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News Article | February 28, 2017
Site: www.eurekalert.org

SCOTTSDALE, Ariz. -- Feb. 28, 2017 -- Colleen's Dream Foundation, a Scottsdale-based nonprofit, today announced a $30,000 grant to the Translational Genomics Research Institute (TGen) to research new ways of treating ovarian cancer. The grant will help fund research that builds on TGen's discovery that mutations in a gene known as SMARCA4 drive a specific type of extremely aggressive ovarian cancer -- Small Cell Carcinoma of the Ovary, Hypercalcemic Type (SCCOHT) -- which most often affects girls and young women. TGen researchers have identified a drug called triptolide -- a derivative of an ancient Chinese medicinal plant known as "thunder god vine" -- which laboratory tests show is potentially effective against a variety of cancer types. The Colleen's Dream grant will enable TGen to test triptolide as a potential drug targeting SCCOHT and other subtypes of ovarian cancer. "We are excited about TGen's research and hope this grant proves useful in TGen's quest to discover new and more effective ways to treat ovarian cancer," said Nicole Cundiff, CEO and co-founder of Colleen's Dream Foundation. "Together, we can help change the ovarian cancer landscape for women across the world." Colleen's Dream is named after Nicole's mother, Colleen Drury, who succumbed to ovarian cancer in 2013. Since its inception in 2012, Colleen's Dream has given nearly $600,000 in grants supporting more than a dozen ovarian cancer research projects. TGen's research will focus on the hypothesis that ovarian cancers, and other cancer types, are triggered in the human genome by large complexes of regulatory proteins known as super-enhancers. "Super-enhancers are master regulators of genetic networks that are critical for cancer growth," said Dr. Will Hendricks, an Assistant Professor in TGen's Integrated Cancer Genomics Division. "We believe that triptolide could disrupt the super-enhancer networks that promote SCOOHT and possibly other subtypes of ovarian cancer." TGen's research is expected to improve the understanding of ovarian cancer biology, unveil the anti-cancer mechanisms of triptolide, and support the eventual development of clinical trials that could immediately help ovarian cancer patients. As part of an initial pilot project, TGen will test the effects of triptolide against ovarian cancers bearing specific genetic mutations. They will also evaluate the ability of triptolide to enhance the effectiveness of therapies currently used to treat ovarian cancers. "There is a tremendous need for new ovarian cancer treatments," said Dr. Jessica Lang, a TGen Postdoctoral Fellow in Dr. Hendricks' lab, specializing in ovarian cancer. "We hope that our work with this novel anti-cancer drug may be making inroads towards improving outcomes for these patients." Translational Genomics Research Institute (TGen) is a Phoenix, Arizona-based non-profit organization dedicated to conducting groundbreaking research with life changing results. TGen is focused on helping patients with neurological disorders, cancer, and diabetes, through cutting edge translational research (the process of rapidly moving research towards patient benefit). TGen physicians and scientists work to unravel the genetic components of both common and rare complex diseases in adults and children. Working with collaborators in the scientific and medical communities literally worldwide, TGen makes a substantial contribution to help our patients through efficiency and effectiveness of the translational process. TGen is allied with City of Hope, a world-renowned independent research and cancer and diabetes treatment center. This precision medicine alliance enables both institutes to complement each other in research and patient care, with City of Hope providing a significant clinical setting to advance scientific discoveries made by TGen. For more information, visit: http://www. . Follow TGen on Facebook, LinkedIn and Twitter @TGen. Colleen's Dream is a qualified 501(c)(3) nonprofit organization founded in 2012 by Nicole Cundiff and her husband, Billy, a 12-year veteran kicker in the NFL. Colleen's Dream is dedicated to funding investigational scientific research with the primary goal of developing and establishing an accurate and accessible early detection test for ovarian cancer. For more information about Colleen's Dream Foundation, or to donate call (480) 269-2266 or visit http://www. .


