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News Article | January 6, 2016
Site: www.scientificcomputing.com

SANTA CLARA, CA — DataDirect Networks (DDN) has announced the winners of the 2015 Pioneer User Awards. The awards recognize and celebrate visionary individuals, organizations and/or multiple people who are embracing leading-edge high performance computing technologies to shatter long-standing technical limits and to accelerate business results and scientific insights. The recipients of the DDN 2015 Pioneer Awards are Dr. Alf Wachsmann, CIO at Max Delbrück Center for Molecular Medicine, Steve Furmedge, Director of Security Services at Public Transport Authority, and the HudsonAlpha Institute for Biotechnology. "Innovation is driven by brilliant minds combining ingenuity and technology to solve problems faster and more accurately than previously conceived possible," said Molly Rector CMO, executive vice president product management and worldwide marketing, DDN. "DDN's innovation in high performance storage and data management solutions is driven by the demands of the science and the business needs of the most data-intensive organizations on the globe. We are thrilled to recognize and celebrate the achievements of the 2015 DDN Pioneer Award recipients who are embracing advanced technologies and innovation to accelerate business results and vital scientific insights while pushing the boundaries of discovery." As the CIO of Germany-based Max Delbrück Center for Molecular Medicine (MDC), which investigates basic biological concepts to understand disease mechanisms and to close the gap between basic biomedical and clinical research, Dr. Alf Wachsmann and his team were the first to test a SAP HANA cluster. Based on the requirements of life sciences researchers at the center, he and his team used their experience in integrating existing decentralized computing resources to form a federated in-memory database system. This approach combined advantages of cloud computing, such as efficient use of hardware resources and provisioning of managed software, with the security of storing and processing sensitive data on local hardware only. Dr. Wachsmann's experience includes systems design and management at the German Electron Synchrotron Lab (DESY) Stanford Linear Accelerator Center (SLAC; now SLAC National Accelerator Lab), and the Okinawa Institute of Science and Technology Graduate University (OIST). He has used DDN storage systems in the United States, Japan and Germany. Steve Furmedge, Director of Security Services at the Public Transport Authority A 30-year law enforcement professional and recognized expert on counter terrorism and security strategies for mass and public transit, Steve Furmedge leads security for the Public Transport Authority (PTA), which is the government agency that oversees Western Australia's public transit infrastructure. Chartered with serving more than two million people in the Perth metropolitan area, as well as more than 240 towns across the state, the PTA connects people and places safely and securely. Furmedge and the PTA IT team deployed a massively scalable, state-of-the-art centralized repository for all CCTV footage for a security system that is expected to grow to 12 PB. The system provides a significant improvement to PTA's counter-terrorism and crime-reduction efforts by enabling real-time monitoring of activity for mass transit and public transportation. These efforts contributed to a 97 percent rate of successful prosecution, reduced graffiti cleanup by 70 percent and prevented a large number of fraudulent complaints and litigations against PTA and staff. Furmedge's innovative and creative thinking helped to create a safe and secure infrastructure that continually maintains Perth's status as one of the top 10 livable cities in the world. Genomics is the language of life and HudsonAlpha scientists decipher its code. Propelled by game-changing technology and a drive for innovation, the expertise of HudsonAlpha researchers impacts the quality of human, plant and animal life around the world. HudsonAlpha is helping to save lives by accelerating genomic data analysis in order to solve some of the most pressing challenges in cancer, childhood genetic disorders, neuropsychiatric disorders and immune-mediated disease. To meet these challenges, HudsonAlpha leverages a unified architecture to meet its end-to-end data lifecycle needs, including the management of 4 PB of annually-generated data from its Illumina XTEN sequencer and downstream analysis using the Edico Genome DRAGEN card. Pioneers Jim Hudson and Lonnie McMillian developed the concept for HudsonAlpha in the early 2000s to develop, maintain and apply cutting-edge genomic technology across a wide spectrum of biology and biomedical research. Other innovators include Dr. Richard Myers who leads the institute, Dr. Shawn Levy who pioneered cutting-edge genomics processing, and Kevin Behn, the lead storage architect who continues to innovate new approaches for its expanding data requirements. In addition, Dr. Howard Jacob recently joined HudsonAlpha to pioneer the integration of genomic research into clinical settings. The Pioneer Award winners were selected by a DDN panel of judges consisting of a Chief Scientist, Customer Advocate, HPC Market Expert and Commercial Market Expert. These awards recognize the use of DDN storage and data management innovation in high performance computing and big data environments. The Pioneer awards acknowledge thought leaders across the globe who strive to accelerate discovery, insights and results within data-intensive HPC and enterprise big data markets by embracing leading-edge technology and innovation. Recognized annually, Pioneer award nominations will open August 1, 2016, for the 2016 Pioneer awards, and winners will be announced next November at the 2016 International Conference for High Performance Computing, Networking, Storage and Analysis (SC16). DataDirect Networks (DDN) is a big data storage supplier to data-intensive, global organizations. For more than 15 years, DDN has designed, developed, deployed and optimized systems, software and solutions that enable enterprises, service providers, universities and government agencies to generate more value and to accelerate time to insight from their data and information, on premise and in the cloud. Organizations leverage the power of DDN technology and the deep technical expertise of its team to capture, store, process, analyze, collaborate and distribute data, information and content at largest scale in the most efficient, reliable and cost effective manner.


