Integrating comprehensive genomic sequencing of non-small cell lung cancer into a public healthcare system

Comprehensive Genomic Profiling of Indian Patients With Lung Cancer

PURPOSE

Genomic profiling has revolutionized non-small cell lung cancer (NSCLC) therapy, but molecular data on Indian patients with NSCLC are limited.

MATERIALS AND METHODS

We analyzed next-generation sequencing (NGS) data of 5,219 Indian patients with lung cancer, tested between May 2022 and August 2023 at CORE Diagnostics, a commercial laboratory in India. Using the PulmoCORE gene panel, we targeted 13 key genes (ALK, BRAF, EGFR, ERBB2, KRAS, MAP2K1, MET, NRAS, PIK3CA, RET, ROS1, TP53, and NTRK) for DNA and RNA sequencing. PD-L1 was tested by immunohistochemistry.

RESULTS

Median patient age was 62 years, and 62.5% were male. Common histologies included adenocarcinoma (57.1%), NSCLC not otherwise specified (19.3%), and squamous cell carcinoma (7%). Genomic alterations were detected in 80.6% patients according to the PulmoCORE panel; 64.2% patients had actionable alterations in at least one of the nine biomarkers with Food and Drug Administration-approved targeted therapies, that is, EGFR, KRAS, ALK, ROS1, BRAF, NTRK1/2/3, MET, RET, and ERBB2. Common alterations included TP53 (37%), EGFR (34.1%), and KRAS (13.3%), ALK (8.8%), and others below 5%. Alterations were more common in adenocarcinoma (76.4%) than in patients with squamous cell carcinoma (29.9%). Sex and age influenced mutation prevalence, with EGFR mutations more common in females and KRAS in males, while ALK, ROS1, and RET fusions were prevalent in younger adults. Most genomic alterations were mutually exclusive, although 25% patients had co-occurring mutations. PD-L1 positivity was higher in males (28.3%) and more common in patients with squamous cell carcinoma (34.2%).

CONCLUSION

Broad molecular profiling is important to detect actionable alterations in Indian patients with lung cancer, for delivering optimal personalized precision medicine. Our study underscores the fact that NGS should be routinely done before planning therapy in Indian patients with advanced lung cancer.

Comprehensive genomic profiling: a public health system perspective

INTRODUCTION

Comprehensive genomic profiling (CGP) is gaining ground in modern precision oncology for its ability to potentially analyze multiple tumor alterations and identify actionable ones, guiding targeted anticancer treatments. However, integrating CGP into healthcare systems demands consideration of the available evidence and collaboration between shareholders.

AREAS COVERED

This review explores CGP's cost-effectiveness and feasibility across diverse healthcare settings, based on searches in PubMed, Google Scholar, gray literature, and extensive snowballing. We further aimed to elucidate barriers to routine CGP implementation and discuss potential solutions.

EXPERT OPINION

Patients generally express satisfaction with CGP, especially if publicly funded, yet face difficulties in understanding test results, and managing lack of actionable mutations and access to novel treatment avenues. Physicians exhibit confidence in recommending and interpreting CGP for patients with refractory disease and considerable life expectancy and performance status, albeit acknowledging potential treatment delays. Health economic studies support CGP's cost-effectiveness, highlighting increased survival, productivity, reduced medical service utilization, and cost diversion to trial sponsors. Nonetheless, challenges persist, including reimbursement policies, limited testing accessibility, and the imperative for physician training and infrastructure enhancement. Addressing these issues through collaborative efforts and policy adjustments is paramount for realizing the full potential of CGP in advancing precision oncology.

