tbuckley/cabot-search huggingface dataset:
A deep learning–enabled workflow to estimate real world progression-free survival in patients with metastatic breast cancer.
Authors: Gowtham Varma, Rohit Kumar Yenukoti, Praveen Kumar-M, Bandlamudi Sai Ashrit, K Purushotham, Subash C, Sunil Kumar Ravi, Verghese Kurien, Avinash Aman, Mithun Manoharan, Shashank Jaiswal, Akash Anand, Rakesh Barve, Viswanathan Thiagarajan, Patrick Lenehan, Scott A. Soefje, Venky Soundararajan
Journal: Journal of Clinical Oncology (2024)

11176 Background: Progression-free survival (PFS) is frequently measured in oncology clinical trials. In analyses outside of the trial setting, various strategies have been utilized to assess real-world PFS (rwPFS), including manual abstraction of clinical records, natural language processing (NLP) of oncology notes and radiology reports, and longitudinal analyses of radiologic images. Here we develop and validate a new semi-automated workflow that combines NLP of clinical notes with structured electronic health record data to facilitate the evaluation of rwPFS in patients with metastatic breast cancer (mBC). Methods: This study analyzes de-identified EHR data using nference nSights. The data is extracted following privacy-preserving protocols and is HIPAA compliant. The overall cohort included 316 patients with HR-positive, HER2-negative mBC who initiated Palbociclib and Letrozole combination therapy between January 1, 2015 and December 31, 2021. We developed and implemented an ensemble of deep-learning NLP frameworks to capture progression events from unstructured clinical notes and radiology reports. A change in the line of therapy, as determined by structured drug order/administration records, was also considered a progression event. We used manually curated “ground-truth” datasets to evaluate the performance of the progression-event capture workflow at the levels of both sentences (N = 1000) and patients (N = 100) by calculating sensitivity, specificity, precision, accuracy, and F1 scores. Progression events and censoring events (death, loss to follow-up, end of study period) were considered to compute rwPFS. Results: At the sentence level, progression events were captured from clinical notes and radiology reports with a sensitivity of 99.8%, specificity of 96.7%, and accuracy of 98.2% (Table). At the patient level, initial progression was correctly captured within a window of +/-30 days with a sensitivity of 92.5%, specificity of 83.0%, and accuracy of 88.0% (Table). In a sample of 100 patients, the median rwPFS was determined to be 25 months (95% CI; 15-35 months) by manual curation and 22 months (95% CI; 15-35 months) by the semi-automated workflow. In the overall cohort, median rwPFS was 20 months (95% CI; 18-25 months). Conclusions: An ensemble of NLP algorithms extracted progression events from clinical notes and radiology reports with high accuracy. A semi-automated workflow enabled rapid and accurate determination of rwPFS in mBC patients receiving a combination chemotherapy regimen. Further evaluation of this workflow to estimate rwPFS in other cancers and therapeutic settings is warranted. [Table: see text]
Patient-reported fatigue and risk of treatment-related adverse events (AEs) in patients receiving systemic therapy in cancer clinical trials.
