Use of Next-Generation Sequencing in Oncology

Faculty Perspectives: Next-Generation Sequencing Testing in Oncology | Part 4 of a 4-Part Series

The advent of next-generation sequencing (NGS) technologies has revolutionized the way we approach and utilize molecular diagnostic testing in oncology. As our knowledge of cancer genomics has expanded rapidly in the past decade, so have the number of molecular targets and biomarkers that we are interested in interrogating. Because of the massively parallel nature of NGS techniques, instead of performing numerous single-gene biomarker assays (eg, fluorescence in situ hybridization, real-time polymerase chain reaction, Sanger sequencing, or pyrosequencing) in series or in parallel, we are able to interrogate hundreds of targets simultaneously. Performed in an optimized way in a molecular laboratory, this approach can result in improved tissue utilization, efficiency, and cost-effectiveness.1

In addition to these benefits, comprehensive NGS testing has also been shown to identify more targetable alterations and therapeutic options than otherwise would have been identified.2 This can be attributed to the fact that for many tumor types, a few genomic drivers are highly recurrent, with a much larger number of targetable findings occurring in a small subset of cases.3 Finally, genome-wide analyses are being proposed as useful biomarkers for various therapeutic options, such as tumor mutational burden in immunotherapy and homologous recombination deficiency score for predicting response to poly (ADP-ribose) polymerase inhibitors.4-6 Because these biomarkers are part of mutational patterns that are present across a tumor genome, they are best accessed via NGS methodologies.

Most of the clinical genomic testing in oncology is currently performed as targeted gene panels, ranging from smaller, more limited “hotspot” panels, which can identify single-­nucleotide variants (SNVs), as well as small insertions and deletions (indels), to larger, more comprehensive panels that cover hundreds of genes, with the capability of identifying SNVs, indels, copy number changes, and gene rearrangements and fusions. The rationale behind the use of these more focused, targeted panels, rather than either whole-genome sequencing (WGS) or whole-exome sequencing (WES), is multifold. First, targeted sequencing allows for greater depth of sequencing, which is often necessary for cancer specimens in which the tumor cellularity may be low or in which subclonal variants may be present at low variant allele fractions. Second, targeted sequencing is a more cost-effective technique than WES or WGS, particularly at the greater sequencing depths achievable in targeted panels. Finally, targeted sequencing allows for the analysis and interpretation to focus on clinically actionable variants, rather than identification of a large number of alterations that may only be characterized as variants of uncertain significance in genes of uncertain relevance.

With increased use of targeted therapies in oncology, the emergence and identification of resistance mechanisms against these therapies are also on the rise.7 Although a classic resistance mechanism to epidermal growth factor receptor (EGFR) targeted therapy is the development of an EGFR T790M mutation, the number of resistance mechanisms identified is quite expansive, and can occur via a variety of mechanisms and in a variety of genes.8,9 Furthermore, it has become increasingly recognized that completely unique driver alterations can occur (eg, the emergence of a RET fusion in a previously EGFR-mutated lung cancer).9 The only reliable way to identify this growing and varied list of resistance mechanisms is to devise an agnostic, comprehensive approach, such as what is possible with NGS-based testing.

Although initial tumor profiling is often performed on biopsied or resection tissue specimens, the utility of performing cancer genotyping on circulating tumor DNA (ctDNA) obtained from a peripheral blood sample is being increasingly realized. This can be useful in a variety of settings, including those in which the procurement of tissue is not possible or is inadequate for molecular testing, as well as in serially monitoring the patient for the development of resistance mechanisms or the presence of residual disease. Limitations to this approach exist, however, including the fact that ctDNA is not present in all patients with cancer and is dependent on the tumor type as well as on the stage of disease.10 It can be a very useful testing option when tumor tissue is not obtainable or not amenable for molecular testing and, based on the factors mentioned earlier for resistance mutation monitoring, can be well-suited for use in NGS-based applications.

