Estimating Treatment Effect of Adjuvant Chemotherapy in Elderly Patients With Stage III Colon Cancer Using Bayesian Networks.

PURPOSE: While adjuvant therapy with capecitabine and oxaliplatin (CAPOX) has been proven to be effective in stage III colon cancer, capecitabine monotherapy (CapMono) might be equally effective in elderly patients. Unfortunately, the elderly are under-represented in clinical trials and patients included may not be representative of the routine care population. Observational data might alleviate this problem but is sensitive to biases such as confounding by indication. Here, we build causal models using Bayesian Networks (BNs), identify confounders, and estimate the effect of adjuvant chemotherapy using survival analyses. METHODS: Patients 70 years and older were selected from the Netherlands Cancer Registry (N = 982). We developed several BNs using constraint-based, score-based, and hybrid algorithms while precluding noncausal relations. In addition, we created models using a limited set of recurrence and survival nodes. Potential confounders were identified through the resulting graphs. Several Cox models were fitted correcting for confounders and for propensity scores. RESULTS: When comparing adjuvant treatment with surgery only, pathological lymph node classification, physical status, and age were identified as potential confounders. Adjuvant treatment was significantly associated with survival in all Cox models, with hazard ratios between 0.39 and 0.45; CIs overlapped. BNs investigating CAPOX versus CapMono did not find any association between the treatment choice and survival and thus no confounders. Analyses using Cox models did not identify significant association either. CONCLUSION: We were able to successfully leverage BN structure learning algorithms in conjunction with clinical knowledge to create causal models. While confounders differed depending on the algorithm and included nodes, results were not contradictory. We found a strong effect of adjuvant therapy on survival in our cohort. Additional oxaliplatin did not have a marked effect and should be avoided in elderly patients.

Identifying Confounders Using Bayesian Networks and Estimating Treatment Effect in Prostate Cancer With Observational Data.

PURPOSE: Randomized controlled trials are considered the golden standard for estimating treatment effect but are costly to perform and not always possible. Observational data, although readily available, is sensitive to biases such as confounding by indication. Structure learning algorithms for Bayesian Networks (BNs) can be used to discover the underlying model from data. This enables identification of confounders through graph analysis, although the model might contain noncausal edges. We propose using a blacklist to aid structure learning in finding causal relationships. This is illustrated by an analysis into the effect of active treatment (v observation) in localized prostate cancer. METHODS: In total, 4,121 prostate cancer records were obtained from the Netherlands Cancer Registry. Subsequently, we developed a (causal) BN using structure learning while precluding noncausal relations. Additionally, we created several Cox proportional hazards models, each correcting for a different set of potential confounders (including propensity scores). Model predictions for overall survival were compared with expected survival on the basis of the general population using data from Statistics Netherlands (Centraal Bureau voor de Statistiek). RESULTS: Structure learning precluding noncausal relations resulted in a causal graph but did not identify significant edges toward treatment; they were added manually. Graph analysis identified year of diagnosis and age as confounders. The BN predicted a treatment effect of 1 percentage point at 10 years. Chi-squared analysis found significant associations between year of diagnosis, age, stage, and treatment. Propensity score correction was successful. Adjusted Cox models predicted significant treatment effect around 3 percentage points at 10 years. CONCLUSION: A blacklist in conjunction with structure learning can result in a causal BN that can be used for confounder identification. Treatment effect found here is close to the 5 percentage point found in the literature.

The feasibility of a Bayesian network model to assess the probability of simultaneous symptoms in patients with advanced cancer.

