Comprehensive Review on the Clinical Impact of Next-Generation Sequencing Tests for the Management of Advanced Cancer

Potential barriers to implementation of next-generation sequencing in cancer management: a U.S. Physician-based survey

BACKGROUND

The purpose of this study was to identify barriers to physicians' NGS use and preferred strategies to alleviate these barriers.

RESEARCH DESIGN AND METHODS

A cross-sectional online survey link was sent to a sample of US oncologists/hematologists, surgeons, and pathologists identified through a panel. The survey collected data, from October-December 2020, on barriers to NGS testing and potential strategies.

RESULTS

Two hundred physicians participated (mean age: 46.2 years; 65% male; 80% White, mean years in clinical practice: 13.7). Despite the use of NGS testing by all physicians, 99.5% reported concerns/barriers. Reimbursement challenges were the most cited reason (87.5%), followed by lack of knowledge of NGS testing methodologies (81.0%), and lack of clinical utility evidence (80.0%). The most common reimbursement challenge was prior authorizations for NGS testing (72.0%), followed by knowledge of new fee codes for reimbursement or corresponding therapy (68.0%), and paperwork/administrative duties (67.5%). Surgeons were more likely to encounter challenges in using NGS testing than other physicians.

CONCLUSIONS

The results highlight the barriers reported by oncologists/hematologists, pathologists, and surgeons, which may impact the evolving role of NGS in the context of the overall management of cancer patients.

Cost-effectiveness of next-generation sequencing for advanced EGFR/ALK-negative non-small cell lung cancer

OBJECTIVES

This study aimed to evaluate the cost-effectiveness of next-generation sequencing (NGS) versus sequential single-gene testing (SGT), including the long-term costs and survival outcomes of relevant treatments for advanced EGFR/ALK-negative non-small cell lung cancer (NSCLC).

MATERIALS AND METHODS

We developed a decision tree linked to a partitioned survival model to estimate the clinical outcomes and costs over the five-year analysis period. The decision tree consisted of treatment types based on molecular biomarker (ROS1, BRAF, NTRK, MET, RET, and KRAS alterations) test results. The probability of receiving each targeted therapy was estimated based on 1) the testing rate, 2) the proportion of alterations detected, and 3) the proportion of patients receiving treatment consistent with the testing results. We estimated the long-term overall survival and progression-free survival for each treatment using parametric estimation by reconstructing patient-level data from clinical trials. The costs of testing, drugs, administration, physician visits, monitoring, adverse events, post-progression, and end-of-life care were included. The utility values were obtained from a previous study. The incremental cost-effectiveness ratio (ICER) was used to evaluate the cost-effectiveness of NGS within a threshold of $38,701 (50,000,000 KRW) per quality-adjusted life year (QALY).

RESULTS

The incremental life-years (LYs) and QALYs for the NGS group versus the SGT group were 0.028 and 0.023, respectively. The total medical cost for the NGS group was $8,375 higher than that for the SGT group. The difference in drug costs accounted for most of the differences in total medical costs. NGS was not cost-effective compared to sequential SGT, with an ICER of $300,233/LY and $359,405/QALY, respectively.

CONCLUSIONS

NGS is not cost-effective for advanced EGFR/ALK-negative NSCLC, but has a survival benefit over sequential SGT. Our findings provide a basis for decision-making regarding the coverage and clinical utilization of NGS in regions where EGFR alterations are prevalent.

Association of Race and Ethnicity with Genomic Testing at a Comprehensive Cancer Center in North Carolina

SIGNIFICANCE

Non-Hispanic Black patients diagnosed with prostate cancer between 2014 and 2019 and treated at a comprehensive cancer center were less likely to use tumor-specific genomic testing compared with non-Hispanic White patients. Disparities in the use of precision oncology technologies should be monitored and addressed to ensure equitable cancer care.

Strategies for the treatment of hormone receptor-positive HER2-low breast cancer based on clinical practice: a round table discussion

Human epidermal growth factor receptor 2 (HER2)-low breast cancer is a newly identified targetable subset of breast tumors, and its clinical characteristics and treatment strategies are controversial. The emergence of novel anti-HER2 antibody-drug conjugate (ADC) has brought promising approaches for HER2-low breast cancer treatment. Several clinical trials have validated the efficacy and safety of trastuzumab deruxtecan (T-Dxd) in HER2-low breast cancer at different treatment settings. The treatment timing, candidate identification, long-term management, and overcoming drug resistance are crucial questions to improve breast cancer patient survival. Here we present a clinical case of hormone receptor-positive (HR+) HER2-low breast cancer patient who experienced neoadjuvant chemotherapy, surgery, adjuvant, and first-line endocrine therapy with limited effectiveness. After the treatment failure of CDK4/6 inhibitors, the utilization of T-Dxd brought a long-term disease response and tolerable low toxicities. In this round table discussion, we summarized opinions and recommendations from breast cancer surgeons and oncologists on treatment strategies for this patient. The discussion mainly focused on the precise diagnosis of HER2-low breast cancer, treatment design at different disease status, regimens selection according to drug response, strategies consideration for overcoming drug resistance and the management of adverse events in long-term survival. These opinions would provide critical insights to improve HER2-low breast cancer treatment and offer valuable suggestions for clinical practice.

