., and Yang, P-C. (2010). MicroRNA in lung cancer. Br J Cancer 103, 1144-8.
3. Rosenfeld, N., Aharonov, R., Meiri, E., Rosenwald, S., Spector, Y., Zepeniuk, M., et al. (2008). MicroRNAs accurately identify cancer tissue origin. Nat Biotechnol 26, 462-9.
4. Le Quesne, J., and Caldas, C. (2010). Micro- RNAs and breast cancer. Mol Oncol 4, 230-41.
5. Mitchell, P. S., Parkin, R. K., Kroh, E. M., Fritz, B. R., Wyman, S. K., Pogosova- Agadjanyan, E. L., et al. (2008). Circulating microRNAs as stable blood-based markers for cancer detection. Proc Natl Acad Sci USA 105, 10513-18.
6. Kroh, E. M., Parkin, R. K., Mitchell, P. S., and Tewari, M. (2010). Analysis of circulating microRNA biomarkers in plasma and serum using quantitative reverse transcription-PCR (qRT-PCR). Methods 50, 298-301.
7. Liu, R., Zhang, C., Hu, Z., Li, G., Wang, C., Yang, C., et al. (2010). A fi ve-microRNA signature identifi ed from genome-wide serum microRNA expression profi ling serves as a fi ngerprint for gastric cancer diagnosis. Eur J Cancer 47, 784 - 91.
8. Bashir, A. (2010). Designing deep sequencing experiments: detecting structural variation and estimating transcript abundance. BMC Genomics 11, 385-99.
9. Montgomery, S. B, Sammeth, M., Gutierrez- Arcelus, M., Lach, R. P., Ingle, C., Nisbett, J., et al. (2010). Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464, 773-7.
10. Hu, Z., Chen, X., Zhao, Y., Tian, T., Jin, G., Shu, Y., et al. (2010). Serum MicroRNA Signatures Identifi ed in a Genome-Wide Serum MicroRNA Expression Profi ling Predict Survival of Non-Small-Cell Lung Cancer. J Clin Oncol 28, 1721-6.
11. Levin, J. Z., Yassour, M., Adiconis, X., Nusbaum, C., Thompson, D. A., Friedman, N., et al. (2010). Comprehensive comparative analysis of strand-specifi c RNA sequencing methods. Nat Methods 7, 709-15.
12. Baumbusch, L. O., Aarøe, J., Johansen, F. E., Hicks, J., Sun, H., Bruhn, L., 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, 379-401.
13. Curtis, C., Lynch, A. G., Dunning, M. J., Spiteri, I., Marioni, J. C., Hadfi eld, J., et al. (2009). The pitfalls of platform comparison: DNA copy number array technologies assessed. BMC Genomics 10, 588-601.
14. MAQC. (2006). The MicroArray Quality Control ( MAQC ) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 24, 1151-61.
15. Southern, E. M. (1975). Detection of specifi c sequences among DNA fragments separated by gel electrophoresis. J Mol Biol 98, 503-17.
16. Alwine, J. C., Kemp, D. J., and Stark, G. R. (1977). Method for detection of specifi c RNAs in agarose gels by transfer to diazobenzyloxymethyl- paper and hybridization with DNA probes. Proc Natl Acad Sci USA 74, 5350-4.
17. Schena, M., Shalon, D., Davis, R. W., and Brown, P. (1995). Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray Science 270, 467-70
18. Mullis, K. B. (1990). Target amplifi cation for DNA analysis by the polymerase chain reaction. Ann Biol Clin (Paris) 48, 579-82.
19. Sanger, F., and Coulson, A. R. (1975). A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J Mol Biol 94, 441-8.
20. Bentley, D. R., Balasubramanian, S., Swerdlow, H., Smith, G. P., Milton, J. (2008). Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456, 53-9.
21. Margulies, M., Egholm, M., Altman, W. E., Attiya, S., Bader, J. S., Bemben, L. A. et al. (2005). Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376-80.
22. McKernan, K. J., Peckham, H. E., Costa, G. L., McLaughlin, S. F., Fu, Y., Tsung, E. F., et al. (2009). Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res 19, 1527-41.