Although patients with advanced cancer often experience multiple symptoms simultaneously, clinicians usually focus on symptoms that are volunteered by patients during regular history-taking. We aimed to evaluate the feasibility of a Bayesian network (BN) model to predict the presence of simultaneous symptoms, based on the presence of other symptoms. Our goal is to help clinicians prioritize which symptoms to assess. Patient-reported severity of 11 symptoms (scale 0-10) was measured using an adapted Edmonton Symptom Assessment Scale (ESAS) in a national cross-sectional survey among advanced cancer patients. Scores were dichotomized (< 4 and ≥ 4). Using fourfold cross validation, the prediction error of 9 BN algorithms was estimated (Akaike information criterion (AIC). The model with the highest AIC was evaluated. Model predictive performance was assessed per symptom; an area under curve (AUC) of ≥ 0.65 was considered satisfactory. Model calibration compared predicted and observed probabilities; > 10% difference was considered inaccurate. Symptom scores of 532 patients were collected. A symptom score ≥ 4 was most prevalent for fatigue (64.7%). AUCs varied between 0.60 and 0.78, with satisfactory AUCs for 8/11 symptoms. Calibration was accurate for 101/110 predicted conditional probabilities. Whether a patient experienced fatigue was directly associated with experiencing 7 other symptoms. For example, in the absence or presence of fatigue, the model predicted a 8.6% and 33.1% probability of experiencing anxiety, respectively. It is feasible to use BN development for prioritizing symptom assessment. Fatigue seems most eligble to serve as a starting symptom for predicting the probability of experiencing simultaneous symptoms.

Prognostic factors analysis for oral cavity cancer survival in the Netherlands and Taiwan using a privacy-preserving federated infrastructure.

The difference in incidence of oral cavity cancer (OCC) between Taiwan and the Netherlands is striking. Different risk factors and treatment expertise may result in survival differences between the two countries. However due to regulatory restrictions, patient-level analyses of combined data from the Netherlands and Taiwan are infeasible. We implemented a software infrastructure for federated analyses on data from multiple organisations. We included 41,633‬ patients with single-tumour OCC between 2004 and 2016, undergoing surgery, from the Taiwan Cancer Registry and Netherlands Cancer Registry. Federated Cox Proportional Hazard was used to analyse associations between patient and tumour characteristics, country, treatment and hospital volume with survival. Five factors showed differential effects on survival of OCC patients in the Netherlands and Taiwan: age at diagnosis, stage, grade, treatment and hospital volume. The risk of death for OCC patients younger than 60 years, with advanced stage, higher grade or receiving adjuvant therapy after surgery was lower in the Netherlands than in Taiwan; but patients older than 70 years, with early stage, lower grade and receiving surgery alone in the Netherlands were at higher risk of death than those in Taiwan. The mortality risk of OCC in Taiwanese patients treated in hospitals with higher hospital volume (≥ 50 surgeries per year) was lower than in Dutch patients. We conducted analyses without exchanging patient-level information, overcoming barriers for sharing privacy sensitive information. The outcomes of patients treated in the Netherlands and Taiwan were slightly different after controlling for other prognostic factors.

Predicting Lung Cancer Survival Using Probabilistic Reclassification of TNM Editions With a Bayesian Network.

PURPOSE: The TNM classification system is used for prognosis, treatment, and research. Regular updates potentially break backward compatibility. Reclassification is not always possible, is labor intensive, or requires additional data. We developed a Bayesian network (BN) for reclassifying the 5th, 6th, and 7th editions of the TNM and predicting survival for non-small-cell lung cancer (NSCLC) without training data with known classifications in multiple editions. METHODS: Data were obtained from the Netherlands Cancer Registry (n = 146,084). A BN was designed with nodes for TNM edition and survival, and a group of nodes was designed for all TNM editions, with a group for edition 7 only. Before learning conditional probabilities, priors for relations between the groups were manually specified after analysis of changes between editions. For performance evaluation only, part of the 7th edition test data were manually reclassified. Performance was evaluated using sensitivity, specificity, and accuracy. Two-year survival was evaluated with the receiver operating characteristic area under the curve (AUC), and model calibration was visualized. RESULTS: Manual reclassification of 7th to 6th edition stage group as ground truth for testing was impossible in 5.6% of the patients. Predicting 6th edition stage grouping using 7th edition data and vice versa resulted in average accuracies, sensitivities, and specificities between 0.85 and 0.99. The AUC for 2-year survival was 0.81. CONCLUSION: We have successfully created a BN for reclassifying TNM stage grouping across TNM editions and predicting survival in NSCLC without knowing the true TNM classification in various editions in the training set. We suggest binary prediction of survival is less relevant than predicted probability and model calibration. For research, probabilities can be used for weighted reclassification.

