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portfolio_onc.Rmd
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---
title: "Oncology Portfolio"
output: html_document
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---
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*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](https://www.mskcc.org/departments/epidemiology-biostatistics/biostatistics/project-genie-bpc-genomics-evidence-neoplasia-information-exchange-biopharma-collaborative) (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](https://www.aacr.org/Newsroom/Pages/News-Release-Detail.aspx?ItemID=1354)). 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.
<font size="4"><i> Related Publications </font></i>
* 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](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btac796/6909009). Bioinformatics (2023)
- {genieBPC} is available on [CRAN](https://cran.r-project.org/web/packages/genieBPC/index.html) and [GitHub](https://genie-bpc.github.io/genieBPC/), and was included on the RStudio blog August 2022 list of [Top 40 New CRAN Packages](https://rviews.rstudio.com/2022/09/26/august-2022-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](https://aacrjournals.org/clincancerres/article/29/17/3418/728542). Clinical Cancer Research (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](https://ascopubs.org/doi/full/10.1200/CCI.21.00105). 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](https://jamanetwork.com/journals/jamaoncology/article-abstract/2785693). 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](https://jamanetwork.com/journals/jamanetworkopen/article-abstract/2782339). JAMA Network Open (2021)
<font size="4"><i> Related Presentations </font></i>
* 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](https://www.aacrmeetingnews.org/news/minisymposium-explores-real-world-examples-of-project-genie-applications/)), 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.](https://ww2.amstat.org/meetings/wsds/2020/onlineprogram/AbstractDetails.cfm?AbstractID=309549) 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.](https://ascopubs.org/doi/abs/10.1200/JCO.2020.38.15_suppl.9622) Contributed poster presentation, American Society of Clinical Oncology (ASCO) Annual Meeting (2020)
### Exercise Oncology
In collaboration with the [Exercise Oncology](https://www.mskcc.org/research-areas/topics/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:
* Lavery JA, Boutros PC, Knight D, Tammela T, Moskowitz CS, Jones LW. [Association of exercise with pan-cancer incidence and overall survival](https://pubmed.ncbi.nlm.nih.gov/38181796/). Cancer Cell (2024)
* Lavery JA, Boutros PC, Scott JM, Tammela T, Moskowitz CS, Jones LW. [Pan-Cancer Analysis of Postdiagnosis Exercise and Mortality](https://ascopubs.org/doi/abs/10.1200/JCO.23.00058). Journal of Clinical Oncology (2023)
* Michalski M, Rowed K, Lavery JA, et al [Validity of Estimated Cardiorespiratory Fitness in Patients With Primary Breast Cancer](https://www.sciencedirect.com/science/article/pii/S2666087322002289?via%3Dihub) 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](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9135110/) Cancer Epidemiology, Biomarkers & Prevention (2022)