Identification of clinically actionable biomarkers via routine comprehensive genomic profiling across a large community health system

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Background: Precision therapies and immunotherapies have revolutionized cancer care, with novel genomic biomarker-associated therapies being introduced into clinical practice rapidly. We assessed the utility of comprehensive genomic profiling (CGP)-based testing for identifying biomarkers associated with approved therapies, and therapies in precision medicine basket clinical trials (CT) across a large cohort of advanced cancer patients in the Providence health system. Methods: Advanced cancer patients were tested utilizing the Providence CGP workflow between 2019-2021. Clinical actionability was assessed for CGP and compared with results from an in silico 50-gene panel based on a previously utilized lab-developed test at Providence. Clinical actionability was assessed based on OncoKB and alterations were assigned as: FDA recognized (Level 1), standard of care (Level 2), FDA approved/investigational drug in another indication or having compelling clinical evidence (Level 3). CT matching was assessed based on enrollment criteria for ASCO-TAPUR, NCI-MATCH and My Pathway CTs at time of testing. Pooled electronic medical record and genomic data were curated and standardized. Results: Of the 3,218 advanced cancer patients tested with CGP, 52% were female, 80% were white, and median age was 67 years. Across 31 tumor types, the most commonly tested were lung (26%), bowel/colon (16%), and breast (9%). Overall, 48% of patients tested with CGP harbored at least one actionable biomarker (OncoKB Levels1/2/3). Clinical actionability was significantly higher in the CGP cohort compared to the in silico cohort based on presence of at least one Level 1 biomarker (45% vs. 19%, p < 0.001). CGP cohort had higher proportion of patients with multiple/co-occurring Level 1 biomarkers compared to in silico cohort (20% vs. 9%, p < 0.001). Of the most prevalent tumor types, 57% lung, 94% bowel/colon, and 37% breast had Level 1 alterations with CGP testing. Notably, 49% of CGP cohort vs. 23% in silico cohort (p < 0.001) harbored a biomarker matching to one or more arms of the three basket CTs. Conclusions: CGP and small panel testing can both identify patients eligible for approved therapies and/or basket CTs with CGP having significantly higher clinical actionability and CT eligibility. We expect value of CGP to increase as biomarker actionability transforms clinical practice.

Pathogenic fusion detection in solid malignancies utilizing RNA-DNA based comprehensive genomic profiling (CGP) testing

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Background: Gene fusions caused by chromosomal rearrangements comprise a key category of oncogenic driver mutations. However, given the diverse array of potentially novel loci where each proto-oncogene can translocate, many assays including DNA-based CGP have technical limitations that disallow the detection of all relevant fusion partners potentially leading to false negatives. Hybrid Capture RNA sequencing renders a more comprehensive evaluation of genes and allows detection of novel and known fusion partners. Here we assessed the impact of utilizing in-house CGP testing with a paired RNA-DNA hybrid assay in the identification of pathogenic fusions and their potential clinical actionability for patients with solid tumors across a large US health system. Methods: Patients in the Providence health system diagnosed with advanced solid tumor malignancies over a two-year period (2019-2021) received reflex CGP testing at the time of diagnosis utilizing an internally validated workflow. DNA/RNA sequencing results as well as histology and staging information were curated from deidentified electronic medical records and in-house databases, and tumor types were mapped to OncoTree tissue categories. Potential clinical actionability was assessed based on OncoKB therapeutic levels 1-3 and clinical trial eligibility matched to the biomarker inclusion criteria for ASCO TAPUR, NCI-MATCH and MyPathway studies (both without time limits and at time of testing). Results: The median patient age at diagnosis was 67 years, 52% of patients were female, and the majority (80%) were white. Across all tested advanced solid tumors, 6.7% (217/3218) were found to harbor a pathogenic fusion. The tumor types most enriched in this set of pathogenic fusions were prostate (30%), lung (27%), CUP (10%) and breast (9%). 29% (n = 64) of the identified pathogenic fusions were identified as actionable based on OncoKB criteria (levels 1-3), and 31% (n = 69) matched to one or more arms in the ASCO TAPUR, NCI-MATCH or MyPathway basket clinical trials. The most frequent actionable fusion driver genes identified were ALK (12%), FGFR 1-3 (12%), RET (7%) NTRK 1-3 (3%), and ROS1 (2%) and a subset of these key drivers were fused with novel gene pairs. A subset of fusions co-occurred with other targetable biomarkers, with the most common comprising tumor mutational burden high (TMB-H) (13%), PIK3CA (7%) and high microsatellite instability (MSI-H) (2%). Conclusions: In-house CGP testing utilizing an RNA-DNA based assay identified actionable fusion targets across tumor types, with many novel fusion partners that may be undetectable by prior generation sequencing assays. While many of these actionable targets are rare individually, the expanding totality of actionable gene alterations supports the growing utility of CGP for identifying patients who are candidates for approved targeted therapies and clinical trials.

Real-world burden of chemotherapy-induced myelosuppression in patients with small cell lung cancer: a retrospective analysis of electronic medical data from community cancer care providers

AIMS

Chemotherapy-induced myelosuppression, which commonly exhibits as neutropenia, anemia, or thrombocytopenia, represents a substantial burden for patients with cancer that affects health-related quality of life and increases healthcare resource utilization (HCRU). We evaluated the burden of myelosuppression among chemotherapy-treated patients with small cell lung cancer (SCLC) using real-world data from community cancer care providers in the Western United States.