Trends in Real-World Clinical Outcomes of Patients with Anaplastic Lymphoma Kinase (ALK) Rearranged Non-Small Cell Lung Cancer (NSCLC) Receiving One or More ALK Tyrosine Kinase Inhibitors (TKIs): A Cohort Study in Ontario, Canada

The treatment landscape for patients with advanced ALK-positive NSCLC has rapidly evolved following the approval of several ALK TKIs in Canada. However, public funding of ALK TKIs is mostly limited to the first line treatment setting. Using linked provincial health administrative databases, we examined real-world outcomes of patients with advanced ALK-positive NSCLC receiving ALK TKIs in Ontario between 1 January 2012 and 31 December 2021. Demographic, clinical characteristics and treatment patterns were summarized using descriptive statistics. Kaplan-Meier analysis was performed to evaluate progression-free survival (PFS) and overall survival (OS) among the treatment groups. A total of 413 patients were identified. Patients were administered alectinib (n = 154), crizotinib (n = 80), or palliative-intent chemotherapy (n = 55) in the first-line treatment. There was a significant difference in first-line PFS between the treatment groups. The median PFS (mPFS) was not reached for alectinib (95% CI, 568 days-not reached), compared to 8.2 months (95% CI, 171-294 days) for crizotinib (HR = 0.34, p < 0.0001) and 2.4 months (95% CI, 65-100 days) for chemotherapy (HR = 0.14, p < 0.0001). There was no significant difference in first-line OS between the treatment groups. In patients who received more than one line of treatment, there was a significant difference in mOS between patients who received two or more lines of ALK TKIs compared to those who received one line of ALK TKI (mOS = 55 months (95% CI, 400-987 days) and 26 months (95% CI, 1448-2644 days), respectively, HR = 4.64, p < 0.0001). This study confirms the effectiveness of ALK TKIs in real-world practice and supports the potential benefit of multiple lines of ALK TKI on overall survival in patients with ALK-positive NSCLC.

Biomarkers to Inform Prognosis and Treatment for Unresectable or Metastatic GEP-NENs

Importance

Evidence-based treatment decisions for advanced gastroenteropancreatic neuroendocrine neoplasms (GEP-NENs) require individualized patient-centered decision-making that accounts for patient and cancer characteristics.

Objective

To create an accessible guidance document to educate clinicians and patients on biomarkers informing prognosis and treatment in unresectable or metastatic GEP-NENs.

Methods

A multidisciplinary panel in-person workshop was convened to define methods. English language articles published from January 2016 to January 2023 in PubMed (MEDLINE) and relevant conference abstracts were reviewed to investigate prognostic and treatment-informing features in unresectable or metastatic GEP-NENs. Data from included studies were used to form evidence-based recommendations. Quality of evidence and strength of recommendations were determined using the Grading of Recommendations, Assessment, Development and Evaluations framework. Consensus was reached via electronic survey following a modified Delphi method.

Findings

A total of 131 publications were identified, including 8 systematic reviews and meta-analyses, 6 randomized clinical trials, 29 prospective studies, and 88 retrospective cohort studies. After 2 rounds of surveys, 24 recommendations and 5 good clinical practice statements were developed, with full consensus among panelists. Recommendations focused on tumor and functional imaging characteristics, blood-based biomarkers, and carcinoid heart disease. A single strong recommendation was made for symptomatic carcinoid syndrome informing treatment in midgut neuroendocrine tumors. Conditional recommendations were made to use grade, morphology, primary site, and urinary 5-hydroxyindoleacetic levels to inform treatment. The guidance document was endorsed by the Commonwealth Neuroendocrine Tumour Collaboration and the North American Neuroendocrine Tumor Society.

Conclusions and Relevance

The study results suggest that select factors have sufficient evidence to inform care in GEP-NENs, but the evidence for most biomarkers is weak. This article may help guide management and identify gaps for future research to advance personalized medicine and improve outcomes for patients with GEP-NENs.