23. Griffi ths-Jones, S., Saini, H. K., van Dongen, S., and Enright, A. J. (2008). miRBase: tools for microRNA genomics. Nucleic Acids Res 36, D154-8.
24. Chiang, H. R., Schoenfeld, L. W., Ruby, J. G., Auyeung, V. C., Spies, N., Baek, D., et al. (2010). Mammalian microRNAs: experimental evaluation of novel and previously annotated genes. Genes Dev 24, 992-1009.
25. Nelson, P.T., Wang, W-X., Wilfred, B. R., and Tang, G. (2009). Technical variables in highthroughput miRNA expression profi ling: much work remains to be done. Biochim Biophys Acta 1779, 758-65.
26. Ach, R. A, Wang, H., and Curry, B. (2008). Measuring microRNAs: comparisons of microarray and quantitative PCR measurements, and of different total RNA prep methods. BMC Biotechnol 8, 69-85.
27. Campo Dell'Orto, M., Zangrando, A., Trentin, L., Li, R., Liu, W. M., te Kronnie, G., et al. (2007). New data on robustness of gene expression signatures in leukemia: comparison of three distinct total RNA preparation procedures. BMC Genomics 8, 188-203.
28. Debey, S., Schoenbeck, U., and Hellmich, M. (2004). Comparison of different isolation techniques prior gene expression profi ling of blood derived cells: impact on physiological responses, on overall expression and the role of different cell types. Pharmacogenomics 4, 193-207.
29. Git, A., Dvinge, H., Salmon-Divon, M., Osborne, M., Kutter, C., Hadfi eld, J., et al. (2010). Systematic comparison of microarray profi ling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression. RNA 16, 991-1006.
30. Git, A., Spiteri, I., Blenkiron, C., Dunning, M. J., Pole, J. C., Chin, S. F., et al. (2008). PMC42, a breast progenitor cancer cell line, has normal-like mRNA and microRNA transcriptomes. Breast Cancer Res 10, R54.
31. Kim, S. J., Dix, D. J., Thompson, K. E., Murrell, R. N., Schmid, J. E., Gallagher, J. E., et al. (2007). Effects of Storage, RNA Extraction, Genechip Type, and Donor Sex on Gene Expression Profi ling of Human Whole Blood. Clin Chem 53, 1038-45.
32. Fan, H. C., Blumenfeld, Y. J., Chitkara, U., Hudgins, L., and Quake, S. R. (2008). Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood. Proc Natl Acad Sci USA 105, 16266-71.
33. Bustin, S. A., Benes, V., Garson, J. A., Hellemans, J., Huggett, J., Kubista, M., et al. (2009). The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments. Clin Chem 55, 611-22.
34. Heid, C. A., Stevens, J., Livak, K. J., Williams, P. M. (1996). Real time quantitative PCR. Genome Res 6, 986-94.
35. Chen, C., Ridzon, D. A., Broomer, A J., Zhou, Z., Lee, D. H., Nguyen, J. T., et al. (2005). Real-time quantifi cation of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 33, e179-88.
36. Schmittgen, T. D., Lee, E. J., Jiang, J., Sarkar, A., Yang, L., Elton, T. S., et al. (2008). Realtime PCR quantifi cation of precursor and mature microRNA. Methods 44, 31-8.
37. Schneeberger, C., Speiser, P., Kury, F., and Zeillinger, R. (1995). Quantitative detection of reverse transcriptase-PCR products by means of a novel and sensitive DNA stain. PCR Methods Appl 4, 234-8.
38. Shi, R., and Chiang, V. (2005). Facile means for quantifying microRNA expression by realtime PCR. Biotechniques 39, 519-25.
39. Morrison, T., Hurley, J., Garcia, J., Yoder, K., Katz, A., Roberts, D., et al. (2006). Nanoliter high throughput quantitative PCR. Nucleic Acids Res 34, e123-31.
40. Spurgeon, S. L., Jones, R. C., and Ramakrishnan, R. (2008). High throughput gene expression measurement with real time PCR in a microfl uidic dynamic array. PLoS One 3, 1662-9.
41. Kloosterman, W. P., Wienholds, E., Bruijn, E. D., Kauppinen, S., Plasterk, R. H. A. (2006). In situ detection of miRNAs in animal embryos using LNA-modifi ed oligonucleotide probes. Nat Methods 3, 2005-7.
