Molecular Pathology

• Anjali Seth, PhD
• Yue Lynn Wang, MD (Rotation Site Director, Fox Chase Cancer Center)

The primary aim of the molecular pathology laboratory is to provide clinical diagnostic/prognostic services for the molecular analysis of clinical material submitted to the anatomical and clinical laboratories of the Temple University Hospital. The goal of the molecular pathology rotation is to provide a comprehensive understanding of the role of molecular pathology in clinical and anatomic pathology. Residents rotating through the molecular pathology laboratory are given extensive handouts on the theoretical basis underlying the principles of a variety of molecular techniques such as polymerase chain reaction (PCR), fragment analysis and sequencing using capillary electrophoresis as well as a variety of next generation sequencing methods.  The residents are trained to perform as well as interpret the molecular diagnostic test results. Testing in the molecular diagnostics laboratory includes areas of infectious diseases such as HIV viral load quantification and genotyping, hepatitis C viral quantification and genotyping, CMV, EBV and BK virus quantification assays. The molecular menu also includes hypercoagulation assays for Factor V Leiden and prothrombin gene mutation analysis. Next generation sequencing panels for detection of actionable mutations in solid tumors has been introduced in the laboratory recently. The laboratory also provides clinical service and training in areas if lymphoid malignancies such as gene rearrangement assays for diagnosis and monitoring of lymphoid tumors.

During the six-week rotation, the residents will spend time reading material describing the theoretical basis of the amplification techniques that are used in the Molecular Pathology Laboratory for diagnostic purposes. This will include:

• The principle underlying the methods used for the extraction and isolation of nucleic acids (DNA and RNA) from various tissue sources such as blood, plasma, serum, urine, cerebrospinal fluids and formalin fixed paraffin embedded tissues.
• The various constituents of the amplification reaction mixture and their importance to a successful assay. This part will include information about how to design primers for PCR, the criteria necessary for optimizing the PCR reaction, the importance of the concentration of deoxynucleotides, magnesium, etc.
• The choice of detection systems (e.g., capillary electrophoresis, DNA sequencing (Sanger and Next Generation sequencing) for identifying a variety of DNA and RNA targets.
• Interpretation and troubleshooting of the results.
• QA/QC issues with regards to the prevention of contamination of the specimens.

During the rotation, the resident will be given ample opportunity to observe the techniques being utilized in the molecular pathology laboratory in order to enable them to understand and correlate the theoretical with the practical. The residents will work closely with lab personnel observing a variety of esoteric tests and will learn to correlate molecular pathology results with other anatomic and clinical pathology tests.

The residents will spend time on interpretation of the results obtained by amplification. They will also be exposed to some challenging and unusual cases that have been obtained in the laboratory during the past years.