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Validation and Implementation of Targeted Capture and Sequencing for the Detection of Actionable Mutation, Copy Number Variation, and Gene Rearrangement.

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Presentation on theme: "Validation and Implementation of Targeted Capture and Sequencing for the Detection of Actionable Mutation, Copy Number Variation, and Gene Rearrangement."— Presentation transcript:

1 Validation and Implementation of Targeted Capture and Sequencing for the Detection of Actionable Mutation, Copy Number Variation, and Gene Rearrangement in Clinical Cancer Specimens  Colin C. Pritchard, Stephen J. Salipante, Karen Koehler, Christina Smith, Sheena Scroggins, Brent Wood, David Wu, Ming K. Lee, Suzanne Dintzis, Andrew Adey, Yajuan Liu, Keith D. Eaton, Renato Martins, Kari Stricker, Kim A. Margolin, Noah Hoffman, Jane E. Churpek, Jonathan F. Tait, Mary-Claire King, Tom Walsh  The Journal of Molecular Diagnostics  Volume 16, Issue 1, Pages (January 2014) DOI: /j.jmoldx Copyright © 2014 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

2 Figure 1 Scheme showing the data analysis pipeline. QA, quality assurance. The Journal of Molecular Diagnostics  , 56-67DOI: ( /j.jmoldx ) Copyright © 2014 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

3 Figure 2 Copy number variants (CNVs) detection directly by UW-OncoPlex sequencing. Adjusted log2 ratio of read depth of sequencing data are plotted for individual baits (y axis) across captured genomic regions (x axis). Overlaid horizontal black lines indicate genomic microarray results in the target regions for the same sample, illustrating high concordance of CNV detection between UW-OncoPlex and genomic microarray. Amplifications or deletions of specific genes are indicated (boxes), with corresponding array CGH calls highlighted (arrowheads). Depicted are examples from a melanoma (FFPE06) and colon cancer sample (FFPE02). The Journal of Molecular Diagnostics  , 56-67DOI: ( /j.jmoldx ) Copyright © 2014 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

4 Figure 3 Novel gene rearrangements detected. Chromosomal ideograms, gene-level schematics of events, and confirmatory bidirectional Sanger sequencing are displayed for three chromosomal rearrangements. Predicted sequences of rearrangements inferred from genomic sequence data are displayed above electropherograms, with exact chromosomal breakpoints indicated (Hg19 coordinates). UTR, untranslated region. The Journal of Molecular Diagnostics  , 56-67DOI: ( /j.jmoldx ) Copyright © 2014 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

5 Figure 4 Scheme showing the framework for variant interpretation and reporting. The Journal of Molecular Diagnostics  , 56-67DOI: ( /j.jmoldx ) Copyright © 2014 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

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