David W. Hall

The rapid development of therapies linked to molecular biomarkers has increased the importance of next-generation sequencing (NGS)-based tumor profiling to guide treatment decisions. Technology has enabled more comprehensive clinical testing; however, the optimal economic approach deserves investigation. This study evaluated the impact of testing using whole-exome, whole-transcriptome sequencing (WES/WTS) versus 50-gene panel tests from a US payer perspective. A previously published Microsoft Excel-based model was used to compare WES/WTS and four 50-gene panels for testing within triple-negative breast cancer (TNBC), colorectal cancer (CRC), non-small cell lung cancer (NSCLC), and castrate resistant prostate cancer (CRPC). Genomic alteration prevalence and test sensitivity were based on a previous analysis of WES/WTS results in clinical samples. Model inputs related to the patient population, costs, clinical trial uptake, and market share were based on published literature. Results included the number of patients directed to a different therapy and the per-member per-month (PMPM) impact to a health plan when increasing utilization of WES/WTS testing. In a one-million-member hypothetical plan, 858 patients were eligible for tumor profiling. Across the four 50-gene panel tests, the number of patients switching treatment when using WES/WTS testing was 1-2 (TNBC), 4-6 (CRC), 1-6 (NSCLC), and 3-5 (CRPC). PMPM cost differences when replacing use of 50-gene panels with WES/WTS testing ranged from a cost-savings of $0.0517 in NSCLC to a $0.0268 increase in CRPC. Per-patient costs when using WES/WTS testing were driven by medical and pharmacy costs, with testing representing only 1.1-2.1% of total costs. Limitations include simplifications required in modeling and exclusion of recently approved therapeutic options due to the quickly evolving landscape. WES/WTS testing resulted in more patients directed to targeted therapies with a minimal budget impact and should be considered in clinical decision-making to improve patient outcomes.

PURPOSE: With an increase in approved targeted therapies for non–small cell lung cancer (NSCLC), tumor profiling that maximizes identification of patients eligible for these treatments is essential. In this study, we compare testing approaches for newly diagnosed advanced or metastatic NSCLC. METHODS: An economic model was developed to estimate the annual costs and clinical outcomes associated with testing alternatives. Patients were assigned alterations on the basis of rates observed in published literature. Treatment approaches included no genomic testing; sequential single-gene testing; or a whole-exome, whole-transcriptome (WES/WTS) comprehensive genomic profiling to inform use of targeted therapies. The budget impact and survival implications of WES/WTS were compared head to head with the other testing approaches, and uncertainty was assessed in sensitivity analyses. In scenario analyses, tests that incorporate both DNA and RNA were compared with tests using DNA sequencing alone when assuming the prevalence of fusions that can only be identified by RNA ranged from 2.5% to 14%. RESULTS: Compared with no testing, WES/WTS reduced costs by $8,809 in US dollars (USD) per patient tested while increasing median overall survival by an average of 3.9 months. When compared with sequential single-gene testing, use of WES/WTS decreased costs by $14,602 (USD) per patient and had a minimal survival benefit. A test that included both RNA and DNA sequencing reduced costs by $400-$1,724 (USD) and increased identification of actionable alterations by 2.3%-13.0% across the range of fusion prevalence. CONCLUSION: Use of WES/WTS improved clinical outcomes while reducing costs. These findings should be considered when choosing between tumor profiling approaches.

Background and Objectives: Identification of colorectal cancer (CRC) patients at high risk of recurrence could be of substantial clinical use. We evaluated the association of ctDNA status, using a tumor‐informed assay, with recurrence‐free survival (RFS).Methods: Stage III CRC patients were enrolled between 2016 and 2020. Tumor tissue and serial (every 3 months for years 1–3, biannually for years 4–5) blood samples were collected. Utilizing whole‐exome sequencing and selection of 50–200 variants for tumor informed assays, ctDNA status was determined using plasma cell‐free DNA.Results: Of 137 patients enrolled, 124 with 1029 ctDNA results were included in the analyses. Median follow‐up was 4.8 years. Plasma ctDNA status was strongly associated with risk of recurrence during the surveillance period (hazard ratio (HR) 49.6, 95% CI: 16.6–148.3; p < 0.0001), and at the postsurgical (HR 9.6, 95% CI: 3.2–29.5) and postdefinitive therapy timepoints (HR: 16.7, 95% CI: 6.9–40.3). The estimated 3‐year RFS for ctDNA positive and ctDNA negative patients were, respectively, 54.5% and 96.1% after surgery, and 18.2% and 90.0% after definitive therapy. Multivariable analysis indicated ctDNA but not CEA was strongly prognostic for recurrence.Conclusions: Our tumor‐informed ctDNA assay was strongly prognostic for recurrence in patients with stage III colorectal cancer at all timepoints.

