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Review
. 2013 Aug;7(4):743-55.
doi: 10.1016/j.molonc.2013.04.008. Epub 2013 May 15.

Translating next generation sequencing to practice: opportunities and necessary steps

Sitharthan Kamalakaran  1 , Vinay Varadan, Angel Janevski, Nilanjana Banerjee, David Tuck, W Richard McCombie, Nevenka Dimitrova, Lyndsay N Harris
Affiliations
Review

Translating next generation sequencing to practice: opportunities and necessary steps

Sitharthan Kamalakaran et al. Mol Oncol. 2013 Aug.

Abstract

Next-generation sequencing (NGS) approaches for measuring RNA and DNA benefit from greatly increased sensitivity, dynamic range and detection of novel transcripts. These technologies are rapidly becoming the standard for molecular assays and represent huge potential value to the practice of oncology. However, many challenges exist in the transition of these technologies from research application to clinical practice. This review discusses the value of NGS in detecting mutations, copy number changes and RNA quantification and their applications in oncology, the challenges for adoption and the relevant steps that are needed for translating this potential to routine practice.

Keywords: Genomics; Next generation sequencing; Oncology; Personalized medicine.

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Figures

Figure 1
Figure 1
A model for enabling sequencing based personalized oncology. A CLIA certified laboratory generates NGS data (Layer 1) that is transferred to a High Performance Computing environment where the requisite quality control and analysis of the data is performed (Layer2). Clinical Decision support algorithms will extract clinically relevant pieces of information from the processed data (Layer 3). Examples of clinically relevant information could be the identification of an activating PIK3CA mutation, ERBB2 amplification, a gene signature such as breast cancer subtype or a gene fusion. This clinically relevant information is then interactively viewed through desktop/mobile devices (Layer 4).
Figure 2
Figure 2
Major challenges for introducing sequencing based oncology into routine practice.
Figure 3
Figure 3
The current status and future vision for oncology – replacement of multitude of single gene/panel tests by one comprehensive molecular profile.
See this image and copyright information in PMC

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