tbuckley/cabot-search huggingface dataset:
Unstructured EMR data hold the key to oncology studies: Methods for validating NLP-extracted phenotypes from EMR notes.
Authors: Elizabeth H. Eldridge, Elizabeth Trowbridge, Mui Van Zandt, Atif Adam, Christina D. Mack
Journal: Journal of Clinical Oncology (2024)

11133 Background: Natural language processing (NLP) parsers are advanced algorithms designed to parse values of interest from free-text stored in Electronic Medical Records (EMR). Given the importance of information stored in free-text for use in oncology research, it is crucial to understand how accurately NLP algorithms are extracting oncology-specific measures of interest. We focus on validating NLP-parsers that identify three measures critical to oncology research by evaluating how closely the NLP-parser results match manual chart abstractor review: AJCC summary cancer stage group (cancer stage), AJCC TNM stage (TNM stage), and surgical treatment of cancer (surgery). Methods: Following deployment of the parsers on 8,000 non-identifiable free-text notes housed in an aggregated non-identifiable U.S. EMR database, manual chart abstraction was performed on a random selection of notes (n=300) dated between 2008 to 2023 to validate the parsers’ accurate capture of cancer stage, TNM stage, and surgical treatment of cancer. We report true positives (TP), false positives (FP) and positive percent value (PPV). Results: The PPV of AJCC Cancer Stage was 99.0% (n=297 TP, n=3 FP). The PPV of the TNM stage NLP-parser was 97.3% for tumor stage (n=292 TP, n=8 FP), 99.0% for nodal stage (n=297 TP, n=3 FP), and 96.7% for presence of metastases (n=290 TP, n=10 FP). The PPV of the surgery parser was 87.8% (n=468 TP, n=65 FP). Conclusions: These NLP-parsers performed very well identifying the measures of interest, providing confidence in use of these derived measures which are central to oncology research. Validation is a necessary initial step in processing real-world data for use in real-world evidence generation, with unique considerations needed in the oncology research space due to key information being documented in EMR free-text rather than structured data fields.
Association between comorbidity clusters and mortality in patients with cancer: A machine learning analysis of data from the US National Health and Nutrition Examination Survey 1999–2018.
Authors: Chun Sing Lam, Rong Hua, Herbert H. Loong, Chun-Kit Ngan, Yin Ting Cheung
Journal: Journal of Clinical Oncology (2024)

11132 Background: Multimorbidity is common among patients with cancer; however, research on cancer prognosis has predominantly focused on cancers in isolation. This study identified comorbidity clusters among patients with cancer using machine learning and examine their associations with survival outcomes in a nationally representative sample of the US. Methods: This study used 10 survey cycles of the National Health and Nutrition Examination Survey from 1999 to 2018. Participants aged ≥20 years with a self-reported history of cancer were included. Comorbidities were ascertained through self-reports and quantitative measurements. Machine learning techniques, including Bernoulli mixture model and partition-based methods, were used to identify comorbidity clusters. Cox proportional hazards models were used to analyze the associations between comorbidity clusters and mortality outcomes, including all-cause mortality and cause-specific mortality (cancer, cardiovascular disease [CVD], and respiratory diseases), adjusting for relevant covariates. Results: The study included 4,390 participants. Four comorbidity clusters were identified: Low Comorbidity, Metabolic, CVD, and Respiratory. After adjusting for confounders, participants in the Respiratory Cluster had the highest risk of all-cause mortality (adjusted hazard ratio[aHR]=1.62, 95% confidence interval [CI]=1.26-2.08, p&lt;0.001), followed by the CVD Cluster (aHR=1.50, 95%CI = 1.26-1.80, p&lt;0.001) and the Metabolic Cluster (aHR=1.15, 95%CI=1.02-1.29, p=0.03) compared to the Low Comorbidity Cluster. The Metabolic, CVD, and Respiratory clusters were associated with higher risks of cardiovascular disease-related mortality (aHR=1.48-3.05, p&lt;0.003), but no significant differences in cancer mortality were observed among the clusters. The effects of comorbidity clusters on all-cause mortality were modified by income-to-poverty ratio ( p for interaction=0.04), diet quality ( p for interaction=0.02), time since cancer diagnosis ( p for interaction=0.009), and cancer prognosis ( p for interaction=0.005). Conclusions: High comorbidity burden clusters showed increased all-cause and CVD-related mortality. Moreover, diet quality and socioeconomic status modified these associations. Machine learning approaches can provide valuable insights into complex multimorbidity profiles in patients with cancer. Further research is needed to deepen understanding of the relationships between multimorbidity, mortality, and cancer-specific outcomes.
Commercial health plan spending on oncology drugs approved via the accelerated approval pathway and later withdrawn from the market.
Authors: Tejas Patel, Eamonn Curran, Sarah S Hellems
Journal: Journal of Clinical Oncology (2024)

