Solving the “Manifold Manifest” Problem: A Case Study

Labs that perform sequencing in support of scientific research or clinical trials generally receive their samples in a batch of tens or hundreds of samples accompanied by a sample manifest. The manifest, usually a CSV or Excel file, provides the lab with the sample metadata required to successfully process samples and report results.

What makes this a challenge is that the manifests can arrive in many different formats and labs have to dedicate significant manual effort to edit them into a standard format that can be accessioned into their LIMS. If labs could convince their customers to provide the manifests in a single standard format, the problem would be solved, but their customers are focused on other priorities, forcing labs to persist with their manual editing.

One of our clients, a busy contract research organization (CRO), asked us to design and build a solution to this “manifold manifest” problem to drastically reduce the cost and time required to accession batches of samples while also reducing errors associated with manual processes.

A custom-built solution to import the data

Semaphore collaborated with the lab to design and build an application that lets users upload manifest CSV files and automatically import the data into the LIMS. A custom user interface streamlines the mapping of columns in the customer manifest file to the appropriate LIMS fields, resulting in a significant reduction in the time required to accession samples and great improvement in the quality of data entering the LIMS. Once a manifest is uploaded, the application validates the data at each step of the accessioning process, and tracks all edits before fully accessioning samples into the LIMS.

Key features of the app include:

  • A dashboard that allows managers to track the manifest files that will be in various stages of processing at any point in time.
  • An easy-to-use interface with Excel-like functionality to assist in editing of manifest data including trim, combine, and apply all functions.
  • Auto-save of in-progress work, ensuring that the valuable time of lab staff is never wasted if their work is interrupted.
  • Compatibility with barcode scanners. This enables staff to scan and organize large numbers of samples that arrive as slides in slide boxes.
  • Ability to map the physical location of individual samples within their boxes or racks.
  • Validation of data types and completeness before accessioning samples into the LIMS.
  • No data deletion to satisfy HIPAA compliance.
  • Validated database that preserves all client manifest data in its raw form.
  • Full audit log that can be filtered by date, changes, complete/incomplete status, manifest text, and many other factors. The log also retains the context of every information point associated with every manifest imported into the portal.
  • Integration with freezer management.
  • Ability to report back results in the same key-pair values that the customer submitted the sample data in.
  • Single source of truth established for incoming manifests from clients, and eliminating multiple versions of Excel.

Good working relationships are built on collaboration & trust

Semaphore’s development process includes meeting regularly with client stakeholders to demo partially completed work. Through these demos, the large client team could see their ideas take shape, ask questions, and give feedback. We also discovered that some client stakeholders were concerned about an external consultant building such an important tool in the lab’s operations. Over time, the meetings enabled these stakeholders to become more comfortable with the collaboration. We moved on from answering questions about what could go wrong to gathering the information we needed to create an application that met everyone’s expectations.

Another key to effective collaboration is having access to subject matter experts when questions arise. Over the course of this project, the client assigned a single point of contact who was responsible for finding the answers to our questions. If we asked for clarification on any point, they responded within 24 hours, and if they were unable to respond that quickly, they held their team accountable. Because they made the project a priority and had rigorous processes in place, productivity remained high for the duration of the project. Meetings followed a clear agenda and were constructive and valuable. Furthermore, tickets outlining feature requirements were well-defined and comprehensive, giving everyone certainty that the project was heading in the right direction.

More speed, fewer errors with automatic import

Since we completed the initial work in May 2020, we’ve delivered all the source code and documentation for the app to the client so that their internal development team can maintain it themselves. We’ve continued to support the client with teaching, talking, and triaging. During the warranty period when the project revealed gaps in the client’s workflows, we helped their team to identify and overcome the issues so that everything is now running smoothly.

The client has been thrilled to see:

  • A significant boost in productivity.
  • More efficient processes.
  • Fewer data input errors.
  • Reduced costs.
  • Employees freed up to work on more complex and interesting problems.

By replacing manual processes with automatic data import, the lab has also seen an increased efficiency for creating and delivering custom data outputs for clients, and the lab is also now in a better position to scale throughput.

The new application provides a significantly faster method for importing patient sample data into the LIMS and one that is much less prone to error. Most importantly, perhaps, the lab staff report that the application is easy to use and has become a valuable tool in their day-to-day work. Not only is it a vital upstream lab tool, but through better lab processes and data management, it also provides a positive ripple effect of improving many other downstream business processes such as bioinformatics and data delivery.

If you’d like to talk about how a custom lab application could drastically improve your lab’s efficiency, contact us today.

As a Project Manager at Semaphore, Cameron has over 10 years of experience in quality assurance testing and has successfully led numerous LIMS and enterprise-level software projects. He is passionate about quality standards and delivering the best possible product to clients.