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Clinical Application of Next-Generation Sequencing in Oncology

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

The clinical application of assays that utilize next-generation sequencing (NGS) technology is accelerating rapidly in the field of oncology.1 Targeted NGS assays that evaluate tens to hundreds of genes are available for prospective clinical use at academic cancer centers2,3 or through commercial vendors,4 whereas broader NGS approaches, such as whole-exome sequencing (WES) or whole-genome sequencing (WGS), are being utilized primarily in research settings at this time. Genomic profiling of specific genes, to identify somatic or germline alterations that predict sensitivity or resistance to US Food and Drug Administration (FDA)-approved cancer therapies for advanced disease, is considered the standard of care in a number of solid tumor types, including non–small-cell lung cancer (NSCLC), breast cancer, ovarian cancer, and colorectal cancer, as well as in melanoma. Notably, the FDA has recently approved 2 tissue-agnostic cancer therapies: larotrectinib for solid tumors that harbor neurotrophic receptor tyrosine kinase (NTRK) gene fusions5 and pembrolizumab for tumors that demonstrate microsatellite instability-high (MSI-H) status or mismatch repair deficiency (dMMR).6 Furthermore, a diversity of investigational genomic biomarkers, including such complex biomarkers as tumor mutational burden (TMB) and homologous recombination deficiency, have been or currently are being evaluated in clinical trials across virtually every type of cancer.

Targeted NGS assays permit the robust characterization of a large number of standard and investigational biomarkers (both single and complex) simultaneously, which cannot be achieved with the use of multiple, traditional single-gene assays. For example, the current National Comprehensive Cancer Network guidelines for NSCLC list numerous standard or emerging genomic biomarkers, including NTRK and TMB, and recommend that “testing should be conducted as part of broad molecular profiling.”7

Tumor NGS also facilitates efficient matching to clinical trials, with 11% of patients who underwent targeted NGS using the comprehensive MSK-IMPACT (Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets) assay as part of an institution-wide effort being matched to a genome-directed treatment protocol.2 NGS assays, which utilize plasma cell-free DNA (cfDNA) input, are also clinically available through a variety of commercial vendors.8-10 Although these assays enable genomic profiling in patients who lack readily accessible tissue and may capture intratumor heterogeneity, they typically assess a narrower panel of genes. Other roles for cfDNA NGS are under active investigation, including minimal molecular residual disease detection,11 response assessment,12 and cancer screening.13

Clinical NGS assays vary widely with respect to multiple factors, including the scope of the genes evaluated, sensitivity for specific alteration types, and germline variant calling.14 Oncologists should understand the advantages and disadvantages of various NGS options in the context of cancer type; disease state; available tumor material (eg, primary tissue, metastatic tissue, or plasma); and other considerations. The interpretation of NGS results may also present challenges to both treating oncologists and patients. The number and complexity of potential genomic variants that may be identified by NGS profiling is extensive, and even experienced oncologists may fail to recognize actionable variants or, conversely, may match off-label therapies to inappropriate variants. Improvements in clinical decision-making support tools are critically needed, particularly with respect to the reports that accompany commercial NGS assay results, as these often link variants to FDA-approved therapies and clinical trials in a wide-ranging fashion that may deliver outdated or inaccurate information. Con­sultation with molecular tumor boards or referral to tertiary cancer centers should be considered in appropriate scenarios.

Oncologists should also appreciate the dynamic nature of translational cancer genomics, recognizing that the true clinical significance of variants identified on prior testing may be elucidated only by future scientific advances well beyond the initial clinical review of a static NGS report. Additionally, oncologists should consider negative NGS results carefully, as false-negatives may occur because of various factors, including poor DNA quality (eg, tissue specimens derived from bone biopsies15 or plasma specimens obtained during low cfDNA shed) or the lack of inclusion of altered genes within the NGS panel. Testing with orthogonal methods or repeat biopsy (including “liquid biopsy” using plasma cfDNA) may be indicated, particularly when the clinical suspicion for an actionable genomic alteration is high, such as in a female nonsmoker with metastatic lung adenocarcinoma.