News Article | May 8, 2017
Site: www.eurekalert.org

PHOENIX, Ariz. -- May 8, 2017 -- Dr. Daniel Von Hoff -- Distinguished Professor, Physician-In-Chief, and Director of Molecular Medicine at the Translational Genomics Research Institute (TGen) -- will receive a gold medal for excellence in clinical medicine from his alma mater, Columbia University. Columbia University College of Physicians and Surgeons Alumni Association will present the award May 13 in New York City to Dr. Von Hoff, a world-renowned expert in new therapies for patients with cancer. "This medal represents the highest honor which the Alumni Association can bestow in recognition of your outstanding accomplishments," said Dr. Kenneth A. Forde, chair of the P&S Alumni Association Honors and Awards Committee, which represents some of the nation's most accomplished medical professionals. This year marks the 250th anniversary of P&S, and its founding as the first medical school in Colonial America to award an Medical Doctorate degree. "This recognition is especially gratifying as it is being presented by notable fellow graduates of my medical school, and I am deeply humbled and appreciative to be counted among those devoted to the welfare of patients," said Dr. Von Hoff, who has been instrumental in developing numerous new cancer treatments. He also is a Senior Consultant-Clinical Investigations for City of Hope, Chief Scientific Officer at HonorHealth Research Institute, and Professor of Medicine at Mayo Clinic. Dr. Von Hoff currently co-leads an international Stand Up To Cancer (SU2C) Pancreatic Cancer Dream Team, developing new treatments for this disease. It is one of three SU2C Dream Team grants awarded to TGen. He graduated cum laude from Carroll University (1969), and received his M.D. from Columbia University College of Physicians and Surgeons (1973). He completed his internship and residency in internal medicine at the University of California, San Francisco, then completed a medical oncology fellowship at the National Cancer Institute. Dr. Von Hoff is a past director of the University of Arizona's Arizona Cancer Center. He also is a past board member and president of the American Association for Cancer Research (AACR), a Fellow of the AACR, and recipient of the distinguished AACR Richard and Hinda Rosenthal Memorial Award. In addition, he is a past board member of the American Association of Clinical Oncology (ASCO) and winner of its prestigious David A. Karnofsky Memorial Award for outstanding contributions to patient care and treatment. He served a six-year term on President Bush's National Cancer Advisory Board (2004-10); is a recipient of the Wallace A. Reed M.D. Award, recognizing his accomplishments in advancing innovative cancer treatments, from the Arizona Medical Association; and received the Award of Excellence from the Hope Funds for Cancer Research, for his work in the clinical development of many new cancer treatments. Dr. Von Hoff and his colleagues have conducted early clinical investigations of many new cancer agents, including: gemcitabine, docetaxel, paclitaxel, topotecan, irinotecan, nanoliposomal irinotecan, fludarabine, mitoxantrone, dexrazoxane, nab-paclitaxel, vismodegib, and others. These treatments are helping many patients with breast, ovarian, prostate, colon, leukemia, advanced basal cell and pancreatic cancers. Translational Genomics Research Institute (TGen) is a Phoenix, Arizona-based non-profit organization dedicated to conducting groundbreaking research with life changing results. TGen is focused on helping patients with neurological disorders, cancer, and diabetes, through cutting edge translational research (the process of rapidly moving research towards patient benefit). TGen physicians and scientists work to unravel the genetic components of both common and rare complex diseases in adults and children. Working with collaborators in the scientific and medical communities literally worldwide, TGen makes a substantial contribution to help our patients through efficiency and effectiveness of the translational process. TGen is allied with City of Hope, a world-renowned independent research and cancer and diabetes treatment center. This precision medicine alliance enables both institutes to complement each other in research and patient care, with City of Hope providing a significant clinical setting to advance scientific discoveries made by TGen. For more information, visit: http://www. . Follow TGen on Facebook, LinkedIn and Twitter @TGen.


