Copy Number Analysis of Archival FFPE Tumor Samples by Oligo Array CGH

Genomic instability is a classic hallmark of cancer and genetic disorders. Microarray-based comparative genomic hybridization (aCGH) has become the accepted technique for studying DNA sequence copy number alterations. While DNA extracted from freshly frozen tissues is optimal for aCGH analysis, in many cases only formalin-fixed, paraffin-embedded (FFPE) tissue material is available. Because DNA extracted from FFPE tissue is often degraded or damaged, these samples present a significant challenge to label and subsequently analyze. The labeled targets from these samples are often short in length with low specific activity and, as a result, can generate noisy aCGH data. To address this critical issue, we have developed an FFPE labeling protocol for Agilent’s high-performance CGH microarray platform that produces exceptional data quality from a variety of FFPE tissues. This protocol is based on Kreatech’s Universal Linkage System (ULS) technology, a non-enzymatic direct labeling methodology, and can be used with degraded FFPE tissue-derived DNA. This new labeling technology also features a simple, single-tube protocol, reducing cost per sample and experimental time. When used on the Agilent inkjet-printed array platform, DNA from a variety of archived FFPE tumor samples yields precise, robust, and high-quality aCGH data. Introduction In recent years, array-based Comparative Genomic Hybridization (aCGH) has evolved to analyze chromosomal changes at progressively higher resolutions (Barrett et al., 2004). Improvements in array quality and data analysis have encouraged many to reanalyze historical samples. However, challenging samples such as degraded or FFPE tissues have remained inaccessible for aCGH technology. Addressing this issue is critical because FFPE samples represent the largest source of archival biological material available for large retrospective prognostic studies of human cancer. In fact, it is estimated that over 400 million FFPE samples exist to date.