Genomic Landscape of Diploid and Aneuploid Microsatellite Stable Early Onset Colorectal Cancer

We applied DNA content based flow cytometry methods to interrogate the genomes of clinical samples from 21 patients with early onset colorectal carcinoma (EOCRC). These included a fresh frozen sample obtained from a surgical resection and 20 archived formalin fixed paraffin embedded (FFPE) samples from a Mayo Clinic tissue bank. Our flow sorting methods are compatible with analyses of biopsies of interest including FFPE samples and frozen biopsies. Notably for this study we distinguished and sorted diploid and aneuploid tumors. We then profiled the exomes of tumor normal pairs for all 21 cases, the whole genome copy number for a subset of 6 samples, and telomere length in diploid and aneuploid nuclei from 9 cases. Additionally, we screened the 20 FFPE cases for EGFR expression with an established IHC assay. We applied DNA content based flow sorting to isolate the nuclei of clonal populations from early onset colorectal carcinoma biopsies. We coupled this strategy with oligonucleotide array CGH (aCGH) thereby obtaining high definition genomic profiles of clonal populations from each tumor. Whole exome sequencing of each flow sorted sample identified somatic pathogenic variants.