CHANDLER, Ariz.--(BUSINESS WIRE)--On May 12, 2017, Governor Doug Ducey signed Arizona’s $9.8 billion 2018-2019 Budget which provides bonding authority for $1 billion for investments in University Research Infrastructure. This investment continues a collaboration between the State of Arizona, Industry Leaders, Philanthropists, and Arizona’s Universities that is driving Arizona towards its goal of becoming a top-tier bioscience state. The Biotechnology Innovation Organization in partnership with TEConomy Partners publishes the biennial report on the economic impact of the bioscience industry that provides a national overview and ranks the 50 states and Puerto Rico across five quintiles or tiers. The 2016 Report, The Value of Bioscience Innovation in Growing Jobs and Improving Quality of Life 2016, was released in June of 2016 at the BIO International Convention in San Francisco. The report includes a wide range of metrics and economic indicators on a national and state basis. As reported in 2016, the top 10 states based on the number of bioscience firms (Tier I) were California, Florida, Illinois, Massachusetts, New Jersey, New York, North Carolina, Pennsylvania, Ohio, and Texas. Could Arizona achieve the growth necessary to reach the top-tiers? Arizona’s leaders began the journey to achieve this goal twenty years ago. In 1997, the Arizona Bioindustry Cluster was founded by Bob Case and Michael E. Berens, Ph.D. laying the foundation for what would become the Arizona Bioindustry Association or AZBio in 2003. Work by the Arizona Legislature and a coalition of community leaders supported voter passage of Proposition 301 in the year 2000. Prop. 301 established a six-tenths of one cent sales tax to support education that included funding for an estimated $1 billion (generated and disbursed over 20 years) for research at Arizona universities. The resulting Technology Research Initiative Fund (TRIF) is administered by the Arizona Board of Regents and has distributed $892 million for the period spanning from 2001-2016 and is well on its way to reach the billion dollar goal by June 30, 2021. The following year, the Flinn Foundation committed to 10 years of major funding for Arizona biosciences and brought together over 100 leaders to begin to craft what would become the Arizona Bioscience Roadmap. Under the stewardship of the Flinn Foundation, the strategic plan for the biosciences in Arizona would include key initiatives along with a commitment to measurement and reporting of the results. The first decade of the new century marked the completion of The Human Genome Project and a new era for life science research and development globally. From 2000 to 2010, Arizona’s Bioscience community activity included the International Genomics Consortium establishing its home in Phoenix and the subsequent creation of the Translational Genomics Research Institute (TGen) which was funded by a $90 million fundraising effort and spun out of IGC. In addition to the funding from Prop. 301, the Arizona legislature approved $440 million for construction of new university research facilities supporting the growth of the Biodesign Institute at Arizona State University, the BIO5 Institute at the University of Arizona, new research facilities at Northern Arizona University and more. An additional $100 million was approved by the voters for bioscience and health care training and facilities at Maricopa Community Colleges. The Virginia G. Piper Charitable Trust committed $50 million to personalized medicine in Arizona and local philanthropists have supported the community with additional resources for research and patient care across the state. Over the last two decades, Arizona’s bioscience industry has focused and grown. Arizona has risen in the rankings to take its place in the second tier of the Bioscience rankings based on number of firms. The Biodesign Institute at Arizona State University has grown from one building to two with a third building under construction. Arizona is now home to the Critical Path Institute, the National Biomarker Development Alliance, the Arizona Alzheimer’s Alliance, the Banner Alzheimer’s Institute, Cancer Treatment Centers of America, and Banner MD Anderson. Barrow Neurological Institute, founded in 1962 as a regional specialty center, has grown into one of the premiere destinations in the world for neurology and neurosurgery. Phoenix Children’s Hospital is now one of the largest children’s hospitals in the country and is ranked in 10 out of 10 specialties. Mayo Clinic has expanded its research and patient care capacity, added proton beam capabilities and will welcome the first class to its Arizona-based Mayo Medical School in 2017. The University of Arizona extended its reach from Tucson