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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.


News Article | April 25, 2017
Site: www.sciencedaily.com

Adding cisplatin to the standard gemcitabine/nab-paclitaxel drug treatment provided a very high rate of tumor shrinkage for patients with advanced pancreatic cancer, according to the results of a pilot clinical trial conducted by the HonorHealth Research Institute and the Translational Genomics Research Institute (TGen). These statistically significant and clinically meaningful improvements in overall response and survival rates resulted from a phase Ib/II clinical study performed at the HonorHealth Research Institute, a partnership of HonorHealth and TGen. The results were presented during the 2017 Gastrointestinal Cancers Symposium, sponsored by the American Society of Clinical Oncology, in San Francisco. Connecting a global network of more than 40,000 cancer professionals, the society serves as the leading resource for best practices in clinical oncology research and academic and community practices. "After just three treatment cycles, we saw tumor markers plummet and some patients' tumors shrink significantly in just nine weeks," said Gayle Jameson, nurse practitioner and principal investigator of the clinical trial, who is highly encouraged by the response. "After treatment, two patients had no evidence of disease and are alive over three years after starting this regimen. This is very rare with traditional chemotherapy." Dr. Daniel Von Hoff, TGen Distinguished Professor and Physician-in-Chief who devised the clinical trial, agreed: "Although a small study, the high response rate and landmark evolving median survival are very encouraging, and this regimen is being expanded for patients with stage IV pancreatic cancer." Dr. Von Hoff also is chief scientific officer at the HonorHealth Research Institute. Of the 24 evaluable patients (those whose response to a treatment could be measured because enough information was collected) who were enrolled in the study: This pilot clinical trial began in 2013 through a partnership between the HonorHealth Research Institute and TGen. It was funded by Stand Up To Cancer, Mattress Firm, the Arizona Diamondbacks, and the Scottsdale-based Seena Magowitz Foundation. Symptoms of pancreatic cancer usually do not appear until the disease progresses to its late stages, making it difficult to treat. Only about one in four patients survives more than a year after diagnosis, and fewer than 10 percent survive more than five years. Pancreatic cancer this year will take the lives of more than 43,000 Americans, making it the nation's third-leading cause of cancer-related death. The results of this trial are encouraging and deserve additional testing prior to becoming a standard of care for patients with advanced pancreatic cancer. Through research, the HonorHealth Research Institute and TGen aim to provide hope and a better chance for patients to live for years instead of months. The current standard of care for advanced pancreatic cancer -- a combination of nab-paclitaxel and gemcitabine -- was developed by TGen and the HonorHealth Research Institute, and approved by the U.S. Food and Drug Administration in 2013.


PHOENIX, Feb. 28, 2017 (GLOBE NEWSWIRE) -- A new test for Lyme Disease may prove to be the most accurate tool available for the difficult-to-diagnose disease, giving hope to thousands of undiagnosed and misdiagnosed patients, if funding can be found to move it through clinical study to production. The test, called LymeSeq™ is poised to transform the speed and precision of diagnosis over current tests. This test will detect multiple strains of Lyme bacteria, plus all major co-infections and non-Lyme causes of disease like Influenza and Staph. LymeSeq, developed by research scientists at Translational Genomics Research Institute (TGen), has been funded by Focus On Lyme. The test may represent a breakthrough in diagnosis and testing for Lyme disease, which are currently about 50 percent accurate. After five years shuttling her daughter specialists across the country and intense antibiotic treatments to battle this disease, Focus On Lyme Executive Director Tammy Crawford got in touch with TGen. Knowing the institute’s experience using genetic sequencing to identify pathogens like tuberculosis and E. coli, Crawford asked if TGen could do the same for Lyme disease and when they said yes, she personally funded the initial research.  The researchers are led by Dr. Paul Keim, the Executive Director of the Pathogen and Microbiome Institute and the Cowden Endowed Chair of Microbiology at Northern Arizona University (NAU), as well as Director of the Pathogen Genomics Division TGen North in Flagstaff, Ariz. Dr. Keim is an internationally recognized expert in DNA-based research methods, a fellow of the American Academy of Microbiology, and a fellow of the American Association for the Advancement of Science. LymeSeq works by targeting and amplifying specific regions of the Lyme bacteria’s DNA as well as specific genes in related bacteria. That amplified DNA gets sequenced, then researchers determine the bacterial species present in the sample by searching for the DNA code specific to Lyme or other bacteria, explained Dr. David Engelthaler, Director of Programs and Operations at TGen North, and Director of the Public Health and Translational Genomics Center at the Pathogen and Microbiome Institute. “LymeSeq has the potential to transform emergency rooms and doctor’s offices world wide, said Holly Ahern, MS, MT (ASCP) and SUNY Adirondack associate professor of microbiology, and a member of the leadership team at Focus on Lyme. Dr. Richard Horowitz, author of "How Can I Get Better? An Action Plan for Treating Resistant Lyme and Chronic Disease,” said, “more than ever, we need an accurate test” referencing the National Science Foundation’s identification of Lyme disease as an emerging pandemic threat, siting the current “problematic two-tiered testing scheme,” for which LymeSeq shows promise of being “superior in every way.” With exciting early signs of high accuracy, the next step is to advance the test into human trials. Crawford’s team of volunteers has raised more than $301,730 towards a goal of $500,000 to bring the test to market. BHHS Legacy Foundation recently stepped forward with an additional $100,000 in grant funding. “With the development of any new medical advancement, the steps are long, arduous and expensive. But we’ve come so far in such a short period of time, we need your help to get us to the finish line,” Crawford said. “We are all volunteers. Every single penny we raise goes towards the research, we keep nothing back.” For more information visit www.focusonlyme.org. To donate, visit: www.focusonlyme.org/donate.