Kircher M.,University of Washington | Witten D.M.,University of Washington | Jain P.,HudsonAlpha Institute for Biotechnology | Jain P.,Oregon Health And Science University | And 4 more authors.
Nature Genetics | Year: 2014

Current methods for annotating and interpreting human genetic variation tend to exploit a single information type (for example, conservation) and/or are restricted in scope (for example, to missense changes). Here we describe Combined Annotation-Dependent Depletion (CADD), a method for objectively integrating many diverse annotations into a single measure (C score) for each variant. We implement CADD as a support vector machine trained to differentiate 14.7 million high-frequency human-derived alleles from 14.7 million simulated variants. We precompute C scores for all 8.6 billion possible human single-nucleotide variants and enable scoring of short insertions-deletions. C scores correlate with allelic diversity, annotations of functionality, pathogenicity, disease severity, experimentally measured regulatory effects and complex trait associations, and they highly rank known pathogenic variants within individual genomes. The ability of CADD to prioritize functional, deleterious and pathogenic variants across many functional categories, effect sizes and genetic architectures is unmatched by any current single-annotation method. © 2014 Nature America, Inc. © 2014 Nature America, Inc.


SAN DIEGO--(BUSINESS WIRE)--Illumina, Inc. (NASDAQ:ILMN) today announced the launch of the iHope Network, a consortium of member institutions who have committed to providing clinical whole genome sequencing (cWGS) to underserved families. Today, the iHope Network consists of clinical laboratory members: Illumina, Genome.One, GeneDx, HudsonAlpha and their affiliate healthcare partners. Through whole-genome sequencing – the process of determining the genetic code or instructions in the cells within a person’s body – the iHope Network and their respective clinical partners strive to end years-long diagnostic odysseys. These odysseys average seven years in length and include multiple inconclusive tests, surgeries and procedures, many of which do not result in answers or treatment options for these children and their families. The iHope Network members have committed to a minimum philanthropic donation of 10 whole genome tests per year (10 patients). Additionally, iHope Network organizations have agreed to donate the variants identified through iHope to public databases, like Clinvar, which are freely accessible, public archives of reports of the relationships among human variations and their related symptoms or diseases. By doing so, the public wealth of knowledge will continue to grow and provide benefit to many more patients who depend on the precision of genomic medicine. With precision medicine and large-scale genomic initiatives being launched across the globe, genomics is reaching an inflection point in public awareness. The iHope program aims to build on that public awareness by demonstrating how next-generation sequencing can create a significant impact – by helping undiagnosed patients and their families find long sought-after answers. “We are delighted to become a participating partner of Illumina’s iHope Network” said Jane Juusola, PhD, FACMG, Director of the Clinical Genomics Program, GeneDx. “As a laboratory founded to address the needs of patients diagnosed with rare genetic diseases, the very principle of the iHope program aligns with our founding mission. Through our donation of 10 whole-genome sequencing tests, we hope to bring closure to the diagnostic odysseys for children with undiagnosed rare diseases.” “We’ve seen firsthand how a diagnosis can help families get a clearer understanding of the journey ahead,” said Marcel Dinger, CEO of Genome.One, a wholly owned subsidiary of the Garvan Institute of Medical Research. “We’re very pleased