11134 Background: The U.S. Food and Drug Administration (FDA) introduced the Accelerated Approval Program in 1992 to expedite the approval of drugs that can be used to treat certain conditions and fill an unmet medical need. Clinical trials conducted to achieve accelerated approval status often use surrogate outcomes as primary endpoints to reduce the time it takes to get FDA approval. Drug manufacturers must conduct further research to verify and report the projected clinical benefit and safety. The FDA may issue traditional approval to previously accelerated approved drug or may request the manufacturer to withdraw a drug from the market based on the clinical benefit and/or safety demonstrated in the confirmatory trial(s). We report members impacted, total drug claims, and total drug cost incurred by a commercial health plan associated with the coverage of oncology drugs approved by the FDA and later withdrawn from the market between 2020 to 2023. Methods: Fifteen unique indications associated with oncology drugs that received accelerated approval and later withdrawn by the FDA were identified between 2020 to 2023. A cohort of patients enrolled in commercial health plan was further identified using the ICD-10 code related to the drug indication being withdrawn. To calculate total paid amount for drugs, de-identified administrative claims data submitted on behalf of this cohort were sorted and summed in this time period using either J-code for drugs covered under medical benefits or national drug code (NDC) for drugs covered under pharmacy benefits. Results: Between 2020 to 2023, 8 oncology drugs were withdrawn because of later failing to demonstrate clinical benefit in the confirmatory trials, 2 drugs were withdrawn due to safety concerns, and 5 drugs were withdrawn due to drug manufacturer unable to complete a confirmatory trial. In this population, we identified 18,430 unique members with 103,743 administrative claims. The total paid amount was $1,392,553,995 in this time period. The average drug cost per administrative claim was $13,423 and the average drug cost per member was $75,559. Conclusions: Drug costs established by manufacturers are not differentiated based on the approval status - accelerated or regular. While drugs approved via accelerated approval pathway may provide benefit to certain patient population, the cost associated with accelerated approved drugs needs more attention. Indication-specific pricing model may help alleviate the cost burden associated with drugs approved via accelerated approval pathway. [Table: see text]
Impact of transitions of care nurse navigation on post-discharge follow-up.
Authors: Celina Lo, Jackie Miller, Valerie Pracilio Csik
Journal: Journal of Clinical Oncology (2024)

11126 Background: Poor discharge communication is among the primary causes of readmissions and many patients are lost to follow-up (F/U) post-discharge (PD). For newly diagnosed (DX) cancer patients, the coordination of care from inpatient (IP) to outpatient (OP) follow-up is critical. At the Sidney Kimmel Cancer Center in Philadelphia, we saw a no show (NS) rate of 6.6% for PD F/U appointments (Oct-Dec 2022) resulting from deficient communication. To improve the IP to OP transition for cancer patients, a Transition of Care Nurse Navigator (ToC NN) pilot was initiated to support patients discharged from Thomas Jefferson University Hospital (TJUH). The goal was to complete 80% of PD visits and reduce the NS rate by 20% by 12/31/23. Methods: The target population are patients that are newly DX solid tumor patients that will be discharged to home/rehab and need an OP Medical Oncology appointment. Through communication with hospitalists, IP Fellows/Residents, and/or Attendings, the ToC NN is referred eligible patients. The ToC NN visits patients during hospitalization or follows-up post-discharge to assess Health Related Social Needs and distress. PD F/U appointments are communicated during the initial contact along with information about the OP resources available and referrals are made based on patient interest/needs to social work, nutrition, or supportive medicine. All communication is documented by the EMR and the oncology care team is notified. The ToC NN follows up with the patient/patient’s family member 48-72 hours after hospital discharge to check in and do a symptom management call. Additional F/U calls are made as needed. The ToC NN serves as the patient’s point of contact (POC) from discharge to OP new patient visit (NPV) appointment. Results: The pilot exceeded the 80% goal of completion of PD visits. It revealed a 41.4% increase of PD NPV completion and a 21.9% decrease of NS rate from the 2022 to 2023 data. Conclusions: The ToC NN services showed significant impact in supporting patients transition from IP to OP. Our findings confirm having a contact after hospital discharge increases the completion of PD visits due to effective communication and support. [Table: see text]
Viral hepatitis screening in patients with early breast cancer receiving cancer therapy: A quality improvement initiative.
Authors: Katherine Klein, Jessica Park Hwang, Vicente Valero, David Luis Ramirez, Jaime Kaushik
Journal: Journal of Clinical Oncology (2024)

