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Subspecialties Oncology, Omics, Technology and innovation, Genetics and epigenetics

The “Impossibly Easy” NGS

sponsored by Thermo Scientific

An interview with Lara Navarro

Lara Navarro is Head Biologist in the Anatomical Pathology Department of the General University Hospital of Valencia, Spain. Her lab, like many others over last decade, has brought in new approaches to cancer sample testing. Not only do they use conventional methods such as immunohistochemistry and immunofluorescence, but they have also implemented complementary molecular biology techniques for genomic profiling. We sat down over Zoom with Lara to discuss her lab’s experience implementing in-house next-generation sequencing (NGS).

Can you tell us about biomarker testing in your lab?

We have 12 to 15 samples each week (so about 50 cases per month), mainly EGFR, ALK, ROS, RET, MET, and Her-2. Before we brought in NGS, our biomarker testing was done gene by gene; we mainly used rtPCR, pyrosequencing, and – of course – Sanger sequencing.

Why did you decide to implement NGS – and were there any worries in your mind?

The main reason for the change was that we were increasingly required to test for multiple biomarkers with the smallest amount of sample possible. We needed a new technique that would allow us to conduct many simultaneous tests.

Our main worry was whether the workflow was going to be realistically implementable in our laboratory. Would it be too time-consuming? Would it require too many resources?We were very surprised (in a positive way!) by the Genexus System. It was so straightforward and so fast that, almost as soon as it was installed, we started using it for routine testing. The workflow is one of the simplest we have here in the laboratory. All the required tasks (such as adding the reagents) are easy to perform and the software checks after the fact to ensure that no errors have been made. The consolidation of the workflow from sample to report, the speed, and the automation all make the system easy to implement and a great fit for our laboratory.

It takes us a maximum of two working days from getting a sample to returning a report.

How does the Genexus System reduce hands-on time in your laboratory?

The process is practically fully automated and requires only about 20 minutes of hands-on time altogether – from nucleic acid extraction to final result and report. I think techniques such as fluorescence in situ hybridization or immunohistochemistry require the same, or perhaps even less, hands-on time – but analyzing genes using Sanger sequencing requires significantly more hands-on time and can take days to yield a result.

For laboratories like ours, speed and efficiency are vital. We receive samples every day and need to process them fast, so we could not have implemented previous incarnations of NGS that required a lot of hands-on time and took several days to produce a result.

What is your turnaround time for results?

It takes us a maximum of two working days from getting a sample to returning a report. To be more precise, it takes us two working mornings, because we don’t work on this type of testing later in the day. If a biomarker test is requested through the department information system on Monday morning, we have the report ready by Wednesday.

What panel do you use – and for what samples?

We use the Oncomine Precision Assay 50-gene panel, which covers all of the biomarkers we need to test. Most of the samples we test are lung cancers, which are notoriously small because most are taken via bronchoscopy. Most of the time, we have only one segment available, which needs to stretch to all of the necessary testing. That is why we value the Oncomine Precision Assay so much; it is an efficient way to use a small sample. We try to use samples with at least 20 percent tumor cells, but we do occasionally have to go as low as 5 percent – and, even when that happens, 98 percent of samples yield a conclusive result.

Although lung cancer constitutes the majority of our samples, we also use the assay for colon cancers, melanomas, gliomas, some breast cancer samples, and some thyroid cancers.

Can you describe the bioinformatics software user experience?

The system employs one user-friendly software interface for the whole workflow, which makes our work very easy. We were also able to create a traceability system so that, at any time, we can see what samples have been sequenced, when they were sequenced, and what else our laboratory did with the sample – not to mention downloading the report.

How would you summarize your experience with NGS so far?

Honestly, based on what we had seen in the past with other platforms, we didn’t think it would be possible to implement NGS in our lab. We were pleasantly surprised! With the Genexus System, the level of automation is such that very little hands-on work is needed and our turnaround time is very short. The implementation process went smoothly and, now that we are fully up and running, we no longer experience sample accumulation and work overload. It has changed – very much for the better – the way we test for oncology biomarkers in our lab.

For research use only. Not for use in diagnostic procedures.

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