Taking Genome Sequencing to the next level

by • February 16, 2018 • Academia, Feature Slider, Feature-Home, Featured-Slides-Home, Personalized Medicine, UncategorizedComments Off on Taking Genome Sequencing to the next level283

Marc Fiume, CEO of DNAstack

The world is opening up to the idea of genome sequencing. What was once a far-fetched idea is now beginning to materialize – and we are only at the tip of the iceberg. Information technology like Facebook, Google, Wikipedia and Uber are all prime examples of impactful software platforms that connect people with data that have set the stage for the next act.

When you look at where DNA sequencing began back in the 1970’s with the “Sanger sequencing method” as a process of determining the order of bases in the length of DNA, we’ve come a long way. But still, researchers are at the forefront of this revolution of gathering our personalized genetic information and using it to power the next generation of safer and more effective “precision” medicines.

This is where Marc Fiume and his team from DNAstack, a Toronto-based cloud genomics company, have their role to play. Started in 2014, the company began work with some exciting researchers from around Canada whose hot topics included autism and cancer research. But constantly they were told that the researchers just didn’t have enough samples to make sense of all the data they were collecting and that they really needed a platform that would connect them with other researchers globally who found themselves in the same position. Inspired by the concept of Facebook, they decided to build their own platform where genetic research could transpire among researchers worldwide.

“In the early days there were lots of interesting things you can learn just by looking at one genome,” says Marc Fiume, CEO and co-founder of DNAstack. “It was all about how can we look at a breast cancer gene to understand the mechanism by which cancer evolved in that location in that patient. It started off with a passion for visually debugging individual genomes but more recently it’s turned into cloud computing and sharing across thousands of genomes which helps us understand the mechanisms of disease more comprehensively.”

He refers to the lack of data access as “potentially keeping life-saving information in a basement server room” and is one of his biggest frustrations when it comes to genomic research. Unveiling the sequence of a genome is challenging, time-consuming and expensive. Perhaps that is the reason why such a platform can no longer be just a notion, but become a mandatory tool so we can further our knowledge unified, instead of trying to connect the dots apart.

“If you look at the forecast for where genomics is going to be in 2025, we expect two billion humans to have their genomes sequenced. The amount of data that those two billion genomes will produce is more data than will be uploaded to a social media site like YouTube or Twitter. It is a tsunami of data that will be generated,” he says. “Part of what excites me is the challenge of applying computer science and machine learning in genomics to change the face of healthcare in the future.”

Genome sequencing is a lot like “decoding” of a foreign script or ciphering out a code of each individual’s personal genome. It is a long string of letters that forms a sort of molecular blueprint that is unique for each of us. These “strings” of letters are about six billion long, and currently, researchers are only grasping about a very small per cent of what those letters represent. This is why the need for sharing information should be a necessity.

In an attempt to break this societal self-inflicted mold, Marc worked with Dr. Stephen Scherer from The Centre of Applied Genomics on the “Personal Genome Project Canada” to facilitate the publication of health and genome records online for free. The intention being that whether you are sick or healthy, it is incredibly useful personally and for the research community to have your genome sequenced. Perhaps you have a predisposition to a potentially harmful genetic disease that you were not aware of before and could catch it before it starts, or if you are a carrier, or if you simply want to learn more about your ancestry. All of this is possible with genome sequencing. While some may not be ready to have theirs published online, it could still be made available to you in the privacy of your own home.

Marc and Ryan Cook, the other co-founder of DNAstack, have both tried to decrease the unease attached to publicly airing one’s genome sequence by publishing their own. “It’s about empowering and making key decisions about their healthcare in a way that’s not scary and also to break down barriers about data sharing,” comments Marc.

There are now 56 genome researchers that are bearing it all for the world to see, and encouragingly are following up on some of the data that they have found.

“Genomics is a continuation of the desire we have to better understand ourselves. Precision medicine will just be an extension of that trend,” he adds.

It wasn’t always easy for Marc and the company though. They have had some hurdles along the way – as do many – who are breaking ground and exploring unfamiliar territory. Conquering inertia is one of the hardest parts, and not one easily broken.

“Creating a culture that is accepting of new technologies allows us to create a vision,” Marc explains. “Helping the community realize that by securely and responsibly sharing information that we can make these discoveries faster and that there are significant underappreciated costs to not do it. We are leaving life-saving information in the basement server room – throwing the baby out with the bath water. Genomics has so far been disconnected from the greatest tool we have for sharing information –  the internet –  and we’ve seen how radical internet technologies like Google and Wikipedia have changed our ability to discover and exchange information worldwide.”

DNAstack is located within JLABS at the MaRS Discovery Centre in the bustling downtown centre of Toronto; with such a healthcare and energetically buzzing corridor – how could a young company like DNAstack go wrong?

“It’s such a collaborative space. I love it,” says Marc. “When we consider the impact that Toronto has in genomics, we punch way above our weight; and if you look at MaRS itself you’ve got the Center for Applied Genomics just down the street, Sick Kids Hospital just across the street, Ontario Institute for Cancer Research, JLABS, Vector Institute, UofT. I haven’t seen a single city block that has so much expertise in genomics as the MaRS corridor. For us, being geographically close to world-leading science allows us to feel a kind of energy that allows us to competes with other genomics hubs like Boston, San Francisco, and San Diego. That energy that everyone brings just keeps you going – definitely a driver.”

The Launch

DNAstack recently launched their Canadian Genomics Cloud platform that is designed to better connect data, researchers and systems across the country to accelerate genomic discoveries and the implementation of precision medicine. It was invented by Canadian leaders with decades of experience in genomics, sequencing, cloud computing, software, security, and policy to democratize access to best-in-class infrastructure while respecting the unique national and provincial requirements for data privacy and security. Their aim is to service the needs of Canadian genome scientists from research institutions, clinical laboratories, pharmaceutical companies, hospitals, and industry.

“Most Canadian genome scientists have been at a systemic disadvantage because they lack access to powerful computational infrastructure they need to manage and make sense of exponentially growing data. They spend a significant amount of their time, money, and effort setting up bricks and mortar data centres when they should really be focused on science, not infrastructure,” Marc explains. “We think that this is going to massively improve our ability to collaborate and will massively reduce the wasted investment into local infrastructures that aren’t scalable for the future. The hope is to demonstrate that Canada now does have the capacity to do a precision medicine initiative at scale. Canada is really ready for this.”

 

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