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

Ambry Genetics, 15 Argonaut, Aliso Viejo, CA 92656, USA
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Academic Editor: Camile S. Farah
Cancers 2015, 7(3), 1313-1332; https://doi.org/10.3390/cancers7030837
Received: 19 May 2015 / Revised: 30 June 2015 / Accepted: 10 July 2015 / Published: 17 July 2015
(This article belongs to the Special Issue Next Generation Sequencing Approaches in Cancer)
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. View Full-Text
Keywords: next generation sequencing; cancer panels; target enrichment; copy number; molecular inversion probes; somatic; germline next generation sequencing; cancer panels; target enrichment; copy number; molecular inversion probes; somatic; germline
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Gray, P.N.; Dunlop, C.L.; Elliott, A.M. Not All Next Generation Sequencing Diagnostics are Created Equal: Understanding the Nuances of Solid Tumor Assay Design for Somatic Mutation Detection. Cancers 2015, 7, 1313-1332.

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