Single Nucleus DNA Sequencing of Flow Sorted Archived Frozen and Formalin Fixed Paraffin Embedded Solid Tumors

We applied DNA content based flow cytometry methods to interrogate the genomes of clinical samples from 8 patients with ovarian cancer. These included 6 high grade serous ovarian carcinomas, a low grade serous carcinoma, and an endometriod carcinoma. Archived samples obtained from surgical resections from a University of California San Francisco (UCSF) tissue bank. Notably for this study we distinguished and sorted diploid and aneuploid tumors. We then profiled the the whole genome copy number for each sample. These data were used to provide standards for single cell analyses of the same tissues including FFPE samples. We applied DNA content based flow sorting to isolate the nuclei of clonal populations from ovarian carcinoma biopsies. We coupled this strategy with oligonucleotide array CGH (aCGH) thereby obtaining high definition genomic profiles of clonal populations from each tumor.