Genocea’s use of Freezerworks as LIMS equals quality data and big savings

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Samantha Kecman,
Senior Analytical Associate

How configuring Freezerworks to operate as a LIMS significantly reduced both IT and personnel costs for a small biotech

Genocea Biosciences, located in Cambridge, Massachusetts, is a biotechnology company that discovers and develops T cell-directed vaccines and immunotherapies utilizing ATLAS™, a transformational technology platform for T cell antigen discovery. Like many small biotech companies, Genocea faces the challenge of conducting clinical trials utilizing groundbreaking and often expensive technologies with limited resources. To efficiently develop new drugs and therapies, a small biotech firm must be flexible to survive and prosper, and thrive by thinking creatively. Such creativity, when expanded to areas such as workflow and data management, can serve small biotechs well, and provide opportunities to stretch limited resources.

Nicolle Siddall, a Research Associate at Genocea, recently spoke at a Freezerworks Users’ Conference. She shared how the company is saving thousands of dollars in IT costs by capitalizing on the configurable nature of the sample management software program to allow it to serve as a LIMS. Besides tracking sample and aliquot locations, Freezerworks is now storing and managing the assay data for Genocea’s growing list of clinical trials. With Freezerworks, Genocea staff are securely storing information and reporting quality data to statisticians in a timely manner, meeting the company’s deadlines and objectives.

Challenge: High cost of LIMS, LIMS development

Although Genocea had access to a formal LIMS, using the program presented problems for the company.

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Nicolle Siddall, Research Associate II and
Amy Baccari, Senior Research Associate

“It wasn’t user friendly, and without a full time IT employee to program and troubleshoot workflows we couldn’t fully implement all it offered,” Siddall explained. Contrasting the LIMS with Freezerworks, which Siddall described as “user-friendly”, the staff started considering whether it was possible to expand the use of Freezerworks to serve as their LIMS and data management software, holding the assay data along with the physical location of their growing inventory of samples. Should the idea be feasible, it would save the startup “potentially hundreds of thousands of dollars over a five year period,” Shane Larson, Manager of Translational Immunology at Genocea estimated.

In order to meet the requirements, it was necessary for Freezerworks to store all trial assay data from the following assays

  • Intracellular cytokine staining
  • Real-time quantitative PCR
  • IgG ELISA
  • Neutralizing Antibody
  • Microbiology Culture and PCR

Also vital for successful operation, Freezerworks would need to accept electronic uploads of large numbers of assay results, as well as link each data point with the proper sample aliquot. Operators perform assays on sample sets that include two to eight subjects, each with multiple collection points, tested simultaneously. Although the copy of Freezerworks in operation at Genocea was not customized for automatic data capture, a component of a traditional LIMS, the team at Genocea thought the process could be handled by use of the electronic transfer of Excel files generated from the various assay readers into Freezerworks through the use of macros. These macros could be written and validated by existing laboratory staff.

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Drug therapies in the Genocea pipeline. This article focuses primarily on GEN-003. Click to enlarge

Having a six month window to get the project up and running, Siddall said the flexibility and user friendliness of Freezerworks, combined with what they regarded as a responsive and very helpful support department (Siddall gave special mention to Implementation Specialist Beth Medema), convinced them the solution was to use Freezerworks to serve as both a sample and assay data manager. Since Freezerworks was already successfully implemented for managing samples and corresponding aliquots, allowing operators to quickly locate and pull those for testing, storing data within Freezerworks was attractive in consolidating workflow. Another major factor was the compliancy Freezerworks offered with the FDA’s 21 CFR Part 11 regulations for electronic records. This was very important since the data for the project would be submitted to the agency.

“We were familiar with Freezerworks and received prompt support from their IT department,” Siddall explained. “We had a six month period to get this off and running, to configure Freezerworks to hold metrics for all clinical assays and to implement the process into our workflow.”

Excel Macro development

Although not a programmer, Senior Research Associate Amy Baccari proved adept at learning how to develop Excel macros to automate the process of adding instrument-generated experimental data into Freezerworks. Such macros are vital for eliminating data entry errors while saving a significant amount of time. Using Visual Basic, Baccari coded macros in accordance with each assay’s unique setup to successfully transfer data from instrument to Freezerworks. The macro functions include:

  • Capture of raw data text files generated from Softmax™, Flojo™, StepOne™ and ImmunoSpot® machines
  • Application of formatting to highlight assay acceptance criteria for samples and controls
  • Implementation of conditional formatting to flag various metrics that are out of specification
  • Transposition of data for import into Freezerworks
  • Import of all assay metrics into Freezerworks
  • Linking of assay data to the appropriate aliquot record in Freezerworks

Workflow

When clinical operators at Genocea perform experiments, they first go to Freezerworks to select the aliquots to be included in the experiment. The staff has configured a Freezerworks “list view” for each assay. Each list view is a scrollable display of the aliquots selected for the assay.

