ct of Long - term Storage in TRIzol on Microarray - Based B & P e Expression Profiling

Downlo kground: Although TRIzol is widely used for preservation and isolation of RNA, there is suspicion that ged sample storage in TRIzol may affect array-based gene expression profiling (GEP) through premarmination during reverse transcription. thods: GEP on Illumina arrays compared paired aliquots (cryopreserved or stored in TRIzol) of primary es of multiple myeloma (MM) and acute myeloid leukemia (AML). Data were analyzed at the “probe (a single consensus value) or “bead level” (multiple measurements provided by individual beads). ults: TRIzol storage does not affect standard probe-level comparisons between sample groups: different vation methods did not generate differentially expressed probes (DEP) within MM or AML sample s, or substantially affect the many DEPs distinguishing between these groups. Differences were found e set enrichment analysis, but these were dismissible because of instability with permutation of sample unbalanced restriction to TRIzol aliquots, inconsistency between MM and AML groups, and lack of ical plausibility. Bead-level comparisons found many DEPs within sample pairs, but most (73%) were d changed. There was no consistent evidence that TRIzol causes premature reverse transcription termi. Instead, a subset of DEPs were systematically due to increased signals in TRIzol-preserved samples robes near the 5′ end of transcripts, suggesting better mRNA preservation with TRIzol. clusions: TRIzol preserves RNA quality well, without a deleterious effect on GEP. Samples stored froith and without TRIzol may be compared by GEP with only minor concern for systematic artifacts. zen w Impact: The standard practice of prolonged sample storage in TRIzol is suitable for GEP. Cancer Epidemiol Biomarkers Prev; 19(10); 2445–52. ©2010 AACR.