to Phoenix which now includes the The University of Arizona College of Medicine-Phoenix and the The University of Arizona Cancer Center at Dignity Health St. Joseph's Hospital and Medical Center on the Phoenix Biomedical Campus. The number of life science companies in Arizona is now over 1,400 and multi-billion dollar exits include the sale of Ventana Medical Systems, Inc. to Roche for $3.4 Billion and Abraxis Biosciences for $2.9 billion to Celgene. Today, companies that were born in Arizona are now publicly traded including Insys, HTG Molecular, and SensTech while others have been acquired by AMAG Pharmaceuticals, Caris Diagnostics, Thermo Fischer, IMS Health, Merz, Stryker and more. These companies have continued to grow in Arizona joining global leaders including BARD, Medtronic, and W.L. Gore. The combined benefits of Arizona’s world-class healthcare institutions and diverse population demographics are driving the number of active clinical trials in the state which have more than doubled over the period from 2012 – 2017 based on data at ClinicalTrials.gov. Long-time residents and new industry partners are benefiting from Arizona’s business-friendly public policy and regulatory environment, affordable operating cost structures, stable and reliable energy suppliers, well-managed water resources, talent, and an affordable cost of living in communities that provide their employees the opportunity for an excellent quality of life. Free from the business disruptions that can be caused by earthquakes, hurricanes, tornadoes, and floods, Arizona has become a go-to site for both high-tech manufacturing and corporate data centers. The Arizona Innovation Challenge, which made its first awards in 2011 and is powered by the Arizona Commerce Authority, awards the most money in the country for a technology commercialization challenge – $3 million ($1.5 million twice yearly) to the world’s most promising technology ventures. Awards range from $100,000 to $250,000 per company. Over this 20-year span, Arizona has gained a reputation as the state with the “collaborative gene” and attracts thought leaders looking to discover, develop, and deliver life-changing and life-saving innovations to patients. Globally recognized thought leaders have left the hallowed halls of Harvard, the National Institutes of Health and other world-class institutions to innovate and collaborate in Arizona. One real-world example of this collaboration is Arizona State University’s International School of Biomedical Diagnostics. A global center for research, teaching and service in the emerging field of biomedical diagnostics, the school pulls expertise from faculty across ASU, in collaboration with Dublin City University (DCU), Ventana Medical Systems, and other industry partners. ASU faculty come from: the Biodesign Institute, College of Health Solutions, Ira A. Fulton Schools of Engineering, School of Life Sciences in the College of Liberal Arts and Sciences, the W. P. Carey School of Business, and the Consortium for Science, Policy & Outcomes. The initiative also leverages the expertise of the National Biomarker Development Alliance that is led by ASU. Under the leadership of President Michael Crow, Arizona State University has been named the Most Innovative University in the United states for two years running and out-ranking Stanford and MIT. Throughout the Arizona Bioscience Roadmap’s first decade, Battelle tracked performance data that was released annually by the Flinn Foundation. The performance metrics released in 2014 serve as the benchmark for the second decade of the Roadmap, with new data reported on a biennial basis. The most current data is available in “2015 Progress of the Biosciences in Arizona,” a report produced by TEConomy Partners (a spinoff of Battelle) that was released in March 2016. The Flinn Foundation will continue to track the progress of the bioscience sector each year by highlighting the state’s major developments. In April of 2017, the Flinn Foundation released its most recent update, the 2016 Progress of the Biosciences in Arizona. Could Arizona achieve the growth necessary to reach the top-tiers? Absolutely. Now, twenty years into the process, Arizona’s Bioindustry has a new funding catalyst. With the Governor’s vision and the Legislature’s support, an additional $1 billion dollars will be invested in university research infrastructure beginning in July of 2018. Arizona’s leaders are already discussing what the next iteration of Prop. 301 will look like as it approaches its renewal on or before 2020. The Arizona Legislature has passed HB2191 which authorizes an additional $10 million in Angel Investor Tax Credits spread over the next four years and SB1416 which continues Arizona’s Quality Jobs