Besides identifying information for each aliquot, a freezer location is also displayed so the operators can easily locate and pull the aliquots for the experiment. At this point, the operators also use the Freezerworks Batch Update feature to create a Transaction record for all aliquots included in the Experiment number for the assay. A printout is then generated for quality control, and an export file of the spreadsheet is generated to link each aliquot with the generated assay metrics.

After the assay is completed, the Excel macro compares the export file with the data from the assay software. First, the macro pulls the analyzed data, matches the correct data of the aliquot and applies conditional formatting based on assay criteria, allowing operators to easily assess the performance of the experiment. A text file is created and adjusted for batch import, to store all assay metrics into the appropriate aliquot records.

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Click to enlarge

“I can’t emphasize enough the importance and benefit of the macro. It has opened up a brand new world for us, eliminating errors and saving time,” Siddall explained.

Control Results and Repeat Tests: Freezerworks has a feature that allows for the creation of sub-aliquots: aliquots that are linked to the original or “parent aliquot”. Normally, this feature is used to trace the development of physical aliquots that are grown and split off from the parent, so that sample and vial lineage can be traced over time. Genocea receives multiple aliquots for a sample, and therefore utilizes the sub-aliquot feature for traditional purposes, but they also require storage capacity for results run from multiple assays on an individual aliquot. The reason for this is that when generating clinical data, it is necessary to store all assay data – whether it has passed or failed the specific assay acceptance criteria. If the data from a re-tested sample subsequently passed the assay acceptance criteria and was uploaded into the same aliquot, it would over-write the initial failed data. Therefore, a solution had to be identified to prevent this from occurring.

To do this, Genocea has Freezerworks generate sub-aliquots for storing both control results for an experiment and repeat tests. A sub-aliquot is identified by having an identifier in the “Parent Aliquot field” that corresponds to the unique identifier of the original aliquot. Thus, all aliquots that need to be re-assayed are documented by the presence of a parent aliquot identifier. The presence of a sub-aliquot indicates a repeat test was run on the original aliquot. Therefore, all assay results are stored for each aliquot, and data are managed through the use of both Unique and Parent Identifiers. This allows the quality control team access to all assay results, which is vital for verifying that accurate data are submitted to the statisticians. Once again, Excel macros collect the parent aliquot identifiers for an aliquot being re-assayed and for all controls tested. The operator must indicate if a sample is being re-assayed in the macro plate set-up because it will generate the data import files based on these variables.

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Above: An aliquot with one sub-aliquot. This list view within Freezerworks indicates an aliquot (the top row) was included in an HSV-2 Neutralization Assay. The Controls failed for this assay, so the assay was re-run. The presence of a Parent Identifier in the second line indicates it is a re-run of the first aliquot, because the Parent ID of the “sub-aliquot” matches the Unique ID of the first aliquot.

genocea-parent-aliquotsLeft: How sub-aliquots are displayed in relation to parent aliquots from the Freezerworks Entry screen: Sub-aliquots are listed below the parent aliquot when the row is expanded (Aliquot 4 is a sub-aliquot of Aliquot 1). For Genocea, this indicates the aliquot was re-run once.

Quality assurance and statistical analysis
With Freezerworks managing both workflow and assay data, Genocea’s quality control team verifies that the data are properly documented through a meticulous process. Each assay has a QC checklist for the experiment that is performed. The QC analyst uses the checklist to verify that all samples, aliquots, and data points are properly documented and accurately uploaded into Freezerworks. Once verified, the data are arrayed in an Excel-readable text file, generated within Freezerworks, and are exported for statistical analysis. Freezerworks List Views are specifically created by the lab staff for data downloads for analysis from each assay. Genocea has successfully finalized and exported from Freezerworks multiple datasets for analysis from each assay and goals for all programs have been successfully met.

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Cost saving Benefits of utilizing Freezerworks for sample and assay data management

Genocea expects to continue the savings calculated below on a yearly basis as it expands use of Freezerworks for future trials.

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For more information, contact Freezerworks at sales@freezerworks.com.