Authors: Joseph M. Unger, Riha Vaidya, Michael Jordan Fisch, Salene M. W. Jones, Norah Lynn Henry, Dawn L. Hershman
Journal: Journal of Clinical Oncology (2024)

11015 Background: Fatigue in patients with cancer is common and negatively impacts quality of life. Patient-reported outcomes (PROs) assess a patient’s direct report of their symptoms and well-being; research has highlighted their potential to predict cancer outcomes. We examined whether fatigue prior to treatment was associated with AEs. Methods: We analyzed 18 phase II and III cancer treatment clinical trials with baseline fatigue data conducted by SWOG between 1988-2018. The Common Terminology Criteria for Adverse Events was used. Symptomatic AEs were defined as those aligned with the NCI’s PRO-CTCAE; laboratory-based or measurable AEs were designated as objective (hematologic v nonhematologic). Thirteen symptomatic and 14 objective AE categories were examined. Fatigue was derived from multiple scales (e.g., FACT, EORTC QLQ-C30 and PROMIS-Fatigue 7a). Each measure was mapped to a 5-point Likert scale. Binary categories were compared (e.g., &lt; some vs. &gt; = some fatigue). Generalized estimating equations were used with a binomial distribution and logit link, adjusting for age, sex, race, and BMI, with clustering by study. Results: We examined N = 8,040 patients receiving systemic therapy. Among 18 trials (prostate, 5; lung, 3; colorectal, 2; lymphoma, 2; breast, 2; bladder, 1; melanoma, 1; ovarian, 1, pancreas, 1), n = 108,059 AEs were examined. Patient fatigue was present at levels of “a little” or greater in 75.8%, “some” or greater in 42.8%, and “quite a lot” or “very much” in 17.7%. Patients with some or greater fatigue were nearly twice as likely to have severe or worse toxicity (OR = 1.92, 95% CI, 1.53-2.40, p &lt; .001) or life-threatening toxicity (OR = 1.93, 95% CI, 1.44-2.59, p &lt; .001) and nearly threefold more likely to have fatal toxicity (OR = 2.76, 95% CI, 1.37-5.53, p = .004). Similar patterns were seen at a threshold of “quite a lot”. A dose response pattern was evident; patients reporting quite a lot/very much compared to no fatigue were &gt; 5 times more likely to experience fatal toxicity (OR = 5.63, p = .002). These patterns were consistent in symptomatic, objective hematologic, and objective non-hematologic AEs. Conclusions: Baseline fatigue was highly predictive of subsequent risk of AEs. These findings suggest that in an era of precision medicine, patient-reported fatigue may be an important component of determining toxicity risk and could aid in treatment decision making.[Table: see text]
Impact of boarding time on in-hospital mortality in patients with cancer presenting to the emergency department.
Authors: Patricia A. Brock, Denise Manon Langabeer, Valda D Page, Aiham Qdaisat
Journal: Journal of Clinical Oncology (2024)

11036 Background: Longer emergency department (ED) boarding times for admitted patients is associated with increased morbidity and mortality. 1 While research over the years has shown an association between boarding time to mortality in a variety of patient demographics, no specific research has been explored in a cancer population. Patients with cancer visit the emergency department frequently and have a high rate of admission compared to other patients. 2 This study evaluates boarding times and mortality rates in patients presenting to an oncologic ED. Methods: A retrospective analysis was performed on 183,524 ED visits located at a comprehensive cancer center between March 2016 and December 2022. Eligibility criteria included patients 19 years and older admitted to the hospital excluding direct intensive care unit admission. Boarding time was defined from the time the physician made an order to admit to the hospital to the time of ED departure. Demographics and clinical characteristics were examined using descriptive statistics. Categorical data was analyzed using chi-square test and continuous variables employed the nonparametric Mann–Whitney U test. Boarding time was grouped into quartiles. Univariate and multivariable logistic regression analyses examined clinical factors, including boarding time and in-hospital mortality. Results: The eligible number of visits supporting the study equaled 83,629. Overall median boarding time was 2.7 hours (interquartile range: 1.5–5.1 hours) and in-hospital mortality was 5.5% (n=4607). Longer boarding time was significantly associated with in-hospital mortality. Patients with boarding time ≥5.1 hours had 1.19 (95% confidence interval [95%CI]: 1.09-1.30; P&lt;0.001) odds of in-hospital mortality when compared to the reference group (boarding time &lt;1.5 hours) when controlling for other risk factors including comorbidities and emergency severity index (ESI) between 1 through 5. Similar results were observed for patients with boarding times of ≥1.5- &lt;2.7 hours and ≥2.7- &lt;5.1 hours with odds ratio of 1.12 (95%CI: 1.02-1.22; P=0.013) and 1.11 (95%CI: 1.02-1.21; P=0.020), respectively. Higher Charlson comorbidity index and levels 1 and 2 ESI were also associated with poor survival outcome (P&lt;0.001 for both). Conclusions: This study found an association between boarding time and in-hospital mortality in cancer patients presenting to the ED. Patients with longer boarding times were likely to experience mortality during their hospital admission. High comorbidity score and high-risk ESI were also identified as risk factors for poor survival outcome. These results emphasize the need for improved strategies to expedite the admission process and optimize care for cancer patients in the ED to reduce mortality rates. Further research and interventions targeting reduction in boarding times are warranted to improve outcomes for this vulnerable population.
