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John Pfeifer, MD, PhD

Professor, Pathology & Immunology
Vice Chair for Clinical Affairs, Pathology & Immunology
Director, Molecular Genetic Pathology Fellowship


Additional Titles

  • Professor, Obstetrics and Gynecology

Clinical Interests

  • Gynecological Pathology
  • Molecular Genetic Pathology
  • Pulmonary Pathology

Research Interests

My academic interests are primarily focused on investigation of the role of molecular genetic testing in the analysis of tissue specimens, specifically on the methods and clinical settings in which molecular testing provides independent information that increases diagnostic accuracy, provides more accurate prognostic estimates, or can be used to guide therapy. The clinical/experimental model for most of these studies has been the group of so-called malignant small round cell tumors, a category of poorly differentiated sarcomas that can be very difficult to distinguish based on conventional histopathologic evaluation. Over the past few years we have shown that molecular testing has independent diagnostic utility, and that testing supports tumor classification schemes that redefine the clinicopathologic spectrum of disease for specific malignancies (with concomitant prognostic and therapeutic implications).

Current studies are focused on the application of so-called next generation DNA sequencing methods (also known as nexgen, deep, or resequencing methods) to analysis of patient specimens. While nexgen methods have traditionally been used for genome-wide analysis, we are exploring technologies that make it possible to use the methods to focus on defined chromosomal regions or individual genetic loci to detect a wide spectrum of genetic aberrations ranging from single base pair changes, to insertions and deletions, to translocations.

Finally, as an outgrowth of our studies of mesenchymal hamartoma of the liver (and the frequently associated tumor undifferentiated embryonal sarcoma), we have cloned the breakpoint of the associated t(11;19) translocation. One of the genes involved in the translocation is MALAT1, which is thought to encode an RNA that functions as part of the spliceosome. Transgenic mice are currently being produced to enable more detailed study of this potential novel route of tumorigesis.

Editorial Responsibilities

Present Editorial Board American Journal of Clinical Pathology
Present Editorial Board Modern Pathology
Present Member NCCN Soft Tissue Sarcoma Panel
Present Ad hoc reviewer Human Pathology
Present Ad hoc reviewer Diagnostic Cytopathology
Present Ad hoc reviewer Expert Opinion on Medical Diagnostics
Present Ad hoc reviewer Clinical Orthopaedics and Related Research
Present Ad hoc reviewer Journal of Molecular Diagnostics
Present Ad hoc reviewer Thyroid
Present Ad hoc reviewer Hepatology


Service to the Department

2004 – 2007 Director, Pathology Residency Program
Present Director, Molecular Pathology Laboratory, Division of Anatomic Pathology
Present Director, Molecular Genetic Pathology Fellowship Program
Present Member, Resident Selection Committee

Service to the University

Present Member, Protocol Review and Monitoring Committee, Siteman Cancer Center
Present Medical Student (2nd Year) lectures on Inflammation and Tissue Repair, Amyloid; laboratory sections on Pulmonary Pathophysiology



Pub Med Search

Duncavage E, Zehnbauer B, Pfeifer JD. Prevalence of Merkel cell polyomavirus in Merkel cell carcinoma. Mod Pathol. 2009;22:516-521, 2009 Abstract
Lennerz JKM, Perry A, Mills JC, Huettner PC, Pfeifer JD. Mucoepidermoid carcinoma of the cervix. Another tumor with the t(11;19) – associated CRTC1-MAML2 gene fusion. Am J Surg Path. 2009;33:835-843, 2009 Abstract
Duncavage EJ, Le B-M, Wang D, Pfeifer JD. Merkel Cell Polyomavirus: A specific marker for Merkel Cell Carcinoma in histologically similar tumors. Am J Surg Pathol. 2009;33:1771-1777, 2009Abstract
Rajaram V, Knezevich S, Bove KE, Perry A, Pfeifer JD. DNA sequence of the translocation breakpoints in undifferentiated embryonal sarcoma arising in mesenchymal hamartoma of the liver harboring the t(11;19)(q11;q13.4) translocation. Genes Chromosomes Cancer 2007;46:508-513, 2007 Abstract
Suba EJ, Pfeifer JD, Raab SS. Patient identification error among prostate needle core biopsy specimens: are we ready for a “DNA timeout?”. J Urol. 2007;178:1245-1248, 2007 Abstract
Bridge RS, Rajaram V, Dehner LP, Pfeifer JD, Perry A. Molecular diagnosis of Ewing sarcoma/primitive neuroectodermal tumor in routinely processed tissue: a comparison of two FISH strategies and RT-PCR in malignant round cell tumors. Mod Pathol 2006;19:1-8, 2006 Abstract
Covinsky M, Gong S, Rajaram V, Perry A, Pfeifer JD. EWS-ATF1 fusion transcripts in gastrointestinal tumors previously diagnosed as malignant melanoma. Hum Pathol 2005;36:74-81, 2005 Abstract
O’Sullivan M, Budhraja V, Sadovsky Y, Pfeifer JD. Tumor heterogeneity affects the precision of microarray analysis. Diag Mol Pathol 2005;14:65-71, 2005 Abstract
Cook JR, Pfeifer JD, Dehner LP. Adult mesenchymal hamartoma of the liver: association with distinct clinical features and histologic changes. Hum Pathol 2002;33:893-898, 2002 Abstract
Hill DA, O’Sullivan MJ, Zhu X, Vollmer RT, Humphrey PA, Dehner LP, Pfeifer JD.. Practical application of molecular genetic testing as an aid to the surgical pathologic diagnosis of sarcomas: a prospective study. Am J Surg Pathol. 2002 Aug;26(8):965-77, 2002 Abstract
O’Sullivan MJ, Perlman EJ, Furman J, Humphrey PA, Dehner LP, Pfeifer JD. Visceral primitive peripheral neuroectodermal tumors – a clinicopatholgic and molecular study. Hum Pathol 2001;32:1109-1115, 2001 Abstract

Elease Barnes