Assessing the Value of Next-Generation Sequencing Tests in a Dynamic Environment

How is Value Defined in Molecular Testing in Cancer? A Scoping Review

OBJECTIVE

To identify how value is defined in studies that focus on the value of molecular testing in cancer and the extent to which broadening the conceptualisation of value in healthcare has been applied in the molecular testing literature.

METHODS

A scoping review was undertaken using Joanna Briggs Institute (JBI) guidance. Medline, Embase, EconLit and Cochrane Library were searched in August 2023. Articles were eligible if they reported costs relative to outcomes, novel costs, or novel outcomes of molecular testing in cancer. Results were synthesised and qualitative content analysis was performed with deductive and inductive frameworks.

RESULTS

Ninety-one articles were included in the review. The majority (75/91) were conventional economic analyses (comparative economic evaluations and budget impact assessments) and undertaken from a healthcare system perspective (38/91). Clinical outcomes dominate the assessment of value (61/91), with quality-adjusted life-years (QALYs) the most common outcome measure (45/91). Other definitions of value were diverse (e.g. psychological impact, access to trials), inconsistent, and largely not in keeping with evolving guidance.

CONCLUSIONS

Broader concepts of value were not commonly described in the molecular testing literature focusing on cancer. Conventional approaches to measuring the health costs and outcomes of molecular testing in cancer prevail with little focus on non-clinical elements of value. There are emerging reports of non-clinical outcomes of testing information, particularly psychological consequences. Intrinsic attributes of the testing process and preferences of those who receive testing information may determine the realised societal value of molecular testing and highlight challenges to implementing such a value framework.

Precision Medicine Testing and Disparities in Health Care for Individuals With Non-Small Cell Lung Cancer: A Narrative Review

PROBLEM IDENTIFICATION

Precision medicine initiatives provide opportunities for optimal targeted therapy in individuals with non-small cell lung cancer. However, there are barriers to these initiatives that reflect social determinants of health.

LITERATURE SEARCH

MEDLINE®, CINAHL®, PsycINFO®, Embase®, and Google ScholarTM databases were searched for articles published in English in the United States from 2016 to 2020.

DATA EVALUATION

Data that were collected included individual demographic information, specific diagnosis, status of targeted genomic testing, and receipt of targeted therapy. All studies were retrospective and involved database review of insurance claims or medical records.

SYNTHESIS

Individuals with non-small cell lung cancer received less genetic testing and targeted therapy if they were of a lower socioeconomic status, had public health insurance or no health insurance, were Black, or lived in rural communities.

IMPLICATIONS FOR NURSING

Social determinants of health affect health equity, including in precision medicine initiatives for individuals with lung cancer. Gaining an understanding of this impact is the first step in mitigating inequities.

Utility of Multimodality Molecular Profiling for Pediatric Patients with Central Nervous System Tumors

Background

As our molecular understanding of pediatric central nervous system (CNS) tumors evolves, so too do diagnostic criteria, prognostic biomarkers, and clinical management decision-making algorithms. Here, we explore the clinical utility of wide-breadth assays including whole-exome sequencing (WES), RNA sequencing (RNAseq), and methylation array profiling as an addition to more conventional diagnostic tools for pediatric CNS tumors.

Methods

This study comprises an observational, prospective cohort followed at a single academic medical center over three years. Paired tumor and normal control specimens from 53 enrolled pediatric patients with CNS tumors underwent WES. A subset of cases also underwent RNAseq (n=28) and/or methylation array analysis (n=27).

Results

RNAseq identified driver and/or targetable fusions in 7/28 cases, including potentially targetable NTRK fusions, and uncovered possible rationalized treatment options based on outlier gene expression in 23/28 cases. Methylation profiling added diagnostic confidence (8/27 cases) or diagnostic subclassification endorsed by the WHO (10/27 cases). WES detected clinically pertinent Tier 1 or Tier 2 variants in 36/53 patients. Of these, 16/17 SNVs/indels and 10/19 copy number alterations would have been detected by current in-house conventional tests including targeted sequencing panels.

Conclusions

Over a heterogeneous set of pediatric tumors, RNAseq and methylation profiling frequently yielded clinically relevant information orthogonal to conventional methods while WES demonstrated clinically-relevant added-value primarily via copy number assessment. Longitudinal cohorts comparing targeted molecular pathology workup versus broader genomic approaches including therapeutic selection based on RNA-expression data will be necessary to further evaluate the clinical benefits of these modalities in practice.

