Molecular characterization of serous ovarian carcinoma using a multigene next generation sequencing cancer panel approach

Abstract

BackgroundHigh grade serous ovarian cancer is one of the poorly characterized malignancies. This study aimed to elucidate the mutational events in Malaysian patients with high grade serous ovarian cancer by performing targeted sequencing on 50 cancer hotspot genes.ResultsNine high grade serous ovarian carcinoma samples and ten normal ovarian tissues were obtained from Universiti Kebangsaan Malaysia Medical Center (UKMMC) and the Kajang Hospital. The Ion AmpliSeq™ Cancer Hotspot Panel v2 targeting “mutation-hotspot region” in 50 most common cancer-associated genes was utilized. A total of 20 variants were identified in 12 genes. Eleven (55%) were silent alterations and nine (45%) were missense mutations. Six of the nine missense mutations were predicted to be deleterious while the other three have low or neutral protein impact. Eight genes were altered in both the tumor and normal groups (APC, EGFR, FGFR3, KDR, MET, PDGFRA, RET and SMO) while four genes (TP53, PIK3CA, STK11 and KIT) were exclusively altered in the tumor group. TP53 alterations were present in all the tumors but not in the normal group. Six deleterious mutations in TP53 (p.R175H, p.H193R, p.Y220C, p.Y163C, p.R282G and p.Y234H) were identified in eight serous ovarian carcinoma samples and none in the normal group.ConclusionTP53 remains as the most frequently altered gene in high grade serous ovarian cancer and Ion Torrent Personal Genome Machine (PGM) in combination with Ion Ampliseq™ Cancer Hotspot Panel v2 were proven to be instrumental in identifying a wide range of genetic alterations simultaneously from a minute amount of DNA. However, larger series of validation targeting more genes are necessary in order to shed a light on the molecular events underlying pathogenesis of this cancer.Electronic supplementary materialThe online version of this article (doi:10.1186/1756-0500-7-805) contains supplementary material, which is available to authorized users.

Next-Generation Sequencing-based genomic profiling of brain metastases of primary ovarian cancer identifies high number of BRCA-mutations

“…Consistently, TP53, BRCA1 , and BRCA2 were the most frequently altered genes in the TCGA ovarian serous cystadenocarcinoma data. Moreover, in line with other studies on the pattern of somatic mutations in human cancer genomes [ 15 , 25 ], we observed a higher rate of transitions than transversions. Even if metastatic tumor spread is a very complex process consisting of many different events, the mutational spectrum of our BM specimens was surprisingly simple, which is consistent with the findings of Beltrame et al, who reported that the genomic architecture of relapsed disease was less heterogenous than that of the primary disease [ 26 ].…”

“…To date, most research efforts have focused on defining the molecular characteristics of primary OC [ 6 , 14 , 15 ]. Only very limited data are available on molecular aberrations in BM of OC [ 16 – 18 ].…”

High-grade versus low-grade serous carcinoma of the ovary – current differential diagnosis and perspectives

“…Mutation of TP53 gene is the most frequent genomic alteration of high-grade carcinomas, while KRAS and BRAF mutations are more likely encountered in low-grade ones 2,16,17 . In one study DNA derived from tumor was detected in the vaginas of 60% of patients with ovarian cancer with intact fallopian tubes and harbored the exact same TP53 mutation 18 .…”

Diagnosis of pancreatic lesions collected by endoscopic ultrasound-guided fine-needle aspiration using next-generation sequencing

“…Somatic mutations (substitutions, insertions, or deletions) were designed to amplify 207 amplicons covering ~2790 Catalogue of Somatic Mutations in Cancer (COSMIC) mutations from the 50 most commonly reported oncogenes and tumor suppressor genes (Ion Torrent™; Thermo Fisher Scientific, Inc.). Sequencing library preparation was performed according to the manufacturer's instructions (18,19). …”