title: Glioma test array for use with formalin-fixed, paraffin-embedded tissue: array comparative genomic hybridization correlates with loss of heterozygosity and fluorescence in situ hybridization.
abstract: Array-based comparative genomic hybridization (aCGH) is a powerful, high-throughput tool for whole genome analysis. Until recently, aCGH could only be reproducibly performed on frozen tissue samples and with significant tissue amounts. For brain tumors however, paraffin-embedded tissue blocks from small stereotactic biopsies may be the only tissue routinely available. The development of methods to analyze formalin-fixed, paraffin-embedded (FFPE) material therefore has the potential to impact molecular diagnosis in a significant way. To this end, we constructed a BAC array representing chromosomes 1, 7, 19, and X because 1p/19q deletion and EGFR gene amplification provide clinically relevant information for glioma diagnosis. We also optimized a two-step labeling procedure using an amine-modified nucleotide for generating aCGH probes. Using this approach, we analyzed a series of 28 FFPE oligodendroglial tumors for alterations of chromosomes 1, 7, and 19. We also independently assayed these tumors for 1p/19q deletion by fluorescence in situ hybridization and by loss of heterozygosity analyses. The concordance between aCGH, standard loss of heterozygosity and fluorescence in situ hybridization was nearly 100% for the chromosomes analyzed. These results suggest that aCGH could offer an improved molecular diagnostic approach for gliomas because of its ability to detect clinically relevant molecular alterations in small FFPE specimens.
authors.affiliation: Department of Pathology, Cancer Center and Neurosurgical Service, Massachusetts General Hospital and Harvard Medical School, Boston 02129, USA.
authors.forename: Gayatry
authors.initials: G
authors.lastname: Mohapatra
authors.forename: Rebecca A
authors.initials: RA
authors.lastname: Betensky
authors.forename: Ezra R
authors.initials: ER
authors.lastname: Miller
authors.forename: Bjorn
authors.initials: B
authors.lastname: Carey
authors.forename: Leah D
authors.initials: LD
authors.lastname: Gaumont
authors.forename: David A
authors.initials: DA
authors.lastname: Engler
authors.forename: David N
authors.initials: DN
authors.lastname: Louis
mesh_terms: D003080:Cold Temperature; D004247:DNA / Q000235:genetics; D005260:Female; D005557:Formaldehyde; D016678:Genome / Q000235:genetics*; D005910:Glioma / Q000235:genetics*; D006801:Humans; D017404:In Situ Hybridization, Fluorescence / Q000379:methods*; D019656:Loss of Heterozygosity / Q000235:genetics; D008297:Male; D016612:Paraffin Embedding / Q000379:methods*; D046888:Tissue Array Analysis / Q000379:methods*
chemical_list: D005557:Formaldehyde; D004247:DNA