Assessment of Capture and Amplicon-Based Approaches for the Development of a Targeted Next-Generation Sequencing Pipeline to Personalize Lymphoma Management

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Presentation transcript:

Assessment of Capture and Amplicon-Based Approaches for the Development of a Targeted Next-Generation Sequencing Pipeline to Personalize Lymphoma Management Stacy S. Hung, Barbara Meissner, Elizabeth A. Chavez, Susana Ben-Neriah, Daisuke Ennishi, Martin R. Jones, Hennady P. Shulha, Fong Chun Chan, Merrill Boyle, Robert Kridel, Randy D. Gascoyne, Andrew J. Mungall, Marco A. Marra, David W. Scott, Joseph M. Connors, Christian Steidl The Journal of Molecular Diagnostics Volume 20, Issue 2, Pages 203-214 (March 2018) DOI: 10.1016/j.jmoldx.2017.11.010 Copyright © 2018 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 1 Validation of capture with Sanger and whole-genome sequencing (WGS). A: Sanger sequencing validates 100% of somatic mutations called by capture-sequenced lymphoma cases having an allele frequency of ≥10% and with variant read support of at least 10 reads (dashed lines). This experiment provided rationale to use a threshold of 10/10 (at least 10 variant reads and 10% allele frequency) for reporting mutations. B: Overlap of single-nucleotide variant and insertion/deletion mutation calls between capture and WGS across 66 patients and within the 32-gene panel. n = 588 (A). The Journal of Molecular Diagnostics 2018 20, 203-214DOI: (10.1016/j.jmoldx.2017.11.010) Copyright © 2018 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 2 A: Design and evolution of the lymphoma-specific 32-gene targeted sequencing panel. B: Coverage is homogeneous across the target space and across panel versions. All panel versions have a mean coverage that achieves the desired minimum target coverage of 100× (dashed line). Samples having a mean coverage <50× were removed from the analysis. CLL, chronic lymphocytic leukemia; DLBCL, diffuse large B-cell lymphoma; FL, follicular lymphoma; V, version. The Journal of Molecular Diagnostics 2018 20, 203-214DOI: (10.1016/j.jmoldx.2017.11.010) Copyright © 2018 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 3 Frequency of mutations across all mutated genes in chronic lymphocytic leukemia (A), diffuse large B-cell lymphoma (B), and follicular lymphoma (C), divided into the classes frameshift insertion/deletion (indel), in-frame indel, missense, nonsense, splice site, and start lost counts. Genes carrying more than one class of mutation are categorized as multiple mutations. The Journal of Molecular Diagnostics 2018 20, 203-214DOI: (10.1016/j.jmoldx.2017.11.010) Copyright © 2018 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions