Abstract
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.
Highlights
The challenges associated with DNA derived from formalin-fixed, paraffin-embedded (FFPE) samples have prevented widespread application of FFPE DNA to many of the technologies available for high-quality DNA, some options with lower genomic coverage are available [1,2,3]
We show the feasibility and limitations of a genome-wide assessment of genotype, loss of heterozygosity (LOH), and copy number using FFPE DNA on the Affymetrix Mapping 500K array set, which includes the Mapping 250K Nsp Array and the Mapping 250K Sty Array (Santa Clara, CA)
These results show that FFPE DNA can be suitable for a combined study of genotype, LOH, and copy number on a whole-genome scale
Summary
The challenges associated with DNA derived from formalin-fixed, paraffin-embedded (FFPE) samples have prevented widespread application of FFPE DNA to many of the technologies available for high-quality DNA, some options with lower genomic coverage are available [1,2,3]. We show the feasibility and limitations of a genome-wide assessment of genotype, loss of heterozygosity (LOH), and copy number using FFPE DNA on the Affymetrix Mapping 500K array set, which includes the Mapping 250K Nsp Array and the Mapping 250K Sty Array (Santa Clara, CA). These arrays use a process termed whole-genome sampling analysis A subset of digested fragments are PCR amplified in a complexity reduction step before hybridization to the arrays. PCR proved to be the critical step when processing FFPE samples. Note: Supplementary data for this article are available at Cancer Research Online (http://cancerres.aacrjournals.org/)
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