Uiring atU-BRAFV600 State DetectionFigure 3. Dispensation order for 5 mutated BRAF variants detected by U-BRAFV600 assay. *A5 = Awt +3Amt. Recognition patters are indicated in black boxes, individual mutation features are marked in grey boxes dispensation order’s nucleotides, which are involved into mt:wt ratio, are bolded. doi:10.1371/journal.pone.0059221.11089-65-9 gleast two reads to support a variant, and removing variants due to typical Illumina sequencing artifacts [11].ResultsWe analyzed BRAF state in 75 formalin-fixed paraffinembedded (FFPE) samples of cutaneous melanoma metastases from 29 patients (age 62625, male-to-female ratio 1.9). By Sanger sequencing, we identified five different types of BRAF mutations reported by our group previously [12] in 18 of 29 patients (62 , Table 1).Novel Pyrosequencing-based U-BRAFV600 AssayTo prove these data, we performed the pyrosequencing analysis with the conventional dispensation order G1A2C3G4[A5T6]G7A8T9 generated by Pyromark Q24 software Version 2.0.6 (Calyculin A site Qiagen) flanking the hotspot mutation T1799A at codon V600 and ending with the first nucleotide of codon S602. Negative nucleotide dispensations G1 and C3 were included as internal controls. Although T1799A mutation was determined by this dispensation order, the variant mutations beyond V600E resulted in unsolved aberrant pyrograms (Figure S1a). To overcome this limitation, we designed the novel dispensation order U-BRAFV600?G1T2A3C4A5C6G7A8T9[A10C11T12]-G13A14T15C16T17[A18G19]. Because the knowledge of specific variant in each case could explain the altered pyrogram tracing created by a change in order and/or quantity of incorporation of each nucleotide, we embedded the two recognition patterns [A10C11T12] and [A18G19], enabling the simultaneous identification of hotspot V600E mutation together with variant mutations with two-nucleotide substitutions p.V600E2 (c.TG1799_1800AA) and p.V600K (c.GT1798_1799AA), tandem mutation p.V600E;K601I (c.TG1799_1800AA;A1802T) and complex in-frame mutation VKS600_602.DT (c.TGAAAT1799_1804.ATA) [12]. Here, the presence of variant mutations affects the pyrogram sequence pattern by re-distribution of nucleotide incorporation in the mutant DNA sequence, resulting in a unique pyrogram for each BRAF mutation (Figure 1). Both recognition patterns differentiate the individual mutations by the presence of the corresponding peaks characteristic for each mutation variant. Furthermore, the ratio A8:T12 distinguishes between mutations V600E2 (5:1) and V600K (3:1) (Figure 2). We found that at least 400 ng PCR product is required for successful analysis by U-BRAFV600 assay, although in this case the signal intensity is constantly reduced by each dispensation step (Figure 3a). In our study, up to 1 reduction was observed per dispensation step from the initial intensity value of dispensation nucleotide T2 resulting in formula [“reduction factor”6N] ,U-BRAFV600 State DetectionTable 2. Recognition patterns for 36 BRAF mutations by U-BRAFV600 assay.MutationRecognition Patterns C6 A10 C11 T12 A18 G19 ????????????????Unique properties of each mutation within one groupmt:wt ratioCOSMIC database1 p.V600E(1) p.T599del p.V600L p.V600M p.V600R(2) p.K601E p.K601N 2 p.V600E;K601I???????????????+???????????????+A8 = Amt; T9 = Twt absence of A8; absence of mutant T2, C4 and A5 absence of A8; G7 = Gwt; T9 = [Twt +2Tmt] absence of A8; G7 = Gwt; 23115181 T9 = [Twt+Tmt] A5 = Awt; G13 = [Gwt +2Gmt] absence of A8; G13 = [Gwt +2Gmt]; A14 = [3Awt +2Amt] abs.Uiring atU-BRAFV600 State DetectionFigure 3. Dispensation order for 5 mutated BRAF variants detected by U-BRAFV600 assay. *A5 = Awt +3Amt. Recognition patters are indicated in black boxes, individual mutation features are marked in grey boxes dispensation order’s nucleotides, which are involved into mt:wt ratio, are bolded. doi:10.1371/journal.pone.0059221.gleast two reads to support a variant, and removing variants due to typical Illumina sequencing artifacts [11].ResultsWe analyzed BRAF state in 75 formalin-fixed paraffinembedded (FFPE) samples of cutaneous melanoma metastases from 29 patients (age 62625, male-to-female ratio 1.9). By Sanger sequencing, we identified five different types of BRAF mutations reported by our group previously [12] in 18 of 29 patients (62 , Table 1).Novel Pyrosequencing-based U-BRAFV600 AssayTo prove these data, we performed the pyrosequencing analysis with the conventional dispensation order G1A2C3G4[A5T6]G7A8T9 generated by Pyromark Q24 software Version 2.0.6 (Qiagen) flanking the hotspot mutation T1799A at codon V600 and ending with the first nucleotide of codon S602. Negative nucleotide dispensations G1 and C3 were included as internal controls. Although T1799A mutation was determined by this dispensation order, the variant mutations beyond V600E resulted in unsolved aberrant pyrograms (Figure S1a). To overcome this limitation, we designed the novel dispensation order U-BRAFV600?G1T2A3C4A5C6G7A8T9[A10C11T12]-G13A14T15C16T17[A18G19]. Because the knowledge of specific variant in each case could explain the altered pyrogram tracing created by a change in order and/or quantity of incorporation of each nucleotide, we embedded the two recognition patterns [A10C11T12] and [A18G19], enabling the simultaneous identification of hotspot V600E mutation together with variant mutations with two-nucleotide substitutions p.V600E2 (c.TG1799_1800AA) and p.V600K (c.GT1798_1799AA), tandem mutation p.V600E;K601I (c.TG1799_1800AA;A1802T) and complex in-frame mutation VKS600_602.DT (c.TGAAAT1799_1804.ATA) [12]. Here, the presence of variant mutations affects the pyrogram sequence pattern by re-distribution of nucleotide incorporation in the mutant DNA sequence, resulting in a unique pyrogram for each BRAF mutation (Figure 1). Both recognition patterns differentiate the individual mutations by the presence of the corresponding peaks characteristic for each mutation variant. Furthermore, the ratio A8:T12 distinguishes between mutations V600E2 (5:1) and V600K (3:1) (Figure 2). We found that at least 400 ng PCR product is required for successful analysis by U-BRAFV600 assay, although in this case the signal intensity is constantly reduced by each dispensation step (Figure 3a). In our study, up to 1 reduction was observed per dispensation step from the initial intensity value of dispensation nucleotide T2 resulting in formula [“reduction factor”6N] ,U-BRAFV600 State DetectionTable 2. Recognition patterns for 36 BRAF mutations by U-BRAFV600 assay.MutationRecognition Patterns C6 A10 C11 T12 A18 G19 ????????????????Unique properties of each mutation within one groupmt:wt ratioCOSMIC database1 p.V600E(1) p.T599del p.V600L p.V600M p.V600R(2) p.K601E p.K601N 2 p.V600E;K601I???????????????+???????????????+A8 = Amt; T9 = Twt absence of A8; absence of mutant T2, C4 and A5 absence of A8; G7 = Gwt; T9 = [Twt +2Tmt] absence of A8; G7 = Gwt; 23115181 T9 = [Twt+Tmt] A5 = Awt; G13 = [Gwt +2Gmt] absence of A8; G13 = [Gwt +2Gmt]; A14 = [3Awt +2Amt] abs.