Mp35-03 Investigating Tobacco Use and Genetic Ancestry in the Genomics of Urothelial Bladder Cancer Using Natural Language Processing and Next Generation Tumor Sequencing

You have accessJournal of UrologyBladder Cancer: Epidemiology & Evaluation II (MP35)1 May 2024MP35-03 INVESTIGATING TOBACCO USE AND GENETIC ANCESTRY IN THE GENOMICS OF UROTHELIAL BLADDER CANCER USING NATURAL LANGUAGE PROCESSING AND NEXT GENERATION TUMOR SEQUENCING Kelly R. Pekala, Xuechun Bai, Justin Jee, Tomin Perea-Chamblee, Michele Waters, Chris Fong, Ronglai Shen, Niki Schultz, Richard Matulewicz, Eugene Pietzak, and Jian Carrot-Zhang Kelly R. PekalaKelly R. Pekala , Xuechun BaiXuechun Bai , Justin JeeJustin Jee , Tomin Perea-ChambleeTomin Perea-Chamblee , Michele WatersMichele Waters , Chris FongChris Fong , Ronglai ShenRonglai Shen , Niki SchultzNiki Schultz , Richard MatulewiczRichard Matulewicz , Eugene PietzakEugene Pietzak , and Jian Carrot-ZhangJian Carrot-Zhang View All Author Informationhttps://doi.org/10.1097/01.JU.0001009372.61513.54.03AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: Smoking and tobacco use are the leading causes of bladder cancer. There is some evidence that there may be an interaction between genetic ancestry and smoking that predisposes patients of African ancestry to lung cancer with fewer smoking pack years. The relationship between genetic ancestry, tobacco smoking, and tumor genetics has not yet been explored in bladder cancer. METHODS: We applied a natural language processing algorithm, previously validated in lung cancer, to determine patients' smoking status within a large dataset of urothelial bladder cancer patients who were selected for next-generation tumor-normal sequencing (MSK-IMPACT). Genetic ancestry was inferred from the sequencing data using SNPs. Given the nature of admixture in the population of the United States, we considered ancestry as a continuous variable. We tested common or clinically actionable genetic alterations (TERT, TP53, Microsatellite instability (MSI), Tumor Mutational Burden (TMB)-high)) with the interaction of ancestry and smoking status using a multivariate logistic regression model that adjusts for age, biologic sex, stage, and smoking status followed by a false discovery rate (FDR) correction. RESULTS: We identified 1733 patients within the MSK-IMPACT bladder cancer dataset, including 57 with at least 50% African ancestry and 36 with at least 80% East Asian ancestry. We found that the natural language processing algorithm applied to the initial consultation note had 95% concordance with manual curation of the electronic medical record when a patient's smoking status was separated into 3 labels (former or current/never/unknown) and had 91% concordance when using 4 labels (former/current/never/unknown). Using former or current smokers compared to never smokers, and genetic ancestry as a continuous variable, no significant ancestry-smoking interaction was observed in bladder urothelial carcinoma for TERT, TP53, MSI, or TMB-high. CONCLUSIONS: Within our analysis, we did not identify an ancestry-smoking interaction in bladder urothelial carcinoma. However, we plan to evaluate additional genes of interest, explore different classifiers of smoking intensity, and this relationship in larger and more ethnically diverse datasets. Download PPT Source of Funding: This work was supported by the Sidney Kimmel Center for Prostate and Urologic Cancers, Ruth L. Kirschstein National Research Service Award T32CA082088 © 2024 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 211Issue 5SMay 2024Page: e581 Advertisement Copyright & Permissions© 2024 by American Urological Association Education and Research, Inc.Metrics Author Information Kelly R. Pekala More articles by this author Xuechun Bai More articles by this author Justin Jee More articles by this author Tomin Perea-Chamblee More articles by this author Michele Waters More articles by this author Chris Fong More articles by this author Ronglai Shen More articles by this author Niki Schultz More articles by this author Richard Matulewicz More articles by this author Eugene Pietzak More articles by this author Jian Carrot-Zhang More articles by this author Expand All Advertisement PDF downloadLoading ...