Genome-wide comparison of paired fresh frozen and formalin-fixed paraffin-embedded gliomas by custom BAC and oligonucleotide array comparative genomic hybridization: facilitating analysis of archival gliomas

摘要: Array comparative genomic hybridization (aCGH) is a powerful tool for detecting DNA copy number alterations (CNA). Because diffuse malignant gliomas are often sampled by small biopsies, formalin-fixed paraffin-embedded (FFPE) blocks the only tissue available genetic analysis; FFPE tissues also needed to study intratumoral heterogeneity that characterizes these neoplasms. In this paper, we present combination of evaluations and technical advances provide strong support ready use oligonucleotide aCGH on gliomas. We first compared using bacterial artificial chromosome (BAC) arrays in 45 paired frozen gliomas, demonstrate high concordance rate between an individual clone-level analysis sensitivity specificity, assuring under certain array conditions, can perform nearly identically. However, because offer advantages BAC coverage practical availability, next developed method labeling from allows efficient arrays. To utility tissues, applied approach biphasic anaplastic oligoastrocytomas CNA differences obtained two components. Therefore, be sensitive specific tools CNAs DNA, novel techniques enable routine DNA. combination, should facilitate genome-wide rare, and/or histologically heterogeneous tissues.