to be part of the iHope Network that will help people who are currently unable to access clinical whole-genome sequencing and help to raise awareness about the value of WGS for rare and genetic disease.” “The evidence is clear that genomic medicine can directly benefit patients. And there are millions of patients who need whole-genome sequencing today, and who cannot afford it,” said Howard J. Jacob, Ph.D., Executive Vice President for Genomic Medicine and Chief Genomic Medicine Officer, HudsonAlpha Institute for Biotechnology. “The more people who are helped through this initiative, the better the likelihood whole-genome sequencing will be integrated into clinical practice around the globe. We are proud to join the iHope Network and help save lives.” The ultimate goal of the iHope Network is to increase awareness and adoption of cWGS and demonstrate to the community that clinical whole genomes are a needed resource for all pediatric patients facing rare and undiagnosed diseases. An iHope Network Summit will take place later this year. To learn more about the program or to become part of the iHope Network, please visit: www.illumina.com/ihope. GeneDx is a world leader in Genomics with an acknowledged expertise in rare and ultra rare genetic disorders, as well as one of the broadest menus of sequencing services available among commercial laboratories. GeneDx provides testing to patients and their families in more than 55 countries. GeneDx is a business unit of BioReference Laboratories, a wholly owned subsidiary of OPKO Health, Inc. To learn more, please visit www.genedx.com. About Genome.One and the Garvan Institute of Medical Research Genome.One (www.genome.one) is a pioneering health information company providing genetic answers to life’s biggest health questions through clinical Whole Genome Sequencing. Genome.One aims to enhance the lives of patients, families and communities across the world. Genome.One is a wholly owned subsidiary of the Garvan Institute of Medical Research, Sydney, Australia. Garvan’s mission is to make significant contributions to medical science that will change the directions of science and medicine and have major impacts on human health. HudsonAlpha Institute for Biotechnology is a nonprofit institute dedicated to innovating in the field of genomic technology and sciences across a spectrum of biological challenges. Opened in 2008, its mission is four-fold: sparking scientific discoveries that can impact human health and well-being; bringing genomic medicine into clinical care; fostering life sciences entrepreneurship and business growth; and encouraging the creation of a genomics-literate workforce and society. The HudsonAlpha biotechnology campus consists of 152 acres nestled within Cummings Research Park, the nation’s second largest research park. Designed to be a hothouse of biotech economic development, HudsonAlpha’s state-of-the-art facilities co-locate nonprofit scientific researchers with entrepreneurs and educators. The relationships formed on the HudsonAlpha campus encourage collaborations that produce advances in medicine and agriculture. Under the leadership of Dr. Richard M. Myers, a key collaborator on the Human Genome Project, HudsonAlpha has become a national and international leader in genetics and genomics research and biotech education, and includes more than 30 diverse biotech companies on campus. To learn more about HudsonAlpha, visit: http://hudsonalpha.org/. Illumina is improving human health by unlocking the power of the genome. Our focus on innovation has established us as the global leader in DNA sequencing and array-based technologies, serving customers in the research, clinical and applied markets. Our products are used for applications in the life sciences, oncology, reproductive health, agriculture, and other emerging segments. To learn more, visit www.illumina.com and follow @illumina.


