Rapid access to biomarker data in a community setting: Integration of next-generation sequencing into routine pathologic workflow

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Background: Biomarker data in the form of next generation sequencing (NGS) are critical to the delivery of precision cancer care. Onsite testing is often limited to large academic centers, requiring smaller community centers to rely on samples send outs. Turnaround time for biomarkers can be lengthy and can adversely affect the delivery of optimal therapy in many tumor types. This study aims to evaluate the feasibility of rapidly delivered comprehensive NGS in a community center using a novel workflow in the laboratory by integrating NGS into the routine immunohistochemistry (IHC) service. Methods: An automated NGS workflow utilizing the Genexus integrated sequencer with the Oncomine precision assay GX (OPA, Thermofisher Scientific), was validated for clinical use and integrated into the routine diagnostic IHC service. During the study period (Oct 2020 – Oct 2021), NGS biomarker data was generated and reported alongside IHC biomarkers where applicable. A retrospective chart review was performed to assess the early experience and performance characteristics of this novel approach to biomarker testing. Results: A total of 578 solid tumor samples underwent genomic profiling. Median turnaround time for biomarker results was 3 business days (IQR 2-5). The majority (n = 481, 83%) of cases were resulted in fewer than 5 business days. Tumor types included lung cancer (n = 310, 54%), melanoma (n = 97, 17%), and colorectal cancer (n = 68, 12%). Specimen types included surgical resections (n = 104, 18%), core biopsies (n = 411, 71%), and cytology specimens (n = 63, 11%). NGS testing detected key driver alterations at expected prevalence rates in respective tumor types; lung EGFR (16%), ALK (3%), RET (1%), melanoma BRAF (43%), colorectal RAS/RAFwild-type (33%), among others. Conclusions: This is the first study demonstrating the clinical feasibility and turnaround time statistics of automated comprehensive NGS performed and interpreted in parallel with diagnostic histopathology and immunohistochemistry in a community setting. This novel approach of integrating biomarkers, IHC, and morphology offers rapid turnaround by removing the need for outsourcing biomarker data. This model could be adopted by other community centers to improve rapid access to biomarker data and therapeutic decision making.

Mitigating the risk of COVID-19 in a large community oncology clinic and its impact on the patient experience

e18631

Background: Cancer patients have a high risk of severe illness from COVID-19 infection, and the William Osler Health System oncology clinic (WOHS-OC) is in Brampton, ON, Canada, a COVID-19 hotspot with high community COVID-19 prevalence. As such, heightened symptom screening prior to entering the WOHS-OC, asymptomatic COVID-19 testing pre-chemotherapy, staff personal protective equipment (PPE) use, enhanced cleaning, and clinic capacity limits (including implementation of virtual visits) were employed in the outpatient WOHS-OC. This study examined patient's perspectives regarding the implemented containment and mitigation strategies in the WOHS-OC during the second wave of the COVID-19 pandemic. Methods: Consenting patients in the WOHS-OC from Dec 01 2020 to Feb 01 2021 were provided a written questionnaire regarding their care during the second wave of the COVID-19 pandemic. Questions about satisfaction with COVID-19 protocols were rated on an analogue scale from 1-5, with 1 being the worst and 5 being the best possible satisfaction. Patient demographics (age, sex, type of cancer, and treatment type) were obtained through electronic medical records. Patients also consented to a second survey should they contract COVID-19 regarding, symptoms and risk factors for contracting the virus. Results: Fifty-six patients with various solid and hematological malignancies consented to the study; median age 59.5, male (30%), type of treatment; chemotherapy (55%), immunotherapy (9%), targeted therapy (23%), biologic therapy (14%), endocrine therapy (11%). Patients felt safe coming to the oncology clinic (95% of respondents), and 100% of patients were screened for symptoms on entry. Prior to cancer treatment, 49% of participants were contacted to do a screening COVID-19 swab. In 57% of patients, at least one clinic visit was changed to virtual (telephone or video). Communication during virtual visits was felt to be adequate with 89% of patients rating communication 4 or 5. Rating of virtual visits compared to in-person visits was widely distributed (57% rated virtual 4 or 5 compared to in person). Infection control practices were rated highly (4 or 5; physical distancing 83%, enhanced cleaning 93%, staff screening 89%, and staff PPE 96%). No patients that consented to the survey contracted COVID-19 during the study period. Conclusions: COVID-19 mitigation strategies in the WOHS-OC made patients feel safe during the second wave of the pandemic. Additionally, despite high levels of community transmission, no patients responding to the survey tested positive for COVID-19 during the study period. Patients were satisfied with communication during virtual visits, however there was a wide distribution of follow-up preferences. Future interventions should be aimed at standardizing pre- treatment COVID-19 testing and delineating areas of virtual care that patients identify as needing improvement.

