Abstract for presentation at 11th International Congress of Human Genetics

High resolution detection of copy number changes and LOH using the Affymetrix® 500K Mapping SNP Array on formalin-fixed, paraffin-embedded tumor tissue

  • Dr Sharoni Jacobs, Affymetrix, Inc, United States
  • Ms Ella Thompson, Peter MacCallum Cancer Centre, Australia
  • Dr Raji Pillai, Affymetrix, Inc, United States
  • Dr Giulia Kennedy, Affymetrix, Inc, United States
  • Dr Dione Bailey, Affymetrix, Inc, United States
  • Ian Campbell, Peter MacCallum Cancer Centre, Australia

    • Using the Affymetrix GeneChip® Mapping arrays containing up to one hundred thousand SNPs for whole genome, high-resolution detection of copy number, genotype, and loss of heterozygosity (LOH) predictions has been previously shown in many different tumors and disease samples with high quality DNA. In this study, we demonstrate the utility of using the Mapping 500K Arrays to include analysis of DNA derived from formalin-fixed, paraffin-embedded (FFPE) tissues. FFPE material tends to yield degraded DNA and is thus sub-optimal for use in many downstream applications. We have previously demonstrated the ability to use FFPE samples on the 10K array for reliable LOH and genotype assessments (Thompson 2005). We performed the whole genome sampling analysis (WGSA) on DNA derived from FFPE tumors and compared this to the DNA derived from matching fresh frozen tissue to assess the suitability of using archival tissue with this system. In addition, DNA isolated from normal blood was also included for comparison during LOH and copy number analyses. Average call rates for the FFPE samples were reduced as compared to normal samples, but filtering for the SNPs on smaller fragment sizes increased the average call rate to >95%. Furthermore, average concordance rates between FFPE and fresh frozen samples from the same tumor surpassed >99% on the smaller fragment sizes. Copy number and LOH analyses were also highly concordant between the FFPE and fresh frozen tumor samples, indicating the feasibility of a complete analysis of FFPE-derived samples using this platform. Importantly, small regions of copy number change were identified in both the paraffin and fresh frozen samples that could not be discerned using arrays with less resolution. In conclusion, we have shown that the Mapping 500K Array can be applied to FFPE-derived samples for genotype, copy number, and LOH analysis, thereby potentially allowing thousands of archival samples to be studied using this integrated system.

    Conference Organiser - ICMS Pty Ltd