Whole-genome gene expression profiling of formalin-fixed, paraffin-embedded tissue samples.

ABSTRACT:

Background

We have developed a gene expression assay (Whole-Genome DASL), capable of generating whole-genome gene expression profiles from degraded samples such as formalin-fixed, paraffin-embedded (FFPE) specimens.

Methodology/principal findings

We demonstrated a similar level of sensitivity in gene detection between matched fresh-frozen (FF) and FFPE samples, with the number and overlap of probes detected in the FFPE samples being approximately 88% and 95% of that in the corresponding FF samples, respectively; 74% of the differentially expressed probes overlapped between the FF and FFPE pairs. The WG-DASL assay is also able to detect 1.3-1.5 and 1.5-2 -fold changes in intact and FFPE samples, respectively. The dynamic range for the assay is approximately 3 logs. Comparing

SUBMITTER: April C 

PROVIDER: S-EPMC2780295 | biostudies-literature | 2009 Dec

REPOSITORIES: biostudies-literature