Accelerating Precision Medicine with High Performance Computing Clusters

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1 Accelerating Precision Medicine with High Performance Computing Clusters Scalable, Standards-Based Technology Fuels a Big Data Turning Point in Genome Sequencing Executive Summary Healthcare is in worldwide transformation, fueled by megatrends such as global aging, electronic medical records, increasing sources and types of medical data, and a rise in collaborative, coordinated care. Precision medicine adds a significant new approach to this landscape, targeting diagnostics and treatments based on an individual s unique history and genetic profile. While genome sequencing has been historically costly and complex, new high performance computing (HPC) clusters are enabling a critical turning point in medical innovation reducing costs and increasing efficiency to the point where precision medicine is poised to become a healthcare reality decades sooner than once anticipated. By sequencing, sharing and evaluating genomic data in a single day rather than weeks, healthcare professionals can develop precision treatment regimes that stand to positively affect the future of medical care for a global population. This white paper offers a closer look at the concept of precision medicine and its astonishing value to the evolving study of life sciences and medical treatment. Dedicated Computing s HPC clusters, based on advanced Intel architectures, illustrate the best technology practices empowering innovators in precision medicine effectively managing massive volumes of data, processing secure information quickly, and ensuring standards-based platforms that enable ease of deployment and deliver right-sized computing for the range of precision medicine environments. 1

2 Turning data into insight Treatments Tailored to Your DNA Genomics is the study of complex gene sets, their activity in human cells and their role in influencing biology. Using HPC clusters, researchers have access to the fast, efficient analytics that reduce costs, deliver immediate results and make genome sequencing feasible for a broad range of healthcare practices. Fueled by this scalable, standards-based computing technology, clinicians will be able to tailor treatments to specific individuals based on personal genetic predispositions instead of treating patients based on a general standard of care for a certain illness. As genomics studies become more pervasive worldwide, applied data is expected to improve diagnosis and treatment on an individual level; for example helping patients get the best care based on the molecular makeup of their specific tumor or other illness. Genetic data can guide clinicians in not only accurately predicting an individual patient s response to therapy, but also anticipating its likelihood of recurrence. Healthcare today is driven by data more accurate and timely information, shared most effectively among practitioners to ensure the best care. Genomics, and the push for precision medicine, seeks to advance this concept even further by creating options for precision medicine based on an individual s particular genetic makeup. Technology is at the core of this ambitious goal, reducing costs associated with genomics and bringing intuitive, purpose-built systems into the hands of researchers at all levels. As healthcare faces transformation worldwide, driven by megatrends such as global aging, increasing healthcare costs, coordinated care, and a significant upswell in data and data sources alike, precision medicine is poised to make a real difference improving treatment results and reducing the long-term cost of care. Essentially, the world is creating a database; genome projects are underway globally, in large part fueled by new HPC clusters that are overcoming longstanding roadblocks of cost, efficiency, scalability and ease of use. Fields such as next-generation genome sequencing and bioinformatics are quickly capitalizing on these new scalable computing platforms, accelerating the promise of global genomics projects by decades. Once thought to be feasible worldwide by 2050, technologydriven precision medicine is now anticipated to have significant global impact as early as HPC clusters are enabling faster genome sequencing for a broad new league of researchers, bringing standards-based, cost-effective, accessible technology to the widest range of medical research environments. 2

3 Greater control of quality and cost A Turning Point: Big Data in a Single Day Volumes of healthcare data come from many essential sources, such as pharmacies and labs, clinical information, general practitioner and specialist records, claims and insurance transactions. Part of the modern healthcare challenge is that disparate streams must be integrated and processed more quickly, ensuring usefulness of timely data in a treatment scenario and enabling well-informed choices. In reality, the one size fits all standard of care must evolve to deliver higher value at lower costs. More effective use of personal data is a healthcare imperative, as the industry is anticipating a ~35 percent compound annual growth rate (CAGR) of data volume over the next four years. The widespread rise of electronic medical records (EMR) one of the largest growth areas, expected to jump from 219PB to 2.3XB reflects the potential value and volume of healthcare data, with real-time information available in both routine and emergency medical settings. Medicine has experienced a decade of progress in this arena, as healthcare organizations have not only streamlined capture and sharing of patient data, but also taken strides in making years of stored research data usable, searchable and actionable by the healthcare sector as a whole. All this data has created a tipping point, where new threads of knowledge can provide greater insight into the quality of care and its associated cost. Unhealthy Cost Growth 2009 U.S. GDP $14.4 TRILLION $600B over expected benchmark U.S. HEALTHCARE COSTS $2.53 TRILLION Unhealthy Healthcare Cost Growth A recent McKinsey and Company report (prepared for the Center for U.S. Health System Reform Business Technology Office), points out that healthcare costs in the U.S. have risen sharply over the last two decades. Their data showed that by 2009, these costs represented nearly 17.6 percent of the $14.4 trillion Gross Domestic Product (GDP), or about $600B more than the benchmark anticipated for a nation of the size and wealth of the U.S. 3

