Next-Generation Sequencing (NGS) Informs Therapy Decisions in Patients with Metastatic Cancer
Whom, When, and How Often to Test?
Erin F. Cobain
Arul M. Chinnaiyan
University of Michigan Rogel Cancer Center
@UMRogelCancer
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ext-generation sequencing (NGS) is routinely used in the clinical care of patients with advanced, metastatic cancer to identify potential therapeutic targets. In some disease settings, NGS has been incorporated into standard-of-care practice to identify a biomarker predictive of benefit from an FDA-approved therapy. In other settings, it is used to identify genomic alterations that may allow for use of a targeted therapy within the context of a clinical trial or off-label. In addition, NGS may also identify inherited cancer predisposition in approximately 15% of patients. Identification of inherited factors that may have contributed to cancer development has important implications for both the patient and family members. Here we explore the evidence that supports use of NGS in all patients with metastatic cancer, as well as the factors that should be considered with regards to timing and type of NGS testing utilized.

Next-Generation Sequencing to Personalize Care in Advanced Cancer

In the last decade, there has been great interest in utilizing next-generation sequencing (NGS) to personalize therapy of patients with metastatic cancer. This has largely stemmed from the recognition that even among tumors of similar histology, cancer is often markedly heterogeneous both at the molecular level and in clinical behavior and treatment response. With the advent of NGS, the tools to uncover the unique molecular features of a tumor became widely available, and numerous clinical studies have determined that delivery of targeted, biomarker-directed therapies may improve patient outcomes. Examples of so-called precision medicine success stories include the use of inhibitors of epidermal growth factor receptor (EGFR) and anaplastic lymphoma kinase (ALK) in EGFR- or ALK-driven non-small cell lung cancer (NSCLC), use of BRAF plus MEK inhibitors in BRAF V600E-mutant melanoma, and use of a phosphatidylinositol 3-kinase (PI3K) inhibitor in PI3K-mutated hormone receptor-positive breast cancer. Given these examples, testing for the presence of these clinically actionable genomic alterations has been incorporated into standard-of-care practice.

Broadening the Indications for NGS

These advancements have increased enthusiasm for applying this strategy more broadly across disease types, using NGS to identify potentially actionable genomic alterations and subsequently guide patients toward sequencing-directed therapy. Retrospective institutional studies such as those from Memorial Sloan Kettering and the University of Michigan have determined that among patients with advanced cancer undergoing comprehensive NGS, approximately 10%-15% are ultimately able to receive therapy informed directly by sequencing results, most often within the context of a clinical trial. Although many more patients were found to have potentially actionable genomic alterations, matching patients with appropriate clinical trials is often logistically challenging due to geographic constraints and patient factors such as poor overall health due to advanced cancer.

With the recognition that increased access to biomarker-directed clinical trials informed by NGS testing was an unmet need, two large national studies employing this strategy were developed, the American Society of Clinical Oncology Targeted Agent and Profiling Utilization Registry (TAPUR) and the National Cancer Institute (NCI) Molecular Analysis for Therapy Choice (MATCH).

Early results from TAPUR and NCI MATCH have established new treatment paradigms, particularly with regard to the use of immune checkpoint inhibitor therapies. For example, a cohort of patients with metastatic breast cancer and high tumor mutational burden (TMB) in the TAPUR study benefited from pembrolizumab (PD-1 inhibitor), and mismatch repair (MMR) deficient non-colorectal cancers benefited from nivolumab (PD-1 inhibitor). Without NGS testing, these patient populations would not have received this treatment.

Both retrospective studies and ongoing clinical trials employing NGS to identify patients with advanced cancer who may be candidates for sequencing-directed therapy have allowed us to understand the following important lessons that inform the potential clinical utility of this testing: (1) there is a reasonable likelihood of identifying a somatic genomic alteration that provides a rationale for treatment with sequencing-directed targeted therapy within the context of a clinical trial, (2) there is a reasonable likelihood of identifying a pathogenic germline variant (PGV) conferring increased cancer risk (up to 17% of patients) which may have therapeutic implications for patients and cancer screening implications for affected family members, and (3) although rare, exceptional responses to targeted therapy informed by NGS testing have been observed, of particular relevance for patients with rare cancers where limited standard treatment options may be available.

Timing and Type of NGS in Variable Disease Settings: Two Case Examples

The above raises the important question: should all patients with metastatic cancer undergo comprehensive NGS to identify potential therapeutic targets, including potential pathogenic germline variants? While we believe the answer to this question is yes, the appropriate implementation of NGS in oncology clinical practice requires more nuanced considerations than a simple yes or no answer. We must consider disease type and state, timing of testing, and the potential role for serial testing to detect emerging mechanisms of resistance to therapy and potential new therapeutic targets. Below, we highlight two case examples that illustrate these considerations in vastly different clinical circumstances, providing insight into developing a framework for optimal utilization of this technology.

CASE EXAMPLE 1: 53-year-old male with diagnosis of an intra-abdominal sarcomatoid carcinoma of unknown primary origin.

