Implementation and Cost Analysis of Performing Molecular Assays using FFPE Tissue Blocks in the Clinical Laboratory at VA Palo Alto Health Care System

Graduation Date


Document Type

Master's Thesis

Degree Name

Master of Science

Department or Program

Clinical Laboratory Sciences

Department or Program Chair

Mary Sevigny, PhD

First Reader

Kristin Jensen, MD

Second Reader

Dean Fong, DO


This project outlines the multi-level processes of implementation of a new molecular platform in a clinical laboratory to process Formalin-Fixed Paraffin-Embedded (FFPE) tissue blocks.

At VA Palo Alto Health Care System, FFPE samples for BRAF, KRAS and EGFR mutation detection assays are usually sent out to reference laboratories. However, with the increasing demand and cost of these tests, it would be more cost effective to bring these assays to be performed in-house. The activities for this project will focus on three assays- BRAF, KRAS and EGFR- as a starting point to bring solid tumor oncology testing at the clinical laboratory at VA PAHCS.

The project’s overall design was broken down according to the following activities: (1) Lay out an implementation plan, (2) Conduct thorough market research, (3) Perform cost analysis and (4) Design and execute a validation/verification plan.

After market research, 4 major platforms were considered based on the potential to test for the intended assays. Side by side comparison of their individual features and cost analysis has brought us to the conclusion that Roche Cobas z480 and their mutation kits are the most likely to be chosen for implementation at VAPAHCS. Its main advantage over the other three platforms is the fact that it is the only method that is currently FDA approved for all three assays of interest. It also provides a reasonable amount of cost savings and the initial investments in equipment is recovered in a short amount of time.

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