Tax Credit, Arizona's Research and Development Tax Credits and other business incentives. Both bills have been sent to the Governor for his signature. Arizona’s leaders are continuing the journey to take the state into the top tiers of the bioscience rankings. The Flinn Foundation has extended its commitment to steward the Arizona Bioscience Roadmap through the year 2025 with the support of the 100-person Arizona Bioscience Roadmap Steering Committee and the Arizona Bioindustry Association (AZBio) Board of Directors is committed to the vision of making Arizona a top-tier bioscience state and works collaboratively to make that vision a reality. A key component in Arizona’s life science ecosystem, the Arizona Bioindustry Association (AZBio) is the only statewide organization exclusively focused on Arizona’s bioscience industry. AZBio membership includes patient advocacy organizations, life science innovators, educators, healthcare partners, municipalities and leading business organizations. AZBio is the statewide affiliate of the Biotechnology Innovation Organization (BIO) and works in partnership with AdvaMed, MDMA, and PhRMA to advance innovation and to ensure that the value delivered from life-changing and life-saving innovation benefits people in Arizona and around the world. For more information visit www.AZBio.org and www.AZBio.TV To learn more about Arizona’s Bioindustry:


News Article | May 23, 2017
Site: www.marketwired.com

LOS ALTOS, CA--(Marketwired - May 23, 2017) - Portworx, the leading provider of container data services for DevOps, today announced that is has been named to the list of "Cool Vendors" in the Gartner "Cool Vendors in Storage Technologies, 2017" report by Dave Russell, Arun Chandrasekaran, Julia Palmer, Raj Bala, Alan Dayley, Pushan Rinnen and Garth Landers at Gartner, Inc. Per the report's authors, "As infrastructure and operations (I&O) teams struggle to meet the demand for increased storage capacity, I&O leaders focused on storage will need to explore innovative technologies to support evolving business requirements." The vendors included in this research report are disruptive private storage vendors recognized for their abilities to address common pain points. The report also provides recommendations for I&O leaders focused on infrastructure agility: "It has become painfully evident that storage capacity demands, and expectations for far more rapid provisioning of that storage, have far outpaced the ability of I&O team's capabilities," according to the report. The analysts go on to state, "We have chosen the five disruptive private storage vendors highlighted in this research because they exemplify innovative approaches to addressing the top storage pain point of managing data growth to support business demands. These vendors accomplish this through automated, scalable storage solutions across a variety of workloads and use cases." Portworx is the solution for stateful containers, designed for DevOps. With Portworx, users can manage any database or stateful service on any infrastructure using any container scheduler, including Kubernetes, Mesosphere DC/OS, and Docker Swarm. Portworx solves the five most common problems DevOps teams encounter when running containerized databases and other stateful services in production: persistence, high availability, data automation, support for multiple data stores and infrastructure, and security. Portworx technology is ideally suited for solution verticals such as databases, messaging queues, continuous integration and continuous deployment (CICD), big data, and content management. "The insights in the Gartner Cool Vendors report are consistent with feedback from our growing base of Fortune 1000 customers, which include GE Digital, Lufthansa Airlines and TGen," said Murli Thirumale, co-founder and CEO, Portworx. "Persistent storage is a major challenge as enterprises deploy stateful containers in production. Portworx addresses this challenge head-on by enabling customers to run any stateful containerized app on any infrastructure with any scheduler." To read the full Gartner Cool Vendors in Storage Technology 2017 report visit: http://www.gartner.com/reprints/portworx?id=1-404ZX84&ct=170512&st=sb Gartner Disclaimer Gartner does not endorse any vendor, product or service depicted in our research publications, and does not advise technology users to select only those vendors with the highest ratings or other designation. Gartner research publications consist of the opinions of Gartner's research organization and should not be construed as statements of fact. Gartner disclaims all warranties, expressed or implied, with respect to this research, including any warranties of merchantability or fitness for a particular purpose.