Due to lack of clear standard upfront systemic therapy recommendations, the patient underwent comprehensive NGS testing which identified a pathogenic germline variant in the MSH2 gene conferring mismatch repair (MMR) deficiency and high tumor mutational burden (TMB). The patient received nivolumab, an immune checkpoint inhibitor, within the context of a clinical trial and had a complete pathologic response which has persisted for two years and is ongoing. For this individual, there was incredible value to the pursuit of NGS in upfront disease management. The results informed a highly beneficial therapeutic strategy and allowed for family members to undergo testing for inherited cancer susceptibility and pursue enhanced cancer surveillance if affected.

CASE EXAMPLE 2: 64-year-old female with metastatic hormone receptor-positive, human epidermal growth factor 2 (HER2) receptor-negative breast cancer involving bone and liver.

The patient developed metastatic recurrence while receiving adjuvant aromatase inhibitor therapy for treatment of early-stage disease. Initial NGS on a liver biopsy revealed an activating ESR1 mutation, likely conferring resistance to aromatase inhibitor therapy, and notably lacking a PIK3CA mutation. The patient received fulvestrant, a selective estrogen receptor down-regulator, in combination with CDK4/6 inhibitor therapy, which resulted in clinical benefit for approximately two years. This was followed by exemestane in combination with everolimus, which resulted in clinical benefit for approximately six months. When disease was endocrine-therapy-refractory, the patient underwent repeat NGS on a second liver biopsy, which identified high TMB (not present with original metastatic biopsy), indicating that high TMB, a highly clinically actionable genomic alteration, likely emerged as a mechanism of endocrine-therapy resistance. This patient ultimately received pembrolizumab on clinical trial. In this second case example, initial NGS was somewhat informative, although NGS did not directly impact upfront treatment selection. NGS testing was more relevant in the setting of endocrine-therapy-refractory disease, which allowed for identification of high TMB. This highlights the potential value of serial testing that can detect emerging clinically actionable genomic alterations.

With the knowledge that serial testing may be of value in select clinical circumstances, use of “liquid biopsy” for detection of tumor-specific molecular alterations via circulating tumor DNA (ctDNA) or sequencing of circulating tumor cells (CTCs) would be ideal for monitoring tumor evolution given that it is far less invasive than tissue biopsy. Indeed, early studies have indicated that serial monitoring of patients in this manner may be clinically informative. However, one potential limitation of this approach is that ctDNA does not allow for sequencing of as many genes due to lower tumor content compared to tissue-based sampling. This may limit the ability to detect molecular features such as high TMB or gene fusions, which are often best identified via RNA-based transcriptomic sequencing. However, for circumstances where the goal is to identify specific point mutations that confer potential benefit from or resistance to a particular therapy, liquid biopsy monitoring may be ideal. In addition, for those patients with higher disease burden and thus higher tumor content, broader testing is feasible (Table 1).

Table 1. Comparison of Tumor-Based NGS versus Liquid Biopsy Sequencing Strategies
Tissue-based NGS
ctDNA
CTCs
Adequate Tumor Content
Yes
Sometimes
Sometimes
Identification of Clinically Actionable Genomic Alterations
Yes
Yes
Yes
Unambiguous Zygosity of Genomic Alterations
Yes
No
Yes (single cell)
TMB and MSI Status Detectable
Yes
Sometimes
Sometimes
Representative of Total Disease Burden
Unknown
Yes
Yes
Cellular Phenotyping Possible (i.e., PD-L1 staining)
Yes
No
Yes
Suitable for Longitudinal Monitoring (i.e., Serial Sampling)
No
Yes
Yes
Adequate Tumor Content
TISSUE-BASED NGS
Yes
CTDNA
Sometimes
CTCs
Sometimes
Identification of Clinically Actionable Genomic Alterations
TISSUE-BASED NGS
Yes
CTDNA
Yes
CTCs
Yes
Unambiguous Zygosity of Genomic Alterations
TISSUE-BASED NGS
Yes
CTDNA
No
CTCs
Yes (single cell)
TMB and MSI Status Detectable
TISSUE-BASED NGS
Yes
CTDNA
Sometimes
CTCs
Sometimes
Representative of Total Disease Burden
TISSUE-BASED NGS
Unknown
CTDNA
Yes
CTCs
Yes
Cellular Phenotyping Possible (i.e., PD-L1 staining)
TISSUE-BASED NGS
Yes
CTDNA
No
CTCs
Yes
Suitable for Longitudinal Monitoring (i.e., Serial Sampling)
TISSUE-BASED NGS
No
CTDNA
Yes
CTCs
Yes

Conclusions Regarding Utilization of NGS in Advanced Cancer

In summary, the evidence to date suggests that undergoing tumor and normal NGS testing (i.e., comparisons of tumor vs. matched normal DNA to identify variants) should be considered for all patients with advanced cancer. This type of testing has the potential to identify tumor-specific somatic genomic alterations that may predict clinical benefit from targeted therapeutics as well as to identify pathogenic germline variants conferring increased cancer risk, which may have direct therapeutic implications (see Case Example 1). However, the optimal timing for this testing is highly dependent on clinical circumstance. In disease settings where upfront systemic therapy options are highly effective with minimal toxicity, this testing may be best employed later in the therapeutic algorithm to capture clinically actionable genomic events that occur throughout tumor evolution. In contrast, in rare cancers or disease settings with few effective standard therapies, this testing may be of maximum benefit at initial diagnosis. Finally, there is likely value to serial NGS in select circumstances, where liquid biopsy approaches may be incorporated to avoid repeat tissue biopsies (see Case Example 2).
References available upon request.
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