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The power of Exome+

Recently, my colleague Dr. Keith Dunaway wrote a great article describing how Helix’s proprietary Exome+® assay compares to other DNA testing technologies on the market. The development of Exome+ was a massive technical achievement driven by the combined Helix and Illumina R&D teams. But while we’re proud of the technical achievement, the reason why we spent so much time designing Exome+ is even more important. In a nutshell, Exome+ is a revolutionary way to go both broader and deeper than most existing technologies, at a price point that democratizes the genome to be available to millions of people and thousands of developers.

We started Helix in 2015 with a simple but powerful mission: to empower every person to improve their life through DNA. We knew we would accomplish this mission by creating the first open platform for genomics, where thousands of partners could develop DNA-powered products in a diverse range of areas. We knew that consumers were interested in non-clinical applications like ancestry and nutrition, but that they were also interested in clinically relevant insights into their health. And we knew that genomics was just getting started, with new genetic discoveries almost every week. That led us to a challenging technical dilemma because we needed to deliver on three main promises:

1. Clinical-grade data to power deep health products. We needed high-quality data to power products in areas like cancer predisposition, cardiovascular risk, and carrier screening that partners were developing. We knew this would require next generation sequencing, which is the state-of-the-art DNA sequencing technology today. We would need to read every letter in a gene and also detect complex types of variations that involve more than a change in a single base pair. Put simply, we needed to go deeper than older technologies like microarrays would allow. Partners like Mayo Clinic and Sema4 demanded it, and we had to deliver.

2. A new kind of DNA platform, where our users can be sequenced once and use that data in diverse ways for years to come. We needed to capture a broad dataset so that our partners could innovate and develop new apps as scientific knowledge increases. Internally, we called this requirement “future-proofing”—and it meant that we needed to go broad as well as deep, capturing 100 times more data than previously available and including data that scientists don’t understand today but are likely to understand in the future.

3. A price point that millions, and eventually billions, of people can afford. Our mission is to empower every person to improve their life through DNA, not just a select few. We decided that getting to “every person” meant that the upfront cost had to be under $100 to start. And frankly, we still aren’t satisfied—we aim to continue innovating to eventually reach people in every corner of the world.

No product that was already on the market could serve all of these needs. Most previous consumer tests used microarrays, which are inexpensive and do fine for ancestry testing, but have resolution too low for the vast majority of health applications (criteria #1). They also only look at known variants, and do not capture locations that aren’t already studied, so fail miserably at being future-proof (criteria #2). Whole genome sequencing is comprehensive, meeting criteria #1 and #2, but is prohibitively expensive (criteria #3). Whole exome sequencing came the closest, but it wouldn’t provide reverse compatibility with insights based on microarray data, and like WGS, it is generally quite expensive.

Exome+: Great for users, great for partners

That’s why we set out to develop Exome+: a comprehensive assay that includes a full clinical-grade exome, in addition to hundreds of thousands of other regions of interest in the genome. The data we generate is sufficient for servicing the vast majority of DNA products in any category, and will support future discoveries for many years to come. Exome+ enables us to deliver on that simple premise we founded the company on: get sequenced once, from a single saliva sample, and unlock a world of DNA-powered products—with new ones launching as geneticists unlock more information about the human genome—offered by Helix’s rigorously screened partners. Or, as one of my favorite childhood book series would say, Choose Your Own Adventure.
But Exome+ isn’t just about users—it’s great for our partners, too. First, because of the vast amount of data we capture upfront, partners can offer on-demand apps to Helix users who were first sequenced through a different product. From our early users, we’ve seen that on-demand DNA is a novel experience that delights users. Second, partners also benefit from an enormous development sandbox, enabling them to build diverse products that are limited only by their creativity and the limits of scientific knowledge. Third, partners can drive their own research, working hand-in-hand with Helix scientists to combine their proprietary datasets—phenotypic, environmental, or fitness data, for example—with robust genetic data to find new associations that would be challenging to discover alone. And finally, our partners know that they have the ability to continually update and improve their products. As scientific knowledge improves, new genes are just an API call away, because Exome+ has already captured the data upfront.

Nearly three years into the Helix journey, I often marvel at how far we have come. The power and flexibility of Exome+ has led to new and unexpected opportunities. For example, the combination of the Helix Store with our pay-as-you-go model—where partners only pay for the data that they need, and can come back for more as their needs evolve—has enabled consumer-centric research projects to be executed at massive population scale. We recently kicked off such a partnership with the Healthy Nevada Project and the Institute for Health Innovation. In the pilot phase, the Healthy Nevada Project had used microarrays, but quickly realized the limitations. To proceed, they needed clinical-grade exome data sequenced in a CLIA- and CAP-accredited lab, but also wanted the optionality of looking at array-type data if needed. With Exome+, we were able to help them achieve this flexibility. Using apps from Helix to encourage volunteers to participate, the Healthy Nevada Project will be one of the first research initiatives to pair longitudinal EMR data with CLIA/CAP exome data, and we will have more announcements soon as we enroll and sequence 40,000 volunteers in Nevada in just a few months.
In my role at Helix, I speak with partners, researchers, clinicians, and developers every day. I often hear surprise and delight that we’re able to deliver clinical-grade capability at a consumer-accessible price. Ultimately, the proof that Exome+ is the right choice lies in the products that we and our partners are able to offer. We have more products live on the Store than we would have dreamed of a few years ago. And in 2018 and beyond, we’re excited to show how Exome+ is making a difference in proactive health screening as we launch the next wave of products with world-class health partners.

Exome+® is a trademark of Helix OpCo LLC.