4 Days of now work done in hours Genomic sequencing holds unique value in this data spectrum the practice is all about individualized data, applied intelligently to enable treatment options that are both predictive and preventive in nature. This type of advanced genetics data once took weeks to gather and analyze in the super-computer environment of a government lab, keeping costs sky-high and severely limiting the value of the data itself due to lack of immediacy. Today, using HPC clusters, researchers can gather and analyze the same data in a single day, even in much smaller clinical settings. With high speed, cost-effective genome processing, labs can ultimately sequence an individual s genome multiple times during the course of treatment, monitoring progress, relapse or resistance to prescribed medications. New, Faster Time to Insight HOURS HOURS HOURS TIME REQUIRED FOR GENOMIC ANALYSIS Two Examples of Faster Insight Data-driven healthcare is at a turning point, fueled by computing advances that both speed and simplify processes, adding new medical value with the immediacy of sophisticated genetic data. For example, according to use cases provided by Intel, one pediatric oncology center successfully reduced its genomics analysis time from seven days to four hours. With this speed of data access, clinicians can sequence patients multiple times during treatment, monitoring for signs of relapse or drug resistance and adjusting treatment strategies accordingly. Another research team provisioned a large cloud-based computing cluster to screen ten million compounds in just 11 hours, defining three compounds to continue to next stage testing. Using traditional research methods, this is the equivalent of 39 years of science at a cost of $44MM; by capitalizing on HPC clusters, it was achieved at a fraction of the time and cost. Source: High-Performance Computing in Personalized Medicine. high-performance-computing-personalized-medicine-video.html. Intel, Accessed June 29,

5 Faster time to insight Inherent Value in HPC Clusters Clusters accelerate genome sequencing processes because multiple computers are working together, each solving its own piece of the puzzle. Huge data files are generated, which are then broken down into thousands of much smaller fragments for effective analytics. By interpreting and identifying relevant markers and genotypes, researchers can then apply algorithms to help guide physicians in determining ideal therapies for a specific patient. So what is an HPC cluster and what makes it different from traditional computing environments? The term cluster refers to multiple computers working together on a particular task or problem. While a cluster incorporates state-of-the-art processing, advanced hardware-based security and flexible storage features, it responds to scaling unlike traditional computing systems. Adding resources, such as more nodes to handle more processes, generates faster results without adding significant cost. Because genomic sequencing and bioinformatics are parallelizable processes which can be allocated to various nodes of the system the cluster enables fast, efficient performance. Purpose-Built for Better Outcomes Dedicated Computing s family of HPC clusters is purpose-built for analytics and storage in bioinformatics research. Powered by Intel XEON processors and developed based on Intel Cluster Ready architecture, systems are fully integrated and optimized for both performance and scalability readily supporting the massive amounts of data that must be analyzed, interpreted and stored. Containing securely maintained open source software stacks and cluster management features, systems from Dedicated Computing are designed to accelerate time-to-market, minimize costly validation and verification and enable 24x7x365 system monitoring for increased uptime. 5

