title: Reliable high-throughput genotyping and loss-of-heterozygosity detection in formalin-fixed, paraffin-embedded tumors using single nucleotide polymorphism arrays.
abstract: Most human cancers show genetic instabilities leading to allelic imbalances, including loss of heterozygosity (LOH). Single nucleotide polymorphism (SNP) arrays can be used to detect LOH. Currently, these arrays require intact genomic DNA as obtained from frozen tissue; however, for most cancer cases, only low-quality DNA from formalin-fixed, paraffin-embedded (FFPE) tissue is available. In this study, we tested Illumina BeadArrays to genotype FFPE tissue and detect LOH/allelic imbalances in matched colorectal tumor and normal tissue. Genotypes were compared between leukocyte and FFPE normal tissue as well as between frozen and FFPE tumor tissue. Identical genotypes and LOH profiles were obtained from normal and tumor isolates. LOH was mainly observed on chromosomes 4, 5q, 12q, 14q, 15q, 17p, 18, and 20p, which are commonly detected regions in colorectal cancer. LOH profiles of the BeadArrays were compared with profiles obtained by Affymetrix GeneChip 10K arrays, showing identical LOH patterns. These data show that genome-wide genotyping of FFPE tissue with the BeadArray gives reliable results and is a powerful technique for LOH analysis.
authors.affiliation: Department of Pathology, Leiden University Medical Center, the Netherlands.
authors.forename: Esther H
authors.initials: EH
authors.lastname: Lips
authors.forename: Jan Willem F
authors.initials: JW
authors.lastname: Dierssen
authors.forename: Ronald
authors.initials: R
authors.lastname: van Eijk
authors.forename: Jan
authors.initials: J
authors.lastname: Oosting
authors.forename: Paul H C
authors.initials: PH
authors.lastname: Eilers
authors.forename: Rob A E M
authors.initials: RA
authors.lastname: Tollenaar
authors.forename: Eelco J
authors.initials: EJ
authors.lastname: de Graaf
authors.forename: Ruben
authors.initials: R
authors.lastname: van't Slot
authors.forename: Cisca
authors.initials: C
authors.lastname: Wijmenga
authors.forename: Hans
authors.initials: H
authors.lastname: Morreau
authors.forename: Tom
authors.initials: T
authors.lastname: van Wezel
mesh_terms: D015179:Colorectal Neoplasms / Q000235:genetics* / Q000473:pathology; D004247:DNA / Q000737:chemistry / Q000235:genetics; D004273:DNA, Neoplasm / Q000737:chemistry / Q000235:genetics; D005557:Formaldehyde; D005838:Genotype; D006801:Humans; D007962:Leukocytes / Q000737:chemistry / Q000502:physiology; D019656:Loss of Heterozygosity; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D016612:Paraffin Embedding; D020641:Polymorphism, Single Nucleotide; D016707:Tissue Fixation
chemical_list: D004273:DNA, Neoplasm; D005557:Formaldehyde; D004247:DNA