Regression models for average hazard.

Limitations of using the traditional Cox's hazard ratio for summarizing the magnitude of the treatment effect on time-to-event outcomes have been widely discussed, and alternative measures that do not have such limitations are gaining attention. One of the alternative methods recently proposed, in a simple 2-sample comparison setting, uses the average hazard with survival weight (AH), which can be interpreted as the general censoring-free person-time incidence rate on a given time window. In this paper, we propose a new regression analysis approach for the AH with a truncation time τ. We investigate 3 versions of AH regression analysis, assuming (1) independent censoring, (2) group-specific censoring, and (3) covariate-dependent censoring. The proposed AH regression methods are closely related to robust Poisson regression. While the new approach needs to require a truncation time τ explicitly, it can be more robust than Poisson regression in the presence of censoring. With the AH regression approach, one can summarize the between-group treatment difference in both absolute difference and relative terms, adjusting for covariates that are associated with the outcome. This property will increase the likelihood that the treatment effect magnitude is correctly interpreted. The AH regression approach can be a useful alternative to the traditional Cox's hazard ratio approach for estimating and reporting the magnitude of the treatment effect on time-to-event outcomes.

Artificial Intelligence in Oncology: Current Landscape, Challenges, and Future Directions.

Artificial intelligence (AI) in oncology is advancing beyond algorithm development to integration into clinical practice. This review describes the current state of the field, with a specific focus on clinical integration. AI applications are structured according to cancer type and clinical domain, focusing on the four most common cancers and tasks of detection, diagnosis, and treatment. These applications encompass various data modalities, including imaging, genomics, and medical records. We conclude with a summary of existing challenges, evolving solutions, and potential future directions for the field. SIGNIFICANCE: AI is increasingly being applied to all aspects of oncology, where several applications are maturing beyond research and development to direct clinical integration. This review summarizes the current state of the field through the lens of clinical translation along the clinical care continuum. Emerging areas are also highlighted, along with common challenges, evolving solutions, and potential future directions for the field.

Biomarker Inference and the Timing of Next-Generation Sequencing in a Multi-Institutional, Cross-Cancer Clinicogenomic Data Set.

PURPOSE: Observational clinicogenomic data sets, consisting of tumor next-generation sequencing (NGS) data linked to clinical records, are commonly used for cancer research. However, in real-world practice, oncologists frequently request NGS in search of treatment options for progressive cancer. The extent and impact of this dynamic on analysis of clinicogenomic research data are not well understood. METHODS: We analyzed clinicogenomic data for patients with non-small cell lung, colorectal, breast, prostate, pancreatic, or urothelial cancers in the American Association for Cancer Research Biopharmaceutical Consortium cohort. Associations between baseline and time-varying clinical characteristics and time from diagnosis to NGS were measured. To explore the impact of informative cohort entry on biomarker inference, statistical interactions between selected biomarkers and time to NGS with respect to overall survival were calculated. RESULTS: Among 7,182 patients, time from diagnosis to NGS varied significantly by clinical factors, including cancer type, calendar year of sequencing, institution, and age and stage at diagnosis. NGS rates also varied significantly by dynamic clinical status variables; in an adjusted model, compared with patients with stable disease at any given time after diagnosis, patients with progressive disease by imaging or oncologist assessment had higher NGS rates (hazard ratio for NGS, 1.61 [95% CI, 1.45 to 1.78] and 2.32 [95% CI, 2.01 to 2.67], respectively). Statistical interactions between selected biomarkers and time to NGS with respect to survival, potentially indicating biased biomarker inference results, were explored. CONCLUSION: To evaluate the appropriateness of a data set for a particular research question, it is crucial to measure associations between dynamic cancer status and the timing of NGS, as well as to evaluate interactions involving biomarkers of interest and NGS timing with respect to survival outcomes.

Identifying Oncology Clinical Trial Candidates Using Artificial Intelligence Predictions of Treatment Change: A Pilot Implementation Study.