6 Analysis accelerated Working with Optimized Intel Cluster Ready Solutions To further simplify implementation of cluster technology, Dedicated Computing offers purpose-built cluster solutions to the life sciences market working in close partnership with Intel as an active participant in the Intel Cluster Ready program. Intel Cluster Ready is an architecture that defines application and component interoperability and makes it easier and faster to realize the performance advantages of HPC clusters. It helps alleviate and abstract the challenges of integrating a collection of independent hardware and software components for cluster performance. Powered by Intel Xeon processors and built upon Intel Cluster Ready architecture, Dedicated Computing s fully integrated and optimized cluster solutions enable clinicians to simulate, analyze and visualize complex, data-intensive models potentially much faster. Interoperability is pre-validated, removing risk and complexity in specifying a cluster solution and also has the potential to reduce the total cost of ownership over the cluster s lifetime. Deployment considers the ideal balance between performance and power dissipation required for the lab environment; improved memory bandwidth may accelerate processing and can have tangible impact on the amount of time required to analyze the workload. These standards-based systems readily drop into existing business systems within a health network, scaling as needed and minimizing the burden of secure data integration with other systems such as EMR or laboratory information systems (LIS). Dedicated Computing also helps scientists address the extraordinary defense of protected health information (PHI); end-users are poised to benefit from a range of hardware-assisted security technologies, including accelerated encryption, anti-theft, identity protection and malware detection. Dedicated s processes and architecture support a layered approach to security, enabling compliance with industry regulations like HIPAA. Scaling the Cluster Advantage Across All Research Settings In these high performance computing cluster solutions, a head node is combined with a preferred form of storage and runs a range of software, including a cluster management application which centralizes coordination of the entire system. The head node itself is connected to a LAN or other network, linking the cluster to a human-machine interface (HMI) or local storage components. HPC clusters range from entry level, compact clusters, featuring four multi-core homogeneous nodes, to those with hundreds of heterogeneous computing nodes; systems are combined with 20 Terabytes to multiple Petabytes of object storage used to support massive amounts of data. Genomic data requires object storage (rather than file storage), which is typically included in the head node. Additional nodes or clients connect via a secure fabric interface such as Ethernet, executing parallel workloads that provide the basis for scalable high performance computing. 6

7 Development simplified A smaller institution might require only a small number of clients, while a super-lab could scale up significantly. Scalability translates to affordability and ease of use, allowing all levels of precision medicine settings (i.e., from smaller medical groups to large research organizations) to manage performance requirements unique to their own needs. Further, the scaled approach allows smaller institutions to take advantage of hybrid systems that offer high performance on-site as well as connectivity to cloud-based analytics providers to help manage data; larger installations such as government research centers can deploy a massive infrastructure to handle sequencing and analysis of data entirely on-site. Partnering for Expertise, Integration and Non-Stop Performance Dedicated Computing s relationship with Intel and other partners offers an advantage in architecting secure solutions for life sciences computing. Researchers can readily tap expertise that allows them to focus on their own genomics applications rather than system development. Dedicated Computing s expertise in this arena helps customers make the best choices in features, such as memory, storage systems, software, security protocols, or remote management tools allowing users to best weigh price and performance options. The process of developing parallel workloads is then simplified for scientists and OEMs, armed with insight regarding the build of the operating system, specific security features, remote operations, object storage, or cluster management options. By capitalizing on Intel Cluster Ready architecture, end-users are assured that systems remain interoperable and can be easily configured to best fit their workload. Integrated tools minimize maintenance, ensure non-stop performance and further validate that the cluster remains within certification over time. Managing uptime is an essential consideration, as a downed genome sequencing system can cause a financial impact in lost opportunities and interruptions to the flow of patient information. Intel Cluster Ready certified solutions help here as well with Intel Cluster Checker, a tool included to assist in managing the cluster. This provides routine systemic management with a wide range of health checking modules to ensure ideal performance of the system for all end-users and their customers. Remote system management can also be outsourced, effectively removing another burden from the research community. Scientists can remain focused on their tasks with no need for specialized support skills, yet have access to optimal preventive maintenance and ideal response time for system issues. 7

8 Results in a fraction of the time Improving Outcomes with Next-Generation, Precision Medicine Smarter, personalized care is on the rise, considering the proliferation of patient-specific health information that improves both predictive and preventive medicine. Driven by advances in HPC clusters, the long view on genomics is changing rapidly scalable, cost-effective cluster systems are producing results in a fraction of the time required by traditional computing systems, breaking down long-held barriers to adoption. With continued progress, precision medicine may soon take place at small clinics or even at the patient s bedside. HPC clusters are making an essential difference, supporting healthcare innovators and driving new treatment advances based on increasingly more intelligent application of data. Unforeseen breakthroughs are ahead, as growth in next-generation genomic sequencing inspires broad change in the standard of care in all areas of healthcare, such as diagnostics, clinical trials, therapeutics, infectious diseases, elder care, and prenatal and neonatal screening. By capitalizing on technology, precision medicine has the potential to transform healthcare globally reducing the long-term cost of care, saving lives and improving patient outcomes. Intel and Xeon are trademarks of Intel Corporation in the U.S. and/or other countries. Dedicated Computing N26 W23880 Commerce Circle Waukesha, WI Phone: Toll Free: sales@dedicatedcomputing.com Website: Dedicated Computing is a global technology company committed to solving the business problems of our customers through the design, development and deployment of innovative technology solutions. Copyright 2015 Dedicated Computing. All Rights Reserved. June 30, 2015.