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! A new FDA-cleared method for detection of variants in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene is now available. This new method, the MiSeqDx Cystic Fibrosis 139-Variant Assay, utilizes next generation sequencing (NGS) to detect 139 CFTR variants, which is an increase from the laboratory’s previously detected 23 variants. For more information, please see the laboratory test services guide.

• UPDATE! Quantitative viral load testing for hepatitis B virus (HBV), hepatitis C virus, human immunodeficiency virus, and cytomegalovirus (CMV) is now being performed on the new state-of-the-art cobas 6800 instrument from Roche Diagnostics Corp which can process up to 384 samples in an 8 hour shift. Like the previous assays, the new tests are FDA-cleared real-time PCR methods. The new tests are similar to the current ones, but have improved performance characteristics such as improved analytical sensitivity and the linear ranges for HBV and CMV are now wider. We anticipate being able to provide improved and faster patient care with this new test.

• UPDATE! The BCR-ABL1 Quantitative (p210) methodology has been changed to the Quantidex qPCR BCR ABL IS assay. Results will continue to be reported on the international scale (IS) and also expressed as a log molecular reduction (MR) from the 100%IS baseline. This new method has improvement of the analytical sensitivity allowing quantitation down to MR4.7 (0.002%IS) with a linear reportable range of MR4.7 (0.002%IS) to MR0.3 (50%IS).


Molecular Genetic Testing

• Details about 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.