Staging of psychiatric disorders in patients with limited and advanced/metastatic solid cancer: A pilot study.
Authors: Raffaela Daria Giovanna Sartori, Chiara Airoldi, Davide Dalu, Valentina Biscaldi, Maria Silvia Cona, Anna Gambaro, Lorenzo Ruggieri, Ottavia Amato, Cinzia Fasola, Sabrina Ferrario, Bernardo Dell'Osso, Caterina Adele Viganò, Nicla Maria La Verde
Journal: Journal of Clinical Oncology (2024)

e22545 Background: 38% of cancer patients (pts) receive diagnosis of major depressive disorder. According with the clinimetric approach of the staging of psychiatric disease, the 5-step model of unipolar depression allows for the evaluation of the extent of the disorder, its severity, and characteristics at a specific time in the course of the disease. This study was aimed: a) to assess mental health and quality of life of cancer patients with limited (LS) and advanced/metastatic (AS) solid cancer through the join evaluation of the staging of psychiatric disorders; b) to explore the potential role of severity of oncological disease in anxious/depressive disease development. Methods: A cross-sectional study was conducted at the Oncology Unit of Luigi Sacco Hospital of Milan during the first session of a psychological support path. Patients’ cancer diagnosis and stage, as well as regular engagement in work, leisure and social activities were explored. Hospital and Depression Anxiety Scale (HADS), the Revised Illness Perception Questionnaire (IPQ-R) and Mental Health Continuum Short-Form (MHC-SF) were also administered. Results: 104 pts were included: F 86, M 18, median age 57,5 (27-84), 30% AS, and 70% LS. Pts’ anxious/depressive symptoms were assessed by HADS scoring and they were divided into 3 groups according to the model of unipolar depression: Group 1a (prodromal phase – no symptoms), Group 1b (prodromal phase – mood symptoms) and Group 2 (anxious/depressive disorder). Pts in group 2 were significantly more frequently AS pts, while in group 1a pts in LS stage (χ² = 7.78, p &lt; .05). Based on MHC-SF scores, flourishing and languishing were significantly more frequently reported by pts in group 1a (55,5% and 46% of pts, respectively), and moderate mental health in group 2 (45,9% of pts, χ² = 18.1, p &lt; .001). Regression analysis highlighted non-hobbyist vs. hobbyists, AS vs. LS cancer pts, asthenic vs. non asthenic pts, and moderate vs flourishing metal health were more likely to receive a provisional anxious depressive disorder diagnosis (Stage 2). No association emerged for other physical symptoms, work, and socialization. Conclusions: AS pts with asthenia, no engagement in structured activities and moderate mental health had a higher risk of developing anxious/depressive disorders. Screening psychiatric disorders in cancer pts may improve the physician's ability to recognize earlier phase of psychopathological disease and guide pts to tailored treatment. These may prevent progression of psychiatric disease and promote mental health and positive quality of life.
Efficacy of mammography screening in women aged 40–49 years: An updated systematic review and meta-analysis.
