Whole exome sequencing of vulvar squamous cell carcinoma and corresponding normal tissue
20 September 2018 (online)
Two etiological pathways have been described in vulvar cancer (VSCC): A high-risk human papillomavirus (HPV)-dependent route and an HPV-independent pathway often associated with lichen sclerosus. This whole exome sequencing project is embedded in the AGO-CaRE1 translational analysis of > 700 paraffin tumor samples that are analyzed for prognostic and predictive markers on RNA-and protein levels to identify molecular subtypes and high-risk constellations in VSCC.
Whole exome sequencing of DNA isolated from 34 VSCC samples and matched normal tissue for each individual was performed on an Illumina HiSeq4000. Short variant discovery was carried out using BWA and MuTect2. Variants were annotated using ANNOVAR. For the detection structural variants and copy number aberrations, Pindel, ADTEx and FREEC were employed. Presence of HPV integration sites was assessed using Bowtie2.
All patients (median age 61) received (partial) vulvectomy as primary treatment. In 59% inguino-femoral lymphadenectomy was performed. 17.6% suffered from recurrence after a median of 10 months. TP53 mutations (39%) were most commonly detected. Additionally, we observed mutations described in the COSMIC database in the following genes, which were affected in at least two samples: RYR2, HYDIN, SYNE1, ADAMTS16, ARMCX3, CRISPLD2, DCC, DICER1, DNAH8, DOCK2, FAM155A, FAT2, FBXO41, FN1, HNRNPU, MSL2, PRDM 2, RP1, NPAT, SLC46A3, TGFB1, TOPORS, UGT2B4, VPS13C, and ZIC4. Results of HPV integration and p16 IHC are pending.
This first work and progress analysis of whole exome sequencing of VSCC with corresponding normal tissue has the potential to identify new targets for the treatment of VSCC.