Somatic mutation genotyping was performed using the GynCarta 2.0 mutation panel (Sequenom, Hamburg, Germany) as described previously.[16 (link)] This panel analyzes mutations that are most commonly involved in gynecological malignancies, detecting 171 mutations in 13 genes: BRAF, CDKN2A, CTNNB1, FBXW7, FGFR2, FGFR3, FOXL2, HRAS, KRAS, NRAS, PIK3CA, PPP2R1A, and PTEN.
All 301 samples, plus 49 (16%) samples in duplicate and 11 (4%) samples in triplicate, were genotyped using the iPLEX technology system (Sequenom Inc., San Diego, USA) for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry following the manufacturer’s protocol as described previously.[21 (link)] Non-template H2O samples (N = 14) and wild-type leukocyte DNA (N = 2) were included to obtain negative and wild-type spectra, respectively. Three investigators blinded to tumor identification analyzed the data using MassArray Typer Analyser software (TYPER 4.0.22, Sequenom, Hamburg, Germany) and MutationSurveyor (Softgenetics, State College, Pennsylvania, USA). The mutation spectra of 197 samples were published previously[16 (link)]; however, in that study we only described the mutation spectrum in the context of validating the mutation panel and no analysis concerning clinicopathological parameters or survival was performed.
All 301 samples, plus 49 (16%) samples in duplicate and 11 (4%) samples in triplicate, were genotyped using the iPLEX technology system (Sequenom Inc., San Diego, USA) for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry following the manufacturer’s protocol as described previously.[21 (link)] Non-template H2O samples (N = 14) and wild-type leukocyte DNA (N = 2) were included to obtain negative and wild-type spectra, respectively. Three investigators blinded to tumor identification analyzed the data using MassArray Typer Analyser software (TYPER 4.0.22, Sequenom, Hamburg, Germany) and MutationSurveyor (Softgenetics, State College, Pennsylvania, USA). The mutation spectra of 197 samples were published previously[16 (link)]; however, in that study we only described the mutation spectrum in the context of validating the mutation panel and no analysis concerning clinicopathological parameters or survival was performed.