Precision Oncology in Older Cancer Patients: A Single-Center Experience

In the last two decades, next-generation sequencing (NGS) has facilitated enormous progress in cancer medicine, in both diagnosis and treatment. However, the usefulness of NGS in older cancer patients is unclear. To determine the role of NGS in older cancer patients, we retrospectively assessed demographic, clinicopathologic, and disease-specific data from 100 randomly selected cancer patients (any subtype/stage) who underwent NGS testing in 2020 at our institution and compared the treatment outcomes (progression-free survival [PFS] and overall survival [OS]) in the younger and older patient cohorts (A [n = 34] and B [n = 66]: age < 70 and ≥70 years, respectively). Overall, 27% had targetable mutations, and 8% received NGS-determined targeted therapy (45% and 19% of patients with a targetable mutation in cohorts A and B, respectively; p = 0.2), of whom 38% (3% of the whole cohort) benefited from the therapy (PFS > 6 months). The median OS (from diagnosis) was 192 and 197 weeks in cohorts A and B, respectively (p = 0.08). This pilot study revealed no significant age-stratified difference in the diagnostic approach and treatment strategy. A small, but relevant, proportion of the cohort (3%) benefited from NGS-determined treatment. Nevertheless, older cancer patients with targetable mutations less frequently received targetable therapies.

Persistent Thrombotic Hemangioma With Organizing/Anastomosing Features: A Case Report of a Guanine Nucleotide-Binding Protein Alpha Subunit (GNA)-Mutated Cutaneous Vascular Lesion

Thrombotic hemangioma with organizing/anastomosing features (THOA) is a newly identified variant within the spectrum of hemangiomas that harbor mutations in the guanine nucleotide-binding protein alpha subunit (GNA) genes (like GNAQ or GNA11). While THOA shares similarities with anastomosing hemangioma, it possesses distinct clinical and morphological characteristics that make it a separate entity. All reported cases of THOA have demonstrated benign behavior. However, histologic features such as anastomosing vascular growth, mitotic figures, and endothelial hobnailing may raise concerns for a low-grade malignant vascular neoplasm. We report the case of a 74-year-old female with an unremarkable medical history who presented with a vascular lesion on her upper torso. The lesion persisted after the initial biopsy and was re-excised, displaying similar histologic characteristics. Next-generation sequencing (NGS) revealed a GNAQ mutation (p.Q209H) in both samples. Notably, a TP53 mutation (p.R273H) was detected in the first specimen but was absent in the subsequent excision. The lesion was diagnosed as persistent THOA. This case report discusses the salient features, genetic profile, and prognosis of this uncommon lesion.

Detection of four isomers of the human cytomegalovirus genome using nanopore long-read sequencing

Human cytomegalovirus has a linear DNA genome with a total length of approximately 235 kb. This large genome is divided into two domains, "Long" and "Short". There are four isomers of the cytomegalovirus genome with different orientations of each domain. To confirm the presence of four types of isomers, it is necessary to identify the sequence of the junction between the domains. However, due to the presence of repeat sequences, it is difficult to determine the junction sequences by next-generation sequencing analysis. To solve this problem, long-read sequencing was performed using the Oxford Nanopore sequencer and the junctions were successfully identified in four isomers in strain Merin and ATCC-2011-3. Nanopore sequencing also revealed the presence of multiple copies of the "a" sequence (a-seq) in the junctions, indicating the diversity of the junction sequences. These results strongly suggest that long-read sequencing using the nanopore sequencer would be beneficial for identifying the complex structure of the cytomegalovirus genome.