Authors: Pedro Cotta Abrahão Reis, João Pedro Oliveira, Swathi Vellaichamy, Renato Cagnacci
Journal: Journal of Clinical Oncology (2024)

e22513 Background: The screening of women aged over 50 through mammography has proven to significantly reduce breast cancer mortality in randomized controlled trials (RCTs). Despite prior trials and meta-analyses, new trials have been published and debates persist regarding the effectiveness of mammography screening for women aged 40–49. Therefore, we conducted an updated meta-analysis to assess the impact of mammography screening on reducing breast cancer mortality within this age group. Methods: In adherence to PRISMA guidelines, we systematically searched Pubmed, Cochrane, and Embase libraries for RCTs evaluating the efficacy of mammography screening in lowering breast cancer mortality among patients aged 40–49. Exclusion criteria encompassed non-RCTs, studies lacking reports on breast cancer mortality for individuals aged 40–49, and secondary analyses of included trials. Data extraction was carried out based on the latest available follow-up. We synthesized the relative risk (RR) for breast cancer mortality along with their corresponding 95% confidence intervals (95% CI). Employing a random-effects model, statistical analysis was conducted using RevMan 5.4 version, with an evaluation of I2 statistics for heterogeneity. Results: From 797 initial studies, 10 RCTs were included, comprising 163,634 women in the intervention group and 206,130 in the control group. Median follow-up ranged from 14 to 30 years. In individual studies, statistical significance was only reached in one trial (Table). Breast cancer mortality in the intervention group was significantly lower than in the control group RR 0.86 [95% CI 0.77–0.95]; p = 0.004; I2 = 0%. Conclusions: Despite limited data availability for this age group in certain recent publications with extended follow-up periods, raised questions about the design and reported results in some trials, the comprehensive findings of this meta-analysis suggest that mammography screening retains its effectiveness in reducing breast cancer mortality among women aged 40–49 years. [Table: see text]
Examining knowledge of cancer-related family history in an urban underserved patient population.
Authors: Monet Jones, Daniel Ludi, Irann Martinez, Keith Naylor
Journal: Journal of Clinical Oncology (2024)

e22550 Background: An accurate assessment of family history of cancer is essential in assigning cancer risk, and in decision making regarding the timing and method of cancer screening. However, obtaining a complete and accurate cancer-related family history, including first- and second-degree relatives, is often challenging in underserved communities. Familial dynamics such as single parent households, kinship care, and estrangement may act as barriers to an individual’s knowledge of their family health history. Presently, Electronic Medical Record systems constrain users to a binary documentation of cancer history as either ‘yes’ or ‘no’. However, patients may be unaware or uncertain of their family’s cancer history. These unknowns are not captured, resulting in poor understanding of patient knowledge regarding their family history of cancer. Objective: To assess knowledge of cancer-related family history for first- and second-degree relatives among an urban underserved patient population. Funding source: The American Cancer Society. Methods: University of Illinois Health patients aged 45-75 years without a history of colorectal cancer, who received an order for colorectal cancer screening through fecal immunochemical testing or screening colonoscopy were eligible to participate. A total of 88 respondents completed a 23-item telephone survey assessing knowledge of their family cancer health history using a 5-point Likert scale. Surveys were administered in both English and Spanish languages. Results: Of the 88 survey participants, 50 (57%) were female, 54 (61%) were of black or African American race, and 31 (36%) were of Hispanic or Latino ethnicity. On a single-item question assessing overall knowledge of their cancer-related family history, 35 (39.7%) responded they know it well or very well, versus 13 (14.8%) with little or no knowledge. On knowledge of maternal cancer related history, 8 participants (9.1%) reported little or no knowledge of their mother’s cancer history, and 29 participants (33%) reported little or no knowledge of their maternal relatives’ cancer history. On knowledge of their father’s cancer history, 35 (39.8%) reported little or no knowledge of their father’s cancer history, and 48 participants (54.5%) reported little or no knowledge of their paternal relatives’ cancer history. Conclusions: This original research study addresses the current gap in understanding patient knowledge regarding familial cancer health history. Survey results demonstrate a striking discrepancy between respondent reported overall knowledge of cancer-related family history, and knowledge of their maternal and paternal cancer histories. Moreover, respondents reported increased knowledge of their mother’s versus father’s cancer history p &lt; 0.0001. Improved recognition of unknown family history in first- and second-degree family members may improve cancer-risk assessment.
