Abstract
Formalin-fixed, paraffin-embedded (FFPE) tissues represent an invaluable resource for gene expression analysis, as they are the most widely available materials for studies of human disease. However, degradation of RNA during tissue fixation and storage makes FFPE-derived RNAs hard to work with using conventional microarray technology. Most gene expression studies done using FFPE tissues rely on quantitative RT-PCR (qPCR), but this approach has had limited success because of the short cDNA templates available in these samples.
In this chapter, we describe the DASL® (cDNA-mediated annealing, selection, extension, and ligation) Assay, a flexible, sensitive, and reproducible gene expression profiling system for parallel analysis of several hundred mRNA transcripts on the BeadArray™ platform. This technology is especially useful for determining cancer prognosis or therapy response, because it allows not only prospective studies but also retrospective analyses. Using the DASL Assay, gene expression analyses can be performed on routinely stored tumor specimens from patients with known outcomes.
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Acknowledgments
We thank Amir Arsanjani, Monica Kostelec, and Joshua Modder for acquisition and pathological evaluation of FFPE tissue samples; Eliza Wickham Garcia and Jing Chen for technical assistance; Lixin Zhou for help with the assay design; Eugene Chudin for data analysis; Dimitri Talantov for participation in the project; and Yixin Wang, Tracy Down, and David Barker for helpful discussions and advice.
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© 2008 Humana Press, a part of Springer Science+Business Media, LLC
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Bibikova, M., Yeakley, J.M., Wang-Rodriguez, J., Fan, JB. (2008). Quantitative Expression Profiling of RNA from Formalin-Fixed, Paraffin-Embedded Tissues Using Randomly Assembled Bead Arrays. In: Starkey, M., Elaswarapu, R. (eds) Genomics Protocols. Methods in Molecular Biology™, vol 439. Humana Press. https://doi.org/10.1007/978-1-59745-188-8_11
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DOI: https://doi.org/10.1007/978-1-59745-188-8_11
Publisher Name: Humana Press
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