PURPOSE: Precision oncology clinical trials often struggle to accrue, partly because it is difficult to find potentially eligible patients at moments when they need new treatment. We piloted deployment of artificial intelligence tools to identify such patients at a large academic cancer center. PATIENTS AND METHODS: Neural networks that process radiology reports to identify patients likely to start new systemic therapy were applied prospectively for patients with solid tumors that had undergone next-generation sequencing at our center. Model output was linked to the MatchMiner tool, which matches patients to trials using tumor genomics. Reports listing genomically matched patients, sorted by probability of treatment change, were provided weekly to an oncology nurse navigator (ONN) coordinating recruitment to nine early-phase trials. The ONN contacted treating oncologists when patients likely to change treatment appeared potentially trial-eligible. RESULTS: Within weekly reports to the ONN, 60,199 patient-trial matches were generated for 2,150 patients on the basis of genomics alone. Of these, 3,168 patient-trial matches (5%) corresponding to 525 patients were flagged for ONN review by our model, representing a 95% reduction in review compared with manual review of all patient-trial matches weekly. After ONN review for potential eligibility, treating oncologists for 74 patients were contacted. Common reasons for not contacting treating oncologists included cases where patients had already decided to continue current treatment (21%); the trial had no slots (14%); or the patient was ineligible on ONN review (12%). Of 74 patients whose oncologists were contacted, 10 (14%) had a consult regarding a trial and five (7%) enrolled. CONCLUSION: This approach facilitated identification of potential patients for clinical trials in real time, but further work to improve accrual must address the many other barriers to trial enrollment in precision oncology research.

Perspectives of Oncologists on the Ethical Implications of Using Artificial Intelligence for Cancer Care.

Importance: Artificial intelligence (AI) tools are rapidly integrating into cancer care. Understanding stakeholder views on ethical issues associated with the implementation of AI in oncology is critical to optimal deployment. Objective: To evaluate oncologists' views on the ethical domains of the use of AI in clinical care, including familiarity, predictions, explainability (the ability to explain how a result was determined), bias, deference, and responsibilities. Design, Setting, and Participants: This cross-sectional, population-based survey study was conducted from November 15, 2022, to July 31, 2023, among 204 US-based oncologists identified using the National Plan & Provider Enumeration System. Main Outcomes and Measures: The primary outcome was response to a question asking whether participants agreed or disagreed that patients need to provide informed consent for AI model use during cancer treatment decisions. Results: Of 387 surveys, 204 were completed (response rate, 52.7%). Participants represented 37 states, 120 (63.7%) identified as male, 128 (62.7%) as non-Hispanic White, and 60 (29.4%) were from academic practices; 95 (46.6%) had received some education on AI use in health care, and 45.3% (92 of 203) reported familiarity with clinical decision models. Most participants (84.8% [173 of 204]) reported that AI-based clinical decision models needed to be explainable by oncologists to be used in the clinic; 23.0% (47 of 204) stated they also needed to be explainable by patients. Patient consent for AI model use during treatment decisions was supported by 81.4% of participants (166 of 204). When presented with a scenario in which an AI decision model selected a different treatment regimen than the oncologist planned to recommend, the most common response was to present both options and let the patient decide (36.8% [75 of 204]); respondents from academic settings were more likely than those from other settings to let the patient decide (OR, 2.56; 95% CI, 1.19-5.51). Most respondents (90.7% [185 of 204]) reported that AI developers were responsible for the medico-legal problems associated with AI use. Some agreed that this responsibility was shared by physicians (47.1% [96 of 204]) or hospitals (43.1% [88 of 204]). Finally, most respondents (76.5% [156 of 204]) agreed that oncologists should protect patients from biased AI tools, but only 27.9% (57 of 204) were confident in their ability to identify poorly representative AI models. Conclusions and Relevance: In this cross-sectional survey study, few oncologists reported that patients needed to understand AI models, but most agreed that patients should consent to their use, and many tasked patients with choosing between physician- and AI-recommended treatment regimens. These findings suggest that the implementation of AI in oncology must include rigorous assessments of its effect on care decisions as well as decisional responsibility when problems related to AI use arise.

Genomic Characterization and Clinical Outcomes of Patients with Peritoneal Metastases from the AACR GENIE Biopharma Collaborative Colorectal Cancer Registry.

