Comprehensive next-generation cancer genome sequencing in the era of targeted therapy and personalized oncology

Abstract

DNA sequence analysis has become a significant laboratory test in oncology, permitting treatment to become increasingly personalized for both solid tumors and hematologic malignancies. Traditional approaches to sequence analysis, including Sanger sequencing, pyrosequencing and allele-specific PCR, are now widely used to guide therapy for patients diagnosed with lung and colorectal cancer as well as for melanoma, sarcomas (e.g., gastrointestinal stromal tumors) and subtypes of leukemia and lymphoma. Traditional sequence analysis has been limited in bandwidth and throughput and as a result, has been focused exclusively on testing the most common aberrations in key genes or fully sequencing single genes. The massively parallel or next-generation sequencing (NGS) approach to DNA analysis holds a number of potential advantages over the traditional methods, including the ability to fully sequence large numbers of genes (hundreds to thousands) in a single test. Furthermore, NGS can simultaneously detect deletions, insertions, copy number alterations, translocations and exome-wide base substitutions (including known hot-spot mutations) in all known cancer-related genes. However, significant challenges, particularly with respect to demands on expertise and infrastructure, will have to be overcome to translate NGS to the bedside of the cancer patient. Extensive computational expertise is required to bring NGS into clinical context, and a deep knowledge of cancer medicine and cancer biology will be required to generate truly useful, so-called ‘clinically actionable‘ reports for clinicians. While NGS is on the cusp of being launched as a clinical test, it may be expected that the near future will continue to bring major advances in the technology that will lower the overall cost, speed up the turnaround time, increase the breadth of genome sequencing, and detect epigenetic markers and other important genomic parameters, while becoming applicable to smaller and smaller specimens, including circulating tumor cells and circulating free DNA in plasma.

KEYWORDS::

• colorectal cancer
• massively parallel sequencing
• melanoma
• next-generation sequencing
• non-small-cell lung cancer
• personalized oncology

Acknowledgement

The authors would like to thank Phil Stephens, Mary Pat Lancelotta, Alexis Borisey and Gary Palmer for helpful comments and reading of this manuscript.

Financial & competing interests disclosure

Maureen Cronin is a full-time compensated employee of Foundation Medicine, Inc., Jeffrey Ross is a paid consultant for Foundation Medicine. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Additional information

Funding

Maureen Cronin is a full-time compensated employee of Foundation Medicine, Inc., Jeffrey Ross is a paid consultant for Foundation Medicine. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.