A cut-off based approach for gene expression analysis of formalin-fixed and paraffin-embedded tissue samples.
Microarray analysis of formalin-fixed and paraffin-embedded (FFPE) tissue seems to be of importance for the detection of molecular marker sets in prostate cancer (PC). The compromised RNA integrity of FFPE tissue results in a high degree of variability at the probe level of microarray data as shown by degradation plot. We tested methods that reduce the variability by including all probes within 300 nucleotides, within 600 nucleotides, or up to a calculated breakpoint with reference to the 3'-end. Accepted PC pathways such as the Wnt signaling pathway could be observed to be significantly regulated within FFPE microarray datasets. The best representation of PC gene expression, as well as better comparability to meta-analysis and fresh-frozen microarray data, could be obtained with a 600-nucleotide cutoff. Beyond the specific impact for PC microarray data analysis we propose a cutoff of 600 nucleotides for samples for which the integrity of the RNA cannot be guaranteed.
Srivastava
Prashant K
PK
Department of Cellular and Molecular Pathology, German Cancer Research Center, D-69120 Heidelberg, Germany.
Küffer
Stefan
S
Brors
Benedikt
B
Shahi
Priyanka
P
Li
Li
L
Kenzelmann
Marc
M
Gretz
Norbert
N
Gröne
Hermann-Josef
HJ
D000704:Analysis of Variance; D005404:Fixatives / Q000737:chemistry; D005557:Formaldehyde / Q000737:chemistry; D020869:Gene Expression Profiling / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008297:Male; D016612:Paraffin Embedding; D011471:Prostatic Neoplasms / Q000235:genetics*; D020871:RNA Stability; D012333:RNA, Messenger / Q000032:analysis* / Q000737:chemistry / Q000302:isolation & purification; D015398:Signal Transduction / Q000235:genetics; D051153:Wnt Proteins / Q000235:genetics
D005404:Fixatives; D012333:RNA, Messenger; D051153:Wnt Proteins; D005557:Formaldehyde