Consensus Recommendations to Optimize Testing for New Targetable Alterations in Non-Small Cell Lung Cancer

Non-small cell lung cancer (NSCLC) has historically been associated with a poor prognosis and low 5-year survival, but the use of targeted therapies in NSCLC has improved patient outcomes over the past 10 years. The pace of development of new targeted therapies is accelerating, with the associated need for molecular testing of new targetable alterations. As the complexity of biomarker testing in NSCLC increases, there is a need for guidance on how to manage the fluid standard-of-care in NSCLC, identify pragmatic molecular testing requirements, and optimize result reporting. An expert multidisciplinary working group with representation from medical oncology, pathology, and clinical genetics convened via virtual meetings to create consensus recommendations for testing of new targetable alterations in NSCLC. The importance of accurate and timely testing of all targetable alterations to optimize disease management using targeted therapies was emphasized by the working group. Therefore, the panel of experts recommends that all targetable alterations be tested reflexively at NSCLC diagnosis as part of a comprehensive panel, using methods that can detect all relevant targetable alterations. In addition, comprehensive biomarker testing should be performed at the request of the treating clinician upon development of resistance to targeted therapy. The expert multidisciplinary working group also made recommendations for reporting to improve clarity and ease of interpretation of results by treating clinicians and to accommodate the rapid evolution in clinical actionability of these alterations. Molecular testing of all targetable alterations in NSCLC is the key for treatment decision-making and access to new therapies. These consensus recommendations are intended as a guide to further optimize molecular testing of new targetable alterations.

Upfront Next Generation Sequencing in Non-Small Cell Lung Cancer

In advanced non-small cell lung cancer (NSCLC), patients with actionable genomic alterations may derive additional clinical benefit from targeted treatment compared to cytotoxic chemotherapy. Current guidelines recommend extensive testing with next generation sequencing (NGS) panels. We investigated the impact of using a targeted NGS panel (TruSight Tumor 15, Illumina) as reflex testing for NSCLC samples at a single institution. Molecular analysis examined 15 genes for hotspot mutation variants, including AKT1, BRAF, EGFR, ERBB2, FOXL2, GNA11, GNAQ, KIT, KRAS, MET, NRAS, PDGFRA, PIK3CA, RET and TP53 genes. Between February 2017 and October 2020, 1460 samples from 1395 patients were analyzed. 1201 patients (86.1%) had at least one variant identified, most frequently TP53 (47.5%), KRAS (32.2%) or EGFR (24.2%). Among these, 994 patients (71.3%) had clinically relevant variants eligible for treatment with approved therapies or clinical trial enrollment. The incremental cost of NGS beyond single gene testing (EGFR, ALK) was CAD $233 per case. Reflex upfront NGS identified at least one actionable variant in more than 70% of patients with NSCLC, with minimal increase in testing cost. Implementation of NGS panels remains essential as treatment paradigms continue to evolve.

An Idealized Clinicogenomic Registry to Engage Underrepresented Populations Using Innovative Technology

Current best practices in tumor registries provide a glimpse into a limited time frame over the natural history of disease, usually a narrow window around diagnosis and biopsy. This creates challenges meeting public health and healthcare reimbursement policies that increasingly require robust documentation of long-term clinical trajectories, quality of life, and health economics outcomes. These challenges are amplified for underrepresented minority (URM) and other disadvantaged populations, who tend to view the institution of clinical research with skepticism. Participation gaps leave such populations underrepresented in clinical research and, importantly, in policy decisions about treatment choices and reimbursement, thus further augmenting health, social, and economic disparities. Cloud computing, mobile computing, digital ledgers, tokenization, and artificial intelligence technologies are powerful tools that promise to enhance longitudinal patient engagement across the natural history of disease. These tools also promise to enhance engagement by giving participants agency over their data and addressing a major impediment to research participation. This will only occur if these tools are available for use with all patients. Distributed ledger technologies (specifically blockchain) converge these tools and offer a significant element of trust that can be used to engage URM populations more substantively in clinical research. This is a crucial step toward linking composite cohorts for training and optimization of the artificial intelligence tools for enhancing public health in the future. The parameters of an idealized clinical genomic registry are presented.