Oncology Portfolio

Since 2017, I have worked as a Research Biostatistician in the Department of Epidemiology and Biostatistics at Memorial Sloan Kettering Cancer Center. Below are a few highlights from research programs that I have been a part of, as well as related publications and presentations.

AACR Project GENIE BPC

American Association for Cancer Research (AACR) project GENIE BPC (Genomics Evidence Neoplasia Information Exchange Biopharma Collaborative) is a cross-institution collaboration between MSKCC, Dana Farber Cancer Institute and Vanderbilt-Ingram Cancer Center with biopharmaceutical partners working towards linking cancer genomic sequencing data with clinical treatment and outcomes data (press release). As a part of the Statistical Coordinating Center, I am involved in writing standard operating procedures for quality assurance, maintaining a quality assurance dashboard, deriving variables that will be publicly released with the data and performing statistical analyses.

For an overview of the GENIE BPC data, see Acebedo et al. Collaborating across sectors in service of open science, precision oncology, and patients: an overview of the AACR Project GENIE (Genomics Evidence Neoplasia Information Exchange) Biopharma Collaborative (BPC). Additional information on accessing these publicly available data sources can be found here.

Publications

• Kehl KL, Lavery JA, Brown S, Fuchs H, Riely G, Schrag D, Newcomb A, Nichols C, Micheel CM, Bedard PL, Sweeney SM, Fiandalo M, Panageas KS, AACR Project GENIE BPC Core Team. Biomarker Inference and the Timing of Next-Generation Sequencing in a Multi-Institutional, Cross-Cancer Clinicogenomic Data Set. JCO Precis Oncol (2024)
• Lavery JA, Brown S, Curry MA, et al. A Data Processing Pipeline for the AACR Project GENIE Biopharma Collaborative Data with the {genieBPC} R Package. Bioinformatics (2023)
  • {genieBPC} is available on CRAN and GitHub, and was included on the RStudio blog August 2022 list of Top 40 New CRAN Packages, out of approximately 200 packages released to CRAN that month.
• Choudhury NJ, Lavery JA, Brown S, et al. 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. Clinical Cancer Research (2023)
• Kehl KL, Uno H, Gusev A, Groha S, Brown S, Lavery JA, Deborah Schrag D, Katherine S. Panageas KS. Elucidating analytic bias due to informative cohort entry in cancer clinico-genomic datasets. Cancer Epidemiol Biomarkers Prev (2023)
• Lavery JA, Lepisto E, Brown S, et al. A Scalable Quality Assurance Process for Curating Oncology Electronic Health Records: The Project GENIE Biopharma Collaborative Approach. JCO Clinical Cancer Informatics (2022)
  
• Brown S, Lavery JA, Shen R, et al. Implications of Selection Bias Due to Delayed Study Entry in Clinical Genomic Studies. JAMA Oncology (2021)
  
• Kehl KL, Riely GJ, Lepisto EM, et al. Correlation Between Surrogate End Points and Overall Survival in a Multi-institutional Clinicogenomic Cohort of Patients With Non–Small Cell Lung or Colorectal Cancer. JAMA Network Open (2021)

Presentations

• Workshop on Genomic Data Curation and Access: Analyzing Clinical and Genomic Oncological Data with the {genieBPC} R Package at the Moffitt Cancer Center Statistical Practice in Cancer Conference (February 2024)
• Defining Real-World Recurrence in the AACR Project GENIE BPC Data. Presented at the American Association for Cancer Research Annual Meeting (April 2021; AACR Meeting News article), the Memorial Sloan Kettering Lung Cancer Oncology Group Seminar Series (May 2021), and the Memorial Sloan Kettering Hospital Research Forum (November 2021)
• A Statistician’s Role in a Quality Assurance of a Multi-Institution Electronic Health Record Curation Project. Contributed oral presentation, Women in Statistics and Data Science (2020)
• Progression-free survival estimates in non-small cell lung cancer when RECIST is unavailable: Project GENIE’s integration of genomic, therapeutic and phenomic data. Contributed poster presentation, American Society of Clinical Oncology (ASCO) Annual Meeting (2020)

Exercise Oncology

In collaboration with the Exercise Oncology service at MSK, I have been a part of a number of protocols and research projects investigating the role of exercise in preventing cancer and improving survival among people with cancer. Select publications are highlighted below:

• Jones LW, Lavery JA, Tsai BL, Moskowitz CS, Lee CP, et al. A Co-clinical Trial of Exercise Therapy in Breast Cancer Prevention. Clin Cancer Res (2025)
• Lavery JA, Boutros PC, Knight D, Tammela T, Moskowitz CS, Jones LW. Association of exercise with pan-cancer incidence and overall survival. Cancer Cell (2024)
• Lavery JA, Boutros PC, Scott JM, Tammela T, Moskowitz CS, Jones LW. Pan-Cancer Analysis of Postdiagnosis Exercise and Mortality. Journal of Clinical Oncology (2023)
• Michalski M, Rowed K, Lavery JA, et al Validity of Estimated Cardiorespiratory Fitness in Patients With Primary Breast Cancer Journal of the American College of Cardiology: CardioOncology (2022)
• Bliss JW, Lavery JA, Underwood WP, Chun SS, Fickera GA, Lee CP, Corcoran S, Maloy MA, Polubriaginof FC, Kelly DW and Scott JM Impact of Exercise on Susceptibility and Severity of COVID-19 in Patients with Cancer: A Retrospective Study Cancer Epidemiology, Biomarkers & Prevention (2022)