Coverage and frequencies of mutations in the gynaecologic-specific mutation panel.

<p>*The absolute number of mutations are reported; >1 mutation was detected in some tumours. COSMIC¹ database accessed February 2013. ‘-’ indicates that data were not applicable.</p

Mutation Spectrum.

<p>The spectrum and frequencies of mutations identified using MALDI-TOF in 546 gynaecological carcinomas. The mutation spectrum is shown (from top to bottom) for cervical (<i>N</i> = 205), endometrial (<i>N</i> = 227), ovarian (<i>N</i> = 89), and vulvar carcinomas (<i>N</i> = 25). From left to right, <i>N</i> is the number of samples with the mutation, ‘%’ is the percentage of mutated samples within the cohort, and bars represent the percentages graphically: blue, 4 mutations per sample (<i>N</i> = 6); red, 3 mutations per sample (<i>N = </i>29); green, 2 mutations per sample (<i>N = </i>65); and yellow, 1 mutation per sample (<i>N = </i>189).</p

Design of GynCarta 2.0.

<p>The panel GynCarta 2.0, (Sequenom, Hamburg, Germany) consists of 13 multiplexes containing 99 assays to detect 171 mutations in 13 genes that are most frequently described to be involved in gynaecological malignancies according to a COSMIC meta-analysis. Assays that were added to create GynCarta 2.0 are depicted in bold.</p

Mutation Frequencies as detected by GynCarta 2.0.

1<p>Cervical, ²endometrial, ³ovarian, and ⁴vulvar carcinomas. ⁵1 cervical and 5 endometrial samples had 2 <i>PIK3CA</i> mutations, and 11 endometrial samples had 2 <i>PTEN</i> mutations in the same tumour. One endometrial sample had 2 <i>CTNNB1</i> mutations and 1 cervical sample had 2 <i>PPP2R1A</i> mutations in the same tumour. Frequencies presented as N(%), where N represents the number of samples showing the mutation. Mutations that were included in the panel but were not detected are not shown.</p

Concordance between MALDI-TOF mutation genotyping and allele-specific qPCR results.

<p>The concordance between MALDI-TOF mutation genotyping (GynCarta, Sequenom, Hamburg, Germany) and allele-specific qPCR for 3 <i>PIK3CA</i> and 7 <i>KRAS</i> mutations was determined for 164 (30% of the total cohort of 546 carcinomas) samples to validate the results. Concordance was calculated for all wild type-wild type matches (1546 in total) and all mutation-mutation matches (45 in total) in all reactions (164*10, 1640 in total). Failed reactions were excluded because comparison was not possible (4*3 for <i>PIK3CA</i> and 4*7 for <i>KRAS</i>; 40 in total). This lead to a concordance of (1546+45)/(1640−40)  = 0.994. WT  =  Wild type; MUT  =  mutant.</p