Precision medicine-based therapies in advanced colorectal cancer: The University of California San Diego Molecular Tumor Board experience

Treatment for advanced colorectal cancer is often limited by complex molecular profiles, which promote resistance to systemic agents and targeted monotherapies. Recent studies suggest that a personalized, combinatorial approach of matching drugs to tumor alterations may be more effective. We implemented a precision medicine strategy by forming a Molecular Tumor Board (MTB), a multidisciplinary team of clinicians, scientists, bioinformaticians and geneticists. The MTB integrated molecular profiling information and patient characteristics to develop N-of-One treatments for 51 patients with advanced colorectal cancer. All patients had metastatic disease and 63% had received ≥3 prior therapy lines. Overall, 34/51 patients (67%) were matched to ≥1 drug recommended by the MTB based on individual tumor characteristics whereas 17/51 (33%) patients received unmatched therapies. Patients who received matched therapy demonstrated significantly longer progression-free survival (hazard ratio [HR], 0.41; 95% CI, 0.21-0.81; P=0.01) and a trend towards higher clinical benefit rates (41% vs. 18% P=0.058) (all multivariate) compared to patients receiving unmatched therapy. The MTB facilitated personalized matching of drugs to tumor characteristics, which was associated with improved progression-free survival in patients with advanced colorectal cancer.

Economic evaluation of genomic/genetic tests: a review and future directions

It has been suggested that health economists need to improve their methods in order to meet the challenges of evaluating genomic/genetic tests. In this article, we set out twelve challenges identified from a rapid review of the literature and suggest solutions to the challenges identified. Two challenges were common to all economic evaluations: choice of perspective and time-horizon. Five challenges were relevant for all diagnostic technologies: complexity of analysis; range of costs; under-developed evidence base; behavioral aspects; and choice of outcome metrics. The final five challenges were pertinent for genomic tests and only these may require methodological development: heterogeneity of tests and platforms, increasing stratification, capturing personal utility; incidental findings; and spillover effects. Current methods of economic evaluation are generally able to cope with genomic/genetic tests, although a renewed focus on specific decision-makers’ needs and a willingness to move away from cost-utility analysis may be required. Certain analysts may be constrained by reference cases developed primarily for the assessment of pharmaceuticals. The combined impact of multiple challenges may require analysts to be particularly careful in setting the scope of their analysis in order to ensure that feasibility is balanced with usefulness to the decision maker. A key issue is the under-developed evidence-base and it may be necessary to rethink translation processes to ensure sufficient, relevant evidence is available to support economic evaluation and adoption of genomic/genetic tests.

Teaching next-generation sequencing to medical students with a portable sequencing device

BACKGROUND

There continues to be a disjoint between the emergence of new diagnostic technologies and venues to train new physicians on how to apply them. Next-generation sequencing (NGS) has become a very important tool for a wide range of clinical applications. Technical complexity and cost have been the major obstacles in incorporating these technologies into the classroom.

GOAL FOR INNOVATION

We opted to use the MinION, which is a new portable DNA sequencer that can produce data in real-time at a relatively low cost, for a NGS hands-on workshop with medical students.

STEPS TAKEN

We conducted a pilot NGS hands-on practical module in order to expose an interested group of medical students to this new portable sequencer device. A pre- and post-survey, using a Likert-type scale survey items and open-ended questions, evaluated participant resistance to new diagnostic tools, familiarity with NGS, and likelihood to use a portable sequencer in clinical practice.

OUTCOMES

Prior to participating in our learning workshop, students did not understand how to incorporate NGS into clinical practice, and expressed that cost and prior training/knowledge were among the limiting factors in their likelihood to use NGS as a diagnostic tool. After participating in the module, students' responses demonstrated a shift in their understanding of the scientific principles and applications of NGS (pre- and post-survey scores p < 0.05).

REFLECTION

The hands-on experience not only helped students become closer to and more comfortable with NGS, but also served as a venue to discuss the science and application of this technology in medicine. Such discussion helped to provide participants with current "genetic literacy" that is often incompletely covered in the typical undergraduate medical education curriculum.

Distribution of Genomic Testing Resources by Oncology Practice and Rurality: A Nationally Representative Study

PURPOSE

Oncologists are increasingly using molecular profiling to inform personalized patient treatment decisions. Despite its promising utility, the integration of genomic testing into diverse clinical health care settings across geographic settings has been understudied.

METHODS

We used data from the National Survey of Precision Medicine in Cancer Treatment, a nationally representative sample of practicing US oncologists, to assess the availability of six genomic testing resources, including on-site pathology, contracts with outside laboratories, on-site genetic counselors, internal policies or protocols for using genomic and biomarker testing, electronic medical record alerts, and genomic or molecular tumor boards. We used multivariate logistic regression models to examine differences in the availability of each genomic testing resource by practice type and rurality while adjusting for payer mix and patient volume.

RESULTS

A larger proportion of multispecialty group and academic practices had genomic testing resources available compared with solo and nonacademic practices. Electronic medical record alerts were the least available resource, whereas contracts with outside laboratories were the most available resource. Compared with urban practices, there were significantly fewer practices located in rural areas that had on-site pathology, on-site genetic counselors, protocols for genomic tests, and molecular tumor boards.

CONCLUSION

Genomic testing resources varied by practice type and geography among a nationally representative sample of practicing oncologists. This variation has important implications for the development of interventions and policies to support the more equitable delivery of precision oncology to patients with cancer.