Impact on Quality of Documentation and Workload of the Introduction of a National Information Standard for Tumor Board Reporting.

PURPOSE: Tumor boards, clinical practice guidelines, and cancer registries are intertwined cancer care quality instruments. Standardized structured reporting has been proposed as a solution to improve clinical documentation, while facilitating data reuse for secondary purposes. This study describes the implementation and evaluation of a national standard for tumor board reporting for breast cancer on the basis of the clinical practice guideline and the potential for reusing clinical data for the Netherlands Cancer Registry (NCR). METHODS: Previously, a national information standard for breast cancer was derived from the corresponding Dutch clinical practice guideline. Using data items from the information standard, we developed three different tumor board forms: preoperative, postoperative, and postneoadjuvant-postoperative. The forms were implemented in Amphia Hospital's electronic health record. Quality of clinical documentation and workload before and after implementation were compared. RESULTS: Both draft and final tumor board reports were collected from 27 and 31 patients in baseline and effect measurements, respectively. Completeness of final reports increased from 39.5% to 45.4% (P = .04). The workload for tumor board preparation and discussion did not change significantly. Standardized tumor board reports included 50% (61/122) of the data items carried in the NCR. An automated process was developed to upload information captured in tumor board reports to the NCR database. CONCLUSION: This study shows implementation of a national standard for tumor board reports improves quality of clinical documentation, without increasing clinical workload. Simultaneously, our work enables data reuse for secondary purposes like cancer registration.

VANTAGE6: an open source priVAcy preserviNg federaTed leArninG infrastructurE for Secure Insight eXchange.

Answering many of the research questions in the field of cancer informatics requires incorporating and centralizing data that are hosted by different parties. Federated Learning (FL) has emerged as a new approach in which a global model can be generated without disclosing private patient data by keeping them at their original location. Flexible, user-friendly, and robust infrastructures are crucial for bringing FL solutions to the day-to-day work of the cancer epidemiologist. In this paper, we present an open source priVAcy preserviNg federaTed leArninG infrastructurE for Secure Insight eXchange, VANTAGE6. We provide a detailed description of its conceptual design, modular architecture, and components. We also show a few examples where VANTAGE6 has been successfully used in research on observational cancer data. Developing and deploying technology to support federated analyses - such as VANTAGE6 - will pave the way for the adoption and mainstream practice of this new approach for analyzing decentralized data.

Integrated analysis of DNA copy number and gene expression microarray data using gene sets.

BACKGROUND: Genes that play an important role in tumorigenesis are expected to show association between DNA copy number and RNA expression. Optimal power to find such associations can only be achieved if analysing copy number and gene expression jointly. Furthermore, some copy number changes extend over larger chromosomal regions affecting the expression levels of multiple resident genes. RESULTS: We propose to analyse copy number and expression array data using gene sets, rather than individual genes. The proposed model is robust and sensitive. We re-analysed two publicly available datasets as illustration. These two independent breast cancer datasets yielded similar patterns of association between gene dosage and gene expression levels, in spite of different platforms having been used. Our comparisons show a clear advantage to using sets of genes' expressions to detect associations with long-spanning, low-amplitude copy number aberrations. In addition, our model allows for using additional explanatory variables and does not require mapping between copy number and expression probes. CONCLUSION: We developed a general and flexible tool for integration of multiple microarray data sets, and showed how the identification of genes whose expression is affected by copy number aberrations provides a powerful approach to prioritize putative targets for functional validation.