A New Frontier for Personal Genomics
We’ve all heard the phrase “an app store for personal genomics”. But what does that actually mean? And what are the technological hurdles involved in building one? Well since the world’s first platform for storing and sharing personal genomics, complete with a suite of genetically-powered apps available to its users, launched towards the end of 2016, we decided to find out more about this new, personalised frontier.
One of the first questions that a recent new staff member on the Front Line Genomics content team asked me, after where do I get coffee and who is in charge of the pens, was whether there was any way for someone who had sequenced some or all of their genetic information to “donate it to science”. This is not a crazy question; after all, we donate blood, and occasionally organs, to science and medicine on a regular basis. Technically speaking, donating our genetic information should be entirely feasible, and dare I say it, straightforward.
There’s no question that over the past few years, something of a revolution has taken place in personal genetics. What began with tests for ancestry has ballooned into an industry covering everything from genetic screening to personal wellness. Many saw the entry of Illumina into the market with spinout company Helix as a key inflection point, and launched a new term and concept into the genomics vernacular: the idea of an ‘app store’ for personal genetics, a place where individual users can channel their data into a range of different services that provide personalised recommendations.
More and more people are getting portions of their genome sequenced through services like 23andMe, Pathway Genomics, or Veritas, to name but a few, whether out of curiosity, for health reasons, or to explore their genetic ancestry. But once that test has been completed, once the analysis has been run, what else can consumers do with their data? In an ideal world they would be able to call up other tests, or to be able to use their information to make more informed lifestyle choices. Or, as my colleague and I considered, even donate it to research.
The growing deluge of personal genetic information has enormous potential value as a tool for research, and even more so if it can be broken out of the silo of individual company databases and stored in a central repository.
This was the opportunity spotted by Dr Brandon Colby, founder of Sequencing.com, a platform that allows its users to store, analyse, and if they are so inclined, share their information. Launched in September 2016, Brandon describes Sequencing.com as simply “a community for people who have genetic data.”
“Sequencing.com is the first universally compatible platform for genomic data,” he explains. “A place to come once you have genetic data and a place to turn that data into valuable information. It doesn’t matter where the genetic data is generated, such as Helix, 23andMe, Veritas, HLI, Ancestry.com or National Geographic, Sequencing.com enables the data from any source to automatically become fully compatible with apps in our app market.”
At launch Brandon said, “Within the next 8 years, we expect that between 100 million and 2 billion human genomes will be sequenced. Sequencing.com has been preparing for this inevitability by creating solutions that unlock the true value of genetic data.”
What Brandon and the team behind Sequencing.com have done is quite remarkable. Theirs is the first “agnostic” platform for genetic data. Simply put, your data could come from any source – whole genome, whole exome, DNA microarrays – or from any company, and your file can be uploaded to Sequencing.com and ready to use immediately and seamlessly.
What does that ‘use’ look like? Very simply, Brandon’s team have turned a community vision into a reality, by creating the world’s first app store for personal genomics. Individual users already have a selection of health and wellness options available to them, including apps like DNA Diet Coach and DNA Fitness Coach that can provide tailored recommendations based on genetic information.
A network of altruists
Beyond personal data, Sequencing.com has wider, more altruistic ambitions. “When researchers come up with a hypothesis to test, they face the high costs of gathering genomic data,” explains Brandon. “At the same time, consumers are looking for a way to make their genomic data useful. We see them converging to create a database that provides free solutions that help accelerate life-saving research.”
Sequencing.com sets out to make that consumer data available to science and healthcare by offering its users the option to become an ‘Altruist’, making their anonymised personal data readily, and freely, available to researchers.
“We don’t automatically opt people into the altruist program. Instead, individuals can choose which data files they want to make available. When a person chooses to be an Altruist and make their anonymised data available in the Altruist Database, the user received Altruism Points. These points are further incentive to people to donate their data to science. Everyone’s points are added up and once certain levels are reached, Sequencing.com makes donations to charities that provide Genome Sequencing to help save children with a severe, undiagnosed illness.”
This kind of data altruism is a worthy objective for the platform, but this approach is heavily reliant on participants who are willing to share. But so far, the results have been encouraging. Users are more inclined to be altruistic with their data than not. According to Brandon, “50-60% of people who import their data are choosing to make it available to the Altruist Database as de-identified genetic data.”
On paper, setting up a platform that stores and shares genomic data sounds straightforward enough. But the problem with bringing together genetic data from multiple different sources is that not all of them sing from the same hymn sheet. Data from Human Longevity Inc. looks different to data from 23andMe, which is different in turn from, say, a whole exome sequence provided by a physician. Getting that data to work across a range of different apps from different developers, in other words creating the truly “agnostic” platform that Brandon describes, was one of the critical hurdles to overcome.
“Sequencing.com provides the world’s only universal genetic data compatibility,” says Brandon. “Apps that are available in our app market gain instant compatibility with genetic data from any source. For example, it doesn’t matter if a user has genetic testing from whole genome sequencing, exome sequencing or even microarrays such as those used by 23andMe, Ancestry.com or National Geographic, because our platform automatically converts the genetic data into the optimal format required by any app.”
New frontier for app developers
All this available data is a goldmine for app developers, many of whom have been exploring the potential uses of genetic information in personal apps from the get go. Through Sequencing.com developers like North Carolina-based Titanovo, the company behind the DNA Diet Coach and DNA Fitness Coach apps already in the Sequencing.com marketplace, gain access to a wide pool of genetic data, all pre-standardised and ready to use.
