From months to days: how nanopore sequencing is transforming genomic investigations at VCGS

At Victorian Clinical Genetics Services (VCGS) in Melbourne, Australia, Sebastian Lunke and his team are exploring how Oxford Nanopore sequencing could help investigate genetic conditions that have been difficult to resolve using standard-of-care approaches. We caught up with Sebastian at the Oxford Nanopore APAC Health Summit 2026.

In our interview below, Sebastian discusses his experience of validating nanopore sequencing for use in a clinical laboratory, his use of Adaptive Sampling for real-time targeted sequencing, and what he thinks is the future of clinical genomics.

Sebastian, why did you decide to try nanopore sequencing at VCGS?

Sequencing is how we read the DNA blueprint that makes you, you. Traditionally, we've had to chop the genome into tiny pieces and then puzzle it back together. That doesn’t work particularly well for all parts of the genome.

Nanopore sequencing gives us a much more holistic picture of DNA. For the first time, we can read regions that were previously difficult to analyse and get a better understanding of what may be causing a disease.

What can nanopore technology detect or resolve that may be difficult with legacy genomic testing approaches?

With older technologies, we couldn't get into all parts of the genome. With long-read sequencing, we can now read parts of the genome that we previously couldn't look at — and there are certain types of conditions where that becomes really important.

One type is repeat expansion disorders, such as Huntington's disease and fragile X syndrome. These diseases are caused by highly repetitive regions of DNA. With short reads, accurately determining repeat size can be difficult. With long reads, we can effectively count how many repeats are present. That opens up a whole raft of genetic diseases that traditionally required highly specialised testing.

Where are the limitations and strengths of a nanopore-based workflow?

Like everything, it's not a magic solution. It's still quite a young technology, and it won't suddenly solve every unsolved case. Early on, we may see a 5–10% increase in the number of cases we can resolve, but that's just the beginning.

One of the strengths of nanopore sequencing is that we can start going beyond DNA, by looking at methylation, transcriptomics, and hopefully proteomics sometime soon. So, it becomes a much more comprehensive picture that allows us to not just read the blueprint, but also to help us interpret it.

Validation is about demonstrating that a technology is safe, accurate, and fit for purpose. We (VCGS) used gold-standard datasets with known answers and made sure the laboratory, bioinformatics, and interpretation workflows all performed as expected.

One thing we've shown is that using nanopore sequencing doesn't require any major rework of our standard procedures. It works with the samples that we receive on a day-to-day basis, which is really exciting.

Since introducing nanopore sequencing, what has changed in your lab?

We can now ascertain many more types of genetic variation. We've talked about repeat expansions, but there are also complex structural variants, insertions, and deletions.

What have you learned from Adaptive Sampling, and where could it add value?

In the past, if we found something in a genome that we couldn’t explain, we had to go through a very laborious process of designing a custom targeted assay specifically for that case. That could take weeks or months of work and required highly specialised expertise.

With Adaptive Sampling, the sequencing device does it for you. It has almost taken the skill out of making these customised assays. We get answers in a matter of weeks that previously could have taken us many months, and sometimes we couldn't do at all and had to send the sample overseas.

Adaptive Sampling is really one of the outstanding features of nanopore sequencing; I'm not aware of another technology that has anything even remotely like it.

It will replace a lot of the traditional techniques and technologies that we already have. There's huge opportunity there, both in terms of solving more cases and being able to address complex variation that previously we just couldn't get to, but also doing that in an efficient and surprisingly cost-efficient manner.

If you then layer on the ability of nanopore sequencing to target not just complex genomic variations, but also methylation, you get a really powerful package of technology. All of a sudden, I can build epigenomic assays, for example, for imprinting disorders.

So, what’s next for nanopore sequencing?

I think we'll initially see the technology used where there is a clear unmet need, particularly when standard testing hasn't found an answer.

Over time, we (VCGS) will continue to demonstrate value, develop the bioinformatics, and add additional information such as DNA methylation. The more evidence we generate, the earlier nanopore sequencing could potentially move into the diagnostic pathway.

What's also powerful is the flexibility. We can scale workflows up or down depending on demand, without impacting our turnaround times too much. The other advantage is that we have everything in one assay, and all the data comes out in a digital format. So, there's no more Sanger fragment analysis traces or RT-qPCR results to analyse.

Personally, I have no doubt that nanopore sequencing will become the primary technology in genomic care in the future. It's not going to happen overnight, but I think the transition is inevitable.

Looking ahead

From difficult-to-access regions of the genome to flexible targeted workflows powered by Adaptive Sampling, Sebastian sees Oxford Nanopore sequencing as offering capabilities that go beyond the status quo — a technology with the potential to consolidate what used to require multiple assays into just one. As researchers continue to streamline workflows and explore applications such as methylation analysis, nanopore sequencing could play an increasingly important role in future genomic investigations.

Watch Sebastian Lunke’s talk at the APAC Health Summit 2026.

Explore our clinical research application page to read more about how nanopore sequencing can deliver comprehensive insights from your research samples.

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