Breaking new ground
Blueprint Genetics was founded in 2011 with a vision of disrupting the genetic testing industry by harnessing leading-edge information technology and robotics to automate the sequencing process and handle unprecedented volumes of tests and samples. Its founders’ ultimate goal was to provide a one-stop shop for screening for the whole field of inherited disorders – over 3,000 types of disease in more than a dozen medical categories – and deliver results within weeks rather than months.
Samuel Myllykangas, CTO at Blueprint Genetics, explains: “We decided to start with a single category: a set of 20 tests for inherited cardiovascular diseases. After four years, we had proved that our business model was successful, and we wanted to broaden our operations to support a much more comprehensive range of screening services. This meant we needed to scale our product offering by a factor of 20, expanding from 20 tests to an offering comprising more than 400.”
The company reviewed its core business processes to identify the best way to scale up its operations.
“We realized that we could easily ramp up the sequencing stage by using the robotics in our lab, and accelerate the data processing stage by investing in more computing power. However, the final interpretation and reporting stage was much more difficult to scale, because it relies so heavily on the expertise of human analysts.”
To interpret the data, these analysts had to look at each unusual gene or mutation, and then look up case histories and medical journal articles in a range of different databases to identify genotype/phenotype combinations acting as markers of particular diseases or disorders. Recognizing these combinations required a lot of domain expertise and experience, and because of the rapid rate at which new medical research is published, there was always a risk that a relevant article or database entry might get overlooked.
“Essentially, the challenge was to find a way to simplify, structure and automate as much of the analysts’ work as possible, to allow them to interpret the data and create the reports more quickly and easily,” remarks Samuel Myllykangas. “We needed something like an ERP system for genetic sequencing – but as far as we were aware, nobody had ever tried to build such a system before. We realized that we needed to break new ground and design a solution for ourselves.”
Finding the right way forward
“We realized that the volume and variety of information involved in interpreting genetic sequencing results meant that this was fundamentally a big data problem,” explains Samuel Myllykangas. “We didn’t have any expertise in that area, so we looked for a partner to help us design the architecture for a solution. IBM had the most complete proposal, encompassing both the data exploration and process management capabilities that we needed.
The solution that Blueprint Genetics has developed consists of two equally important parts. The first is a big data analytics solution that harnesses IBM® BigInsights® for Apache Hadoop to ingest, enrich and store the data generated by Blueprint’s genetic sequencing engine in a Hadoop cluster. Each sample generates 20 or more separate files of different data types, including text, images and structured data, which are combined together into a single record.
The second part of the solution is a comprehensive workflow management system that structures the interpretation process, guides the analysts to work in a standardized and efficient manner, and pre-populates the final reports with as much data as possible to reduce repetitive manual work.
Achieving business transformation
With the new solution in place, Blueprint has already been able to increase productivity by 30 to 50 percent, and expects to see a three-fold increase in overall processing speed and capacity as its analysts gains more experience.
“Over time, we expect to build up a knowledge base that will help accelerate the interpretation of more straightforward cases,” says Samuel Myllykangas. “This will not only speed up the interpretation process – it will also enable our analysts to spend more time focusing on the more unusual and interesting cases, where their expertise really counts.”
Since the solution also encourages a more structured and standardized approach to the interpretation and reporting process, it also makes it easier for Blueprint to train new analysts and ensure that everyone is complying with the appropriate lab standards and regulations.
“The process gives our analysts confidence that they have followed all the correct protocols and haven’t overlooked anything,” notes Samuel Myllykangas. “It also gives us complete traceability, so it is easy to audit our operations and demonstrate proper compliance.”
As a result of accelerating its interpretation and reporting processes, Blueprint has been able to scale up its product offering from 20 tests to 400 within just seven months.
“By eliminating one of the biggest operational bottlenecks, we have been able to achieve our goal of transforming our business from a cardiovascular specialist to an all-encompassing genetic testing service that can test for a comprehensive range of inherited disorders,” says Samuel Myllykangas. “We can now provide the one-stop shop that our clients have been looking for – giving us a significant competitive advantage.”
He concludes: “When we founded our business, it was common for genetic sequencing providers to take months or more to deliver results. As standard, we offer to deliver results within 21 days, and now that we have the solution, we’re achieving average turnaround times of just 14 days.