title: 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.
abstract: 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 are often the only tissue available for genetic analysis; FFPE tissues are also needed to study the intratumoral heterogeneity that characterizes these neoplasms. In this paper, we present a combination of evaluations and technical advances that provide strong support for the ready use of oligonucleotide aCGH on FFPE diffuse gliomas. We first compared aCGH using bacterial artificial chromosome (BAC) arrays in 45 paired frozen and FFPE gliomas, and demonstrate a high concordance rate between FFPE and frozen DNA in an individual clone-level analysis of sensitivity and specificity, assuring that under certain array conditions, frozen and FFPE DNA can perform nearly identically. However, because oligonucleotide arrays offer advantages to BAC arrays in genomic coverage and practical availability, we next developed a method of labeling DNA from FFPE tissue that allows efficient hybridization to oligonucleotide arrays. To demonstrate utility in FFPE tissues, we applied this approach to biphasic anaplastic oligoastrocytomas and demonstrate CNA differences between DNA obtained from the two components. Therefore, BAC and oligonucleotide aCGH can be sensitive and specific tools for detecting CNAs in FFPE DNA, and novel labeling techniques enable the routine use of oligonucleotide arrays for FFPE DNA. In combination, these advances should facilitate genome-wide analysis of rare, small and/or histologically heterogeneous gliomas from FFPE tissues.
authors.affiliation: Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. gmohapatra@partners.org
authors.forename: Gayatry
authors.initials: G
authors.lastname: Mohapatra
authors.forename: David A
authors.initials: DA
authors.lastname: Engler
authors.forename: Kristen D
authors.initials: KD
authors.lastname: Starbuck
authors.forename: James C
authors.initials: JC
authors.lastname: Kim
authors.forename: Derek C
authors.initials: DC
authors.lastname: Bernay
authors.forename: George A
authors.initials: GA
authors.lastname: Scangas
authors.forename: Audrey
authors.initials: A
authors.lastname: Rousseau
authors.forename: Tracy T
authors.initials: TT
authors.lastname: Batchelor
authors.forename: Rebecca A
authors.initials: RA
authors.lastname: Betensky
authors.forename: David N
authors.initials: DN
authors.lastname: Louis
mesh_terms: D045744:Cell Line, Tumor; D022202:Chromosomes, Artificial, Bacterial; D055028:Comparative Genomic Hybridization / Q000379:methods; D005404:Fixatives / Q000494:pharmacology*; D005557:Formaldehyde / Q000494:pharmacology*; D005629:Frozen Sections / Q000379:methods; D055106:Genome-Wide Association Study / Q000379:methods*; D005910:Glioma / Q000235:genetics* / Q000473:pathology; D006801:Humans; D009837:Oligodendroglioma / Q000235:genetics / Q000378:metabolism; D016612:Paraffin Embedding / Q000379:methods*; D012680:Sensitivity and Specificity
chemical_list: D005404:Fixatives; D005557:Formaldehyde