From gene to genome: NGS workflow automation for homogeneity in sequencing

In a SelectScience webinar now available to view on demand, Dr. rer. nat. Manja Meggendorfer, MBA, head of molecular genetics at the Munich Leukemia Laboratory, delivers a presentation on the challenges of NGS workflow automation and the key benefits of automated library preparation in diagnostic workflows, including reliability, safety, and precision.

Meggendorfer also details how the leukemia laboratory achieved uniform output and homogeneity within its sequencing process and how overnight automation reduces turnaround times, ensuring fast conveyance of information to physicians.

Read on for highlights from the live Q&A session or register to watch the webinar at any time that suits you.

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Highlights from the live Q&A session can be found below:

Q: With regard to automation of your NGS workflows, did you start with the three systems for research and routine diagnostics right away, or was it more a stepwise extension of your automation pipeline?

MM: In our lab, we try to automize as much as possible due to the increasing throughput of all our analysis. Mostly, we try to establish new workflows in the research setting and then release them to our routine diagnostic settings. We started, in this case, with the automation of the WGS and transcriptome workflows, and extended subsequently to the routine panel workflows. We started with one system, extended to two, then two or three, and finally a fourth one.

Q: Are there upfront workflow steps for NGS library preparation, such as DNA and RNA isolation, also automated in your Hamilton NGS STAR, or do you use separate workstations for this part of the workflow?

MM: For the DNA and RNA extraction, we currently use the MagNA Pure 96 system from Roche. We don't use an NGS STAR. However, for rare materials like FFPE and fixed DNA samples, we’re trying to establish an NGS STAR extraction method for next year. But currently, we use the 96 MagNA Pure systems.

Q: Have you separated pre- and post-PCR workflow steps in your lab, or do you use the systems as combined pre-post workstations for NGS library preparation?

MM: Due to our ISO accreditation, we try to split the workflows in pre- and post-PCR systems as much as possible. For independent workflows, we have two separate systems for the pre- and post-PCR steps of the library preparation and enrichment. However, for WGS and RNA-seq the library preparation is done on one system. Since this is a research setting, we combine the other pre- and post-PCR steps into one system. But, actually, we try to separate these two parts as far as possible.

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