A Tumor-Targeted DNA Extraction Method for Array CGH Analysis of HER2 Gene Copy Number Status in Newly Diagnosed Breast Cancer
RS Robetorye, SR Gunn, I Yeh. University of Texas Health Science Center at San Antonio, San Antonio, TX; Combimatrix Molecular Diagnostics, Ir, CA
Background: Array-based comparative genomic hybridization (array CGH) is currently actively being evaluated as a clinical tool for the rapid and accurate evaluation of HER2 gene copy number status in newly diagnosed breast cancer. However, currently validated array CGH assays require tumor-targeted high molecular weight (HMW) DNA extraction from fresh or frozen breast tumor tissue. While tumor-targeted DNA extraction insures that the tumor genome is evaluated by array CGH, visualization of the tumor by H&E staining of tissue prior to DNA extraction necessitates transport media that preserves both tissue architecture as well as DNA quality.
Design: Twenty frozen breast cancer samples previously evaluated for HER2 status by array CGH [HER2 positive (n=10)] and [HER2 negative (n=10)] were thawed and stored for at least 48 hours in RNAlater (Applied Biosystems, Foster City, CA). Samples were re-frozen and sectioned for H&E staining followed by tumor-targeted DNA extraction for array CGH analysis. Results from the RNAlater processed samples were compared to results obtained from non-processed samples.
Results: In all cases, high-quality HMW DNA was obtained for array CGH analysis and HER2 copy number was concordant with previously determined HER2 copy number results.
Conclusions: Fresh and/or frozen tissue from newly diagnosed breast cancer can be obtained at the time of surgery and preserved for future tumor-targeted DNA extraction and array CGH evaluation of HER2 gene copy number status. This analysis algorithm makes it possible to store and/or ship samples for 48 hours or more before subsequent histological examination and array CGH analysis is performed.
Wednesday, March 11, 2009 1:00 PM
Poster Session VI # 232, Wednesday Afternoon