Ovarian cancer is a biologically diverse tumor with heterogeneous molecular subtypes. Genetic mutations in various oncogenes have been previously identified in high grade serous ovarian cancer, including RB1, CDK12, BRAF, PI3KCA, and KRAS. To further investigate genetic variants, we screened 104 high grade serous ovarian cancer specimens for 2.855 hotspot regions of 50 oncogenes and tumor suppressor genes using the Ion AmpliSeq™ Cancer Hotspot Panel. The panel contains 207 primer pairs in a single tube, using only 10ng of DNA to allow sequencing. Data analysis was performed via Ion Torrent software version 3.0, Nextgene software version 2.3.2, Excel and Medcalc.

Our analysis resulted in the detection of 240 mutation variants. The most frequent mutation variants detected were in PDGFRA (91.35%), FGFR3 (90.38%), APC (86.54%), RET (82.69%), EGFR (74.04%), and TP53 (52.88%). When only COSMIC hotspot mutations were analyzed, genes with frequent mutations were APC (COSM19349; 91.35%),

KDR (COSM149673; 56.7%), PDGFRA (COSM22413; 36.5%), KIT (COSM28026; 19.23%) and TP53 (COSM10704; 7.69%). The COSM19349 APC hot spot mutation results in a frameshift and has been described in colorectal cancer. The hotspot PDGFRA mutation (COSM22413) is a silent mutation that has been previously reported in gastrointestinal stromal tumors, gliomas and endometrial carcinoma. KDR (COSM149673) is a missense mutation that has been found in stomach cancer. KIT (COSM28026) is a missense mutation that has been confirmed as a somatic mutation in chordomas, hematologic malignancies and Merkel cell carcinoma. The TP53 (COSM10704) hotspot mutation has been found in many different tissues, including serous ovarian cancer, breast cancer and GI tract malignancies.

We used the dbNSFP database (database for nonsynonymous SNPs' functional predictions) via Nextgene for functional prediction analysis using six algorithms (PolyPhen, SIFT, Mutation Taster, LRT and 1000 Genomes). Among the most frequent hotspot mutations, TP53 (COSM10704) was found to be ‘damaging’ via all prediction tools.

KIT (COSM28026) was found to be ‘possibly damaging’ via PolyPhen.

In summary, Ion Torrent sequencing revealed mutation variants in serous ovarian cancer that have not been previously identified. Further studies will be needed to analyze the functional and clinical importance of these variants.

Citation Format: Salome Masghati, Oliver Dorigo, Chintda Santisvkulvong. Mutational analysis of serous ovarian cancer using Ion Torrent sequencing. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3287. doi:10.1158/1538-7445.AM2014-3287

©2014 American Association for Cancer Research.
2014