Abstract 1148: Array comparative genomic hybridization of diffuse intrinsic pontine glioma samples obtained from formalin fixed paraffin embedded autopsy specimens

Abstract

Abstract We have recently optimized the method of formalin fixed paraffin embedded (FFPE) tissue processing for high resolution array comparative genomic hybridization (aCGH). This will facilitate the copy number assessment of number archival clinical surgical pathology specimens as well as biopsies with debated utility. Molecular characterization of archival specimens can potentially clarify the biology of diseases with unclear etiology and poor prognosis such as diffuse intrinsic pontine glioma (DIPG). In the case of DIPG, which is seldom biopsied, at present autopsy samples provide the only practical approach to studying this disorder. Here we performed aCGH on FFPE autopsy specimens obtained from children with DIPG. DNA was extracted from FFPE blocks obtained from autopsy on 14 pediatric DIPG patients using a modified Qiagen DNeasy kit. Non-enzymatic Universal Linkage System (ULS) chemical labeling was used to directly couple fluorescent dyes with the sample and reference DNAs (1ug each), which were then hybridized to 105k oligonucleotide CGH microarrays (Agilent). Arrays were scanned and data analyzed in Nexus Copy Number software. Twenty-one samples from 14 subjects were available for the study from which CGH was successfully performed on 18 samples representing 12 patients. All samples demonstrated DNA aberrations. Frequent DNA copy number changes included gain of 1q, 7p, and loss of 10q. High copy number amplification of known oncogenes was observed, including PDGFRA, EGFR, CCND1, and MYCN. Homozygous deletions of known tumor suppressor genes included PTEN and CDKN2A. Our tissue processing method demonstrates the feasibility of successfully using DNA derived from FFPE autopsy material for aCGH. The pediatric DIPG sample set was highly informative with the majority of specimens showing at least 1 abnormality related to a known cancer gene. Significant heterogeneity among DIPG patients as well as aberrations in candidate drug targets (KIT and EGFR) were observed. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1148.