“One of the key data challenges for an app like ours,” explains Corey McCarren, COO of Titanovo, “is that you need certain SNPS to look at, depending on which region of DNA you use to make your recommendations. Not all datasets are the same. Sequencing.com does the work of compatibility for us.”
While at present Titanovo’s apps offer recommendations based upon a specific selection of genetic markers, in the future Corey explains, they want to move to a much more detailed whole-exome approach, as well as incorporating more data from fitness tracking and even health reports. All this information can contribute to far more detailed, and actionable recommendations for their users.
“One of the benefits of our platform is that we will always be iterating,” he explains. “We’re very aware that these types of genetics-based recommendations are a very new thing, and it’s not accurate to say that these recommendations are the end of the line. We want all our users to have a dataset that’s large enough so that they will benefit from new information.”
Analysis in real time
At the moment, many of the apps available at Sequencing.com analyse a user’s genetic data and provide the results as a report. But for Brandon the next big achievement will be moving from a single one-time analysis to analysis on an on-going basis, “in order to optimize life in real-time throughout each and every day.” Dr Colby stated that “the integration of genomics into mass market will occur when genetic data can be accessed and used instantaneously to provide on-going, real-time benefit to a person throughout the person’s entire life.”
Sequencing.com are taking on this challenge though Real Time Personalization (+RTP) technology®, which is currently patent pending and offered on a subscription basis to app developers. +RTP translates genetic information into software code, making it easy for app developers to code with regardless of their understanding of genetics. When an app is developed with +RTP, it is able to perceive the uniqueness of each user and this enables the app experience to be personalized with real-time, gene-based insights and guidance.
“For example, an app powered by +RTP technology may provide different information to you compared to someone else because the app can access and understand the unique information in your genes,” says Brandon. “The app can then use this information to provide you with a truly personalised user experience.”
“It is all about the engagement,” explains Geralyn Miller, Director, Microsoft Genomics. Microsoft Genomics have partnered with Sequencing.com to further explore how +RTP can be used to personalise a user experience by running a Hack the Genome event in April 2017. The aim of the event is to explore how developers can bring greater personalisation to their apps.
“If you deliver the information once, and the user goes away and does not re-engage, the value of their experience is limited to that single point in time,” says Geralyn. “But if we can deliver information that is impactful to someone, we can extend that interaction period. Wellness is a great example – how can we provide insights from health and genomic data and make them applicable to people who want to maintain a healthy lifestyle.”
“The focus of what we’re doing with Hack the Genome is really how you can take genomic data and add value to it as part of a cloud-based platform and a mobile experience,” she adds. “We want to get meaningful information, based on the genome, into people’s hands in a format to which they are accustomed.”
A key reason for partnering with Sequencing.com, explains Erdal Cosgun, PhD, Data and Applied Scientist with Microsoft Genomics, is the chance to better understand how to optimise mobile applications with genomic data. “This is one of the key outcomes for us from Hack the Genome,” he notes.
In fact, prior knowledge of genomics is not required to take part. “We’re looking to attract a broad audience of people to the event,” explains Erdal. “Students, post-docs, researchers, people who may not have genomic experience, but who are interested in developing applications that use genomic information. We hope that we can show them the benefits of working with Microsoft Azure [Microsoft’s cloud computing platform] as a platform for app development.”
The benefits of +RTP are already being felt by Sequencing.com users in the form of an app called Weather My Way +RTP, a service that provides weather reports tailored to your genetic information, such as suggesting to a people with a specific genetic makeup that they could benefit from a vitamin D supplement on a gloomy day, or, to people with a different genetic makeup, specific sunscreen recommendations when the weather is going to be sunny that day. In fact, Weather My Way +RTP has been such a success for the platform that Brandon describes his users as “hungry” for more apps like it. “We have a lot of positive feedback about Weather My Way +RTP, and many of our users are enthusiastic about the personalization it provides and are asking for more apps like that,” he says.
Taking on the data bottleneck
Data standardisation was the first major hurdle for the fledgling company, and real time analysis is the current mountain to climb. The next major frontier, according to Brandon, will be handling and transferring the hefty data files produced by DNA sequencing.
“While some of the smaller testing methods produce small files – 10-20 MB,” he says, “what we’re seeing from a lot of newer technologies is that the file size varies from 5-150 GB or more per file. So a single file can be larger than some people’s hard drives!”
Trying to upload or transfer a hard drive-sized file is a critical bottleneck for any internet-dependent service. Sequencing.com have sought to overcome this with a dedicated file uploader – Big Yotta – specific to genomic information that allows for secure uploading of any sized files. “For a whole genome file, the transfer can take from 10 hours to two days, which is still too slow,” explains Brandon. “The next challenge we are working on is to increase compression of the files, which will greatly reduce transfer times of whole genome data.”
This bottleneck is hardly news to anyone working with genomic data. Even seemingly simple problems like where to store data become a completely different species of challenge when faced with petabytes of files. The problem is not unique to genomics – in the past two years human beings have created more digital data than in all preceding history, more than 16 trillion gigabytes of digital data. In our not-so-distant future, where anywhere between 100 million and 2 billion human genomes have been sequenced, just having the data will be worthless without the capacity to move, manipulate and analyse it.
“In the near future when every newborn has their genome sequenced at birth, the big challenge will be how do we securely move, store and analyse such an enormous amount of data,” says Brandon. “Sequencing.com is building upon our current innovation to continue to unlock the value of genetic data to all those who have had genetic testing and the billions who will soon have it.