News Article | December 12, 2016
Site: www.eurekalert.org

PHOENIX, Ariz. -- Dec. 12, 2016 -- The National Cancer Institute (NCI) has awarded a 5-year, $1.125 million grant to continue an innovative and unique oncology training program for newly minted physicians developed and overseen by Dr. Daniel Von Hoff, Distinguished Professor and Physician-In-Chief at the Translational Genomics Research Institute (TGen). Convened by the American Association for Cancer Research (AACR) and the American Society of Clinical Oncology (ASCO) -- the world's leading cancer professional organizations -- Dr. Von Hoff's Methods in Clinical Cancer Research Workshop is a one-week boot camp for new oncologists, which has been conducted each summer for the past 21 years. The program's nearly 2,100 graduates now populate leading cancer centers throughout the nation. The workshop draws on the expertise of 40 of the nation's leading oncologists, patient advocates and biostatisticians to provide intensive cancer care instruction each summer to 100 students -- 75 of whom are 2nd- and 3rd-year post-doctoral oncology fellows, and 25 are new faculty members at clinical centers. "Through a rigorous process, we select doctors who appear to have promise. It's a big deal. It's rough. It's one of the most effective courses ever," said Dr. Von Hoff, who also is Professor of Medicine at Mayo Clinic, Chief Scientific Officer for the HonorHealth Research Institute, and past director of the Arizona Cancer Center. He also is a past board member and president of AACR, a Fellow of the AACR, and recipient of the distinguished 1997 AACR Richard and Hinda Rosenthal Memorial Award. In addition, he is a past board member of ASCO and winner of its prestigious David A. Karnofsky Memorial Award for outstanding contributions to patient care and treatment. The course teaches the essentials of effective clinical trial design for therapeutic interventions in the treatment of all cancers. Working around the clock, each summer's class is divided into 12 groups. Each student must write a protocol for a new cancer clinical trial of sufficient quality to pass an Institutional Review Board, a critical step in receiving FDA approval to pursue such a study. Clinical trials are carefully controlled research studies that evaluate promising new drugs, while giving patients access to potentially lifesaving therapeutics. One of the first to take the Methods course when it began in 1996 is Dr. Ramesh K. Ramanathan, Professor of Medicine at Mayo Clinic with a joint appointment at TGen; he is now a gastrointestinal cancer specialist involved in early drug development at Mayo Clinic in Arizona: "This program helped me start a career in academic medicine and prepare me for the exacting work required to design and execute clinical trials that will make a substantial difference in the lives of our patients." Dr. Glen Weiss, a graduate of the 2006 Methods workshop and a Clinical Associate Professor at TGen, is now the Director of all Phase I and II clinical trials at Cancer Treatment Centers of America at Western Regional Medical Center near Phoenix: "This unique training course, under the meticulous watch of Dr. Von Hoff, helped me understand how to design top-flight cancer clinical trials, demanding enough to be approved by the nation's leading oncology experts. It was an invaluable experience." Poor design and conduct of a clinical trial can make it impossible for a study to provide definitive answers about the effectiveness of a new approach. They also can lead to the abandonment of promising avenues of research, even those based on sound basic scientific work, as well as to delays in the introduction of new treatments into the practice of oncology. "On behalf of the American Association for Cancer Research, I would like to thank Dr. Von Hoff for conceptualizing the idea for this course and for his tireless commitment to securing continued financial support for the Methods in Clinical Cancer Research Workshop," said Margaret Foti, PhD, MD (hc), chief executive officer of the AACR. "The Workshop has a proven track record of training early-career clinical researchers who have gone on to become world-renowned leaders in clinical trial design and conduct. We are thrilled to be able to continue this rich tradition, which will increase the number of therapeutic interventions that can be tested and made available in a timely manner to improve the care and treatment of cancer patients worldwide." AACR and ASCO have helped design the Methods workshop to increase the reliability and effectiveness of clinical trials by: 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.