Peritoneal metastases (PM) are common in metastatic colorectal cancer (mCRC). We aimed to characterize patients with mCRC and PM from a clinical and molecular perspective using the American Association of Cancer Research Genomics Evidence Neoplasia Information Exchange (GENIE) Biopharma Collaborative (BPC) registry. Patients' tumor samples underwent targeted next-generation sequencing. Clinical characteristics and treatment outcomes were collected retrospectively. Overall survival (OS) from advanced disease and progression-free survival (PFS) from start of cancer-directed drug regimen were estimated and adjusted for the left truncation bias. A total of 1,281 patients were analyzed, 244 (19%) had PM at time of advanced disease. PM were associated with female sex [OR: 1.67; 95% confidence interval (CI): 1.11-2.54; P = 0.014] and higher histologic grade (OR: 1.72; 95% CI: 1.08-2.71; P = 0.022), while rectal primary tumors were less frequent in patients with PM (OR: 0.51; 95% CI: 0.29-0.88; P < 0.001). APC occurred less frequently in patients with PM (N = 151, 64% vs. N = 788, 79%) while MED12 alterations occurred more frequently in patients with PM (N = 20, 10% vs. N = 32, 4%); differences in MED12 were not significant when restricting to oncogenic and likely oncogenic variants according to OncoKB. Patients with PM had worse OS (HR: 1.45; 95% CI: 1.16-1.81) after adjustment for independently significant clinical and genomic predictors. PFS from initiation of first-line treatment did not differ by presence of PM. In conclusion, PM were more frequent in females and right-sided primary tumors. Differences in frequencies of MED12 and APC alterations were identified between patients with and without PM. PM were associated with shorter OS but not with PFS from first-line treatment. SIGNIFICANCE: Utilizing the GENIE BPC registry, this study found that PM in patients with colorectal cancer occur more frequently in females and right-sided primary tumors and are associated with worse OS. In addition, we found a lower frequency of APC alterations and a higher frequency in MED12 alterations in patients with PM.

Effects of KRAS Genetic Interactions on Outcomes in Cancers of the Lung, Pancreas, and Colorectum.

BACKGROUND: KRAS is among the most commonly mutated oncogenes in cancer, and previous studies have shown associations with survival in many cancer contexts. Evidence from both clinical observations and mouse experiments further suggests that these associations are allele- and tissue-specific. These findings motivate using clinical data to understand gene interactions and clinical covariates within different alleles and tissues. METHODS: We analyze genomic and clinical data from the AACR Project GENIE Biopharma Collaborative for samples from lung, colorectal, and pancreatic cancers. For each of these cancer types, we report epidemiological associations for different KRAS alleles, apply principal component analysis (PCA) to discover groups of genes co-mutated with KRAS, and identify distinct clusters of patient profiles with implications for survival. RESULTS: KRAS mutations were associated with inferior survival in lung, colon, and pancreas, although the specific mutations implicated varied by disease. Tissue- and allele-specific associations with smoking, sex, age, and race were found. Tissue-specific genetic interactions with KRAS were identified by PCA, which were clustered to produce five, four, and two patient profiles in lung, colon, and pancreas. Membership in these profiles was associated with survival in all three cancer types. CONCLUSIONS: KRAS mutations have tissue- and allele-specific associations with inferior survival, clinical covariates, and genetic interactions. IMPACT: Our results provide greater insight into the tissue- and allele-specific associations with KRAS mutations and identify clusters of patients that are associated with survival and clinical attributes from combinations of genetic interactions with KRAS mutations.

Empirical evaluation of language modeling to ascertain cancer outcomes from clinical text reports.

