Esther Lips
Dept. Pathology, Leiden University Medical Center, LEIDEN.
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 were obtained from normal and tumor isolates, respectively. LOH profiles were identical between frozen and FFPE tumor tissue and LOH was mainly observed on chromosomes 4, 5q, 12q, 14q, 15q, 17p, 18, 20p, which are commonly detected regions in colorectal cancer. LOH profiles of the BeadArrays were compared to 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.