%0 Journal Article
%T Biomarker discovery for colon cancer using a 761 gene RT-PCR assay
%A Kim M Clark-Langone
%A Jenny Y Wu
%A Chithra Sangli
%A Angela Chen
%A James L Snable
%A Anhthu Nguyen
%A James R Hackett
%A Joffre Baker
%A Greg Yothers
%A Chungyeul Kim
%A Maureen T Cronin
%J BMC Genomics
%D 2007
%I BioMed Central
%R 10.1186/1471-2164-8-279
%X RNA was extracted from formalin fixed paraffin embedded (FPE) tissue, as old as 28 years, from 354 patients enrolled in NSABP C-01 and C-02 colon cancer studies. Multiplexed reverse transcription reactions were performed using a gene specific primer pool containing 761 unique primers. PCR was performed as independent TaqMan£¿ reactions for each candidate gene. Hierarchal clustering demonstrates that genes expected to co-express form obvious, distinct and in certain cases very tightly correlated clusters, validating the reliability of this technical approach to biomarker discovery.We have developed a high throughput, quantitatively precise multi-analyte gene expression platform for biomarker discovery that approaches low density DNA arrays in numbers of genes analyzed while maintaining the high specificity, sensitivity and reproducibility that are characteristics of RT-PCR. Biomarkers discovered using this approach can be transferred to a clinical reference laboratory setting without having to re-validate the assay on a second technology platform.Over the last decade, many studies have applied gene expression analysis to identify biomarkers for prognostic and/or predictive information in relation to human disease [1-4]. RNA for these studies has come from either frozen or formalin fixed paraffin embedded (FPE) tissue. RNA from frozen tissues is generally regarded as the most desirable for molecular assays, since if collected correctly it is generally intact and can be analyzed by a wide variety of standard molecular biology techniques. However, FPE tissue is the most widely available source of tumor tissue as it is the product of standard tissue processing procedures followed by surgical pathology laboratories. It is clear that RNA obtained from FPE tissue is not full length and the extent of degradation increases with storage time [5]. Therefore, it is generally considered to be challenging to extract RNA from archival FPE tissue for analysis by standard molecular bi
%U http://www.biomedcentral.com/1471-2164/8/279