42. Válóczi, A., Hornyik, C., Varga, N., Burgyán, J., Kauppinen, S., Havelda, Z. (2004). Sensitive and specifi c detection of microRNAs by northern blot analysis using LNA-modifi ed oligonucleotide probes. Nucleic Acids Res 32, e175-82.
43. Wienholds, E., Kloosterman, W. P., Miska, E., Alvarez-Saavedra, E., Berezikov, E., de Bruijn, E., et al. (2005). MicroRNA expression in zebrafi sh embryonic development. Science 309, 310-1.
44. Thomsen, R., Nielsen, P. S., Jensen, T. H. (2005). Dramatically improved RNA in situ hybridization signals using LNA-modifi ed probes. RNA 11, 1745-8.
45. Obernosterer, G., Martinez, J., Alenius, M. (2007). Locked nucleic acid-based in situ detection of microRNAs in mouse tissue sections. Nat Protoc 2, 1508-14.
46. Liu, C. G., Calin, G. A., Meloon, B., Gamliel, N., Sevignani, C., and Ferracin, M., et al. (2004). An oligonucleotide microchip for genome-wide microRNA profi ling in human and mouse tissues. Proc Natl Acad Sci USA 101, 9740-4.
47. Ruby, J. G., Jan, C., Player, C., Axtell, M. J., Lee, W., and Nusbaum, C., et al. (2006). Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 127, 1193-207.
48. Hafner, M., Landgraf, P., Ludwig, J., Rice, A., Ojo, T., Lin, C., et al. (2008). Identifi cation of microRNAs and other small regulatory RNAs using cDNA library sequencing. Methods 44, 3-12.
49. Linsen, S. E., de Wit, E., Janssens, G., Heater, S., Chapman, L., Parkin, R. K., et al. (2009). Limitations and possibilities of small RNA digital gene expression profi ling. Nat Methods 6, 474-6.
50. Tian, G., Yin, X., Luo, H., Xu, X., Bolund, L., and Zhang, X. (2010). Sequencing bias : comparison of different protocols of MicroRNA library construction. BMC Biotechnol 10, 64-73.
51. Landgraf, P., Rusu, M., Sheridan, R., Sewer, A., Iovino, N., and Aravin, A., et al. (2007). A Mammalian microRNA Expression Atlas Based on Small RNA Library Sequencing. Cell 129, 1401-14.
52. Bradford, J. R., Hey, Y., Yates, T., Li, Y., Pepper, S. D., and Miller, C. J. (2010). A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profi ling. BMC Genomics 11, 282-302.
53. Sah, S., McCall, M., Eveleigh, D., Wilson, M., and Irizarry, R. (2010). Performance evaluation of commercial miRNA expression array platforms. BMC Res Notes 3, 80-6.
54. Baldwin, D. (2009). ABRF microRNA Profi ling: Platform Comparison. www.abrf.org/ResearchGroups/Microarray/Activities/ R7-Baldwin.pdf.
55. Chen, Y., Gelfond, J. A., McManus, L. M., and Shireman PK (2009). Reproducibility of quantitative RT-PCR array in miRNA expression profi ling and comparison with microarray analysis. BMC Genomics 10, 407-17.
56. Dreher, A., Rossing, M., Kaczkowski, B., Nielsen, F. C., and Norrild, B. (2010). Differential expression of cellular microRNAs in HPV-11 transfected cells. An analysis by three different array platforms and qRTPCR. Biochem Biophys Res Commun 403, 357-62.
57. Pradervand, S., Weber, J., Lemoine, F., Consales, F., Paillusson, A., and Dupasquier, M., et al. (2010). Concordance among digital gene expression, microarrays, and qPCR when measuring differential expression of microRNAs. Biotechniques 48, 219-22.
58. Sato, F., Tsuchiya, S., Terasawa K., and Tsujimoto G. (2009). Intra-platform repeatability and inter-platform comparability of microRNA microarray technology. PLoS One 4, 5540-52.
59. Yauk, C., Rowan-Carroll, A., Stead, J., and Williams, A. (2010). Cross-platform analysis of global microRNA expression technologies. BMC Genomics 11, 330-57.