Point of Care Molecular Testing: Community-Based Rapid Next-Generation Sequencing to Support Cancer Care

Purpose: Biomarker data are critical to the delivery of precision cancer care. The average turnaround of next-generation sequencing (NGS) reports is over 2 weeks, and in-house availability is typically limited to academic centers. Lengthy turnaround times for biomarkers can adversely affect outcomes. Traditional workflows involve moving specimens through multiple facilities. This study evaluates the feasibility of rapid comprehensive NGS using the Genexus integrated sequencer and a novel streamlined workflow in a community setting. Methods: A retrospective chart review was performed to assess the early experience and performance characteristics of a novel approach to biomarker testing at a large community center. This approach to NGS included an automated workflow utilizing the Genexus integrated sequencer, validated for clinical use. NGS testing was further integrated within a routine immunohistochemistry (IHC) service, utilizing histotechnologists to perform technical aspects of NGS, with results reported directly by anatomic pathologists. Results: Between October 2020 and October 2021, 578 solid tumor samples underwent genomic profiling. Median turnaround time for biomarker results was 3 business days (IQR: 2-5). Four hundred eighty-one (83%) of the cases were resulted in fewer than 5 business days, and 66 (11%) of the cases were resulted simultaneously with diagnosis. Tumor types included lung cancer (310), melanoma (97), and colorectal carcinoma (68), among others. NGS testing detected key driver alterations at expected prevalence rates: lung EGFR (16%), ALK (3%), RET (1%), melanoma BRAF (43%), colorectal RAS/RAF (67%), among others. Conclusion: This is the first study demonstrating clinical implementation of rapid NGS. This supports the feasibility of automated comprehensive NGS performed and interpreted in parallel with diagnostic histopathology and immunohistochemistry. This novel approach to biomarker testing offers considerable advantages to clinical cancer care.

Rapid point of care NGS in colorectal cancer

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Background: Next generation sequencing (NGS) is the laboratory cornerstone of precision oncology treatment. In advanced colorectal cancer (CRC), current guidelines recommend testing RAS, BRAF and MMR biomarkers as standard of care. The added value of comprehensive genomic profiling is so far unclear. Traditional NGS operations are complicated, requiring specialized equipment and personnel. In many jurisdictions, cancer patients are treated in publicly-funded community hospitals, where NGS is not typically utilized and access to testing via send-out services is associated with lengthy turnaround times. Here, we have validated and implemented one of the world's first "point of care" NGS services. Our early experience on NGS implementation and impact in CRC patients is described. Methods: All NGS studies were performed using the Oncomine Precision Assay (OPA) on the genexus integrated sequencer. NGS was performed at the request of the treating physician. All NGS was performed in a local community pathology lab by histotechnologists, simultaneously responsible for IHC testing (such as MMR) and interpreted by anatomic pathologists in conjunction with routine diagnostic pathology services. Retrospective chart review was performed for all patients undergoing sequencing studies and key data, including turnaround time and NGS findings were extracted from the electronic medical record for analysis. Results: A total of 51 cases with CRC were tested using point of care NGS from November 2020-August 2021, initiated by treating physicians. The median turnaround time for results was 3 days. Oncogenic driver events were identified in 46 (90%) cases, including canonical mutations in KRAS, NRAS and BRAF (Table). Actionable mutations were identified in 13 (25%) samples that would not have been identified with single-gene testing. Conclusions: Here, we show that comprehensive NGS can reveal occult resistance mechanisms to standard therapy and identify actionable biomarkers in a substantial proportion of patients with CRC. NGS added valuable information compared to guideline-recommended testing standards. Our study demonstrates that local testing can have rapid turnaround times. To our knowledge, this is the first report of “point of care” NGS in CRC. Further follow up is needed to explore the utility of these expanded roles for NGS testing. [Table: see text]