Finally, although the merits and effects of NGS-based testing in oncology are well-recognized and acknowledged by many oncologists, pathologists, and patients, particularly in such tumor types as non–small-cell lung cancer and acute myeloid leukemia, barriers to the implementation and use of these technologies still exist. NGS technologies are highly complex and require extensive knowledge, skill, and experience, both in the performance of the testing and in the interpretation of the results. Nonetheless, this level of expertise may not be present in all healthcare settings.

The lack of universal insurance coverage for these tests is also a significant burden, both to the laboratories that want to perform these tests and to the providers and patients who would like to have these tests performed. The recent National Coverage Determinations provided by the Centers for Medicare & Medicaid Services allow for 1 NGS test per primary tumor per patient, with national coverage required for US Food and Drug Administration-approved tests and coverage of laboratory-developed tests to be determined by local Medicare Administrative Contractors.11

Private payers and insurance companies still have variable policies regarding NGS test reimbursement in oncology. Although it is the hope that payers will continue to expand their coverage for NGS tests in oncology care, this is still a gray area, particularly with respect to how these coverage determinations will affect serial testing, such as that currently being used for monitoring resistance mechanisms and residual disease. As NGS testing has already been incorporated into routine clinical use for several types of tumors, both in academic and in community settings, our continually expanding knowledge of cancer genomics will serve to further the demand for this comprehensive and efficient testing methodology.


  1. Pennell NA, Mutebi A, Zhou Z-Y, et al. Economic impact of next generation sequencing vs sequential single-gene testing modalities to detect genomic alterations in metastatic non-small cell lung cancer using a decision analytic model. J Clin Oncol. 2018;36(15 suppl):9031.
  2. Mehrad M, Roy S, Bittar HT, Dacic S. Next-generation sequencing approach to non–small cell lung carcinoma yields more actionable alterations. Arch Pathol Lab Med. 2018;142:353-357.
  3. Fumagalli C, Vacirca D, Rappa A, et al. The long tail of molecular alterations in non-small cell lung cancer: a single-institution experience of next-generation sequencing in clinical molecular diagnostics. J Clin Pathol. 2018;71:767-773.
  4. Samstein RM, Lee CH, Shoushtari AN, et al. Tumor mutational load predicts survival after immunotherapy across multiple cancer types. Nat Genet. 2019 Jan 14. Epub ahead of print.
  5. Hellmann MD, Ciuleanu T-E, Pluzanski A, et al. Nivolumab plus ipilimumab in lung cancer with a high tumor mutational burden. N Engl J Med. 2018;378:2093-2104.
  6. Telli ML, Timms KM, Reid J, et al. Homologous recombination deficiency (HRD) score predicts response to platinum-containing neoadjuvant chemotherapy in patients with triple-negative breast cancer. Clin Cancer Res. 2016;22:3764-3773.
  7. Neel DS, Bivona TG. Resistance is futile: overcoming resistance to targeted therapies in lung adenocarcinoma. NPJ Precis Oncol. 2017 Mar 20. Epub ahead of print.
  8. Westover D, Zugazagoitia J, Cho BC, et al. Mechanisms of acquired resistance to first- and second-generation EGFR tyrosine kinase inhibitors. Ann Oncol. 2018;29(suppl 1):i10-i19.
  9. Piotrowska Z, Isozaki H, Lennerz JK, et al. Landscape of acquired resistance to osimertinib in EGFR-mutant NSCLC and clinical validation of combined EGFR and RET inhibition with osimertinib and BLU-667 for acquired RET fusion. Cancer Discov. 2018;8:1529-1539.
  10. Bettegowda C, Sausen M, Leary RJ, et al. Detection of circulating tumor DNA in early- and late-stage human malignancies. Sci Transl Med. 2014;6:224ra24.
  11. Centers for Medicare & Medicaid Services & Food and Drug Administration website. Decision Memo for Next Generation Sequencing (NGS) for Medicare Benefi­ciaries with Advanced Cancer (CAG-00450N). Accessed January 25, 2019.
Last modified: July 22, 2021