Marinov G.K.,California Institute of Technology | Williams B.A.,California Institute of Technology | McCue K.,California Institute of Technology | Schroth G.P.,Illumina | And 3 more authors.
Genome Research | Year: 2014

Single-cell RNA-seq mammalian transcriptome studies are at an early stage in uncovering cell-to-cell variation in gene expression, transcript processing and editing, and regulatory module activity. Despite great progress recently, substantial challenges remain, including discriminating biological variation from technical noise. Here we apply the SMART-seq single-cell RNA-seq protocol to study the reference lymphoblastoid cell line GM12878. By using spike-in quantification standards, we estimate the absolute number of RNA molecules per cell for each gene and find significant variation in total mRNA content: between 50,000 and 300,000 transcripts per cell. We directly measure technical stochasticity by a pool/ split design and find that there are significant differences in expression between individual cells, over and above technical variation. Specific gene coexpression modules were preferentially expressed in subsets of individual cells, including one enriched for mRNA processing and splicing factors. We assess cell-to-cell variation in alternative splicing and allelic bias and report evidence of significant differences in splice site usage that exceed splice variation in the pool/split comparison. Finally, we show that transcriptomes from small pools of 30-100 cells approach the information content and reproducibility of contemporary RNA-seq from large amounts of input material. Together, our results define an experimental and computational path forward for analyzing gene expression in rare cell types and cell states. © 2014 Marinov et al.


Cooper G.M.,HudsonAlpha Institute for Biotechnology | Shendure J.,University of Washington
Nature Reviews Genetics | Year: 2011

Genome and exome sequencing yield extensive catalogues of human genetic variation. However, pinpointing the few phenotypically causal variants among the many variants present in human genomes remains a major challenge, particularly for rare and complex traits wherein genetic information alone is often insufficient. Here, we review approaches to estimate the deleteriousness of single nucleotide variants (SNVs), which can be used to prioritize disease-causal variants. We describe recent advances in comparative and functional genomics that enable systematic annotation of both coding and non-coding variants. Application and optimization of these methods will be essential to find the genetic answers that sequencing promises to hide in plain sight. © 2011 Macmillan Publishers Limited. All rights reserved.