The Association of Drug-Funding Reimbursement With Survival Outcomes and Use of New Systemic Therapies Among Patients With Advanced Pancreatic Cancer

Importance

Gemcitabine-nab-paclitaxel (GEMNAB) and fluorouracil, leucovorin, irinotecan, and oxaliplatin (FOLFIRINOX) both improve survival of patients with advanced pancreatic cancer when compared with single-agent gemcitabine in clinical trials.

Objective

To describe changes in the survival of patients with advanced pancreatic cancer associated with sequential drug-funding approvals and to determine if there exist distinct patient populations for whom GEMNAB and FOLFIRINOX are associated with survival benefit.

Design, Setting, and Participants

This population-based, retrospective cohort study examined all incident cases of advanced pancreatic cancer treated with first-line chemotherapy in Ontario, Canada (2008-2018) that were identified from the Cancer Care Ontario (Ontario Health) New Drug Funding Program database. Statistical analysis was performed from October 2020 to January 2021.

Exposures

First-line chemotherapy for advanced pancreatic cancer.

Main Outcomes and Measures

The main outcomes were the proportion of patients treated with each chemotherapy regimen over time and overall survival for each regimen. Cox proportional hazards regression models were used to compare overall survival between treatment regimens after adjustment for confounding variables, inverse probability of treatment weighting, and matching.

Results

From 2008 to 2018, 5465 patients with advanced pancreatic cancer were treated with first-line chemotherapy in Ontario, Canada. The median (range) age of patients was 66.9 (27.8-93.4) years; 2447 (45%) were female; 878 (16%) had prior pancreatic resection, and 328 (6%) had prior adjuvant gemcitabine. During the time period when only gemcitabine and FOLFIRINOX were funded (2011-2015), 49% (929 of 1887) received FOLFIRINOX. When GEMNAB was subsequently funded (2015-2018), 9% (206 of 2347) received gemcitabine, 44% (1034 of 2347) received FOLFIRINOX, and 47% (1107 of 2347) received GEMNAB. The median overall survival increased from 5.6 months (95% CI, 5.1-6.0 months) in 2008 to 2011 to 6.9 months (95% CI, 6.5-7.4 months) in 2011 to 2015 to 7.6 months (95% CI, 7.1-8.0 months) in 2015 to 2018. Patients receiving FOLFIRINOX were younger and healthier than patients receiving GEMNAB. After adjustment and weighting, FOLFIRINOX was associated with better overall survival than GEMNAB (hazard ratio [HR], 0.75 [95% CI, 0.69-0.81]). In analyses comparing patients treated with GEMNAB and gemcitabine, GEMNAB was associated with better overall survival (HR, 0.86 [95% CI, 0.78-0.94]).

Conclusions and Relevance

This cohort study of patients with advanced pancreatic cancer receiving first-line palliative chemotherapy within a universal health care system found that drug funding decisions were associated with increased uptake of new treatment options over time and improved survival. Both FOLFIRINOX and GEMNAB were associated with survival benefits in distinct patient populations.

Feasibility outcomes of a randomised, multicentre, pilot trial comparing standard 6-monthly dosing of adjuvant zoledronate with a single one-time dose in patients with early stage breast cancer

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Adjuvant bisphosphonates are an established standard in postmenopausal breast cancer.

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Guidelines note the need to explore different agents, doses, and intervals of bisphosphonates.

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Feasibility of randomizing to 6-monthly vs one dose of IV zoledronate was demonstrated.

