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Jennifer A. Hempelmann, Sheena M. Scroggins, Colin C

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1 MSIplus for Integrated Colorectal Cancer Molecular Testing by Next-Generation Sequencing 
Jennifer A. Hempelmann, Sheena M. Scroggins, Colin C. Pritchard, Stephen J. Salipante  The Journal of Molecular Diagnostics  Volume 17, Issue 6, Pages (November 2015) DOI: /j.jmoldx Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

2 Figure 1 Study design and summary of results. Diagnostic testing algorithm and results are depicted. The number of specimens at each stage is indicated numerically at corresponding nodes. Fifteen specimens were tested for both microsatellite instability (MSI) status and mutational hotspots; thus, inclusion in these categories is not mutually exclusive. IHC, immunohistochemistry. The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx ) Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

3 Figure 2 Correlation of allele fraction by MSIplus and targeted gene-capture next-generation sequencing. Allele fractions are estimated by either the MSIplus assay or the UW-OncoPlex targeted gene-capture sequencing panel. The subset of 55 specimens for which data from both assays were available is shown. Dashed gray line indicates a theoretical perfect correlation between the two estimations. The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx ) Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

4 Figure 3 Inferring microsatellite instability (MSI) status by MSIplus. Data are stratified according to testing results by MSI-PCR. The mSINGS score (the fraction of interrogated microsatellite loci that are unstable) is plotted for each specimen. The dashed lines at mSINGS scores of 0.27 and 0.54 indicate the cutoffs for delineating MSI-positive and MSI-negative specimens by MSIplus: mSINGS scores falling below these values were interpreted as negative, scores above those values were interpreted as positive, and scores falling between the values could not be reliably interpreted. Arrowheads indicate specimens misclassified by MSI-PCR; asterisk indicates specimen misclassified by MSIplus, as resolved by alternative clinical testing results (immunohistochemical and/or genetic testing). For specimens that were typed multiple times, one representative mSINGS score is displayed. The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx ) Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

5 Figure 4 Correlation of locus instability measured by microsatellite instability (MSI)-PCR and MSIplus. The mSINGS score (the fraction of interrogated microsatellite loci that are unstable) is plotted against the fraction of unstable loci determined by MSI-PCR. Overall mSINGS score for the MSIplus assay is shown separately from mSINGS score calculated for the five loci in common with MSI-PCR. Dashed gray line indicates a theoretical perfect correlation between the two measures of instability. The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx ) Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions


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