11125 Background: ASCO guidelines recommend screening all patients for hepatitis B virus (HBV) before initiation of cancer therapy. Comprehensive screening for HBV includes measuring HBV surface antigen (HBsAg), HBV core antibody (anti-HBc), and antibody to HBV surface antigen (anti-HBs). ASCO also recommends hepatitis C virus (HCV) screening in patients with cancer. Cancer patients receiving cancer therapy represent a vulnerable population and reactivation of undetected hepatitis virus can lead to devastating consequences such as liver failure and death. At MD Anderson Cancer Center, rates of hepatitis screening for all cancer patients has been historically low. For example, rates are around 29% for HBV screening in patients receiving cancer therapy in 2019-2021. The aim of this quality improvement study is to increase rates of HBV and HCV screening in early breast cancer patients in the Breast Medical Oncology clinic at MD Anderson before undergoing cancer therapy to at least 50%. Methods: Quality improvement measures were implemented by 1) creation of an order panel in the electronic medical record (EMR) which contains all tests needed for comprehensive HBV and HCV screening (HBsAg, anti-HBc, HBsAb, and anti-HCV), and 2) an educational session to providers in the Breast Medical Oncology clinics. Data was collected for patients seen at MD Anderson initiating cancer therapy (start of cycle 1) between April 1, 2023 until September 30th, 2023. Inclusion criteria were early breast cancer patients (Stage I-III) and receiving chemotherapy at MD Anderson. Exclusion criteria were Stage IV disease, or those receiving chemotherapy at an outside institution. Results: A total of 340 patients were screened, and 219 were determined to meet inclusion criteria for data extraction. In total, 105 patients (48%) received comprehensive HBV screening, with 137 (63%) receiving at least one HBV test. A total of 122 (56%) patients were screened for HCV. Combining data for both HBV and HCV, 88 (40%) received both comprehensive HBV and HCV screening (HBsAg, anti-HBc, anti-HBs, anti-HCV). A majority of patients (91% for HBV and 93% for HCV) were screened prior to cycle 1 of cancer therapy. The EMR order panel was utilized in 51 (23%) of patients. Anti-HBc was positive in 8 of those tested, and HBsAg was positive in 1 patient. No patients tested positive for HCV. Conclusions: Screening rates for HBV and HCV individually were near or exceeded our goal, however rates of combined HBV and HCV screening were lower. Going forward, additional education to providers as well as increased awareness of the available order panel will be needed to ensure we are comprehensively screening for both HBV and HCV in our patients. [Table: see text]
Racial/ethnic differences in incidence of squamous cell carcinoma in California.
Authors: Deepti Behl, Carol Parise
Journal: Journal of Clinical Oncology (2024)

