Patients with cancer have been disproportionately affected by the COVID-19 pandemic. This effect has included the adverse outcomes in patients with cancer who develop COVID-19, the impact of the ...COVID-19 pandemic on the delivery of cancer care, and the severe disruption to cancer research. However, patients with cancer are a heterogeneous population, and recent studies have now documented factors that allow risk stratification of patients with cancer in order to optimize care. In this review, we highlight data at the intersection of COVID-19 and cancer, including the biological interplay between the two diseases and practical recommendations for the treatment of patients with cancer during the pandemic. We additionally discuss the potential long-lasting impact of the pandemic on cancer care due to its deleterious effect on cancer research, as well as biological insights from the cancer research community that could help develop novel therapies for all patients with COVID-19.
Patients with cancer have been disproportionately affected by the COVID-19 pandemic. This effect has included the adverse outcomes in patients with cancer who develop COVID-19, the impact of the COVID-19 pandemic on the delivery of cancer care, and the severe disruption to cancer research. However, patients with cancer are a heterogeneous population, and recent studies have now documented factors that allow risk stratification of patients with cancer in order to optimize care. In this review, we highlight data at the intersection of COVID-19 and cancer, including the biological interplay between the two diseases and practical recommendations for the treatment of patients with cancer during the pandemic. We additionally discuss the potential long-lasting impact of the pandemic on cancer care due to its deleterious effect on cancer research, as well as biological insights from the cancer research community that could help develop novel therapies for all patients with COVID-19.
Current models for correlating electronic medical records with -omics data largely ignore clinical text, which is an important source of phenotype information for patients with cancer. This data ...convergence has the potential to reveal new insights about cancer initiation, progression, metastasis, and response to treatment. Insights from this real-world data will catalyze clinical care, research, and regulatory activities. Natural language processing (NLP) methods are needed to extract these rich cancer phenotypes from clinical text. Here, we review the advances of NLP and information extraction methods relevant to oncology based on publications from PubMed as well as NLP and machine learning conference proceedings in the last 3 years. Given the interdisciplinary nature of the fields of oncology and information extraction, this analysis serves as a critical trail marker on the path to higher fidelity oncology phenotypes from real-world data.
Objective To evaluate the phenotyping performance of three major electronic health record (EHR) components: International Classification of Disease (ICD) diagnosis codes, primary notes, and specific ...medications.
Materials and Methods We conducted the evaluation using de-identified Vanderbilt EHR data. We preselected ten diseases: atrial fibrillation, Alzheimer’s disease, breast cancer, gout, human immunodeficiency virus infection, multiple sclerosis, Parkinson’s disease, rheumatoid arthritis, and types 1 and 2 diabetes mellitus. For each disease, patients were classified into seven categories based on the presence of evidence in diagnosis codes, primary notes, and specific medications. Twenty-five patients per disease category (a total number of 175 patients for each disease, 1750 patients for all ten diseases) were randomly selected for manual chart review. Review results were used to estimate the positive predictive value (PPV), sensitivity, and F-score for each EHR component alone and in combination.
Results The PPVs of single components were inconsistent and inadequate for accurately phenotyping (0.06–0.71). Using two or more ICD codes improved the average PPV to 0.84. We observed a more stable and higher accuracy when using at least two components (mean ± standard deviation: 0.91 ± 0.08). Primary notes offered the best sensitivity (0.77). The sensitivity of ICD codes was 0.67. Again, two or more components provided a reasonably high and stable sensitivity (0.59 ± 0.16). Overall, the best performance (F score: 0.70 ± 0.12) was achieved by using two or more components. Although the overall performance of using ICD codes (0.67 ± 0.14) was only slightly lower than using two or more components, its PPV (0.71 ± 0.13) is substantially worse (0.91 ± 0.08).
Conclusion Multiple EHR components provide a more consistent and higher performance than a single one for the selected phenotypes. We suggest considering multiple EHR components for future phenotyping design in order to obtain an ideal result.
Genome-wide and phenome-wide association studies are commonly used to identify important relationships between genetic variants and phenotypes. Most studies have treated diseases as independent ...variables and suffered from the burden of multiple adjustment due to the large number of genetic variants and disease phenotypes. In this study, we used topic modeling via non-negative matrix factorization (NMF) for identifying associations between disease phenotypes and genetic variants. Topic modeling is an unsupervised machine learning approach that can be used to learn patterns from electronic health record data. We chose the single nucleotide polymorphism (SNP) rs10455872 in LPA as the predictor since it has been shown to be associated with increased risk of hyperlipidemia and cardiovascular diseases (CVD). Using data of 12,759 individuals with electronic health records (EHR) and linked DNA samples at Vanderbilt University Medical Center, we trained a topic model using NMF from 1,853 distinct phenotypes and identified six topics. We tested their associations with rs10455872 in LPA. Topics enriched for CVD and hyperlipidemia had positive correlations with rs10455872 (P < 0.001), replicating a previous finding. We also identified a negative correlation between LPA and a topic enriched for lung cancer (P < 0.001) which was not previously identified via phenome-wide scanning. We were able to replicate the top finding in a separate dataset. Our results demonstrate the applicability of topic modeling in exploring the relationship between genetic variants and clinical diseases.
