Prediction of qualitative outcome of oligonucleotide microarray hybridization by measurement of RNA integrity using the 2100 Bioanalyzer capillary electrophoresis system.
RNA quality is critical to achieve valid results in microarray experiments and to save resources. The RNA integrity number (RIN) can be measured with minimal sample consumption by microfluidics-based capillary electrophoresis. To determine whether RIN can predict the qualitative outcome of microarray hybridization, we measured RIN in total RNA samples from 484 different experiments by the 2100 Bioanalyzer system and correlated with the percentage of present calls (%pc) of downstream oligonucleotide microarrays. The correlation coefficient for RNA and %pc in all 408 samples for which the bioanalyzer algorithm was able to produce an RIN was 0.475 (p < 0.05), ranging from 0.039 to 0.673 for different tissue- and assay-type subgroups. Multivariate analysis found RIN to be the best predictor of microarray quality as assessed by %pc, outperforming the 28S to 18S ratio. For a %pc threshold of 25% and 35%, we determined optimal cut points for RIN at 7.15 and 8.05, respectively. Using the suggested cut points, RIN can support the final decision whether a certain RNA sample is appropriate for successful microarray hybridization.
Department of Hematology, Oncology, and Transfusion Medicine, Charité-University Hospital Benjamin Franklin, Hindenburgdamm 30, 12203 Berlin, Germany. philipp.kiewe@charite.de
Philipp
P
Kiewe
Saskia
S
Gueller
Martina
M
Komor
Andrea
A
Stroux
Eckhard
E
Thiel
Wolf-Karsten
WK
Hofmann
D000465:Algorithms; D000818:Animals; D019075:Electrophoresis, Capillary / Q000295:instrumentation / Q000379:methods; D020869:Gene Expression Profiling / Q000295:instrumentation / Q000379:methods; D006801:Humans; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation / Q000379:methods; D012313:RNA / Q000032:analysis* / Q000235:genetics; D020871:RNA Stability; D012372:ROC Curve; D015203:Reproducibility of Results
D012313:RNA