Application of whole genome tiling arrays to formalin-fixed paraffin embedded tissue: Opening up the archives to cancer gene discovery. E.A. Maher¹, R.R. Selzer², D. Castrillon¹, P.S. Eis². 1) University of Texas Southwestern Medical Center, Dallas, TX; 2) NimbleGen Systems, Inc.
   Study of the human cancer genome has largely been based on DNA extracted from tumor tissue frozen at the time of operative resection. While even in the most committed academic centers, relatively few tumors are saved in accessible tumor banks, thus limiting the potential value of these samples for cancer gene discovery. Historically, archival tissue has been inaccessible to high resolution genomic technologies, including array comparative genomic hybridization (aCGH), since the quality of DNA extracted from formalin-fixed paraffin embedded tissue (FFPE) has been poor. Fragment lengths are generally 50-150 bp, well below minimum length necessary for gene-specific array CGH. However, recent modifications to DNA extraction methods has enabled extraction of long intact fragments of DNA (>15 kb) from FFPE tumors (Maher et al., submitted) providing an opportunity to profile these specimens. Using DNA from FFPE glioblastomas and other solid tumors (archival time ranged from 1-10 years), we performed whole genome analysis using 25 kb-resolution tiling-path aCGH (NimbleGen Systems, Inc.). Full complexity genomic DNA from FFPE was labeled and analyzed in a 2-color format (Cy3/Cy5). The FFPE data were compared to data generated from frozen tumor DNA. No differences were detected among the profiles when examined for signal-to-noise ratios and a series of quality control parameters and, most importantly, detection capability of both large and small copy number alterations was similar for FFPE and frozen tumor DNA. Indeed, in a small number of glioblastomas, the classical amplifications including EGFR, MDM2, CDK4, PDGFRA and classical deletions including p16, PTEN, and RB were easily detected. In addition, many novel focal loci were identified. This study demonstrates the feasibility of using FFPE DNA for high resolution genomic analysis. Applying this technology to archived cancer specimens that have full clinical annotation and are readily available in most pathology departments provides an unprecedented opportunity for comprehensive investigation of the cancer genome.