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19 March 2022

Demystifying the Next-Generation Sequencing Workflow: Part 2

In the second part of our series discussing next-generation sequencing (NGS), we highlight the aspects of the NGS workflow that are particularly challenging for clinical laboratories (If you missed the first blog in this series discussing the NGS workflow, take a look at it here.).

Clinical diagnostic laboratories have specific requirements to maintain chain of custody of all samples and data generated across the testing workflow, and this requirement is especially challenging for NGS-based tests, where many daughter samples are generated across the multi-day workflow. Clinical diagnostic labs also must retain patient data for at least 2 years after the test result is issued, which is challenging in the case of NGS, where a lot of data is generated. 

Here’s how your LIMS partner can help you overcome the challenges associated with performing NGS in the clinical diagnostic laboratory.

Specimen Tracking and Storage

The NGS workflow is a multi-step process that creates many daughter samples that must be stored and traced back to the original parent specimen. Laboratories need good naming conventions for each of the daughter tubes and the data that is generated along the NGS workflow. Further, the clinical diagnostic laboratory needs to ensure that the lab is equipped with sufficient and organized freezer space to accommodate the original patient specimen and each of the daughter tubes. 

As a laboratory implements the NGS workflow, the laboratory team should work very closely with the lab’s LIMS vendor to ensure chain of custody is maintained across the specimens and data generated in the NGS workflow. A good LIMS (and LIMS partner) will accommodate laboratory-specific naming conventions and ensure links between sample and data are established and maintained across the workflow within the LIMS database. Further, the LIMS should be able to map tube position in the freezer box to a storage location recorded in the LIMS database. 

The issues of chain of custody across daughter tubes and generated data is a concern for any testing scenario within the diagnostic laboratory, and it is especially critical for labs performing NGS testing because of the number of daughter tubes and the amount of data generated. Fortunately, a solid LIMS and LIMS partner will be able to help your laboratory overcome these issues.

Integrations: Instruments and External Software

The NGS workflow relies on many different instruments to create the data needed for quality control and the sequencing data itself. Most clinical diagnostic laboratories performing NGS testing prefer to integrate these instruments with the LIMS software. These integrations are important to the clinical diagnostic lab because these labs need to manage the instruments (e.g. calibration, preventative maintenance, etc.) and retain the data generated for each patient. Often these instruments have associated analytic software that generates important data for the diagnostic testing workflow and needs to be stored as part of the patient record.

Instrument integration is a very important consideration for laboratories planning an NGS workflow. This is another aspect of the NGS workflow where the laboratory needs to work very closely with their LIMS partner to ensure that the integrations are completed in a time-efficient manner. Ideally, the diagnostic laboratory’s LIMS vendor will have extensive in-house experience integrating with the instrumentation and software that is used commonly across the NGS workflow. 

Data Storage: Cloud Connectivity

The NGS workflow generates terabytes of data, which must be retained as part of the patient record. These large data files create a challenge for the traditional clinical diagnostic laboratory. In order to accommodate the quantity of data generated, it is essential that the clinical lab discuss the data storage requirements with your LIMS partner as early in the implementation process as possible to ensure that the costs are known and the technical set up is appropriately provisioned to accommodate the data requirements. A cloud environment is a critical element of implementing a NGS testing process, and it is very important that the lab’s LIMS partner is experienced and knowledgeable about the data storage and retention challenges presented by the NGS workflow.


The NGS workflow presents some unique, but surmountable, challenges for the clinical diagnostic laboratory environment. The NGS workflow generates a large number of daughter samples that must be stored and traced back to the original patient specimen, uses specialized instrumentation and software, and generates a massive amount of data that must be traceable across the workflow and must be stored and retrieved by the laboratory. These challenges can be addressed efficiently in partnership with the laboratory’s LIMS vendor. If your laboratory is considering adding NGS testing to your clinical laboratory, contact our team at ApolloLIMS. We have extensive experience addressing the challenges associated with the NGS workflow, and we can provide a LIMS solution that meets the needs of your NGS workflows.