Abstract 4534: Large-scale DNA copy number analysis as a biomarker study in the ACTS-CC trial (TRICC0706), a phase III trial of adjuvant chemotherapy with S-1 and UFT/LV in stage III colon cancer in Japan
Authors: Toshiaki Ishikawa, Hiroyuki Uetake, Shigeyuki Matsui, Megumi Ishiguro, Takashi Kobunai, Kenichi Sugihara
Journal: Cancer Research (2012)

Abstract Background: The ACTS-CC trial is a phase III study designed to validate the non-inferiority of S-1 to UFT/LV, a standard treatment in Japan, as adjuvant chemotherapy for stage III colon cancer. The initial safety results were reported at ASCO 2011. In a biomarker study of the ACTS-CC trial, DNA copy number was studied using formalin fixed, paraffin-embedded (FFPE) specimens. Methods: Blocks of resected tumor specimens for this biomarker study were obtained after receiving informed consent from 779 of 1535 patients enrolled between April 2009 and January 2010. Laser-captured microdissection was performed to extract genomic DNA (gDNA) from 10-αm-thick FFPE specimens of colon cancer. DNA concentrations were measured by spectrophotometry (NanoDrop, Thermo Fisher Scientific Inc., Wilmington, DE). DNA quality was assessed and classified into 4 grades according to DNA fragment length by arbitrary primed PCR (AP-PCR) followed by microfluidic analysis (Bioanalyzer: Agilent Technology, Santa Clara, CA): grade-a, β700 bp; grade-b, &amp;lt;700 bp and β400 bp; grade-c, &amp;lt;400 bp and β200 bp; and grade-d, &amp;lt;200 bp. Genomic copy-number alterations in cancer were analyzed by high-density single-nucleotide polymorphism (SNP) arrays (Human 250K StyI array, Affymetrix, Santa Clara, CA) using samples of grade-a or grade-b quality. For GeneChip arrays, 250 ng of DNA was used according to the manufacturer's protocols. Results: Initial DNA amount was sufficient for GeneChip assays in 647 of 779 samples. DNA quality assessment after AP-PCR revealed that the proportions of grade-a, grade-b, grade-c, and grade-d samples were 25.3%, 48.9%, 18.9%, and 6.9%, respectively. Samples of grade-a or grade-b DNA quality were used for target preparation. After complexity reduction by restricted enzymatic digestion followed by adaptor ligation, PCR amplification, and DNA purification, 162 of 647 purified PCR products were successfully amplified to 90 μg, sufficient for target hybridization. Throughout these stepwise processes, 162 of 779 samples were successfully analyzed by GeneChip. Somatic copy-number alterations of stage III colon cancer will be further investigated. Conclusions: Genome-wide copy number was successfully analyzed for only 21% of initial samples. However, this pre-planned study was designed to identify valid biomarkers. Not only 162 carefully selected genome-wide datasets to screen candidate loci associated with clinical outcomes, but also 617 genomic DNA samples usable as independent validation sets for real-time PCR-based assay were obtained. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4534. doi:1538-7445.AM2012-4534