Treatment patterns in systemic anticancer therapy (SACT) are extremely varied and complex. While professional society guidelines exist that suggest recommended treatment strategies, these guidelines ...are produced through an extremely laborious and sometimes opaque manual process, making it impossible for such guidelines to cover all relevant treatment scenarios. To complement these manually curated guidelines, we leveraged a database of 5818 clinical trials and 7012 supporting references from 1943-present to calculate a quantifiable "relevance score". In a pilot evaluation, this score was strongly associated with professional society guideline recommendations, while also providing relevance information on thousands of additional therapies. We show that this score also accurately illustrates trends in SACT adoption over time. We foresee that this score, which comprehensively evaluates the relevance of SACT overall and by cancer subtype, will have utility for clinical practitioners as well as researchers in real-world data.
Purpose
Immunocompromised individuals, such as those diagnosed with cancer, are at a significantly higher risk for severe illness and mortality when infected with SARS-CoV-2 (COVID-19) than the ...general population. Two oral antiviral treatments are approved for COVID-19: Paxlovid® (nirmatrelvir/ritonavir) and Lagevrio® (molnupiravir). There is a paucity of data regarding the benefit from these antivirals among immunocompromised patients with cancer, and recent studies have questioned their efficacy among vaccinated patients, even those with risk factors for severe COVID-19.
Methods
We evaluated the efficacy and safety of nirmatrelvir/ritonavir and molnupiravir in preventing severe illness and death using our database of 457 patients with cancer and COVID-19 from Brown University-affiliated hospitals.
Results
Sixty-seven patients received nirmatrelvir/ritonavir or molnupiravir and were compared to 45 concurrent controls who received no antiviral treatment despite being eligible to receive it. Administration of nirmatrelvir/ritonavir or molnupiravir was associated with improved survival and lower 90-day all-cause and COVID-19-attributed mortality (
p
< 0.05) and with lower peak O
2
requirements (ordinal odds ratio OR 1.52, 95% confidence interval CI 0.92–2.56).
Conclusion
Acknowledging the small size of our sample as a limitation, we concluded that early antiviral treatment might be beneficial to immunocompromised individuals, particularly those with cancer, when infected with SARS-CoV-2. Larger-scale, well-stratified studies are needed in this patient population.
Graphical Abstract
Objective
Ibrutinib is an irreversible inhibitor of Bruton tyrosine kinase (BTK) in B lymphocytes as well as other kinases including interleukin‐2‐inducible T‐cell kinase (ITK) in CD4+ Th2 regulatory ...T cells. Increased infections have been observed in patients taking ibrutinib. The overall incidence has not been systematically evaluated.
Methods
The published literature and conference s of prospective clinical trials using ibrutinib in hematologic malignancies were identified and reviewed using PubMed, Google Scholar, and HemOnc.org per PRISMA guidelines. Infectious events with a focus on pneumonia were collated per the Common Terminology Criteria for Adverse Events Version 4.03 grading.
Results
Infectious complications are common, occurring in 56% of patients taking single‐agent ibrutinib and 52% of those on combination therapy. Approximately one in 5 patients developed pneumonia, which was the major contributor to a 2% rate of death from infections. Many of the cases of pneumonia were due to opportunistic pathogens.
Conclusions
Ibrutinib use requires prudent consideration of the impacts on host immunity. We identified a high rate of serious adverse infectious events within prospective clinical trials. Data suggest a role of both BTK and ITK inhibition for the increased events. There was considerable variability in the reporting of adverse events between trials, journals, and conference reports.
Electronic health records (EHRs) have become ubiquitous tools and represent the standard of care for 96% of hospitals and 86% of ambulatory physicians in the United States. With adoption of EHRs came ...the promise of improved efficiency, higher-quality care, and lower costs. Unfortunately, some clinicians are now spending twice as much time on documentation as they spend seeing patients, and the documentation paradigm of problem-oriented medical records is contributing to this imbalance. It is time to consider new innovations. The collaborative wiki format offers many opportunities to ease the burden of documentation as well as to increase the usefulness of the recorded clinical data. Wikis support multiple authorship, have built-in features to track edits and changes, allow for contextual linkages (e.g., linking medical problems to their treatment), and support new technologies such as application programming interfaces, which allow for safe and secure exchange of information. In this Perspective, the authors describe the rationale for considering this approach to clinical documentation and propose a pilot to learn about its effectiveness. They believe wiki-based documentation will become increasingly attractive, especially as new legislation and directives from policymakers seek to reduce the crushing documentation burden and as the U.S. health care system transitions from an episode-based payment structure to a value-based, outcomes-focused system.
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