Molecular Pathology

Published by daniel, on August 04, 2014

Molecular Pathology

The Molecular Pathology Laboratory offers molecular diagnostic testing for a variety of clinical indications across the health-care continuum, including testing for disease susceptibility, population screening, diagnosis, prognosis, therapeutic decision making, and disease monitoring. The test menu has many applications in the areas of hereditary diseases, neoplastic diseases, infectious diseases, and for identity testing. The laboratory uses a spectrum of molecular techniques and platforms to evaluate nucleic acids isolated from patient samples, including real-time PCR, capillary electrophoresis, and pyrosequencing.

The Molecular Pathology Laboratory works closely with other laboratories in the Division of Precision and Computational Diagnostics, including the Center for Personalized Diagnostics and the Cytogenetics Laboratory, to provide integrated and cutting-edge precision molecular and genomic diagnostic services to patients. All faculty members are Board-Certified in Pathology, Clinical Molecular Genetics, and/or Molecular Genetic Pathology.

Notable areas of expertise, summarized below, include molecular genetic testing, identity testing, molecular virology, and molecular profiling of common liquid and solid tumors. Please refer to requisition form [PDF] for full test menu and the online Lab Service Test Guide for specific test details and requirements.


In the News

PLM news brief: Transplant study requires molecular pathology techs on-call virtually around the clock for Hepatitis C virus (HCV) genotyping

Penn Medicine press release: First Clinical Trial Transplants Hepatitis C-Infected Kidneys at Penn Medicine


Testing Highlights

• UPDATE! DNA testing for high risk (HR) human papillomavirus (HPV) will now also include concurrent testing for low risk (LR) HPV types for fine needle aspirate (FNA) or paraffin-embedded tissue (PET) specimens. Testing is offered using the Linear Array HPV Genotyping Test (Roche Diagnostics, Inc).

• UPDATE! Leukemia Translocation Panel (LTx) methodology has changed and includes detection of up to the four following gene fusions: RUNX1/RUNX1T1, CBFB/MYH11, PML/RARA and BCR/ABL1.

• Testing for the most common genetic abnormality in ALS and frontotemporal degeneration, C9orf72, is available for diagnostic and predictive testing indications.


Molecular Genetic Testing

• Neurodegenerative disease genetics is an area of expertise. Diagnostic and predictive testing for frontotemporal degeneration (FTD) and amyotrophic lateral sclerosis are available. The laboratory works closely with the Penn Center for Neurodegenerative Disease Research (CNDR) and the Penn FTD Center to provide clinical testing for research and clinical trial participants.
• Details about available neurogenetic and other molecular genetic tests are available through the Genetic Test Registry.


Identity Testing

• Chimerism analysis, performed using short tandem repeat PCR, supports the active bone marrow transplant service in the UPenn Health System. The laboratory has 20 years of experience with the technical and analytical aspects of chimerism analysis, including for reduced-intensity and cord blood transplants. Cellular subset analysis is performed for CD3+ and CD33/CD66b+ subset samples.
• Additional applications of identity testing which are available include maternal cell contamination, assessment of graft-versus-host disease, assessment of recipient versus donor origin of tumor, hydatidiform molar evaluation, and sample identification.


Molecular Oncology Testing

• Comprehensive qualitative and quantitative molecular oncology testing is available for diagnosis, disease monitoring, and therapeutic decision making.
• A variety of assays, including MGMT methylation analysis by pyrosequencing and BCR-ABL quantitative PCR, are offered to detect common genetic alterations in solid and hematologic malignancies.
• The Molecular Pathology Laboratory works in conjunction with the Center for Personalized Diagnostics for the testing of molecular oncology specimens. Please inquire with the laboratory for questions or additional information.


Molecular Virology Testing

• Molecular testing is performed for the identification of specific viral infections, including common respiratory pathogens such as influenza A/B and respiratory syncytial virus.
• For selected viruses, quantitative assessment of viral infections as well as monitoring of viral loads is offered in the laboratory.
• Genotyping of hepatitis C and human papillomavirus is also available.
• Sample types acceptable for molecular virology testing depend on the assay requested.



The one-year ACGME-accredited Molecular Genetic Pathology (MGP) fellowship program trains fellows in the practice of molecular pathology and genomics, the application and interpretation of molecular laboratory techniques, and diagnostic laboratory administration. Over the course of the one-year ACGME accredited fellowship the fellow gains experience in the application of molecular pathology through service work, didactic lectures, resident teaching, involvement in laboratory administration, hands-on test development and/or research projects, as well as rotations in cytogenetics, genomics, HLA, virology, biochemical genetics, and clinical adult and pediatric genetics.