“Precision Medicine”: Moving Next-Generation Sequencing into the Clinic Today

Kellie Carey discussing her treatment with her doctor. Image by Jesse Neider for The Wall Street Journal

Just a few weeks ago, the case of Kellie Carey made it to the front page of the Wall Street Journal. Initially, her prognosis in 2010 was very dire. Three months. Lung Cancer.

As I write this article, Ms. Carey is still alive because they were able to prescribe a drug based on the results of sequencing her tumor.  It turned out that Ms. Carey has one of at least 15 lung cancer variations, which were classified in the last decade using next-generation sequencing of tumors. Based on this knowledge, some major cancer centers are beginning to rethink their approach to treating the disease, and drug companies have begun the laborious process of creating drugs to specifically target one specific type of cancer.

According to the WSJ: “Doctors now talk about a ‘precision medicine’ approach in which those pinpoint drugs can treat tumors far more effectively than catchall chemotherapy.”

Ms. Carey is just one example. Here at Golden Helix, we are seeing this shift in our daily work as the latest research is now used more and more to diagnose diseases and find the best possible treatment for a particular patient. Clinicians and researchers are working hand in hand in a way that wasn’t previously possible. This trend is particularly evident in major cancer centers as well as children’s hospitals. While research may lead the way to clinical diagnosis, it is also the case that clinical data is reviewed by researchers to deepen our understanding of the cause and effect leading to a disease or trait.

The clinical applicability of DNA and RNA analytical tools is quickly becoming a reality. As a company, this means our tools must serve both worlds. We have empowered researchers for over 15 years to conduct complex analytical work, and we are committed to doing the same for clinicians, albeit with a few different considerations in mind.

Research Tool vs. Clinical Tool Considerations 
While researchers may have different goals and areas of focus, common considerations come to light when evaluating software. It must be:

  • Scalable: Our flagship product, SNP & Variation Suite (SVS), can handle everything from a single gene panel to a whole genome sequence. In fact, some of our clients are conducting research on hundreds of exomes and whole genomes. And it can be run on a desktop.
  • Visual: We’ve received a lot of kudos for our Golden Helix GenomeBrowse® visualization tool which gives researchers an interactive experience of viewing their NGS data in a streamlined and intuitive way. In our upcoming major release of SVS 8.0, we will integrate GenomeBrowse to share the same, amazing visualization experience with our SVS clients.
  • Transparent: Researchers are very sensitive to any software package that is a “black box.” Understanding what algorithms and methods have been implemented is critical so that results can be externally validated. To that end, we document all of the algorithms in SVS and the science behind them and publish it all online. We have yet to find a competitor who does that.

On the clinical side, there are a few other requirements that we have to keep in mind. Software must also be:

  • Simple: Clinicians are required to spend a lot of time with patients. Any tool they implement must therefore be intuitive and easy-to-use to make the most of their office time. Utilizing a pipeline and workflow created by their counterparts on the research and development side, clinicians don’t need to explore. They need results fast, in an easy-to-read format.
  • Compliant: Clinical applications are surrounded by a regulated set of processes and procedures because the results need to be repeatable and verifiable. They become part of the patient record. Unlike anonymous DNA samples used in the research realm, patients require a level of certainty that only comes through proven workflows.

Moving Forward 
To date, Golden Helix has been able to contribute to the explosion of knowledge by making researchers more efficient. One of our customers told us that a few years ago, conducting a trio analysis with conventional tools took him 14 days. With Golden Helix software, he is now able to analyze 100 trios within two hours.

But even two hours won’t work in the clinic. By automating most of the steps needed, we plan to further reduce the actual touch time it takes to conduct these analysis. Look for our upcoming webcast on SVS workflow automation, which could help diagnose patients, like Ms. Carey, in mere minutes using a repeatable, time-effective solution built on the SVS platform.

Andreas Scherer

About Andreas Scherer

Dr. Andreas Scherer has managed global software and services businesses working for publicly traded companies such as Netscape and AOL as well as privately held companies. As part of his academic work, he has developed algorithms to conduct DNA sequence analysis. In the last decade, he has focused on accelerating R&D processes of Fortune 500 pharmaceutical, biotech, and medical device companies. As a result of this work, he is intimately familiar with the domestic and international life sciences market. Dr. Scherer holds a PhD in Computer Science from the University of Hagen, Germany, and a Master of Computer Science from the University of Dortmund, Germany. He is author and co- author of over 20 international publications and has written books on project management, the Internet, and artificial intelligence. His latest book, “Be Fast Or Be Gone,” is a prizewinner in the 2012 Eric Hoffer Book Awards competition and has been named a finalist in the 2012 Next Generation Indie Book Awards. Follow Andreas on Twitter @andreasscherer or connect with him on LinkedIn.
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