Background

Adjuvant zoledronate is widely used in patients with early stage breast cancer (EBC), but its optimal duration and dosing interval is still unknown. While a single-dose of zoledronate can improve bone density for many years, a proper evaluation of its effects on breast cancer-related outcomes would require a large trial. In this pilot study we evaluated the feasibility of performing such a trial.

Methods

Eligible patients with EBC were randomised to receive either one dose of zoledronate or 7 doses (6-monthly dosing for 3 years). Feasibility was assessed by a combination of primary outcomes including: activation of at least 6 Ontario sites within a year, active participation (i.e. approaching eligible patients for study participation) of at least half of the medical oncologists, and enrolment of at least 100 patients across all sites within 9 months of the sixth site being activated.

Results

All 6 sites were activated within 1 year and of 47 medical oncologists, 27 (57%) approached patients. Between November 2018 and April 2020, 211 eligible patients were randomised, 106 (50.2%) to a single dose of zoledronate and 105 (49.8%) to 6-monthly dosing. Baseline characteristics of randomised patients included; median age 59 (range 36–88), ER and/or PR positive (85%), Her2 positive (23%), menopausal status (premenopausal [19%], perimenopausal [6.7%] and postmenopausal [74%]) and 74% received neo/adjuvant chemotherapy.

Conclusions

All study feasibility endpoints were met in this trial comparing alternative schedules for adjuvant zoledronate. We will now seek funding for performing a larger efficacy trial.

Trial registration: NCT03664687.

Impact of an immuno-oncology (IO) education/monitoring program on patient’s self-efficacy and adverse event reporting from immune checkpoint inhibitors (ICIs)

2032

Background: ICIs have unique side effects of immune related adverse events (irAEs). For early detection and management of irAEs, at a large community hospital we implemented a standard IO nursing baseline assessment, education and monitoring program. We studied it’s impact on a patient’s irAE reporting and self-efficacy (confidence to manage symptoms) of ICIs. Methods: Prospective study conducted at William Osler Health System, Brampton, Canada from May 2018-December 2019. Patients aged > = 18, English speaking that received an ICI for cancer were included. Patients underwent a standardized baseline nursing assessment and education class. Patients identified at the assessment as high risk (risk of grade 3/4 irAE >20%) had weekly nurse proactive calls. Cancer Behaviour Inventory – Brief Version (CBI-B) (Heitzmann et al, 2011) was used to evaluate patient’s self-efficacy. Results: Eighty patients were enrolled. Median follow up of 4.1 months. Baseline demographics: median age 69, 70% males, 77% Caucasian, 81% ECOG 0/1, 66% had English as their first language and 19% highest education was elementary, 30% high school, 26% trade diploma and 21% post-secondary. Fourty-one percent had limited cancer health literacy (measured by CHLT6 (Dumenci et al, 2014)). ICIs prescribed were 70% monotherapy anti-PD1/PDL1, 13% combination nivolumab/ipilimumab, 17% anti-PD1/PDL1 + chemotherapy/other therapies. Majority had a diagnosis of non-small cell lung cancer (55%), melanoma (19%) and renal cell carcinoma (9%). A statistically significant improvement in the average CBI-B scores were found pre and post baseline assessment/education (p < 0.001) and this improvement was maintained over time at follow-up visits (non-significant change in scores from post education results). Fourty-three percent of patient’s experienced > 1 irAE. Most were grade 1/2 at time of detection (65%). Method of detection was mainly by patient self-reporting (62%), followed by proactive calls (27%). Only 3 patients had detection of an irAE with an ER visit. Rate of discontinuation of ICIs due to toxicity was 8.8%. Conclusions: In this diverse patient population with almost half of patients having limited cancer health literacy, a standardized IO baseline assessment, education and monitoring program resulted in improved patient self-efficacy with most irAEs detected by self-reporting and proactive calls. Our IO program can be a model for other oncology programs.

