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Genome-Wide, High-Resolution Detection of Copy Number, Loss of Heterozygosity, and Genotypes from Formalin-Fixed, Paraffin-Embedded Tumor Tissue Using Microarrays

¹ Affymetrix, Inc., Santa Clara, California; ² Victorian Breast Cancer Research Consortium Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia; ³ Department of Pathology, University of Melbourne, Parkville, Victoria, Australia; and Departments of ⁴ Hematology/Oncology and ⁵ Regeneration Medicine for Hematopoiesis, University of Tokyo, Tokyo, Japan

Requests for reprints: Sharoni Jacobs, Affymetrix, Inc., 3420 Central Expressway, Santa Clara, CA 95051. Phone: 408-731-5880; Fax: 408-481-0435; E-mail: sharoni_jacobs{at}affymetrix.com.

Formalin-fixed, paraffin-embedded (FFPE) material tends to yield degraded DNA and is thus suboptimal for use in many downstream applications. We describe an integrated analysis of genotype, loss of heterozygosity (LOH), and copy number for DNA derived from FFPE tissues using oligonucleotide microarrays containing over 500K single nucleotide polymorphisms. A prequalifying PCR test predicted the performance of FFPE DNA on the microarrays better than age of FFPE sample. Although genotyping efficiency and reliability were reduced for FFPE DNA when compared with fresh samples, closer examination revealed methods to improve performance at the expense of variable reduction in resolution. Important steps were also identified that enable equivalent copy number and LOH profiles from paired FFPE and fresh frozen tumor samples. In conclusion, we have shown that the Mapping 500K arrays can be used with FFPE-derived samples to produce genotype, copy number, and LOH predictions, and we provide guidelines and suggestions for application of these samples to this integrated system. [Cancer Res 2007;67(6):2544–51]

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