NEWARK, Calif., Dec. 08, 2016 (GLOBE NEWSWIRE) -- CymaBay Therapeutics, Inc. (Nasdaq:CBAY), today announced the appointment of Robert Booth, Ph.D. and Caroline Loewy to the company’s Board of Directors, effective December 6, 2016. "I am excited to welcome Dr. Robert Booth and Caroline Loewy to the CymaBay board. A major objective for us in 2016 has been to enrich our board of directors with experienced, respected, and highly accomplished drug development executives as we continue to advance our clinical programs. Robert and Caroline have significant strategic and operational experience in drug development and biotechnology,” said Harold Van Wart, Ph.D., Chief Executive Officer of CymaBay. “Robert is a veteran of the industry and a superb scientist with wide ranging expertise in many aspects of drug development. Caroline brings years of financial and operational experience with development stage biotechnology companies and a particular focus in supporting the advancement of therapies for rare diseases.” Dr. Robert Booth is the Founder and Chief Executive Officer of Virobay, Inc., a drug discovery and development company. He served concurrently as an Operating Partner and Senior Advisor at TPG Biotech. Dr. Booth is also the Executive Chairman and co-founder of Ab Initio Biotherapeutics and of CuraSen Therapeutics. Dr. Booth was appointed to the position of Consulting Professor in the School of Medicine at Stanford University in 2016. From 2002 to 2006, Dr. Booth was the Chief Scientific Officer at Celera Genomics, where he was responsible for leading all discovery and development activities. Dr. Booth conceived and initiated the Btk tyrosine kinase inhibitor program that was licensed to Pharmacyclics and from which Imbruvica was discovered and developed. Dr. Booth served on the board of directors of Pharmacyclics until its acquisition by Abbvie for $21 billion in 2015. Dr. Booth was at Roche from 1989 to 2002, in positions of increasing responsibility and was the Senior Vice President and Business Unit Leader for Roche in Palo Alto, California. Dr. Booth was a member of the Global Research Management Team and a member of the Business Development Committee, which oversaw licensing opportunities for Roche. The biology team for which Dr. Booth was responsible discovered and contributed to the development of Invirase, the first HIV protease inhibitor to be launched. Dr. Booth currently serves as a member of the board of directors of Glialogix, Inc., CuraSen Therapeutics and Ab Initio Biotherapeutics and Virobay, Inc. He has approximately 50 published scientific articles and is an inventor on 9 patents. Caroline Loewy is a biopharmaceutical and financial executive with over 25 years of experience in the field. She is a Co-Founder and the Chief Business Officer and Chief Financial Officer of Achieve Life Sciences, as well as a consultant providing strategic advisory services for biopharmaceutical companies. Caroline has previously held the position of Chief Financial Officer of both public and private biopharmaceutical companies Tobira Therapeutics, Corcept Therapeutics, and Poniard Pharmaceuticals. Prior to her roles in company management, Caroline spent 11 years as a senior biotechnology equity research analyst at Morgan Stanley and Prudential Securities. Caroline has leveraged her experience in the medical arena and financial expertise to benefit those affected by rare disease. She is a founding board member of the Global Genes Project, one of the leading rare disease patient advocacy organizations in the world, and is a member of the National Advisory Council of the Translational Genomics Research Institute (TGen) Center for Rare Childhood Disorders. Caroline is also a founding board member of the KCNQ2 Cure Alliance, promoting education and research into the rare disorder affecting her son. CymaBay Therapeutics, Inc. (CBAY) is a clinical-stage biopharmaceutical company developing therapies to treat diseases with high unmet medical need, including serious rare and orphan disorders. Seladelpar is a potent, selective, orally active PPARδ agonist. CymaBay has recently completed a Phase 2 study of seladelpar in patients with primary biliary cholangitis as well as a pilot Phase 2 study in patients with homozygous familial hypercholesterolemia, establishing proof-of-concept in both indications. Previously, a Phase 2 study of seladelpar in patients with mixed dyslipidemia established that it has an anti-atherogenic lipid profile. Arhalofenate, CymaBay’s other product candidate, is a potential Urate-Lowering Anti-Flare Therapy that has completed five Phase 2 studies in gout patients. Arhalofenate has been found to reduce painful flares in joints while at the same time promoting excretion of uric acid by the kidney. This dual action addresses both the signs and symptoms of gout while managing the underlying pathophysiology of hyperuricemia.


