Research article
Characterization of the effect of sample quality on high density oligonucleotide microarray data using progressively degraded rat liver RNA
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* Corresponding author: Karol L Thompson karol.thompson@fda.hhs.gov
1 Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
2 Affymetrix Inc., Santa Clara, CA, USA
3 Current- Illumina Inc., San Diego, CA, USA
BMC Biotechnology 2007, 7:57 doi:10.1186/1472-6750-7-57
Published: 13 September 2007Abstract
Background
The interpretability of microarray data can be affected by sample quality. To systematically explore how RNA quality affects microarray assay performance, a set of rat liver RNA samples with a progressive change in RNA integrity was generated by thawing frozen tissue or by ex vivo incubation of fresh tissue over a time course.
Results
Incubation of tissue at 37°C for several hours had little effect on RNA integrity, but did induce changes in the transcript levels of stress response genes and immune cell markers. In contrast, thawing of tissue led to a rapid loss of RNA integrity. Probe sets identified as most sensitive to RNA degradation tended to be located more than 1000 nucleotides upstream of their transcription termini, similar to the positioning of control probe sets used to assess sample quality on Affymetrix GeneChip® arrays. Samples with RNA integrity numbers less than or equal to 7 showed a significant increase in false positives relative to undegraded liver RNA and a reduction in the detection of true positives among probe sets most sensitive to sample integrity for in silico modeled changes of 1.5-, 2-, and 4-fold.
Conclusion
Although moderate levels of RNA degradation are tolerated by microarrays with 3'-biased probe selection designs, in this study we identify a threshold beyond which decreased specificity and sensitivity can be observed that closely correlates with average target length. These results highlight the value of annotating microarray data with metrics that capture important aspects of sample quality.