BACKGROUND: Longitudinal data on key cancer outcomes for clinical research, such as response to treatment and disease progression, are not captured in standard cancer registry reporting. Manual extraction of such outcomes from unstructured electronic health records is a slow, resource-intensive process. Natural language processing (NLP) methods can accelerate outcome annotation, but they require substantial labeled data. Transfer learning based on language modeling, particularly using the Transformer architecture, has achieved improvements in NLP performance. However, there has been no systematic evaluation of NLP model training strategies on the extraction of cancer outcomes from unstructured text. RESULTS: We evaluated the performance of nine NLP models at the two tasks of identifying cancer response and cancer progression within imaging reports at a single academic center among patients with non-small cell lung cancer. We trained the classification models under different conditions, including training sample size, classification architecture, and language model pre-training. The training involved a labeled dataset of 14,218 imaging reports for 1112 patients with lung cancer. A subset of models was based on a pre-trained language model, DFCI-ImagingBERT, created by further pre-training a BERT-based model using an unlabeled dataset of 662,579 reports from 27,483 patients with cancer from our center. A classifier based on our DFCI-ImagingBERT, trained on more than 200 patients, achieved the best results in most experiments; however, these results were marginally better than simpler "bag of words" or convolutional neural network models. CONCLUSION: When developing AI models to extract outcomes from imaging reports for clinical cancer research, if computational resources are plentiful but labeled training data are limited, large language models can be used for zero- or few-shot learning to achieve reasonable performance. When computational resources are more limited but labeled training data are readily available, even simple machine learning architectures can achieve good performance for such tasks.

Machine learning for genetics-based classification and treatment response prediction in cancer of unknown primary.

Cancer of unknown primary (CUP) is a type of cancer that cannot be traced back to its primary site and accounts for 3-5% of all cancers. Established targeted therapies are lacking for CUP, leading to generally poor outcomes. We developed OncoNPC, a machine-learning classifier trained on targeted next-generation sequencing (NGS) data from 36,445 tumors across 22 cancer types from three institutions. Oncology NGS-based primary cancer-type classifier (OncoNPC) achieved a weighted F1 score of 0.942 for high confidence predictions ([Formula: see text]) on held-out tumor samples, which made up 65.2% of all the held-out samples. When applied to 971 CUP tumors collected at the Dana-Farber Cancer Institute, OncoNPC predicted primary cancer types with high confidence in 41.2% of the tumors. OncoNPC also identified CUP subgroups with significantly higher polygenic germline risk for the predicted cancer types and with significantly different survival outcomes. Notably, patients with CUP who received first palliative intent treatments concordant with their OncoNPC-predicted cancers had significantly better outcomes (hazard ratio (HR) = 0.348; 95% confidence interval (CI) = 0.210-0.570; P = [Formula: see text]). Furthermore, OncoNPC enabled a 2.2-fold increase in patients with CUP who could have received genomically guided therapies. OncoNPC thus provides evidence of distinct CUP subgroups and offers the potential for clinical decision support for managing patients with CUP.

The GENIE BPC NSCLC Cohort: A Real-World Repository Integrating Standardized Clinical and Genomic Data for 1,846 Patients with Non-Small Cell Lung Cancer.

PURPOSE: We describe the clinical and genomic landscape of the non-small cell lung cancer (NSCLC) cohort of the American Association for Cancer Research (AACR) Project Genomics Evidence Neoplasia Information Exchange (GENIE) Biopharma Collaborative (BPC). EXPERIMENTAL DESIGN: A total of 1,846 patients with NSCLC whose tumors were sequenced from 2014 to 2018 at four institutions participating in AACR GENIE were randomly chosen for curation using the PRISSMM data model. Progression-free survival (PFS) and overall survival (OS) were estimated for patients treated with standard therapies. RESULTS: In this cohort, 44% of tumors harbored a targetable oncogenic alteration, with EGFR (20%), KRAS G12C (13%), and oncogenic fusions (ALK, RET, and ROS1; 5%) as the most frequent. Median OS (mOS) on first-line platinum-based therapy without immunotherapy was 17.4 months [95% confidence interval (CI), 14.9-19.5 months]. For second-line therapies, mOS was 9.2 months (95% CI, 7.5-11.3 months) for immune checkpoint inhibitors (ICI) and 6.4 months (95% CI, 5.1-8.1 months) for docetaxel ± ramucirumab. In a subset of patients treated with ICI in the second-line or later setting, median RECIST PFS (2.5 months; 95% CI, 2.2-2.8) and median real-world PFS based on imaging reports (2.2 months; 95% CI, 1.7-2.6) were similar. In exploratory analysis of the impact of tumor mutational burden (TMB) on survival on ICI treatment in the second-line or higher setting, TMB z-score harmonized across gene panels was associated with improved OS (univariable HR, 0.85; P = 0.03; n = 247 patients). CONCLUSIONS: The GENIE BPC cohort provides comprehensive clinicogenomic data for patients with NSCLC, which can improve understanding of real-world patient outcomes.