News Article | November 23, 2016
Site: www.eurekalert.org

PHOENIX, Ariz. -- Nov. 23, 2016 -- Faster and more precise information about how best to treat cancer patients should be possible thanks to a $200,000 Compute the Cure grant announced today from the NVIDIA Foundation to the Translational Genomics Research Institute (TGen). The grant will help TGen accelerate the computer processing of transcriptomes from thousands of cells gleaned from patient tumor samples, using a complex computational algorithm. Transcriptomes are all the messenger RNA (mRNA) molecules expressed from an individual's genes. This process will advance the practice of precision medicine by quickly informing doctors with the best options for attacking each individual patient's cancer. "When you analyze actual patient data, your goal is to help physicians better understand treatment options, providing these answers to the doctors as soon as you possibly can. There is a lot at stake for our patients, and time is critical," said Dr. Seungchan Kim, an Associate Professor and head of TGen's Biocomputing Unit. Specifically, the grant will enable TGen to perfect its prototype statistical analysis tool called EDDY (evaluation of differential dependency), reducing its analysis turn-around from months to days. By simultaneously sequencing the mRNAs of thousands of individual cancer cells from the same tumor, it will help physicians understand why some cancer cells respond to treatment, and some don't, leading to more precisely targeted therapeutics. "We can actually separate all these individual cells and then look in more fine detail at how each cell responds to each compound," Dr. Kim said. "With that information we can propose which treatment might be best for each patient. You might have to use more than one compound to get all the tumor cells." According to TGen's project proposal, single-cell RNA sequencing addresses several shortcomings of the traditional averaging of RNA expression from multiple cells. In isolating the specific genetic profile of individual cells, subtle changes in biological behavior are brought into sharp focus, enabling new research directions such as microevolution, dynamic RNA processes and the biological mechanisms involved in rare diseases. The challenge for researchers is that each cell contains billions of pieces of genetic information. Initial attempts to simultaneously analyze thousands of tumor cells proved time consuming. Using a CPU -- a central processing unit, which is designed to conduct many different tasks -- EDDY ran for two months and was still not able to complete the analysis of an initial batch of more than 4,700 samples, even using hundreds of CPUs simultaneously. However, using a GPU -- a graphics processing unit created by NVIDIA, which is designed to accomplish simple tasks but in massive parallel computing units -- researchers anticipate EDDY will be able to analyze thousands of samples in a matter of days. Working with the University of California San Francisco, TGen will apply this GPU-accelerated process to a study of brain cancer patients, analyzing their tumors, proposing therapies and monitoring the results. "That is the promise of this grant proposal," said Dr. Harshil Dhruv, an Assistant Professor in TGen's Cancer and Cell Biology Division. "With the GPU, we can speed up the computation significantly, process the patient data within a few days, and give that information back to the oncologists so they can make an informed decision about how best to help the patient." Compute the Cure is the NVIDIA Foundation's philanthropic initiative to fund computational efforts to advance cancer research, diagnostics and treatment, support non-profits that provide patient care and support services, and engage its employees in fundraising activities. Through this initiative, the NVIDIA Foundation has donated nearly $3 million to cancer causes since 2011. The award to TGen was selected by a group of NVIDIA employees, with the support of researchers at the National Cancer Institute, from among nearly 20 proposals submitted from across the globe. "Advanced computation is indispensable to the search for cancer cures, so we're supporting researchers who embrace this view, like TGen's Dr. Kim. We're impressed with his novel use of single-cell transcriptomic profiling, the broad experience of his research team, and the potential of his GPU-accelerated analysis method to advance the clinical practice of precision medicine in cancer," said John Montrym, chief architect at NVIDIA, and an NVIDIA Foundation Compute the Cure review committee member. 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. For more information, visit: http://www. . Follow TGen on Facebook, LinkedIn and Twitter @TGen.


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. .


DUARTE, Calif., and PHOENIX, Dec. 1, 2016 /PRNewswire/ -- City of Hope, a world-renowned independent research and cancer and diabetes treatment center, and Translational Genomics Research Institute (TGen), a leading biomedical research institute, announced today that they have formed an...


DUARTE, California, y PHOENIX, 30 de noviembre de 2016 /PRNewswire-HISPANIC PR WIRE/ -- City of Hope, un reconocido centro de investigación independiente y tratamiento contra el cáncer y la diabetes, y Translational Genomics Research Institute (TGen), un destacado instituto de...

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