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

Author(s): April C, Klotzle B, Royce T, Wickham-Garcia E, Boyaniwsky T, Izzo J, Cox D, Jones W, Rubio R, Holton K, Matulonis U, Quackenbush J, Fan JB

Publication: PLoS One, 2009, Vol. 4, Page e8162

PubMed ID: 19997620 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   The purpose of this study was to compare DASL analysis of FF and FFPE tissue and determine the effects of template quantity on DASL analysis. Lung tumor and normal adjacent tissue blocks were stored for 3 years, and ovarian tumor blocks were stored 8-13 years.

   Summary of Findings:

   Approximately 90% of probes that hybridized in FF lung tissues were also detected in the corresponding FFPE lung tissue with a correlation of 0.62. The fold change between normal adjacent and tumor tissue was greater in FF lung specimens than in FFPE specimens. There were 4793 differentially expressed genes identified in both FFPE and FF tissue, 9948 transcripts identified as differentially expressed only in FF lungs, and 1680 identified only in FFPE lungs. When as little as 5 ng template RNA from FFPE tissue was used, more than 85% of the probes that hybridized with 200 ng template FFPE RNA were detected. When less template was used, the number of probes that hybridized decreased; however, 1 ng still yielded comparable results to 200 ng (r2= 0.75).

   Biospecimens

   • Tissue - Lung

   Preservative Types

   • Formalin
   • Frozen

   Diagnoses:

   • Neoplastic - Carcinoma
   • Neoplastic - Normal Adjacent

   Platform:

   Analyte	Technology Platform
   RNA	DASL

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Biospecimen Preservation	Type of fixation/preservation	Formalin (buffered) Frozen
   DASL Specific	Template/input amount	200 ng 50 ng 10 ng 5 ng 1 ng 250 pg

   View more