Practice-Level Variation in Molecular Testing and Use of Targeted Therapy for Patients With Non-Small Cell Lung Cancer and Colorectal Cancer.

Importance: All patients with newly diagnosed non-small cell lung cancer (NSCLC) and colorectal cancer (CRC) should receive molecular testing to identify those who can benefit from targeted therapies. However, many patients do not receive recommended testing and targeted therapies. Objective: To compare rates of molecular testing and targeted therapy use by practice type and across practices. Design, Setting, and Participants: This cross-sectional study used 100% Medicare fee-for-service data from 2015 through 2019 to identify beneficiaries with new metastatic NSCLC or CRC diagnoses receiving systemic therapy and to assign patients to oncology practices. Hierarchical linear models were used to characterize variation by practice type and across practices. Data analysis was conducted from June 2019 to October 2022. Exposures: Oncology practice providing care. Outcomes: Primary outcomes were rates of molecular testing and targeted therapy use for patients with NSCLC and CRC. Secondary outcomes were rates of multigene testing for NSCLC and CRC. Results: There were 106 228 Medicare beneficiaries with incident NSCLC (31 521 [29.7%] aged 65-69 years; 50 348 [47.4%] female patients; 2269 [2.1%] Asian, 8282 [7.8%] Black, and 91 215 [85.9%] White patients) and 39 512 beneficiaries with incident CRC (14 045 [35.5%] aged 65-69 years; 17 518 [44.3%] female patients; 896 [2.3%] Asian, 3521 [8.9%] Black, and 32 753 [82.9%] White patients) between 2015 and 2019. Among these beneficiaries, 18 435 (12.9%) were treated at National Cancer Institute (NCI)-designated centers, 8187 (5.6%) were treated at other academic centers, and 94 329 (64.7%) were treated at independent oncology practices. Molecular testing rates increased from 74% to 85% for NSCLC and 45% to 65% for CRC. First-line targeted therapy use decreased from 12% to 8% among patients with NSCLC and was constant at 5% for patients with CRC. For NSCLC, molecular testing rates were similar across practice types while rates of multigene panel use (13.2%) and targeted therapy use (16.6%) were highest at NCI-designated cancer centers. For CRC, molecular testing rates were 3.8 (95% CI: 1.2-6.5), 3.3 (95% CI, 0.4-6.1), and 12.2 (95% CI, 9.1-15.3) percentage points lower at hospital-owned practices, large independent practices, and small independent practices, respectively. Rates of targeted therapy use for CRC were similar across practice types. After adjusting for patient characteristics, there was moderate variation in molecular testing and targeted therapy use across oncology practices. Conclusions and Relevance: In this cross-sectional study of Medicare beneficiaries, molecular testing rates for NSCLC and CRC increased in recent years but remained lower than recommended levels. Rates of targeted therapy use decreased for NSCLC and remained stable for CRC. Variation across practices suggests that where a patient was treated may have affected access to recommended testing and efficacious treatments.

Elucidating Analytic Bias Due to Informative Cohort Entry in Cancer Clinico-genomic Datasets.

BACKGROUND: Oncologists often order genomic testing to inform treatment for worsening cancer. The resulting correlation between genomic testing timing and prognosis, or "informative entry," can bias observational clinico-genomic research. The efficacy of existing approaches to this problem in clinico-genomic cohorts is poorly understood. METHODS: We simulated clinico-genomic cohorts followed from an index date to death. Subgroups in each cohort who underwent genomic testing before death were "observed." We varied data generation parameters under four scenarios: (i) independent testing and survival times; (ii) correlated testing and survival times for all patients; (iii) correlated testing and survival times for a subset of patients; and (iv) testing and mortality exclusively following progression events. We examined the behavior of conditional Kendall tau (Tc) statistics, Cox entry time coefficients, and biases in overall survival (OS) estimation and biomarker inference across scenarios. RESULTS: Scenario #1 yielded null Tc and Cox entry time coefficients and unbiased OS inference. Scenario #2 yielded positive Tc, negative Cox entry time coefficients, underestimated OS, and biomarker associations biased toward the null. Scenario #3 yielded negative Tc, positive Cox entry time coefficients, and underestimated OS, but biomarker estimates were less biased. Scenario #4 yielded null Tc and Cox entry time coefficients, underestimated OS, and biased biomarker estimates. Transformation and copula modeling did not provide unbiased results. CONCLUSIONS: Approaches to informative clinico-genomic cohort entry, including Tc and Cox entry time statistics, are sensitive to heterogeneity in genotyping and survival time distributions. IMPACT: Novel methods are needed for unbiased inference using observational clinico-genomic data.