News Article | May 8, 2017
Site: www.scientificcomputing.com

Product developers talk about time to market. Web service providers measure time to first byte. For James Lowey, the key metric is time to life. Lowey is CIO at the Translational Genomics Research Institute (TGen), a nonprofit focused on turning genomics insights into faster diagnostics and treatments that are more effective. TGen’s genetics research is being applied to rare childhood diseases, cancer, neurological disorders, diabetes and others. “We’ve got patients waiting,” Lowey told the panel audience. “We need to diagnose and treat them. They need results now, not in weeks or months. We’re working to accelerate the movement of insights from the bench to the bedside.” It’s no surprise that each new generation of processors helps organizations like TGen deliver genetic results—and clinical answers—more quickly. Lowey described TGen’s farm of Intel Xeon processor E5 v3 based Dell blade servers based on Intel Scalable System Framework (Intel SSF). Using the blade servers, TGen has reduced processing time for critical genomics processing tasks from two weeks to seven hours, making it fast enough to be clinically relevant. Digital imaging is another area where HPC-enabled speedups are advancing clinical care. Panelist Simon K. Warfield described innovative imaging techniques his team is applying to increase understanding of the brain’s complex circuitry. Dr. Warfield is the Thorne Griscom Professor of Radiology at Harvard Medical School and the founder and director of the Computational Radiology Lab (CRL) at Boston Children's Hospital. CRL is an Intel Parallel Computing Center that is modernizing the algorithms and data structures of medical image computing on Intel Xeon and Intel Xeon Phi processors. The lab is improving cache performance, vectorization performance and multi-threading performance, as well as creating more sophisticated imaging and modeling strategies. CRL can contribute to improved diagnosis and treatment of brain injuries, multiple sclerosis, depression, Alzheimer’s and many other conditions. Consider the novel technique CRL has developed to show more clearly water’s diffusion through the brain—and pinpoint hindrances and restrictions to its flow. In contrast to traditional image processing approaches, CRL’s diffusion-weighted imaging infers new parametric maps from data measurements. Its computational model includes tens or hundreds of 3D images—each up to 10 million pixels each—as its inputs. “This type of analysis is very computationally intensive,” Warfield said. “With the accelerated algorithm and the Intel Xeon Phi processors, we reduced the time needed from 48 hours to 15 minutes of calculations.” That speedup can translate to immediate benefits in for critically ill patients facing brain surgery. That’s because, as Warfield put it, “When you’re talking about surgical planning, life is a matter of time.” Recently, one of the hospital’s neurosurgery teams realized on a Friday that their patient’s conventional magnetic resonance scan was not clear enough to allow them to proceed with a planned brain resection. With the surgery-planning meeting scheduled for Monday, they requested emergency use of CRL’s diffusion imaging algorithm. The patient had a new scan Saturday evening, the data was processed on Sunday, and the information was ready for the team’s decision on Monday. The panel also highlighted precision medicine’s global reach—and its big data challenges. Fang Lin, Director of the Bioinformatics Center at BGI, described BGI’s use of the Lustre file system to help maintain storage performance as its data volumes grow. BGI is a global research leader as well as a provider of genetic testing products. It also operates the China National Genebank, putting it on the forefront of China’s five-year. BGI cranks 20 terabytes of sequencing data every day. The institute stores13petabytes of genomic data and uses a 10 petabyte file system comprising Intel Enterprise Edition for Lustre Software and open source technologies. Dr. David Torrents, a molecular biologist and research professor at the Barcelona Supercomputing Center, shone a spotlight on the importance of collaboration in advancing precision medicine. BSC provides resources to a variety of international centers and consortia. In addition, the institute conducts its own multidisciplinary research in computational biomedicine and related fields. BSC’s alliances also encompass a range of hospitals and medical centers, enabling it to validate and test its models and tools with data from clinical institutions. “We’re at an exciting moment,” Torrents said. “We are not just developing new solutions for personalized medicine, but now are beginning a pilot program in January 2017 to bring them together and apply them in clinical settings, beginning in Catalonia and then throughout Spain.” The panelists say continued leaps forward in precision medicine will come from faster and more sophisticated analysis of larger volumes of more varied data types. “What we want is a more holistic picture, and for that, it’s becoming absolutely