Colorectal cancer (CRC) is a common cancer in younger adults. In patients undergoing liver resection with RAS-altered CRCs, there is evidence suggesting younger patients have worse outcomes than older patients. To explain this pattern, differences in associations between RAS status and other cancer-related biomarkers in tumors from younger versus older patients with CRC were evaluated in a cohort of 925 patients with CRC, 277 (30.0%) of whom were ≤50 years old, and 454 (49.1%) who had RAS-altered tumors. For 3 biomarkers, RNF43, APC, and microsatellite instability (MSI), the association with RAS status was significantly modified by age after adjustment for multiple testing. Specifically, younger patients with RAS-altered tumors were more likely to be MSI-high, RNF43 mutated, and APC wild type. These differences might contribute to the observed pattern of diminished survival in younger versus older patients with CRC with RAS-mutated tumors undergoing liver metastasis resection.

Aims: The availability of targeted therapies for oncology patients is increasing. Available genomic tests to identify treatment-eligible patients include single gene tests and gene panel tests, including the whole-exome, whole-transcriptome OncoExTra^TM test. We assessed the costs and clinical benefits of test choice. Methods: A Microsoft Excel-based model was developed to evaluate test choice in patients with advanced/metastatic non-small cell lung cancer (NSCLC), breast, prostate, and colorectal cancer. Treatment pathways were based on NCCN guidelines and medical expert opinion. Inputs were derived from published literature. Annual economic results and lifetime clinical results with OncoExTra testing were projected per-tested-patient and compared with single gene testing and no testing. Separately, results were estimated for a US health plan without the OncoExTra test and with its use in 5% of patients. Results: Compared with no genomic testing, OncoExTra test use increased costs by $4,915 per patient; however, 82%-92% of individuals across tumor types were identified as eligible for targeted therapy or a clinical trial. Compared with single gene testing, OncoExTra test use decreased costs by $9,966 per-patient-tested while increasing use of approved or investigational targeted therapies by 20%. When considering a hypothetical health plan with 1 million members, 858 patients were eligible for genomic testing. Using the OncoExTra test in 5% of those eligible, per-member per-month costs decreased by $0.003, ranging from cost-savings of $0.026 in NSCLC patients to a $0.009 increase in prostate cancer patients. Cost-savings were driven by reduced treatment costs with increased clinical trial enrollment and reduced direct and indirect medical costs associated with targeted treatments. Conclusions: Limitations include the required simplifications in modeling complex conditions that may not fully reflect evolving real-world testing and treatment patterns. Compared to single-gene testing, results indicate that using NGS test such as OncoExTra identified more actionable alterations, leading to improved outcomes and reduced costs.

The fitness effects of new mutations determine key properties of evolutionary processes. Beneficial mutations drive evolution, yet selection is also shaped by the frequency of small-effect deleterious mutations, whose combined effect can burden otherwise adaptive lineages and alter evolutionary trajectories and outcomes in clonally evolving organisms such as viruses, microbes, and tumors. The small effect sizes of these important mutations have made accurate measurements of their rates difficult. In microbes, assessing the effect of mutations on growth can be especially instructive, as this complex phenotype is closely linked to fitness in clonally evolving organisms. Here, we perform high-throughput time-lapse microscopy on cells from mutation-accumulation strains to precisely infer the distribution of mutational effects on growth rate in the budding yeast, Saccharomyces cerevisiae . We show that mutational effects on growth rate are overwhelmingly negative, highly skewed towards very small effect sizes, and frequent enough to suggest that deleterious hitchhikers may impose a significant burden on evolving lineages. By using lines that accumulated mutations in either wild-type or slippage repair-defective backgrounds, we further disentangle the effects of two common types of mutations, single-nucleotide substitutions and simple sequence repeat indels, and show that they have distinct effects on yeast growth rate. Although the average effect of a simple sequence repeat mutation is very small (∼0.3%), many do alter growth rate, implying that this class of frequent mutations has an important evolutionary impact.

PURPOSE: This review summarizes the published evidence on the clinical impact of using next-generation sequencing (NGS) tests to guide management of patients with cancer in the United States.METHODS: We performed a comprehensive literature review to identify recent English language publications that presented progression-free survival (PFS) and overall survival (OS) of patients with advanced cancer receiving NGS testing.RESULTS: Among 6,475 publications identified, 31 evaluated PFS and OS among subgroups of patients who received NGS-informed cancer management. PFS and OS were significantly longer among patients who were matched to targeted treatment in 11 and 16 publications across tumor types, respectively.CONCLUSION: Our review indicates that NGS-informed treatment can have an impact on survival across tumor types.