Utilizing Electronic Health Records (EHR) and Tumor Panel Sequencing to Demystify Prognosis of Cancer of Unknown Primary (CUP) patients.

Cancer of unknown primary (CUP) is a type of cancer that cannot be traced back to its original site and accounts for 3-5% of all cancers. It does not have established targeted therapies, leading to poor outcomes. We developed OncoNPC, a machine learning classifier trained on targeted next-generation sequencing data from 34,567 tumors from three institutions. OncoNPC achieved a weighted F1 score of 0.94 for high confidence predictions on known cancer types (65% of held-out samples). When applied to 971 CUP tumors from patients treated at the Dana-Farber Cancer Institute, OncoNPC identified actionable molecular alterations in 23% of the tumors. Furthermore, OncoNPC identified CUP subtypes with significantly higher polygenic germline risk for the predicted cancer type and significantly different survival outcomes, supporting its validity. Importantly, CUP patients who received first palliative intent treatments concordant with their OncoNPC-predicted cancer sites had significantly better outcomes (H.R. 0.348, 95% C.I. 0.210 - 0.570, p-value 2.32 × 10-5). OncoNPC thus provides evidence of distinct CUP subtypes and offers the potential for clinical decision support for managing patients with CUP.

Disparities in the Inclusion of Racial and Ethnic Minority Groups and Older Adults in Prostate Cancer Clinical Trials: A Meta-analysis.

Importance: Prostate cancer (PCa) is marked by disparities in clinical outcomes by race, ethnicity, and age. Equitable enrollment in clinical trials is fundamental to promoting health equity. Objective: To evaluate disparities in the inclusion of racial and ethnic minority groups and older adults across PCa clinical trials. Data Sources: MEDLINE, Embase, and ClinicalTrials.gov were searched to identify primary trial reports from each database's inception through February 2021. Global incidence in age subgroups and US population-based incidence in racial and ethnic subgroups were acquired from the Global Burden of Disease and Surveillance, Epidemiology, and End Results 21 incidence databases respectively. Study Selection: All phase 2/3 randomized PCa clinical trials were eligible for age disparity analyses. Trials recruiting exclusively from the US were eligible for primary racial and ethnic disparity analyses. Data Extraction and Synthesis: This study was reported in accordance with Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) reporting guidelines. Data were pooled using a random-effects model. Main Outcomes and Measures: Enrollment incidence ratios (EIRs), trial proportions (TPs) of participants 65 years or older or members of a racial and ethnic subgroup divided by global incidence in the corresponding age group, or US population-based incidence in the corresponding racial and ethnic subgroup, were calculated. Meta-regression was used to explore associations between trial characteristics and EIRs and trends in EIRs during the past 3 decades. Results: Of 9552 participants among trials reporting race, 954 (10.8%) were African American/Black, 80 (1.5%) were Asian/Pacific Islander, and 8518 (78.5) were White. Of 65 US trials, 45 (69.2%) reported race and only 9 (13.8%) reported data on all 5 US racial categories. Of 286 global trials, 75 (26.2%) reported the enrollment proportion of older adults. Outcomes by race and age were reported in 2 (3.1%) and 41 (15.0%) trials, respectively. Black (EIR, 0.70; 95% CI, 0.59-0.83) and Hispanic (EIR, 0.70; 95% CI, 0.59-0.83) patients were significantly underrepresented in US trials. There was no disparity in older adult representation (TP, 21 143 [71.1%]; EIR, 1.00; 95% CI, 0.95-1.05). The representation of Black patients was lower in larger trials (meta-regression coefficient, -0.06; 95% CI, -0.10 to -0.02; P = .002). Conclusions and Relevance: The results of this meta-analysis suggest that Black and Hispanic men are underrepresented in trials compared with their share of PCa incidence. The representation of Black patients has consistently remained low during the past 2 decades.

