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10:58
Profiling of Pre-micro RNAs and microRNAs using Quantitative Real-time PCR (qPCR) Arrays
Published on: December 3, 2010
Quantitative expression profiling of RNA from formalin-fixed, paraffin-embedded tissues using randomly assembled bead
Marina Bibikova1, Joanne M Yeakley, Jessica Wang-Rodriguez
1Illumina Inc., San Diego, CA, USA.
Methods in Molecular Biology (Clifton, N.J.)
|March 29, 2008
Summary
The cDNA-mediated annealing, selection, extension, and ligation (DASL) Assay enables gene expression profiling from degraded RNA in formalin-fixed, paraffin-embedded (FFPE) tissues. This method allows for retrospective cancer studies using routinely stored tumor specimens.
Area of Science:
- Molecular Biology
- Genomics
- Biotechnology
Background:
- Formalin-fixed, paraffin-embedded (FFPE) tissues are a valuable resource for studying human diseases due to their widespread availability.
- RNA degradation in FFPE tissues poses challenges for conventional gene expression analysis methods like microarrays.
- Quantitative RT-PCR (qPCR) has shown limited success with FFPE samples due to short cDNA templates.
Purpose of the Study:
- To introduce the cDNA-mediated annealing, selection, extension, and ligation (DASL) Assay for gene expression profiling.
- To highlight the DASL Assay's utility for analyzing degraded RNA from FFPE tissues.
- To demonstrate the application of the DASL Assay for both prospective and retrospective studies, particularly in cancer research.
Main Methods:
- Description of the DASL Assay, a gene expression profiling system.
- Utilizes the BeadArray platform for parallel analysis of hundreds of mRNA transcripts.
- Designed to work with challenging FFPE-derived RNA samples.
Main Results:
- The DASL Assay is presented as a flexible, sensitive, and reproducible method.
- It enables gene expression analysis on routinely stored tumor specimens.
- Facilitates retrospective analyses of patient outcomes and cancer prognosis/therapy response.
Conclusions:
- The DASL Assay overcomes limitations associated with analyzing degraded RNA from FFPE tissues.
- It provides a robust platform for gene expression profiling in cancer research.
- Enables retrospective studies on patient cohorts with known outcomes using archived FFPE samples.
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