critical to combine many diverse data types together for analysis,” said Lowey. To achieve that holistic picture, researchers want to use deep learning and other forms of artificial intelligence. They also want to apply those AI methods to genomic data in combination with imaging data, lifelong clinical records, population studies, environmental studies, and much more. Different aspects of the precision medicine workflow will have varying processing and storage requirements. So the push continues for faster performance with agile or heterogeneous platform architectures rather than a single “silver bullet” approach. The processors will continue as the primary workhorses, supplemented by embedded resources and FPGA accelerators for parts of the workflow. Distributed compute and storage resources will remain crucial, along with advances in applications and tools. As to the clinical impact of these holistic approaches, look no further than Boston Children’s Hospital. Noninvasive prenatal genomic testing can indicate whether a fetus has the risk factors that predispose it to be born with a malformed heart. If genetic testing shows these factors are present, data-intensive digital imaging can reveal whether the heart is actually deformed. By combining genomic with other medical data in this way, clinicians can provide peace of mind for worried parents-to-be, or help them plan for their child’s future. “We’re starting to connect the genetics that predisposes an individual to heart disease, with the imaging to see if the defect is present, and use that information to influence current treatment,” said Warfield. “That information can also help us plan for the child’s longer-term future. We can predict how they’ll do as teenagers and begin to plan accordingly.” Precision medicine is one of the most promising and meaningful applications of high-performance computing today. “It’s still early days, but we’re moving toward an exciting new era of predictive biology and personalized medicine,” said McManus. “Our panelists gave us a great taste of what’s on the horizon. With continued advances in platform technologies, artificial intelligence, and other areas, we create significant opportunities to increase the science of medicine and ultimately improve human health. Intel is excited to empower scientists and clinicians with technology innovations, resources and expertise as we collaborate to make this new era a reality.” Jan Rowell writes about technology trends in HPC, healthcare, life sciences, and other industries.


News Article | May 8, 2017
Site: www.scientificcomputing.com

Product developers talk about time to market. Web service providers measure time to first byte. For James Lowey, the key metric is time to life. Lowey is CIO at the Translational Genomics Research Institute (TGen), a nonprofit focused on turning genomics insights into faster diagnostics and treatments that are more effective. TGen’s genetics research is being applied to rare childhood diseases, cancer, neurological disorders, diabetes and others. “We’ve got patients waiting,” Lowey told the panel audience. “We need to diagnose and treat them. They need results now, not in weeks or months. We’re working to accelerate the movement of insights from the bench to the bedside.” It’s no surprise that each new generation of processors helps organizations like TGen deliver genetic results—and clinical answers—more quickly. Lowey described TGen’s farm of Intel Xeon processor E5 v3 based Dell blade servers based on Intel Scalable System Framework (Intel SSF). Using the blade servers, TGen has reduced processing time for critical genomics processing tasks from two weeks to seven hours, making it fast enough to be clinically relevant. Digital imaging is another area where HPC-enabled speedups are advancing clinical care. Panelist Simon K. Warfield described innovative imaging techniques his team is applying to increase understanding of the brain’s complex circuitry. Dr. Warfield is the Thorne Griscom Professor of Radiology at Harvard Medical School and the founder and director of the Computational Radiology Lab (CRL) at Boston Children's Hospital. CRL is an Intel Parallel Computing Center that is modernizing the algorithms and data structures of medical image computing on Intel Xeon and Intel Xeon Phi processors. The lab is improving cache performance, vectorization performance and multi-threading performance, as well as creating more sophisticated imaging and modeling strategies. CRL can contribute to improved diagnosis and treatment of brain injuries, multiple sclerosis, depression, Alzheimer’s and many other conditions. Consider the novel technique CRL has developed to show more clearly water’s diffusion through the brain—and pinpoint hindrances and restrictions to its flow. In contrast to traditional image processing approaches, CRL’s diffusion-weighted imaging infers new parametric maps from data measurements. Its computational model includes tens or hundreds of 3D images—each up to 10 million pixels each—as its inputs. “This type of analysis is very computationally intensive,” Warfield said. “With the