11139 Background: Squamous cell lung carcinoma is strongly associated with a history of smoking. Typically, no actionable mutations are found, and treatment options are more limited. It is not known if race has any impact on the incidence of squamous cell cancers, especially for Asian ethnicities since most studies combine multiple Asian populations in an Asian/Pacific Islander (API) category. The purpose of this study was to compare the odds of squamous cell carcinoma versus adenocarcinoma in Hispanic, American Indian, Middle Eastern, and 7 Asian ethnicities when compared with both Black and White men and women. Methods: We accessed 211,987 cases of invasive lung cancer with either squamous cell or adenocarcinoma from the California Cancer Registry 2000-2020. Race was categorized as White, African American/Black, Hispanic, American Indian/Alaskan Native, Middle Eastern, Chinese, Japanese, Korean, Filipino, Southeast Asian (SEA), Pacific Islander, or Asian Indian. Separate logistic regression analyses were used to assess the odds of squamous cell versus adenocarcinoma for each race/ethnicity using White and Black as the reference categories. Analyses were conducted separately for males and females and adjusted for age, smoking status, socioeconomic status, marital status, and Charlson Comorbidity Score. Odds Ratios (OR) and 95% confidence intervals (CI) were computed. Results: When compared with White men, American Indian men had increased odds (OR: 1.39; 95% CI: 1.03, 1.88) and Black, Hispanic, Chinese, Filipino, SEA men had decreased odds of squamous cell carcinoma. Japanese women had increased odds (OR: 1.54; 95% CI: 1.15, 2.07) while Black, Hispanic, Middle Eastern, Filipino, and SEA women had decreased odds of squamous cell carcinoma when compared with White women. When compared with Black men, White men, (OR: 1.11; 95% CI: 1.01, 1.24) American Indian, (OR: 1.56; 95% CI: 1.13, 2.13) and Korean (OR: 1.35; 95% CI: 1.05, 1.73) men had increased odds and Chinese, Filipino, and SEA men had decreased odds of squamous cell carcinoma. White, (OR: 1.13; 95% CI: 1.01, 1.28) Japanese, (OR: 1.75; 95% CI: 1.28, 2.39) and Korean (OR: 1.63; 95% CI: 1.09, 2.42) women had increased odds and Southeast Asians had decreased odds when compared with Black women. Conclusions: Some Asian ethnicities have a higher risk for squamous cell lung cancer than both Black and White men and women even after adjusting for smoking. This is not apparent when the Asian ethnicities are classified as API. Examining individual Asian ethnicities is important since they have little to no shared genetic or cultural variables and are grouped together for convenience rather than any scientifically plausible reason.
Demographics and survival outcomes of stage IV male breast cancer: A retrospective analysis of SEER database.
Authors: Nishanth Thalambedu, Bradley Fugere, Sindhu Malapati
Journal: Journal of Clinical Oncology (2024)

11142 Background: Male Breast Cancer (MBC) is a rare malignancy accounting for &lt;1% of all breast cancer cases in the United States. It is often lately diagnosed due to lack of awareness leading to substantial morbidity and mortality. Previous studies revealed higher risk of death among males compared to females across all stages, but little known about the impact of Hormone Receptor (HR) and Human Epidermal growth factor Receptor 2(HER 2) statuses on prognosis and survival among MBC patients. So, we aim to study the survival outcomes of stage IV MBC patients using SEER (Surveillance, Epidemiology, and End Results) data. Methods: A retrospective analysis was conducted using a SEER database and identified stage IV MBC cases (Any T, Any N, M1) diagnosed between 2010-2015. The selection of these years is based on the reporting of HER2 status on SEER database starting from 2010 and to ensure a current period and a minimum of 5 years of follow-up. Patient demographics, tumor HR/HER 2 status and survival data were extracted and analyzed. Subgroup analyses were performed to show the correlation between HR/HER 2 status and survival. Results: The study included 144 patients. 59.7%(86/144) were above 60 years of age. Majority were Caucasians up to 68.1%(98/144) followed by African Americans 18.7% (27/144), Hispanics 6.9%(10/144) and Asians/Pacific Islanders 6.2%(9/144). Among the subtypes, the most common was HR+/HER2- consisting of 69.4%(100/144) followed by HR+/HER2+ 19.4%(28/144), HR-/HER2- 9.7%(14/144), HR-/HER2+ 1.4%(2/144). The median overall survival varied among different subtypes of breast cancer and was noted to be 31.5 months, 25 months, 4.5 months and 10 months among HR+/HER2-, HR+/HER2+, HR-/HER2- and HR-/HER2+ respectively (Table). In the comparison between HR+/HER2+ and HR-/HER2-, the risk of death differed significantly, as indicated by a hazard ratio of 0.26 (95% CI 0.12-0.56, p = 0.001), highlighting a poor survival of HR-/HER2-. Conclusions: This retrospective analysis provides valuable insights into the demographics and survival outcomes of stage IV MBC patients. Triple negative (HR-/HER2-) subtype continues to have poor outcomes in males as well, emphasizing the need to explore novel treatment strategies to improve outcomes for this unique patient population. Although, treatment regimens for MBC are extrapolated from women, the disparity in survival across all subtypes requires the need to get more men on breast cancer clinical trials when feasible. [Table: see text]
Analysis of healthcare provider management of immune-related adverse events and concordance with NCCN Guidelines.
Authors: Kristen M. Rosenthal, Megan Cartwright, Rachael Andrie, John A. Thompson
Journal: Journal of Clinical Oncology (2024)

