Next generation sequencing and tumor mutation profiling: are we ready for routine use in the oncology clinic?

Debu Tripathy¹^*, Kathleen Harnden², Kimberly Blackwell² and Mark Robson³⁴

*Corresponding author: Debu Tripathy tripathy@med.usc.edu

Author Affiliations

¹University of Southern California, Keck School of Medicine, USC/Norris Comprehensive Cancer Center, 1441 Eastlake Avenue, NTT-3429, Los Angeles 90033, CA, USA

²Duke Cancer Institute, Duke University Medical Center, 2301 Erwin Road, Durham 27710, NC, USA

³Memorial Sloan Kettering Cancer Center, Memorial Hospital, 1275 York Avenue, New York 10065, NY, USA

⁴Weill Cornell Medical College, 1275 York Ave, New York 10065, NY, USA

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BMC Medicine 2014, 12:140 doi:10.1186/s12916-014-0140-3

The electronic version of this article is the complete one and can be found online at:http://www.biomedcentral.com/1741-7015/12/140

Received:	28 July 2014
Accepted:	28 July 2014
Published:	12 August 2014

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

Abstract

Next generation sequencing (NGS) coupled with sophisticated bioinformatics tools yields an unprecedented amount of information regarding tumor genetics, with the potential to reveal insights into tumor behavior. NGS and other multiplex genomic assays are rapidly spilling from the laboratory into the clinic through numerous commercial and academic entities. This raises the important question as to whether we are ready to use these data in clinical decision-making. While genetic lesions are clearly targeted by a new generation of biological cancer therapies, and certain regulatory approvals are actually coupled to single gene assays, we still do not know if the vast information on other genomic alterations is worth the added cost, or even worse, the inappropriate and unproven assignment of patients to treatment with an unapproved drug carrying potentially serious side effects. On the other hand, the trend toward a precision medicine pathway is clearly accelerating, and clinical trials validating pathway-driven personalized cancer therapeutics will be necessary in both the community and academic settings. Lower cost and wider availability of NGS now raises a debate over the merit of routine tumor genome-wide analysis.