Defeating cancer through education, prevention, and youth athletics.
Authors: William Barrett, Sherwin Anderson, Andrew Frankart, Samuel Thompson, William Mackey
Journal: Journal of Clinical Oncology (2024)

e22548 Background: Barriers to effective scientific learning exists for elementary students, particularly in socially and financially disadvantaged settings. Maintaining interest, concentration and focus can be difficult for children, particularly when confronted with complex material and multiple distractions. Methods: We implemented a scientific educational program for children attending an urban community center after-school program entailing tutoring stations conducted during a basketball practice. Five tutoring stations included human physiology, astronomy, geography, geology and cancer. Five children spend 3 minutes with tutors who are medical students or residents while five other children are on the basketball court going through drills with a coach. After 3 minutes the kids on the court and the kids being tutored switch places. The sequence is repeated until each child has rotated through each of the 5 tutoring stations and through each of the 5 basketball drills. After this, each child rotates through each tutoring station for one minute where they are quizzed on what they were taught and the end of practice scrimmage begins with a score based upon each team of fives’ performance on the quiz. Results: The method proved to be highly effective in the children’s ability to understand and retain scientific concepts. Within weeks nearly every child could list the planets of the solar system in order, calculate their pulse and explain its importance, list the most common symptoms of the most prevalent cancers, correctly identify continents, oceans, countries and states on maps and explain the origin of volcanos, earthquakes, hurricanes and tsunamis. Conclusions: This novel teaching method proved highly effective with children being able to maintain interest, focus and concentration in a setting where physical exertion is rapidly alternated with educational instruction. Parents and teachers commented that the kids learned more in 45 minutes with this method than in 2 weeks of conventional classroom teaching. The approach is widely applicable to students from diverse backgrounds.
A novel multi-cancer screening approach based on screening objectives, cancer occurrence mechanism, and cost modeling.
Authors: Chris Chang Yu, Xuedong Du, Yue Lin, Xing Tang
Journal: Journal of Clinical Oncology (2024)

e22509 Background: The current cancer screening approach is relatively expensive and unable to cover all general population. Certain amount of information collected is possibly “overkill” at the expense of costs and technology complexity as statistically only 2-3 individuals in very one thousand individuals have cancer. We propose a novel multi-cancer screening for general population which is based on initial screening objectives, new cancer occurrence mechanism, and cost model. Since the step following cancer screening is cancer diagnosis in which significant tests will be carried out, we strongly believe that cancer screening should mainly focus on (1) separating high cancer risk individuals from low risk group, and (2) reduce screening costs and make screening available for everyone. Methods: We analyzed our own large size, multi-year, multi-cancer data as well as other reported studies. We have also studied new cancer occurrence mechanisms developed in recent years which included correlations between immune system and micro- environment change in human body (both of which could occur before the tumor is formed) and cancer occurrence. Finally, we have analyzed cost numbers for the new and traditional approaches. Results: In our extensive multi-year, multi-cancer general population screening of over 200,000 individuals and follow-up study, only 1.4% tested classified as high risk individuals, while this small group accounted for close to 92% of all cancer cases confirmed to date in the follow-up study when enrollment is normalize for all groups. This is very significant because this demonstrates that as long as screening is statistically meaningful and effective, a lot other information is not needed in screening as high risk people will undergo diagnosis anyway. The new screening approach does not require to obtain full information (for example, traceability (cancer location information), as over 98% of people do not likely have cancer) in order to reduce screening costs. The cost analysis results are shown in Table 1. Conclusions: We proposed a new cancer screening approach which is much more cost effective while it is still workable and meets screening objectives. [Table: see text]