accelerated algorithm and the Intel Xeon Phi processors, we reduced the time needed from 48 hours to 15 minutes of calculations.” That speedup can translate to immediate benefits in for critically ill patients facing brain surgery. That’s because, as Warfield put it, “When you’re talking about surgical planning, life is a matter of time.” Recently, one of the hospital’s neurosurgery teams realized on a Friday that their patient’s conventional magnetic resonance scan was not clear enough to allow them to proceed with a planned brain resection. With the surgery-planning meeting scheduled for Monday, they requested emergency use of CRL’s diffusion imaging algorithm. The patient had a new scan Saturday evening, the data was processed on Sunday, and the information was ready for the team’s decision on Monday. The panel also highlighted precision medicine’s global reach—and its big data challenges. Fang Lin, Director of the Bioinformatics Center at BGI, described BGI’s use of the Lustre file system to help maintain storage performance as its data volumes grow. BGI is a global research leader as well as a provider of genetic testing products. It also operates the China National Genebank, putting it on the forefront of China’s five-year. BGI cranks 20 terabytes of sequencing data every day. The institute stores13petabytes of genomic data and uses a 10 petabyte file system comprising Intel Enterprise Edition for Lustre Software and open source technologies. Dr. David Torrents, a molecular biologist and research professor at the Barcelona Supercomputing Center, shone a spotlight on the importance of collaboration in advancing precision medicine. BSC provides resources to a variety of international centers and consortia. In addition, the institute conducts its own multidisciplinary research in computational biomedicine and related fields. BSC’s alliances also encompass a range of hospitals and medical centers, enabling it to validate and test its models and tools with data from clinical institutions. “We’re at an exciting moment,” Torrents said. “We are not just developing new solutions for personalized medicine, but now are beginning a pilot program in January 2017 to bring them together and apply them in clinical settings, beginning in Catalonia and then throughout Spain.” The panelists say continued leaps forward in precision medicine will come from faster and more sophisticated analysis of larger volumes of more varied data types. “What we want is a more holistic picture, and for that, it’s becoming absolutely critical to combine many diverse data types together for analysis,” said Lowey. To achieve that holistic picture, researchers want to use deep learning and other forms of artificial intelligence. They also want to apply those AI methods to genomic data in combination with imaging data, lifelong clinical records, population studies, environmental studies, and much more. Different aspects of the precision medicine workflow will have varying processing and storage requirements. So the push continues for faster performance with agile or heterogeneous platform architectures rather than a single “silver bullet” approach. The processors will continue as the primary workhorses, supplemented by embedded resources and FPGA accelerators for parts of the workflow. Distributed compute and storage resources will remain crucial, along with advances in applications and tools. As to the clinical impact of these holistic approaches, look no further than Boston Children’s Hospital. Noninvasive prenatal genomic testing can indicate whether a fetus has the risk factors that predispose it to be born with a malformed heart. If genetic testing shows these factors are present, data-intensive digital imaging can reveal whether the heart is actually deformed. By combining genomic with other medical data in this way, clinicians can provide peace of mind for worried parents-to-be, or help them plan for their child’s future. “We’re starting to connect the genetics that predisposes an individual to heart disease, with the imaging to see if the defect is present, and use that information to influence current treatment,” said Warfield. “That information can also help us plan for the child’s longer-term future. We can predict how they’ll do as teenagers and begin to plan accordingly.” Precision medicine is one of the most promising and meaningful applications of high-performance computing today. “It’s still early days, but we’re moving toward an exciting new era of predictive biology and personalized medicine,” said McManus. “Our panelists gave us a great taste of what’s on the horizon. With continued advances in platform technologies, artificial intelligence, and other areas, we create significant opportunities to increase the science of medicine and ultimately improve human health. Intel is excited to empower scientists and clinicians with technology innovations, resources and expertise as we collaborate to make this new era a reality.” Jan Rowell writes about technology trends in HPC, healthcare, life sciences, and other industries.

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