Recently, I was interviewed by CIOReview on Golden Helix. I gave them an overview of our strategy as well as our entire solution stack. Please read the entire article here.
Entering the Clinical Testing Market with VarSeq
The adoption of genetic services is key to our ability to provide personalized medicine in the future. The goal is to better diagnose diseases, predict their outcomes, and to choose the best possible care option for a patient. Our part here at Golden Helix is to essentially build the equivalent of an MRI for the genome. In this process the latest research on disorders is combined with our understanding of the best treatment option at any given time.
Next week, we will launch VarSeq.
VarSeq supports both gene panel based diagnostics as well as the application of clinical workflows based on Next-Gen sequencing data. Working closely with our clients in research hospitals across the world, we were able to incorporate the knowledge we gained from applying SVS in clinical settings over the last several years to VarSeq.
Over the next few weeks we will share more news with you about VarSeq, including demonstrations at the 64th Annual Meeting of the American Society of Human Genetics (ASHG) in San Diego – please stay tuned.
In order for NGS data to become broadly used in a clinical setting, other factors have come into play. This is not only about producing a state-of-the-art software package but also about accelerating clinical testing based on whole exome and genome data. Some of our additional considerations:
- Regulatory Environment: This is a wide open field. The FDA is paying increasing attention to this field. Very publicly, it engaged with 23andMe to review their processes and procedures. While this gives the adoption process a pause in the short-term, it might mean that in the mid and long term, we can hope for a consolidated governance, protecting patients while enabling clinicians to make informed decisions.
- Reimbursement: The adoption of these test in the clinic hinges on the ability for doctors to recover the expense for genetic tests. For this to occur, the quality of the results produced from these tests must be at a very high and reliable level. Also, price points need to become reasonable for payers to accept these tests as part of standard care.
- Physician Education and Acceptance: We are facing the need to educate a wide range of health care specialists involved in designing, conducting, interpreting, and utilizing genetic tests: translational researchers, pathologist, geneticists, genetic counselors, biostatisticians etc. This also includes the personnel supporting these professions such as nurses and assistants.
We share the optimism in our field that these issue will be resolved quickly. Already today, there are a few areas where adoption is expected first with significant testing volume:
- Oncology
- Inflammation
- Rare diseases
- Obstetrics
Beyond these areas, there is strong potential in areas such as obesity, diabetes, and cardiac disorders. In addition to this, there is a huge uptake in adoption expected in the area of pharmacogenomics to determine safety, efficacy, and cost of care. New applications of genetic testing will result in changes to current care teams and processes. It will reshape how pathologists, oncologists, geneticists, genetic counselors, biostatisticians, and bioinformaticians work together.
For over fifteen years, we at Golden Helix have provided tools for the research community to better understand the underlying mechanisms that cause disease. As our field is ripe to take the next step, we will do the same for clinicians, genetic counselors, and any other medical specialist in need of the best possible tool which consistently creates a reliable, clinical diagnosis. By doing so, we have the opportunity to improve patient outcomes and help fight the diseases of our time such as cancer, Alzheimer’s, and diabetes.
Precision Medicine: Moving Next-Generation Sequencing into the Clinic
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.