We carried out a retrospective chart review to identify patients with advanced or recurrent HGSOC treated at the University of Iowa Hospitals and Clinics. We identified 253 such patients and determined that there were 193 with available flash-frozen tumor tissues stored in the Department of Obstetrics and Gynecology Gynecologic Oncology Bank (IRB, ID#200209010) that is part of the Women’s Health Tissue Repository (WHTR, IRB, ID#200910784)24 (link). All tissues archived in the Gynecologic Oncology Bank were originally obtained from adult patients under informed consent in accordance with University of Iowa IRB guidelines. Both genomic DNA (gDNA) and total cellular RNA were purified from the identified tumors (Fig. 1).

Distribution of controls and samples. (A) Normal fallopian tube controls retrieved from patients at the University of Iowa. (B) University of Iowa Hospitals and Clinics patients diagnosed with high grade serous ovarian cancer (HGSOC). (C) Normal fallopian tubes and HGSOC samples in the cancer genome atlas, TCGA, database.

A separate approval was given by the University of Iowa Institutional Review Board (IRB, ID#201202714) to collect 20 normal fallopian tube samples to be used as controls in coordination with the University of Iowa Tissue Procurement Core Facility. Again, all tissues were obtained from adult patients under informed consent in accordance with University of Iowa IRB guidelines. Samples came from the junction of the ampullary and fimbriated end of fallopian tubes of patients who were scheduled to undergo salpingectomy for benign indications. No patient indicating a personal or family history of cancer was included.
Genomic DNAs (gDNAs) were purified from frozen tumor tissues using the DNeasy Blood and Tissue Kit according to manufacturer’s (QIAGEN) recommendations. Yield and purity were assessed on a NanoDrop Model 2000 spectrophotometer and used a 260 nm/280 nm absorbance ratio of ~1.8 with minimal to no degradation as shown through horizontal agarose gel electrophoresis. Among the initial purifications, 97 gDNAs met our quality control standard which included minimal visible degradation (Fig. 1B). These samples were then bisulfite-converted using the EZ-96 Deep-Well Format DNA Methylation Kit (ZYMO Research) following the Illumina Infinium® Methylation Assay alternate incubation instructions. Similarly, gDNAs from the control fallopian tube tissues were purified and subjected to the quality control standard. Twelve of the original twenty tissues yielded material meeting our standard (Fig. 1A).
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