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KRAS Mutation The Journal of Molecular Diagnostics

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1 KRAS Mutation The Journal of Molecular Diagnostics
Wilbur A. Franklin, Jerry Haney, Michio Sugita, Lynne Bemis, Antonio Jimeno, Wells A. Messersmith  The Journal of Molecular Diagnostics  Volume 12, Issue 1, Pages (January 2010) DOI: /jmoldx Copyright © 2010 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

2 Figure 1 Schematic diagram for testing protocol. Tissue blocks were tested using two tissue block sampling methods and three mutation assays including direct sequencing, ARMS/scorpions, and high resolution melting. The Journal of Molecular Diagnostics  , 43-50DOI: ( /jmoldx ) Copyright © 2010 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

3 Figure 2 Raw amplification curves for KRAS mutant tumor sample tested by the ARMS/S method. Each curve represents an amplification product of the same DNA template for one of eight specific primer sets. The curve on the farthest left is for wild-type control primers. The next curve to right represents amplification products for mutant template (GGT→GAT, G12D). The remaining curve is for the wild-type template. A positive result is determined by the cross point, the point on each curve where the slope of the curve becomes linear. There is a clear separation between mutant product (CP 29.6) and non-mutant product (CPs >38.5). The difference between CP for the wild-type control DNA and the mutant DNA (ΔCP) is small (2.4 cycles), indicating a mutation. The Journal of Molecular Diagnostics  , 43-50DOI: ( /jmoldx ) Copyright © 2010 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

4 Figure 3 High resolution melting (HRM) difference point plot for KRAS. A: Normalized high resolution melt curves. PCR products are labeled with a fluorescent dye and the fluorescent signal is plotted as the temperature increases. Strand melting results in a decrease in fluorescent signal. B: The difference plot displays the melting curve of each sample subtracted from a reference curve to visually accentuate the melt curve differences and aid in genotype grouping. Products of three mutant templates are shown in red and pink. Products of wild-type templates are shown in blue. The upper (pink curve) represents the codon 12 mutation G12S, whereas the red curves represent amplification products for a single mutation at codon 12 (G12V) at two different concentrations. The latter two curves are similar shapes but have different heights due to variation in the quantity of PCR amplicon. The Journal of Molecular Diagnostics  , 43-50DOI: ( /jmoldx ) Copyright © 2010 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

5 Figure 4 Mutation Surveyor readout for KRAS codon 12 mutation (GGT→GAT, G12D), forward primer set. Top tracing is for wild-type control. Mutant tracing is shown in the center. The chomatogram peak differences are calculated by the Mutation Surveyor program and plotted in the bottom tracing. Numbers refer to areas under the curve. The horizontal green line indicates the calculated threshold level for the mutation call. Visual inspection of chromatograms are required to indentify mutation peaks that fall below the threshold of detection of the software, as well as for false positives due to band compression or other sequencing artifacts. The Journal of Molecular Diagnostics  , 43-50DOI: ( /jmoldx ) Copyright © 2010 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

6 Figure 5 Example of discrepancy between ARMS/S and direct sequencing. On the left (A), ARMS/S amplification curve for mutant tumor DNA (G12D) is clearly separated from that of non-mutant control DNA with ΔCP of 7.3, a value that is within the range indicating mutation. On the right (B) is a chromogram for direct sequencing results for KRAS codons 12 and 13. In frames 1 and 6, tracings of forward and reverse control DNA strands are shown. Tracings for forward and reverse test DNA strands are shown in frames 2 and 5. Frames 3 and 4 show difference plots for forward and reverse strands calculated by Mutation Surveyor software. There is a low peak (A) corresponding to the expected mutation, but the height of the peak is below the level background and cannot be confidently interpreted as a mutation. The Journal of Molecular Diagnostics  , 43-50DOI: ( /jmoldx ) Copyright © 2010 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

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