Illumina NextSeq 500 System

The Problem

After MiSeq launched, Illumina made significant advancements in sequencing chemistry and wanted to bring the power to sequence a whole human genome to the bench top as well. Along with this new instrument, I wanted to improve upon some of the workflow issues I had seen after MiSeq launched:

  • Coordination between software projects was poor. Illumina had launched BaseSpace (a cloud analysis platform), but it was poorly integrated with the customer workflow and there was duplication of efforts as other software analysis and visualization packages were being developed concurrently.
  • Though I had attempted to improve the end-to end user experience of sequencing with MiSeq, I was barely able to scratch the surface of what was possible.

The Process

As with the MiSeq project, I did extensive ethnographic research at the beginning of the project. From this and my experience with MiSeq, I realized that the focus of my work should not be on the sequencing software (which was already quite good from MiSeq) but on the non-instrument parts of the workflow. By presenting my findings to stakeholders, I was able to strategically pull groups together from different departments and secure funding for the development of a program that wasn't even on the roadmap.

This new program was arranged to support both the development of an on-site analysis server running the BaseSpace software and to add in functionality to set up runs directly in BaseSpace and monitor them remotely. Once this was built, the workflow would be:

  1. Primary Investigator sets up run in BaseSpace.
  2. Lab Technician prepares samples based on instructions in BaseSpace and scans the cartridge barcode to associate it to a run.
  3. Lab Technician inserts the cartridge into any available NextSeq 500.
  4. Run starts automatically and analysis is fed to BaseSpace where it is automatically tied to the intital samples entered.

The Outcome

Unfortunately, I was not able to see this project through to completion since I left the company for a new opportunity. However, the products I laid the groundwork for were all developed and integrated into the sequencing workflow which launched over a year after I left.

Watch a video about the NextSeq 500