Optimizations of DNA isolation and copy number analysis identifies regions of genomic gain/loss in early breast cancer. Homo sapiens

DNA copy number changes with or without accompanying copy neutral changes such as unparental disomy (UPD) is a feature of the cancer genome that is linked to cancer development. However, technical problems with archived formalin-fixed, paraffin-embedded (FFPE) tissue samples have limited their general use in genomic profiling studies done using high-density single nucleotide polymorphism (SNP) microarray. To overcome the current problems with the use of this material in the detection of DNA copy number and copy neutral changes, we have devised two new protocols for extracting DNA from FFPE tissue. Genotyping efficiency and accuracy were improved using our novel protocols. After censoring the larger fragments, we obtained call rates for FFPE DNA equivalent to those for FF tissue DNA, with concordance rates between FFPE and FF tumor exceeding 99%. Identical DNA copy number changes were obtained for FFPE and FF; and between two new extraction protocols in tumor samples by using Affymetrix® high-density oligo-based SNP microarray platform. We observed UPD and recurrent gains and losses in tumor samples. Interestingly, we also identified UPD in the 5q and 13q regions in matching normal blood, FF adjacent breast tissue and tumor tissue in two samples. In conclusion, our new two DNA extraction protocols should substantially improve the ability to use archived material to help elucidate the complexity of early-stage breast cancer genomes. Keywords: SNP based array Overall design: Using the Affymetrix GeneChipR Mapping 250K Assay we studied primary breast tumor and normal samples with different DNA extraction protocols Abbreviations: Tumor (T), Normal (N)_sample number_tissue type (FFPE formalin fixed parafin embedded), FF (fresh frozen), peripheral blood (PBL)_DNA extraction protocol (01, DNA extraction protocol 1; 02, DNA extraction protocol 2; 03, DNA extraction protocol 3)