Pharmacogenomics Lab PGx Quality Control Pfizer

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. Pfizer currently supports approximately 40 trials that require molecular testing of samples. This is up 100% from 2014 and is expected to double again to 80 trials in 2016. 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 are needed to support the existing environment. Data loading and analysis can often take days and introduces responsiveness backlogs and scheduling challenges. The existing LIMS (LabVantage 6 and now version 8) 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 OQ, PQ and IQ requirements of Pfizer.

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.
User interface for uploading sample data
Importing sample data
User interface for reviewing sample data
The application provides a visual display of approved/rejected samples and assay metrics, highlights discrepancies between replicates, and enables searching, grouping and sorting so users can quickly find samples of interest.
User interface for auditing data
The application captures comprehensive auditing information that can be searched and exported to ensure regulatory compliance.