Pharmacogenomic Lab QC Portal

Case Study:

Pfizer
QC web application

Tech Stack:

AngularJS, Docker, NodeJS, Oracle, PL/SQL, Java, Gradle, Selenium

Project Summary

Pfizer sought the capabilities to perform molecular testing of clinical trial samples in their CLIA-certified lab facility. Pharmacogenomics is playing an increasing role in establishing the utility of drug targets. One focus is the use of RNA sequencing (or RNA-Seq) to assess the entire transcriptome of a sample. Several technologies and data types are used to perform the analysis in the lab. These trials either have large sample sizes (200+) or large gene signatures (more than 24 mRNA assays). Ensuring quality and compliance is reliant on data management and thorough, repeatable analysis.

In order to scale the operation into making molecular testing efficient, new tools were needed to support the existing environment. Data loading and analysis can often take days and introduces responsiveness backlogs and scheduling challenges. The existing LIMS was insufficient to be configured to handle the current needs and the next generation sequencing capabilities being acquired and planned for in 2017 and 2018.

5AM collaborated with the Pfizer team to deliver an integrated workflow and visualization web and database solution inside the firewall between October 2015 and February 2016 and again in October 2016 through January 2017. We performed an Inception and Delivery during each time frame. We designed the user interface from the ground up, collaborated with stakeholders and users to design the workflow, using our mockups-to-wireframes-to-HTML approach, and successfully supported the documentation required to deliver the solution in compliance with the OQPQ, and IQ requirements of Pfizer.

PGxQC Close up view
A close-up view of performing quality control of sample data.

The use of pharmacogenomic assays on patient samples in an FDA-regulated environment requires:

  • Robust approval processes
  • Quality control workflows
  • Secure collection of audit logs

5AM designed the web application to enable electronic review and approval of molecular data from a variety of platforms, including:

  • Ion Torrent next-generation sequencing
  • TaqMan Low Density Array (TLDA) gene expression
  • Real-Time PCR-based genotyping

The PGx QC application allows lab managers to:

  • Import, validate and organize data sets
  • Review and approve assay results
  • Export data that has been approved by the lab’s medical director
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