Benefits of NGS in Advanced Lung Adenocarcinoma Vary by Populations and Timing of Examination

Despite the widespread application of next-generation sequencing (NGS) in advanced lung adenocarcinoma, its impact on survival and the optimal timing for the examination remain uncertain. This cohort study included advanced lung adenocarcinoma patients who underwent NGS testing. We categorized patients into four groups: Group 1: treatment-naïve, upfront NGS; Group 2: Treatment-naïve, exclusionary EGFR/ALK/ROS1; Group 3: post-treatment, no known EGFR/ALK/ROS1; Group 4: known driver mutation and post-TKI treatment. A total of 424 patients were included. There were 128, 126, 90, and 80 patients in Groups 1, 2, 3, and 4, respectively. In Groups 1, 2, 3, and 4, targetable mutations were identified in 76.6%, 49.2%, 41.1%, and 33.3% of the patients, respectively (p < 0.001). Mutation-targeted treatments were applied in 68.0%, 15.1%, 27.8%, and 22.5% of the patients, respectively (p < 0.001). In the overall population, patients receiving mutation-targeted treatments exhibited significantly longer overall survival (OS) (aHR 0.54 [95% CI 0.37-0.79], p = 0.001). The most profound benefit was seen in the Group 1 patients (not reached vs. 40.4 months, p = 0.028). The median OS of patients with mutation-targeted treatments was also significantly longer among Group 2 patients. The median post-NGS survival of patients receiving mutation-targeted treatments was numerically longer in Group 3 and Group 4 patients. In conclusion, mutation-targeted therapy is associated with a favorable outcome. However, the opportunities of NGS-directed treatment and the survival benefits of mutation-targeted treatment were various among different populations.

Oncofusions - shaping cancer care

Cancer manifests through a spectrum of mutations, including gene fusions termed oncofusions. These structural alterations influence tumorigenesis across various cancer types. Oncofusions arise primarily from genomic rearrangements and operate through deregulation or hybrid gene formation mechanisms. Notable examples such as BCR::ABL and EWS::FLI1 underscore their clinical significance. Several case studies exemplify the role of identifying and targeting oncofusions in guiding treatment decisions and improving patient outcomes. However, challenges persist in discerning drivers from passenger mutations and addressing acquired resistance. Despite advancements, the complexity of oncofusions warrants further exploration of their full potential as therapeutic targets, requiring a multidisciplinary approach integrating genomics, functional studies, and innovative drug discovery strategies to achieve precision in medicine.

Next-generation sequencing for pediatric CNS tumors: does it add value in a middle-income country setup?

Introduction

Advances in molecular diagnostics led to improved targeted interventions in the treatment of pediatric CNS tumors. However, the capacity to test for these is limited in LMICs, and thus their value needs exploration.

Methods

We reviewed our experience with NGS testing (TruSight RNA Pan-Cancer-seq panel) for pediatric CNS tumors at KHCC/Jordan (March/2022-April/2023). Paraffin blocks' scrolls were shipped to the SickKids laboratory based on the multidisciplinary clinic (MDC) recommendations. We reviewed the patients' characteristics, the tumor types, and the NGS results' impact on treatment.

Results

Of 237 patients discussed during the MDC meetings, 32 patients (14%) were included. They were 16 boys and 16 girls; the median age at time of testing was 9.5 years (range, 0.9-21.9 years). There were 21 samples sent at diagnosis and 11 upon tumor progression. The main diagnoses were low-grade-glioma (15), high-grade-glioma (10), and other histologies (7). Reasons to request NGS included searching for a targetable alteration (20) and to better characterize the tumor behavior (12). The median turnaround time from samples' shipment to receiving the results was 23.5 days (range, 15-49 days) with a median laboratory processing time of 16 days (range, 8-39 days) at a cost of US$1,000/sample. There were 19 (59%) tumors that had targetable alterations (FGFR/MAPK pathway inhibitors (14), checkpoint inhibitors (2), NTRK inhibitors (2), and one with PI3K inhibitor or IDH1 inhibitor). Two rare BRAF mutations were identified (BRAFp.G469A, BRAFp.K601E). One tumor diagnosed initially as undifferentiated round cell sarcoma harbored NAB2::STAT6 fusion and was reclassified as an aggressive metastatic solitary fibrous tumor. Another tumor initially diagnosed as grade 2 astroblastoma grade 2 was reclassified as low-grade-glioma in the absence of MN1 alteration. NGS failed to help characterize a tumor that was diagnosed histologically as small round blue cell tumor. Nine patients received targeted therapy; dabrafenib/trametinib (6), pembrolizumab (2), and entrectinib (1), mostly upon tumor progression (7).

Conclusion

In this highly selective cohort, a high percentage of targetable mutations was identified facilitating targeted therapies. Outsourcing of NGS testing was feasible; however, criteria for case selection are needed. In addition, local capacity-building in conducting the test, interpretation of the results, and access to "new drugs" continue to be a challenge in LMICs.