News Article | January 11, 2016
Site: www.biosciencetechnology.com

Consider the engineering marvel that is your foot. Be it hairy or homely, without its solid support you’d be hard-pressed to walk or jump normally. Now, researchers at the Stanford University School of Medicine and the HudsonAlpha Institute for Biotechnology in Huntsville, Alabama, have identified a change in gene expression between humans and primates that may have helped give us this edge when it comes to walking upright. And they did it by studying a tiny fish called the threespine stickleback that has evolved radically different skeletal structures to match environments around the world. “It’s somewhat unusual to have a research project that spans from fish all the way to humans, but it’s clear that tweaking the expression levels of molecules called bone morphogenetic proteins can result in significant changes not just in the skeletal armor of the stickleback, but also in the hind-limb development of humans and primates,” said David Kingsley, Ph.D., professor of developmental biology at Stanford. “This change is likely part of the reason why we’ve evolved from having a grasping hind foot like a chimp to a weight-bearing structure that allows us to walk on two legs.” Kingsley, who is also a Howard Hughes Medical Institute investigator, is the senior author of a paper describing the work that was published online Jan. 7 in Cell. The lead author is former Stanford postdoctoral scholar Vahan Indjeian, Ph.D., now head of a research group at Imperial College London. The threespine stickleback is remarkable in that it has evolved to have many different body structures to equip it for life in different parts of the world. It sports an exterior of bony plates and spines that act as armor to protect it from predators. In marine environments, the plates are large and thick; in freshwater, the fish have evolved to have smaller, lighter-weight plates, perhaps to enhance buoyancy, increase body flexibility and better slip out of the grasp of large, hungry insects. Kingsley and his colleagues wanted to identify the regions of the fish’s genome responsible for the skeletal differences that have evolved in natural populations. The researchers identified the area of the genome responsible for controlling armor plate size, and then looked for differences there in 11 pairs of marine and freshwater fish with varying armor-plate sizes. They homed in on a region that includes the gene for a bone morphogenetic protein family member called GDF6. Due to changes in the regulatory DNA sequence near this gene, freshwater sticklebacks express higher levels of GDF6, while their saltwater cousins express less. Strikingly, marine fish genetically engineered to contain the regulatory sequence of freshwater fish expressed higher levels of GDF6 and developed smaller armor plates, the researchers found. Kingsley and his colleagues wondered whether changes in GDF6 expression levels might also have contributed to critical skeletal modifications during human evolution. The possibility was not as far-fetched as it might seem. Other studies by evolutionary biologists, including Kingsley, have shown that small changes in the regulatory regions of key developmental genes can have profound effects in many vertebrates. They began by working with colleagues in the laboratory of Gill Bejerano, Ph.D., Stanford associate professor of developmental biology, of computer science and of pediatrics, to compare differences in the genomes of chimps and humans. In previous surveys, they found over 500 places in which humans have lost regulatory regions that are conserved from chimps and many other mammals. Two of these occur near the GDF6 gene. They homed in on one in particular. “This regulatory information was shared through about 100 million years of evolution,” said Kingsley. “And yet, surprisingly, this region is missing in humans.” To learn more about what the GDF6 regulatory region might be controlling, the researchers used the chimp regulatory DNA to control the production of a protein that is easy to visualize in mice. Laboratory mice with the chimp regulatory DNA coupled to the reporter protein strongly and specifically expressed the protein in their hind limbs, but not their forelimbs, and in their lateral toes, but not the big toes of the hind limbs. Mice genetically engineered to lack the ability to produce GDF6 in any part of their bodies had skull bones that were smaller than normal and their toes were shorter than those of their peers. Together, these findings gave the researchers a clue that GDF6 might play a critical role in limb development and evolution. The fact that humans are missing the hind-limb-regulatory region probably means that we express less of the gene in our legs and feet during development, but comparable amounts in our nascent arms, hands and skulls. Loss of this particular regulatory sequence would also shorten lateral toes but not the first toe of feet. This may help explain why the big toe is aligned with other short, lateral toes in humans.. Such a modification would create a more sturdy foot with which to walk upright. “These bone morphogenetic proteins are strong signals for bone and cartilage growth in all types of animals,” said Kingsley. “You can evolve new skeletal structures by changing where and when the signals are expressed, and it’s very satisfying to see similar regulatory principles in action whether you are changing the armor of a stickleback, or changing specific hind-limb structures during human evolution.” The research was supported by the National Institutes of Health and the Howard Hughes Medical Institute.


Cooper G.M.,HudsonAlpha Institute for Biotechnology
Genome Research | Year: 2015

Human genome sequencing is routine and will soon be a staple in research and clinical genetics. However, the promise of sequencing is often just that, with genome data routinely failing to reveal useful insights about disease in general or a person's health in particular. Nowhere is this chasm between promise and progress more evident than in the designation, "variant of uncertain significance" (VUS). Although it serves an important role, careful consideration of VUS reveals it to be a nebulous description of genomic information and its relationship to disease, symptomatic of our inability to make even crude quantitative assertions about the disease risks conferred by many genetic variants. In this perspective, I discuss the challenge of "variant interpretation" and the value of comparative and functional genomic information in meeting that challenge. Although already essential, genomic annotations will become even more important as our analytical focus widens beyond coding exons. Combined with more genotype and phenotype data, they will help facilitate more quantitative and insightful assessments of the contributions of genetic variants to disease. © 2015 Cooper.


Patent
HudsonAlpha Institute for Biotechnology and Stanford University | Date: 2014-03-13

The present disclosure provides for and relates to the identification of novel biomarkers for diagnosis and prognosis of prostate cancer or the biochemical reoccurence of prostate cancer. The biomarkers of the invention show altered methylation levels of certain CpG loci relative to normal prostate tissue, as set forth.


Patent
HudsonAlpha Institute for Biotechnology and Stanford University | Date: 2015-12-22

The present disclosure provides for and relates to the identification of novel biomarkers for diagnosis and prognosis of prostate cancer or the biochemical reoccurrence of prostate cancer. The biomarkers of the invention show altered methylation levels of certain CpG loci relative to normal prostate tissue, as set forth.


