Level of Agreement between Paired Paraffin and Frozen Renal Tumor Samples on SNP Microarray
Selene Koo, Agata Minor, Poluru Reddy, Tatjana Antic, Loren Joseph, Carrie Fitzpatrick, Maria Tretiakova. University of Chicago, Chicago, IL
Background: Copy number alterations occur in many solid tumors including renal cell carcinomas (RCC), which can be classified due to distinctive chromosomal abnormalities. Single nucleotide polymorphism (SNP) microarrays may be useful for RCC characterization, as they provide whole-genome copy number data at higher resolution and can detect copy number-neutral loss of heterozygosity (LOH). While there have been advances in utilizing SNP microarrays in formalin-fixed paraffin-embedded (FFPE) tissue, few comparisons between results from FFPE tissue and fresh-frozen (FF) tissue have been made, and none of those studies investigated paired RCC samples.
Design: Paired, morphologically matched FF and FFPE tumor tissues were obtained from five RCC specimens, including clear cell, papillary, and chromophobe subtypes. Genomic DNA was quantitated using Picogreen, assessed for integrity using gel electrophoresis, and processed according to the standard protocol for Affymetrix Genome-Wide Human SNP Array 6.0. Acquired data were analyzed for copy number changes (CNC) and LOH using the Affymetrix Chromosome Analysis Suite.
Results: Following previously published optimization steps for FFPE samples, including increased amount of starting DNA, number of PCR cycles and DNase fragmentation time, CNC and LOH were compared for FFPE and matched FF samples. Results are summarized in the table.
|Identified in both FFPE and FF||Identified in FFPE, not FF||Identified in FF, not FFPE||% agreement|
|Normal copy number||85||0||2||98%|
|Whole/partial chromosome gain/loss||9||4||7||45%|