Description of Research Expertise

The Liquid Biopsy Laboratory, led by Director Dr. Erica Carpenter, focuses on the identification, capture, and analysis of Circulating Tumor Cells (CTCs) and cell-free DNA (cfDNA) from cancer patients. Blood, bone marrow, pleural effusions, and other non-invasively captured patient samples are used to detect biomarkers which allow: 1) early detection of disease as well as post-therapy monitoring of minimal residual disease, 2) an efficient means of determining clinical and biological response to therapy and, thus, clinical decision making, and, 3) cancer genetic phenotyping to drive personalized medicine that obviates the need for serial biopsies in a population of patients for which these procedures are difficult, risky, and insufficient. The focus of the CTM Center is driven by the needs of clinicians and translational investigators, and realized through collaborative work with investigators in the Penn School of Medicine, the Penn School of Engineering, and the Center for Personalized Diagnostics. Moreover, when it is determined that outsourcing of technology development is preferable, collaborative efforts with industry partners are actively sought, and these efforts have already been initiated in focused areas.

Selected Publications

Charu Aggarwal, MD, MPH; Jeffrey C. Thompson, MD; Taylor A. Black, BA; Sharyn I. Katz, MD, MTR; Ryan Fan, BA;, Stephanie S. Yee, MS; Austin L. Chien, BA; Tracey L. Evans, MD; Joshua M. Bauml, MD; EvanW. Alley, MD, PhD;, Christine A. Ciunci, MD, MSCE; Abigail T. Berman, MD, MSCE; Roger B. Cohen, MD; David B. Lieberman, MS, LCGC;, Krishna S. Majmundar, BS; Samantha L. Savitch, BA; Jennifer J. D. Morrissette, PhD;Wei-Ting Hwang, PhD;, Kojo S. J. Elenitoba-Johnson, MD; Corey J. Langer, MD; Erica L. Carpenter, MBA, PhD: Clinical implications of plasma-based genotyping with the delivery of personalized therapy in metastatic non-small cell lung cancer JAMA Oncology 5 (2): 173-180,2019.

Zijian Yang, Michael J. LaRiviere, Jina Ko, Jacob E. Till, Theresa E. Christensen, Stephanie S. Yee, Taylor A. Black, Kyle Tien, Andrew Lin, Hanfei Shen, Neha Bhagwat, Daniel Herman, Andrew Adallah, Mark H. O’Hara, Charles M. Vollmer, Bryson W. Katona, Ben Z. Stanger, David Issadore, and Erica L. Carpenter: A multi-analyte, liquid biopsy approach for diagnosing and staging of pancreatic adenocarcinoma Clinical Cancer Research 26 (13): 3248-3258,2020.

Jeffrey H. Lin, Austin P. Huffman, Max M. Wattenberg, David M. Walter, Erica L. Carpenter, David M. Feldser, Gregory L. Beatty, Emma E. Furth, Robert H. Vonderheide: Type 1 conventional dendritic cells are systemically dysregulated early in pancreatic carcinogenesis Journal of Experimental Medicine 217 (8): e20190673,2020.

Mark H. O’Hara, MD, Eileen M. O’Reilly, MD, Gauri Varadhachary, MD, Robert A. Wolff, MD, Zev A. Wainberg, MD, Andrew H. Ko, MD, George Fisher, MD, Osama Rahma, MD, , Jaclyn P. Lyman, MSc, Christopher Cabanski, PhD, Rosemarie Mick, MS, , Pier Federico Gherardini, PhD, Lacey Kitch, PhD, Jingying Xu, PhD, Theresa Samuel, MD, Joyson Karakunnel, MD, MSc, Justin Fairchild, MPH, Samantha Bucktrout, PhD, , Theresa M. LaVallee, PhD, Cheryl Selinsky, PhD, Jacob E. Till, MD, PhD, Erica L. Carpenter, PhD, Cécile Alanio, MD, PhD, Katelyn T. Byrne, PhD, Richard O. Chen, MD, , Ovid C. Trifan, MD, PhD, Ute Dugan, MD, PhD, Christine Horak, PhD, Vanessa M. Hubbard-Lucey, PhD, E. John Wherry, PhD, Ramy Ibrahim, MD, Robert H. Vonderheide, MD, DPhil: Agonistic CD40 Monoclonal Antibody APX005M and Chemotherapy with or without Nivolumab for the Treatment of Metastatic Ductal Pancreatic Adenocarcinoma Lancet Oncology 22 (1): 118-131,2021.

C. Aggarwal, MD, MPH, J. C. Thompson, MD, MTR, A. L. Chien, BA, K. J. Quinn, PhD, W. Hwang, PhD, T. A. Black, BA, S. S. Yee, MS, T. E. Christensen, BA, M. J. LaRiviere, MD, B. A. Silva, K. C. Banks, MBA, MS, R. J. Nagy, MS, E. Helman, PhD, A. T. Berman, MD, MSCE, C. A. Ciunci, MD, MSCE, A. P. Singh, MD, J. S. Wasser, MD, J. M. Bauml, MD, C. J. Langer, MD, R. B. Cohen, MD, E. L. Carpenter, MBA, PhD: Baseline plasma tumor mutation burden predicts response to pembrolizumab-based therapy in patients with metastatic non-small cell lung cancer Clinical Cancer Research 26 (10): 2354-2361,2020.

