Comparison of phenol-based and alternative RNA isolation methods for gene expression analyses

The widespread use of gene expressionanalyses has been limited by the lack of critical evaluations of the methods used to extract nucleic acids from human tissues. For evaluating gene expressionpatterns in whole blood or leukocytes, the method of RNA isolation needs to be considered as a critical variablein the design of the experiments. Quantitative real-time PCR (qPCR) is widely used for the quantification of gene expressionin today's clinical prac- tice. Blood samples as a preferred RNA source for qPCR should be carefully handled and prepared in order not to inhibit gene expressionanalyses. The pre- sent study was designed to compare the frequently employed guanidine thio- cyanate-phenol-chloroform-based method (TRI Reagent ® ) with two alterna- tive RNA isolation methods (6100 PrepStation and QIAamp ® ) from whole blood or leukocytes for the purpose of gene expressionanalysis in chronic myeloid leukemia (CML) patients. Based on the results of this study, for the best combination of yield and RNA extractionpurity, taking into account the necessary amount of the clinical sample and performance time, the protocol using phenol-based TRI Reagent ® for RNA extractionfrom leukocytes is suggested as the most suitable protocol for this specific gene expressionana- lysis.