Analytic validation and clinical utilization of the comprehensive genomic profiling test, GEM ExTra®

We developed and analytically validated a comprehensive genomic profiling (CGP) assay, GEM ExTra, for patients with advanced solid tumors that uses Next Generation Sequencing (NGS) to characterize whole exomes employing a paired tumor-normal subtraction methodology. The assay detects single nucleotide variants (SNV), indels, focal copy number alterations (CNA), TERT promoter region, as well as tumor mutation burden (TMB) and microsatellite instability (MSI) status. Additionally, the assay incorporates whole transcriptome sequencing of the tumor sample that allows for the detection of gene fusions and select special transcripts, including AR-V7, EGFR vIII, EGFRvIV, and MET exon 14 skipping events. The assay has a mean target coverage of 180X for the normal (germline) and 400X for tumor DNA including enhanced probe design to facilitate the sequencing of difficult regions. Proprietary bioinformatics, paired with comprehensive clinical curation results in reporting that defines clinically actionable, FDA-approved, and clinical trial drug options for the management of the patient's cancer. GEM ExTra demonstrated analytic specificity (PPV) of > 99.9% and analytic sensitivity of 98.8%. Application of GEM ExTra to 1,435 patient samples revealed clinically actionable alterations in 83.9% of reports, including 31 (2.5%) where therapeutic recommendations were based on RNA fusion findings only.

Fine-needle aspiration as an alternative to core needle biopsy for tumour molecular profiling in precision oncology: prospective comparative study of next-generation sequencing in cancer patients included in the SHIVA02 trial

High-throughput molecular profiling of solid tumours using core needle biopsies (CNB) allows the identification of actionable molecular alterations, with around 70% success rate. Although several studies have demonstrated the utility of small biopsy specimens for molecular testing, there remains debate as to the sensitivity of the less invasive fine-needle aspiration (FNA) compared to CNB to detect molecular alterations. We aimed to prospectively evaluate the potential of FNA to detect such alterations in various tumour types as compared to CNB in cancer patients included in the SHIVA02 trial. An in-house amplicon-based targeted sequencing panel (Illumina TSCA 99.3 kb panel covering 87 genes) was used to identify pathogenic variants and gene copy number variations (CNV) in concomitant CNB and FNA samples obtained from 61 patients enrolled in the SHIVA02 trial (NCT03084757). The main tumour types analysed were breast (38%), colon (15%), pancreas (11%), followed by cervix and stomach (7% each). We report 123 molecular alterations (85 variants, 23 amplifications and 15 homozygous deletions) among which 98 (80%) were concordant between CNB and FNA. The remaining discordances were mainly related to deletions status, yet undetected alterations were not exclusively specific to FNA. Comparative analysis of molecular alterations in CNB and FNA showed high concordance in terms of variants as well as CNVs identified. We conclude FNA could therefore be used in routine diagnostics workflow and clinical trials for tumour molecular profiling with the advantages of being minimally invasive and preserve tissue material needed for diagnostic, prognostic or theranostic purposes.

Real-world data from a molecular tumor board demonstrates improved outcomes with a precision N-of-One strategy

Next-generation sequencing (NGS) can identify novel cancer targets. However, interpreting the molecular findings and accessing drugs/clinical trials is challenging. Furthermore, many tumors show resistance to monotherapies. To implement a precision strategy, we initiated a multidisciplinary (basic/translational/clinical investigators, bioinformaticians, geneticists, and physicians from multiple specialties) molecular tumor board (MTB), which included a project manager to facilitate obtaining clinical-grade biomarkers (blood/tissue NGS, specific immunohistochemistry/RNA expression including for immune-biomarkers, per physician discretion) and medication-acquisition specialists/clinical trial coordinators/navigators to assist with medication access. The MTB comprehensively reviewed patient characteristics to develop N-of-One treatments implemented by the treating physician's direction under the auspices of a master protocol. Overall, 265/429 therapy-evaluable patients (62%) were matched to ≥1 recommended drug. Eighty-six patients (20%) matched to all drugs recommended by MTB, including combinatorial approaches, while 38% received physician's choice regimen, generally with unmatched approach/low degree of matching. Our results show that patients who receive MTB-recommended regimens (versus physician choice) have significantly longer progression-free (PFS) and overall survival (OS), and are better matched to therapy. High (≥50%) versus low (<50%) Matching Score therapy (roughly reflecting therapy matched to ≥50% versus <50% of alterations) independently correlates with longer PFS (hazard ratio [HR], 0.63; 95% confidence interval [CI], 0.50-0.80; P < 0.001) and OS (HR, 0.67; 95% CI, 0.50-0.90; P = 0.007) and higher stable disease ≥6 months/partial/complete remission rate (52.1% versus 30.4% P < 0.001) (all multivariate). In conclusion, patients who receive MTB-based therapy are better matched to their genomic alterations, and the degree of matching is an independent predictor of improved oncologic outcomes including survival.