Improving support for smoking cessation in medical oncology patients: A quality improvement initiative

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Background: Smoking cessation is integral to cancer care. Active smoking is associated with increased toxicity of treatment, poorer response to therapy and is associated with worse overall survival. Patients who quit smoking at diagnosis have better survival outcomes. Cancer Care Ontario has aimed to improve rates of smoking screening and referral to smoking cessation programs based on the validated Ottawa model. Methods: We aimed to implement an “opt-out” referral process for recent or current smokers to a smoking cessation program at the Credit Valley Hospital. We aimed to achieve a referral rate of 20%, based on an institutional baseline of 8.5% and a provincially defined target of 20%. Key stakeholders targeted included nursing, administration, physicians, smoking cessation counsellors and patients. Sequential education interventions were delivered to address gaps in patient and provider knowledge; these included grand rounds, an informal lecture and an educational pamphlet. Results: After the initiative was launched, the referral rate increased from 8.5% to 14.3%. The impact of each intervention is summarized in Table 1. Conclusions: Smoking cessation referrals increased with new process but not to target. Patient refusals lead to a low rate of referral, warranting efforts aimed at addressing patient barriers. Future outcome measures may include smoking cessation rates. [Table: see text]

Chemotherapy choice in advanced pancreatic cancer: What patient and disease factors influence prescription patterns?

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Background: FOLFIRINOX (FFX), gemcitabine+nab-paclitaxel (GnP) and gemcitabine monotherapy (Gem)) are universally funded as first-line chemotherapy regimens for advanced pancreatic cancer (APC) in Ontario, Canada. However, there is scarce real-world data on factors that may influence choice of chemotherapy regimens in APC. Methods: Patients who received first-line chemotherapy for APC between April 2015-March 2016 in Ontario were identified from CCO’s New Drug Funding Program database and linked to the Ontario Cancer Registry and other provincial databases to ascertain baseline factors. Multinomial logistic regressions were used to examine the associations between the prescribed chemotherapy regimen and baseline factors. Results: 546 patients were identified, with a mean age of 65 and 43.6% female. 9.9% and 9.7% had received adjuvant gemcitabine and radiation treatment respectively. 17.6% had previous pancreatic resection. 68.3% had zero Charlson score and 30.6% had ECOG performance status (PS) of 0. 72.7% had metastatic disease. The majority of the patients received FFX (52.4%) compared to GnP (35.7%) and Gem (11.9%). Age and ECOG PS were strongly associated with choice of chemotherapy regimens. (See Table) Conclusions: In Ontario, increased patient age and worse ECOG PS are strongly associated with choice of Gem compared to GnP and FFX. Previous treatments and stage of disease also impact chemotherapy choice. Understanding how providers choose chemotherapy in APC aids in comprehending our practices. Odds ratio (OR) and p value from multinomial logistic regressions. [Table: see text]

Toward improved goals-of-care documentation in advanced cancer: report on the development of a quality improvement initiative

Background

Documentation of advance care planning for patients with terminal cancer is known to be poor. Here, we describe a quality improvement initiative.

Methods

Patients receiving palliative chemotherapy for metastatic lung, pancreatic, colorectal, and breast cancer during 2010-2015 at the Cancer Centre of Southeastern Ontario were identified from electronic pharmacy records. Clinical notes were reviewed to identify documentation of care plans in the event of acute deterioration. After establishing baseline practice, we sought to improve documentation of goals of care and referral rates to palliative care. Using quality improvement methodology, we developed a guideline, a standardized documentation system, and a process to facilitate early referral to palliative care.

Results

During 2010-2015, 456 patients were included in the baseline cohort: 63% with lung cancer, 16% with colorectal cancer, 13% with pancreatic cancer, and 7% with breast cancer. Care goals in the event of an acute illness were documented by medical oncologists in 6% of cases (26 of 456). Of the 456 patients, 47% (n = 214) were seen by palliative care; care goals were documented by palliative care in 48% of the patients seen (103 of 214). With those baseline data in hand, a local practice guideline and process was developed to facilitate the identification of patients for whom advance care planning and early palliative care referral should be considered. A system was also established so that goals-of-care documentation will be supported with a written framework and broadly accessible in the electronic medical record.

Conclusions

Low rates of documentation of advance care planning and referral to palliative care persist and have stimulated a local quality improvement initiative.