Now, researchers at the Stanford University School of Medicine and the HudsonAlpha Institute for Biotechnology in Huntsville, Alabama, have identified a change in gene expression between humans and primates that may have helped give us this edge when it comes to walking upright. And they did it by studying a tiny fish called the threespine stickleback that has evolved radically different skeletal structures to match environments around the world. "It's somewhat unusual to have a research project that spans from fish all the way to humans, but it's clear that tweaking the expression levels of molecules called bone morphogenetic proteins can result in significant changes not just in the skeletal armor of the stickleback, but also in the hind-limb development of humans and primates," said David Kingsley, PhD, professor of developmental biology at Stanford. "This change is likely part of the reason why we've evolved from having a grasping hind foot like a chimp to a weight-bearing structure that allows us to walk on two legs." Kingsley, who is also a Howard Hughes Medical Institute investigator, is the senior author of a paper describing the work that will be published online Jan. 7 in Cell. The lead author is former Stanford postdoctoral scholar Vahan Indjeian, PhD, now head of a research group at Imperial College London. The threespine stickleback is remarkable in that it has evolved to have many different body structures to equip it for life in different parts of the world. It sports an exterior of bony plates and spines that act as armor to protect it from predators. In marine environments, the plates are large and thick; in freshwater, the fish have evolved to have smaller, lighter-weight plates, perhaps to enhance buoyancy, increase body flexibility and better slip out of the grasp of large, hungry insects. Kingsley and his colleagues wanted to identify the regions of the fish's genome responsible for the skeletal differences that have evolved in natural populations. The researchers identified the area of the genome responsible for controlling armor plate size, and then looked for differences there in 11 pairs of marine and freshwater fish with varying armor-plate sizes. They homed in on a region that includes the gene for a bone morphogenetic protein family member called GDF6. Due to changes in the regulatory DNA sequence near this gene, freshwater sticklebacks express higher levels of GDF6, while their saltwater cousins express less. Strikingly, marine fish genetically engineered to contain the regulatory sequence of freshwater fish expressed higher levels of GDF6 and developed smaller armor plates, the researchers found. Kingsley and his colleagues wondered whether changes in GDF6 expression levels might also have contributed to critical skeletal modifications during human evolution. The possibility was not as far-fetched as it might seem. Other studies by evolutionary biologists, including Kingsley, have shown that small changes in the regulatory regions of key developmental genes can have profound effects in many vertebrates. They began by working with colleagues in the laboratory of Gill Bejerano, PhD, Stanford associate professor of developmental biology, of computer science and of pediatrics, to compare differences in the genomes of chimps and humans. In previous surveys, they found over 500 places in which humans have lost regulatory regions that are conserved from chimps and many other mammals. Two of these occur near the GDF6 gene. They homed in on one in particular. "This regulatory information was shared through about 100 million years of evolution," said Kingsley. "And yet, surprisingly, this region is missing in humans." To learn more about what the GDF6 regulatory region might be controlling, the researchers used the chimp regulatory DNA to control the production of a protein that is easy to visualize in mice. Laboratory mice with the chimp regulatory DNA coupled to the reporter protein strongly and specifically expressed the protein in their hind limbs, but not their forelimbs, and in their lateral toes, but not the big toes of the hind limbs. Mice genetically engineered to lack the ability to produce GDF6 in any part of their bodies had skull bones that were smaller than normal and their toes were shorter than those of their peers. Together, these findings gave the researchers a clue that GDF6 might play a critical role in limb development and evolution. The fact that humans are missing the hind-limb-regulatory region probably means that we express less of the gene in our legs and feet during development, but comparable amounts in our nascent arms, hands and skulls. Loss of this particular regulatory sequence would also shorten lateral toes but not the first toe of feet. This may help explain why the big toe is aligned with other short, lateral toes in humans. Such a modification would create a more sturdy foot with which to walk upright. "These bone morphogenetic proteins are strong signals for bone and cartilage growth in all types of animals," said Kingsley. "You can evolve new skeletal structures by changing where and when the signals are expressed, and it's very satisfying to see similar regulatory principles in action whether you are changing the armor of a stickleback, or changing specific hind-limb structures during human evolution."

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