Archive by Author | Melanie Febrer

BaseSpace™ Clarity LIMS NovaSeq™ Integration v2.2

Integration and interoperability between laboratory systems—or lack thereof—remains a challenge for those performing next-generation sequencing (NGS) or other genomics studies.1 To address this challenge, we developed version 2.2 of the integration between BaseSpace Clarity LIMS and the NovaSeq 6000 instrument. This integration now supports the NovaSeq S4 flow cell, as well as the NovaSeq Xp protocol.

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Figure 1: The NovaSeq 6000 version 2.0 Workflow in BaseSpace Clarity LIMS that supports the integration version 2.2

The NovaSeq S4 flow cell delivers up to 6 TB of output in two days and is ideally suited for high intensity sequencing applications. Users can now sequence up to 48 human genomes or 384 exomes per run in less than 48 hours. This innovation paves the way for large-population-scale initiatives at the lowest price per sample, and enables labs to cost effectively perform human whole-genome sequencing.2 And now, users of both BaseSpace Clarity LIMS and the NovaSeq 6000 instrument can access this out-of-the box integration to get up and running with their system sooner.

The new integration helps users track samples throughout the workflow. Specifically, it:

  • Supports S13, S2, and S4 flow cells per sample
  • Supports different applications on the same flow cell
  • Calculates samples and reagents volumes based on the flow cell type
  • Creates an output file for use with liquid handling robots
  • Validates every step in the workflow

The new integration also tracks sequencing run information in BaseSpace Clarity LIMS to help with troubleshooting or trending:

  • Run recipe files (JSON) are automatically generated to set up and initiate the run
  • Sample sheets, which are compatible with BaseSpace Sequence Hub and bcl2fastq
    v 2.19, are automatically generated and placed directly on the NovaSeq 6000 instrument
  • Sequencing run are tracked and run metrics are parsed per lane and per flow cell

If you have questions about this integration, please email Illumina Technical Support.

References

  1. Next-Generation Sequencing Informatics: Challenges and … http://www.bing.com/cr?IG=74008A18392242E59F11965A936C0331&CID=1B0873003B0C6EB91053783A3A0A
    6F0E&rd=1&h=qZ8eqx6ov_OxkAzDtTWfrbsSZM2WP_pCoQuO66f-AVI&v=1&r=http%3a%2f%2fwww.archivesofpathology.org%2fdoi%2f10.5858%2farpa.2015-0507-RA&p=DevEx,5067.1. Accessed November 14, 2017.
  2. Illumina.com. (2017). Illumina Releases NovaSeq S4 Flow Cell and NovaSeq Xp Workflow. [online] Available at: https://www.illumina.com/company/news-center/press-releases/2017/2308795.html [Accessed 16 Nov. 2017].
  3. Upcoming flow cell in the NovaSeq 6000 instrument portfolio

For Research Use Only. Not for Use in Diagnostic Procedures.

BaseSpace™ Clarity LIMS Integration to VeriSeq™ NIPT Solution

We are pleased to announce the launch of the first integration between the Illumina VeriSeq™ Noninvasive Prenatal Testing (NIPT) Solution and BaseSpace Clarity LIMS.

The VeriSeqTM NIPT Solution is an in vitro diagnostic test intended for use as a sequencing‐based screening test for the detection of fetal aneuploidies from maternal peripheral whole blood samples in pregnant women of at least 10 weeks gestation. VeriSeq NIPT provides information regarding aneuploidy status for chromosomes: 21, 18, 13, X, and Y. This product must not be used as the sole basis for diagnosis or other pregnancy management decisions.

To facilitate use of the solution, we have implemented an integration with BaseSpace™ Clarity LIMS, which allows users of both to centralize data into one location from sample accessioning to reporting, without altering the IVD CE Marked VeriSeqTM NIPT Solution.

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Figure 1. The VeriSeq NIPT workflow in BaseSpace Clarity LIMS.

At a high level, the integration includes:

  • Automatic generation of a sample upload sheet that is compatible with Workflow Manager. The sample sheet generated captures VeriSeq NIPT Sample Type and Sex Chromosomes fields required by Workflow Manager.
  • Preconfigured VeriSeq NIPT v1.0 workflow containing a protocol that maps to the VeriSeq NIPT Software Solution for both library prep and reporting.
  • Preconfigured VeriSeq NIPT v1.0 Validation workflow and protocol that allows for validation of the integration.
  • Batching step that includes automated validation to ensure batch size equals 48 or 96 – including No Template Controls (NTCs).
  • Generation of sample sheet that is designed to be used by the VeriSeq NIPT Workflow Manager to start the run.
  • An analysis step that populates NIPT report data back into BaseSpace Clarity LIMS. For BaseSpace Clarity LIMS Silver customers, the report data must be manually uploaded. However, for BaseSpace Clarity LIMS Gold users, the report data are automatically uploaded.

To learn more about the BaseSpace Clarity LIMS integration to the VeriSeq™ NIPT Solution, please contact us.

For Research Use Only. Not for use in diagnostic procedures.