MATERIALS AND METHODS

This was a retrospective, observational analysis of electronic medical records (EMRs) from Providence St. Joseph Health hospital-associated oncology clinics between January 2016 and December 2019. Patient demographics were assessed from the date of first SCLC diagnosis in adult patients with chemotherapy-induced grade ≥3 myelosuppression in first-line (1L) or second-line-and-beyond (2L+) treatment settings. Myelosuppressive adverse events (AEs), treatment patterns, and HCRU were assessed from the date of chemotherapy initiation (index date) until 12 months, date of the last visit, date of death, or study end, whichever occurred earliest.

RESULTS

Of 347 eligible patients with SCLC who had received chemotherapy (mean age 66; 49% female), all had received at least 1L treatment, and 103 (29.7%) had a 2L + treatment recorded within the EMR during the study period. Of 338 evaluable patients with longitudinal laboratory data, 206 (60.9%) experienced grade ≥3 myelosuppressive AEs, most commonly neutropenia, anemia, and thrombocytopenia (44.9, 41.1, and 25.4 per 100 patients, respectively). Rates of granulocyte colony-stimulating factor use and red blood cell transfusions were 47.0 and 41.7 per 100 patients, respectively. There was a trend toward increasing the use of supportive care interventions and visits to inpatient and outpatient facilities in patients with myelosuppressive AEs in more than one cell lineage.

CONCLUSIONS

Chemotherapy-induced myelosuppression places a substantial real-world burden on patients with SCLC in the community cancer care setting. Innovations to protect bone marrow from chemotherapy-induced damage have the potential to reduce this burden.

Cancer case trends following the onset of the COVID-19 pandemic: A community-based observational study with extended follow-up

BACKGROUND

The coronavirus disease 2019 (COVID-19) pandemic has impacted health care delivery worldwide. Cancer is a leading cause of death, and the impact of the pandemic on cancer diagnoses is an important public health concern.

METHODS

This cross-sectional study retrospectively analyzed the electronic medical records of 80,138 cancer patients diagnosed between January 1, 2019, and May 31, 2021. Outcome measures included weekly number of new cancer cases and trends in weekly cancer cases, before and after the pandemic; patient demographics; and positive COVID-19 test rates.

RESULTS

Beginning March 4, 2020, defined as the onset of the pandemic, weekly cancer cases declined precipitously (-110.0 cases per week [95% confidence interval, -190.2 to -29.8]) for 4 weeks, followed by a moderate recovery (+23.7 cases per week [9.1 to 38.4]) of 10 weeks duration. Thereafter, weekly cancer cases trended slowly back toward pre-COVID-19 baseline levels. Following the pandemic onset, there was a cumulative year-over-year decline in cancer cases overall of 7.3%, including a 20.2%, 14.3%, and 12.8% decline in nonmelanoma skin cancer, breast cancer, and prostate cancer, respectively. Changes in case volumes were accompanied by variations in patient characteristics, including region, age, gender, race, insurance coverage, and COVID-19 positive test rates (P < .01 for all). Among patients tested for COVID-19, 5.3% had a positive result.

CONCLUSIONS

The data in this study demonstrate a substantial reduction in cancer diagnoses following the onset of COVID-19, which appear to reach expected pre-COVID norms 12 months later. The largest reduction was noted among cancers that are typically screen-detected or identified as part of a routine wellness examination.

Real-world burden of myelosuppression in patients with small cell lung cancer (SCLC): Retrospective, longitudinal data analysis

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Background: Myelosuppression is a common side effect of chemotherapy (CT) that can compromise patient (pt) and economic outcomes. To evaluate the overall burden of myelosuppression, a longitudinal, patterns of care analysis was conducted among pts with SCLC treated with CT in routine clinical practice. Methods: Data were obtained from Providence St. Joseph Health electronic medical records between Jan 2016 and Dec 2019. Hematologic adverse events, treatment patterns, and hospital-based healthcare resource utilization and costs were assessed during the 12 months from first diagnosis of SCLC in pts who had CT-induced grade 3/4 myelosuppression in 1st or 1st/2nd/3rd-line (1/2/3L) treatment settings. Descriptive statistics were utilized to summarize key findings. Costs of care were calculated from actual treatment costs for inpatient, outpatient, and emergency room services after first diagnosis and treatment with CT. Professional billing was not included due to variability in physician employment by the system. Results: 347 pts were eligible for analysis; mean age (SD) was 66 (9.0) years, 49% were female, and 89% were Caucasian. Prominent comorbidities included chronic obstructive pulmonary disease (52%), diabetes (23%), and peripheral vascular disease (20%). 264 pts (76%) received 1L treatment only, while an additional 83 pts (24%) had both 1L and 2/3L treatment. Of 339 evaluable pts with longitudinal laboratory data, grade 3/4 cytopenias were reported as follows: 45%, neutropenia; 41%, anemia; and 25%, thrombocytopenia. 43% and 15% of pts received red blood cell or platelet transfusions, respectively. 49% of pts received prophylaxis (6%) or treatment (43%) with G-CSF, and 4% of pts were treated with erythropoiesis-stimulating agents. Average total costs of care (post initial-diagnosis and treatment) for pts without grade 3/4 hematologic events (n = 110) were $67,802 per pt throughout the 12 months’ follow-up. On average, annual per pt costs for those with grade 3/4 hematologic events were $131,047 for neutropenia, $95,954 for anemia, and $90,053 for thrombocytopenia. Conclusions: A large and meaningful proportion of pts had grade 3/4 myelosuppression with annual incremental associated costs per pt ranging from $22,251 for pts with thrombocytopenia to $63,245 for pts with neutropenia. Despite the availability of protocols of care and various rescue treatments, CT-induced myelosuppression places a significant real-world burden on pts and the healthcare system.