The validated 17-gene Oncotype DX Genomic Prostate Score® (GPS™) assay risk-stratifies prostate-cancer patients with localized disease. The assay has primarily been utilized in lower risk patients deciding between active surveillance versus definitive therapy. In this retrospective cohort study, we analyze the association of the GPS result with time to biochemical recurrence post-prostatectomy in patients with National Comprehensive Cancer Network® (NCCN) intermediate and higher risk prostate cancer. The 141 patients included in the study were from the NorthShore University HealthSystem diagnosed 2014–2019 with NCCN intermediate (n = 109) or higher risk (n = 32) prostate cancer, treated with radical prostatectomy 2015–2019. The association of GPS result with time to biochemical recurrence was evaluated using univariable and multivariable Cox proportional hazards models in 120 patients with unfavorable intermediate or higher risk. Median (interquartile range) follow-up time was 28 (20 to 38) months. The GPS result was significantly associated with time to biochemical recurrence as both a continuous and dichotomous variable in univariable (hazard ratio [HR] per 20 GPS units 2.36, 95% CI 1.45–3.80, p < 0.001; HR for GPS result 41–100 vs 0–40 3.28, 95% CI 1.61–7.19, p < 0.001) and in multivariable models accounting for NCCN risk group (HR per 20 GPS units 2.14, 95% CI 1.31–3.46, p = 0.003; HR for GPS result 41–100 vs 0–40 3.00, 95% CI 1.43–6.72, p = 0.003) or biopsy Gleason Score and diagnostic PSA or PSA density. These results indicate that the GPS assay was a strong predictor of biochemical recurrence after radical prostatectomy in this unfavorable intermediate and higher risk prostate cancer patient population.

Background: Immune-oncology (I-O) drugs show promise across multiple tumor types, and several biomarkers (BM) predict responsiveness to I-O therapy. In this descriptive study of clinical lab experience (2018-2021), we investigated the prevalence of genomic BMs associated with sensitivity and resistance to I-O drugs across solid tumors. Methods: The GEM ExTra^® assay was used to exome-sequence 2,359 paired samples at 180X and 400X coverage for germline and tumor DNA respectively. Reportable alterations were single base substitutions, indels, copy number alterations, fusions, alternate transcripts, as well as tumor mutational burden (TMB) and microsatellite instability (MSI) status. For I-O sensitive BMs we recorded MSI-High status, TMB-High (> 10 mut/Mb) status, and mutations in POLE/POLD1, MLH1, MSH2/3/6, PMS1/2, PD-L1/-L2, CTLA4, CD28, ARID2, and PBRM1. For I-O resistance BMs, IDO1 amplification and mutations in B2M, JAK1/2, IDO1, KRAS and STK11 were tallied. Results: I-O sensitive BMs varied from 0% to 58% (results in Table 1 for selected tumor types). Overall, TMB-High was in 6% of samples and MSI-High in 3%; all MSI-High were also TMB-High. In the 46% of renal cell carcinoma samples with I-O-sensitive BMs, PBRM1 mutation was common (94%). In 3 TMB-High endometrial samples, POLE/POLD1 was mutated, indicative of an ultra-mutated phenotype. Of note, 35% of colorectal cancer and 8% of melanoma samples with I-O sensitive mutations also had loss-of-function mutations in JAK1/2 and B2M, suggestive of I-O resistance. In non-small cell lung cancer, co-mutation of STK11 and KRAS, suggesting inferior response to I-O therapy, was present in 4% of samples with I-O BMs. IDO1 amplification was present in less than 1% of entire cohort. Conclusions: Our study found I-O sensitive BMs in common and in rare aggressive cancers. The GEM ExTra assay can stratify cancer patients for likely responsiveness to immunotherapy. Citation Format: Pawan Noel, David W. Hall, Sameer S. Udhane, Min Wang, Fadel S. Alyaqoub, Szabolcs Szelinger, Audrey A. Ozols, Janine R. LoBello, Frederick L. Baehner, Gargi D. Basu. Comprehensive genomic profiling to identify biomarkers predictive of response to immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1263.

Here, we report an essentially complete genome assembly for the Ty1-less Saccharomyces paradoxus strain DG1768 (derivative of strain 337) based on PacBio and Illumina shotgun sequence data. We also document the genetic alterations that make this yeast strain a key resource for Ty1 mobility studies.