Germline variants associated with toxicity to immune checkpoint blockade.

Immune checkpoint inhibitors (ICIs) have yielded remarkable responses but often lead to immune-related adverse events (irAEs). Although germline causes for irAEs have been hypothesized, no individual variant associated with developing irAEs has been identified. We carried out a genome-wide association study of 1,751 patients on ICIs across 12 cancer types. We investigated two irAE phenotypes: (1) high-grade (3-5) and (2) all-grade events. We identified 3 genome-wide significant associations (P < 5 × 10-8) in the discovery cohort associated with all-grade irAEs: rs16906115 near IL7 (combined P = 3.6 × 10-11; hazard ratio (HR) = 2.1); rs75824728 near IL22RA1 (combined P = 3.5 × 10-8; HR = 1.8); and rs113861051 on 4p15 (combined P = 1.2 × 10-8, HR = 2.0); rs16906115 was replicated in 3 independent studies. The association near IL7 colocalized with the gain of a new cryptic exon for IL7, a critical regulator of lymphocyte homeostasis. Patients carrying the IL7 germline variant exhibited significantly increased lymphocyte stability after ICI initiation, which was itself predictive of downstream irAEs and improved survival.

Genomic analysis of early-stage lung cancer reveals a role for TP53 mutations in distant metastasis.

Patients with non-small cell lung cancer (NSCLC) who have distant metastases have a poor prognosis. To determine which genomic factors of the primary tumor are associated with metastasis, we analyzed data from 759 patients originally diagnosed with stage I-III NSCLC as part of the AACR Project GENIE Biopharma Collaborative consortium. We found that TP53 mutations were significantly associated with the development of new distant metastases. TP53 mutations were also more prevalent in patients with a history of smoking, suggesting that these patients may be at increased risk for distant metastasis. Our results suggest that additional investigation of the optimal management of patients with early-stage NSCLC harboring TP53 mutations at diagnosis is warranted in light of their higher likelihood of developing new distant metastases.

Deep Learning for Cancer Symptoms Monitoring on the Basis of Electronic Health Record Unstructured Clinical Notes.

PURPOSE: Symptoms are vital outcomes for cancer clinical trials, observational research, and population-level surveillance. Patient-reported outcomes (PROs) are valuable for monitoring symptoms, yet there are many challenges to collecting PROs at scale. We sought to develop, test, and externally validate a deep learning model to extract symptoms from unstructured clinical notes in the electronic health record. METHODS: We randomly selected 1,225 outpatient progress notes from among patients treated at the Dana-Farber Cancer Institute between January 2016 and December 2019 and used 1,125 notes as our training/validation data set and 100 notes as our test data set. We evaluated the performance of 10 deep learning models for detecting 80 symptoms included in the National Cancer Institute's Patient-Reported Outcomes version of the Common Terminology Criteria for Adverse Events (PRO-CTCAE) framework. Model performance as compared with manual chart abstraction was assessed using standard metrics, and the highest performer was externally validated on a sample of 100 physician notes from a different clinical context. RESULTS: In our training and test data sets, 75 of the 80 candidate symptoms were identified. The ELECTRA-small model had the highest performance for symptom identification at the token level (ie, at the individual symptom level), with an F1 of 0.87 and a processing time of 3.95 seconds per note. For the 10 most common symptoms in the test data set, the F1 score ranged from 0.98 for anxious to 0.86 for fatigue. For external validation of the same symptoms, the note-level performance ranged from F1 = 0.97 for diarrhea and dizziness to F1 = 0.73 for swelling. CONCLUSION: Training a deep learning model to identify a wide range of electronic health record-documented symptoms relevant to cancer care is feasible. This approach could be used at the health system scale to complement to electronic PROs.