Stephen J. Bagley, S. Ali Nabavizadeh, Jazmine J. Mays, Jacob E. Till, Jeffrey B. Ware, Scott Levy, Whitney Sarchiapone, Jasmin Hussain, Timothy Prior, Samantha Guiry, Theresa Christensen, Stephanie S. Yee, MacLean P. Nasrallah, Jennifer J.D. Morrissette, Zev A. Binder, Donald M. O’Rourke, Andrew J. Cucchiara, Steven Brem, Arati S. Desai, and Erica L. Carpenter: Clinical utility of plasma cell-free DNA in adult patients with newly diagnosed glioblastoma – a pilot prospective study Clinical Cancer Research 26 (2): 397-407,2020.

Jae W. Lee, Meredith L. Stone, Paige M. Porrett, Stacy K. Thomas, Chad A. Komar, Joey H. Li, Devora Delman, Kathleen Graham, Whitney L. Gladney, Xia Hua, Taylor A. Black, Austin L. Chien, Krishna S. Majmundar, Jeffrey C. Thompson, Stephanie S. Yee, Mark O’Hara, Charu Aggarwal1, Dong Xin, Abraham Shaked, Mingming Gao, Dexi Liu, Mitesh J. Borad, Ramesh K. Ramanathan, Erica L. Carpenter, Ailing Ji, Maria C. de Beer, Frederick C. de Beer, Nancy R. Webb, & Gregory L. Beatty: Hepatocytes direct the formation of a pro-metastatic niche in the liver Nature 567 (7747): 249-252,2019.

S. Ali Nabavizadeh, Jeffrey B. Ware, Samantha Guiry, MacLean P. Nasrallah, Jazmine J. Mays, Jacob E. Till, Jasmin Hussain, Aseel Abdalla, Stephanie S. Yee, Zev A. Binder, Donald M. O’Rourke, Steven Brem, Arati S. Desai, Ronald Wolf, Erica L. Carpenter and Stephen J. Bagley: Imaging and histopathologic correlates of plasma cell-free DNA concentration and circulating tumor DNA in adult patients with newly diagnosed glioblastoma Neuro-Oncology Advances 2 (1): vdaa016,2020.

Ko, Jina; Bhagwat, Neha; Yee, Stephanie; Ortiz, Natalia; Sahmoud, Amine; Black, Taylor; Aiello, Nicole; McKenzie, Lydie; O'Hara, Mark; Redlinger, Colleen; Romeo, Janae; Carpenter, Erica; Stanger, Ben; Issadore, David: Combining Machine Learning and Nanofluidic Technology to Diagnose Pancreatic Cancer Using Exosomes ACS Nano 11 (11): 11182-11193,2017.

Jinzhao Song, Jorrit W. Hegge, Michael G. Mauk, Junman Chen, Jacob E. Till, Neha Bhagwat, Lotte T. Azink, Jing Peng, Moen Sen, Jazmine Mays, Erica Carpenter, John van der Oost, and Haim H. Bau: Highly Specific Enrichment of Rare Nucleic Acid Fractions using Thermus thermophilus Argonaute with Applications in Cancer Diagnostics Nucleic Acids Research 48 (4): e19,2020.

Moen Sen, Friedrich Hahn, Taylor A. Black, Maureen DeMarshall, Warren, Porter, Eileen Snowden, Stephanie S. Yee, Frances Tong, Mitchell Ferguson, Emylee N. Fleshman, Hiroshi Nakagawa, Gary W. Falk, Gregory G. Ginsberg, Michael L. Kochman, Rainer Blaesius, Anil K. Rustgi and Erica L. Carpenter: Flow based single cell analysis of the immune landscape distinguishes Barrett's esophagus from adjacent normal tissue Oncotarget 10 (38): 3592-3604,2019.

Bange E, Marmarelis M, Hwang W-T, Yang Y-X, Thompson JC, Rosenbaum J, Bauml JM, Ciunci C, Alley EW, Cohen RB, Langer CJ, Carpenter EL, Aggarwal C: Impact of KRAS and TP53 co-mutations on outcomes after first-line systemic therapy among patients with STK11-mutated advanced non-small cell lung cancer Journal of Clinical Oncology Precision Oncology 3 : 2019.

Jeffrey C. Thompson, Ryan Fan, Taylor Black, Gordon H. Yu, Samantha L. Savitch, Austin Chien, Stephanie S. Yee, Moen Sen, Wei-Ting Hwang, Sharyn I. Katz, Michael Feldman, Anil Vachani, Erica L. Carpenter: Measurement and Immunophenotyping of Pleural Fluid EpCAM-Positive Cells and Clusters for the Management of Non-Small Cell Lung Cancer Patients Lung Cancer 127 : 25-33,2019.

Neha Bhagwat, Keely Dulmage, Charles H. Pletcher Jr., Ling Wang, William DeMuth, Moen Sen, David Balli, Stephanie S. Yee, Silin Sa, Frances Tong, Liping Yu, Jonni S. Moore, Ben Z. Stanger, Eric P. Dixon & Erica L. Carpenter: An integrated flow cytometry-based platform for isolation and molecular characterization of circulating tumor single cells and clusters Scientific Reports 8 (1): 5035,2018.

Academic Contact Information

#8-104
South Pavilion, 8th Floor
3400 Civic Center Blvd
Philadelphia, PA 19104
Phone: 215-746-4427