11136 Background: Immune checkpoint inhibitors (ICIs) are a mainstay of treatment for many cancers but can cause immune-related adverse events (irAEs) that require prompt recognition and management. In 2017, we developed an online interactive decision support tool [www.clinicaloptions.com/immuneAEtool] for healthcare providers (HCPs) with case-specific recommendations for managing irAEs from a medical oncology expert. In 2019 and 2023, we updated the tool to offer recommendations from the latest National Comprehensive Cancer Network (NCCN) Guidelines. Here, we report a comparison of self-reported irAE management from HCPs using the 2023 tool vs NCCN recommendations and a comparison of practice patterns between the 2023 and 2019 tools. Methods: To use the online tool, HCPs entered the affected organ system, symptom grade/severity, and their planned management strategy. The tool showed the NCCN management recommendation for that irAE and then asked if the recommendation changed their intended management approach. Results: From July to December 2023, 172 HCPs entered 241 case scenarios into the tool; 53% treated &lt;10 patients/month with ICIs, and 38% of HCPs practiced in the United States. The most common irAEs involved the gastrointestinal (GI)/hepatobiliary (hep)/pancreatic (29% of cases) or dermatologic/oral (19%) systems. Overall, the planned irAE management strategy of HCPs matched the NCCN recommendations in 55% of cases, an increase from the 49% concordance rate in our 2019 analysis. In the current analysis, the lowest concordance was observed for infusion-related reactions (20%), musculoskeletal irAEs (46%), and dermatologic/oral mucosa irAEs (46%; Table). Furthermore, US HCPs had a lower overall concordance rate (46%) than non-US HCPs (66%). Approximately one half (56%) of all HCPs indicated that the NCCN recommendations in the tool changed their management plan. Conclusions: These data suggest that many HCPs are challenged to optimally manage irAEs and are not managing their patients in concordance with NCCN guidelines. A detailed analysis of HCP irAE management vs NCCN recommendations, including by organ system and severity, along with a comparison of 2023 vs 2019 practice patterns, will be presented. [Table: see text]
Implementation of standardized electronic documentation of goals of care discussions to improve cancer care.
Authors: Katarina Vasiljevic, Shelly Kane, Brooks Tuyn, Jennifer Schoenecke, Kyle P Edmonds, Kathryn A. Gold
Journal: Journal of Clinical Oncology (2024)

11127 Background: Early documentation of physician-led goals of care (GOC) discussions is important to providing comprehensive and individualized quality care to cancer patients as it can provide all members of the patient care team with a context for the type of care each patient wishes to receive prior to and at end of life. The electronic medical record (EMR) should provide easy access to these conversations to seamlessly integrate outpatient, emergency room and inpatient care of cancer patients. Methods: The institution-wide initiative was introduced via presentations and emails between 8/2021 and 11/2021 to all Moores Cancer Center faculty at UC San Diego Health. A SmartPhrase was created in our EMR Epic as the intervention, including critical components of a GOC discussion: people present during discussion, goal of cancer-directed treatment, anticipated cancer trajectory shared with the patient, and patient’s health care agent. The SmartPhrase was radiolabeled to be easily searchable for any clinician accessing the patient’s chart. Physician documentation was tracked for the purposes of achieving a group goal with a target of greater than 50% documentation of GOC discussions within 30 days of the first day of the first cycle of chemotherapy. Prior to physician education, 4% of patients had a GOC note using a searchable SmartPhrase. In 12/2021, we began sending individual emails to physicians to remind them of eligible patients. Results: By 1/2022, after education, 50% of physicians ordering chemotherapy had used the GOC SmartPhrase and 29% of patients initiating chemotherapy had a GOC note using the SmartPhrase. After initiation of monthly reminder emails, documentation increased to 51% by 10/2022. An increased use of Advanced Care Planning billing codes was also noted. Conclusions: Implementation of an initiative to standardize electronic documentation of GOC conversations improved early documentation of these vital conversations. Radiolabeling of the SmartPhrase made it easily accessible to all members of a patient’s care team.