Although the use of targeted NGS assays is highly compelling in numerous types of cancer and is, arguably, the standard of care in lung adenocarcinoma, clinical scenarios may exist in which NGS testing is less compelling. While treatment with larotrectinib or pembrolizumab for tumors with the appropriate pan-cancer biomarker can result in dramatic clinical benefit, the probability of identifying NTRK gene fusions or MSI-H/dMMR status in most types of cancer is quite low.5,6 Thus, for those patients who are not candidates for clinical trials and are being treated for cancers without standard tumor type–specific genomic biomarkers, oncologists should exercise clinical judgment regarding the optimal application of NGS testing. Lastly, coordination among various stakeholders is needed to ensure that coverage of and access to NGS testing keeps pace with the rapid scientific advances in cancer genomics.

In summary, the application of targeted NGS assays in clinical oncology offers important opportunities to greatly improve patient outcomes both now and in the near future. As the costs associated with sequencing continue to decline, broader NGS assays (eg, WES and WGS), along with NGS testing at unique or multiple timepoints and in earlier disease states, will likely also find roles in clinical cancer care.

References

  1. Freedman AN, Klabunde CN, Wiant K, et al. Use of next-generation sequencing tests to guide cancer treatment: results from a nationally representative survey of oncologists in the United States. JCO Precis Oncol. 2018:1-13.
  2. Zehir A, Benayed R, Shah RH, et al. Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. Nat Med. 2017;23:703-713.
  3. Garcia EP, Minkovsky A, Jia Y, et al. Validation of OncoPanel: a targeted next-generation sequencing assay for the detection of somatic variants in cancer. Arch Pathol Lab Med. 2017;141:751-758.
  4. Frampton GM, Fichtenholtz A, Otto GA, et al. Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing. Nat Biotechnol. 2013;31:1023-1031.
  5. Drilon A, Laetsch TW, Kummar S, et al. Efficacy of larotrectinib in TRK fusion–positive cancers in adults and children. N Engl J Med. 2018;378:731-739.
  6. Le DT, Durham JN, Smith KN, et al. Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade. Science. 2017;357:409-413.
  7. National Comprehensive Cancer Network. NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines®). Non-Small Cell Lung Cancer. Version 3.2019. www.nccn.org/professionals/physician_gls/pdf/nscl.pdf. Accessed March 5, 2019.
  8. Clark TA, Chung JH, Kennedy M, et al. Analytical validation of a hybrid capture–based next-generation sequencing clinical assay for genomic profiling of cell-free circulating tumor DNA. J Mol Diagn. 2018;20:686-702.
  9. Lanman RB, Mortimer SA, Zill OA, et al. Analytical and clinical validation of a digital sequencing panel for quantitative, highly accurate evaluation of cell-free circulating tumor DNA. PloS One. 2015;10:e0140712.
  10. Guibert N, Hu Y, Feeney N, et al. Amplicon-based next-generation sequencing of plasma cell-free DNA for detection of driver and resistance mutations in advanced non-small cell lung cancer. Ann Oncol. 2018;29:1049-1055.
  11. Chaudhuri AA, Chabon JJ, Lovejoy AF, et al. Early detection of molecular residual disease in localized lung cancer by circulating tumor DNA profiling. Cancer Discov. 2017;7:1394-1403.
  12. Phallen J, Leal A, Woodward BD, et al. Early noninvasive detection of response to targeted therapy in non-small cell lung cancer. Cancer Res. 2018 Dec 20. Epub ahead of print.
  13. Cohen JD, Li L, Wang Y, et al. Detection and localization of surgically resectable cancers with a multi-analyte blood test. Science. 2018;359:926-930.
  14. Mandelker D, Zhang L, Kemel Y, et al. Mutation detection in patients with advanced cancer by universal sequencing of cancer-related genes in tumor and normal DNA vs guideline-based germline testing. JAMA. 2017;318:825-835.
  15. Abida W, Armenia J, Gopalan A, et al. Prospective genomic profiling of prostate cancer across disease states reveals germline and somatic alterations that may affect clinical decision making. JCO Precis Oncol. 2017. doi: 10.1200/PO.17.00029.
Last modified: March 18, 2019