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Gray PN, Dunlop CL, Elliott AM. Not All Next Generation Sequencing Diagnostics are Created Equal: Understanding the Nuances of Solid Tumor Assay Design for Somatic Mutation Detection. Cancers (Basel). 2015;7(3):1313-32doi: 10.3390/cancers7030837.
Gray, P. N., Dunlop, C. L., & Elliott, A. M. (2015). Not All Next Generation Sequencing Diagnostics are Created Equal: Understanding the Nuances of Solid Tumor Assay Design for Somatic Mutation Detection. Cancers, 7(3), 1313-32. https://doi.org/10.3390/cancers7030837
Gray, Phillip N, et al. "Not All Next Generation Sequencing Diagnostics are Created Equal: Understanding the Nuances of Solid Tumor Assay Design for Somatic Mutation Detection." Cancers vol. 7,3 (2015): 1313-32. doi: https://doi.org/10.3390/cancers7030837
Gray PN, Dunlop CL, Elliott AM. Not All Next Generation Sequencing Diagnostics are Created Equal: Understanding the Nuances of Solid Tumor Assay Design for Somatic Mutation Detection. Cancers (Basel). 2015 Jul 17;7(3):1313-32. doi: 10.3390/cancers7030837. PMID: 26193321; PMCID: PMC4586770.
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Cancers (Basel). 2015 Jul 17;7(3):1313-32. doi: 10.3390/cancers7030837.

Not All Next Generation Sequencing Diagnostics are Created Equal: Understanding the Nuances of Solid Tumor Assay Design for Somatic Mutation Detection.

Cancers

Phillip N Gray, Charles L M Dunlop, Aaron M Elliott

Affiliations

  1. Ambry Genetics, 15 Argonaut, Aliso Viejo, CA 92656, USA. [email protected].
  2. Ambry Genetics, 15 Argonaut, Aliso Viejo, CA 92656, USA. [email protected].
  3. Ambry Genetics, 15 Argonaut, Aliso Viejo, CA 92656, USA. [email protected].

PMID: 26193321 PMCID: PMC4586770 DOI: 10.3390/cancers7030837

Abstract

The molecular characterization of tumors using next generation sequencing (NGS) is an emerging diagnostic tool that is quickly becoming an integral part of clinical decision making. Cancer genomic profiling involves significant challenges including DNA quality and quantity, tumor heterogeneity, and the need to detect a wide variety of complex genetic mutations. Most available comprehensive diagnostic tests rely on primer based amplification or probe based capture methods coupled with NGS to detect hotspot mutation sites or whole regions implicated in disease. These tumor panels utilize highly customized bioinformatics pipelines to perform the difficult task of accurately calling cancer relevant alterations such as single nucleotide variations, small indels or large genomic alterations from the NGS data. In this review, we will discuss the challenges of solid tumor assay design/analysis and report a case study that highlights the need to include complementary technologies (i.e., arrays) and germline analysis in tumor testing to reliably identify copy number alterations and actionable variants.

Keywords: cancer panels; copy number; germline; molecular inversion probes; next generation sequencing; somatic; target enrichment

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