Abstract 3073: Isothermal whole genome amplification of FFPE samples to detect copy number changes in the progression from colonic adenoma to carcinoma

Abstract

Abstract Screening tumor genomes for somatic aberrations by aCGH is a commonly used high-resolution tool used both in research and clinical diagnostics. Unfortunately, the full utility of this technique is compromised with formalin fixed paraffin embedded (FFPE) tissue samples due to their inherently high degree of DNA degradation and the presence of DNA adducts acquired during the fixation and storage process. DNA degradation tends to worsen with storage time, making the analysis of archived samples even more challenging. We have developed a highly sensitive and robust whole genome amplification system for FFPE tumor samples that takes advantage of the proprietary Single Primer Isothermal Amplification (SPIA®) technology. The system uses 100 ng of routinely isolated FFPE DNA and produces 3-5 µg of DNA suitable for multiple downstream applications such as aCGH, enrichment strategies, and next generation sequencing (NGS). We evaluated the performance of the amplification system in the context of identifying aberrations by aCGH. Data will be presented that highlights the performance of the SPIA amplified material benchmarked against its unamplified counterpart along with the system's effectiveness on an array of sample qualities ranging from highly degraded FFPE DNA to highly intact FFPE DNA samples. Lastly, we employed the amplification system to examine the progression from adenoma to carcinoma using FFPE samples from human colon carcinomas within high-grade adenomas. Colonic epithelia gains numerous genetic alterations when degraded to dysplastic adenoma and then to cancer. While genetic alterations for each entity are well known, little data are available for combined lesions. Our results indicate that the SPIA amplified DNA performs equivalently to unamplified FFPE DNA in detecting copy number variations by aCGH, the system is suitable for a broad range of FFPE sample qualities, and is a flexible solution that allows for higher resolution analyses with NGS platforms. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3073. doi:10.1158/1538-7445.AM2011-3073