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 In Advanced Applications, Cofactor Genomics, Molecular Diagnostics, Q&A

Discover what’s new about sequencing.

Cofactor Genomic’s CSO, Jon Armstrong, shares his thoughts on sequencing innovations. You’ll learn more about what he calls “silicon science”, and why “one size does not fit all”. Learn more about how we take raw data and drive insights for disease.

Q: Is there still a debate over long reads versus short reads?

A: In the early days of sequencing technology, development companies tried to differentiate themselves by how long of a read their platform would generate. I think this was best exemplified by 454’s marketing slogan, “Length Matters.” I think we’ve reached a point now in the maturity of sequencing where we understand that the question of read length that’s required is driven more by the questions that you’re asking and the answers that you’re hoping to receive. I think if I were to amend 454’s past marketing slogan I’d say that really one size doesn’t fit all and the decision of what read length you’re going to use is dependent on the question you’re trying to answer.

Q: Everyone seems to be talking about single-cell sequencing, is that the future?

A: I’m not a fan of answering a question with a question but in this case I would say the future of what? If the question is about the future of cancer diagnostics I would say not in the near future. I think there needs to be some fundamental changes in the way that tumor specimens are archived and preserved, as well as some changes in the way that single-cell RNA sequencing prep is done for that to really become prime time for that application. If the question is about research and discovery work and better understanding tumors, cancer, and some other biology questions then I would say it’s a great tool that we have in our genomics toolkit along with things like Methyl-seq, ChIP-seq and Ribo-seq. These are all things that we can use to better understand some basic fundamental questions, but I would say they’re in the research and development side.

Q: What is the most exciting new sequencing innovation that you think will make an impact in the near future?

A: My initial thought to that question is I don’t know what the technology is yet. The space is moving so quickly and thinking back, I worked on Solexa/ILMN serial #1 around 2006 and that was just over 10 years ago. If you pressed me, I would say it’s most likely to be in software technology and not hardware technology. If you think about the amount of data and the type of data that we generate on a daily basis, we’re going to have to focus on the software technology to be able to derive applicable biomarkers and generate disease models to have an impact in human health. One of the interesting things to that point that I’m seeing now is really talented wet lab scientists coming out of academia into industry that also have a deep understanding of the silicon sciences. That’s super exciting and that’s something we didn’t see 10 years ago. I think it’s these meshing of disciplines that is going to really drive and have a large impact on human health in the future.

Q: What’s so special about RNA? Isn’t DNA what everyone’s focused on?

A: We sequenced DNA for the human genome project so it’s not a large surprise that people have been focusing on that in the recent years. However, I think we can all agree now that DNA hasn’t been the holy grail that many people thought it would be for designing effective precision medicine. When I think about RNA and DNA and other types of molecules like micro-RNA’s, I don’t put them in the same bucket. RNA has attributes that make it a really interesting molecule to use to be able to model disease and define biomarkers. RNA changes based on the state of a cell or a tissue or an organism or disease. If you can leverage these changes to design models for cells or for tissues or for diseases, this is where you can really have an impact on therapeutics, biomarkers, and ultimately human health in the future.


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