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Genomics

  Sector's Activity Matrix

3 Months Ending Apr/22/2014
Previous Developments

New High-Throughput Genotyping System Launched by Applied Biosystems

Foster City, CA (OBBeC) - Applied Biosystems has unveiled that it has commercialized a new analysis system, which it claims, enables researchers to perform high-sample-throughput genotyping studies that are faster, easier and more cost effective than other commercially available methods.

According to the announcement, the TaqMan OpenArray Genotyping System provides life scientists with the ease-of-use, accuracy, and reproducibility of the TaqMan SNP Genotyping Assays and TaqMan DME Assays in a flexible format. This system expands the potential uses of TaqMan technology across a wide range of genotyping applications, providing fast, high-sample-throughput validation and screening tool for researchers in agricultural, pharmaceutical, and other commercial industries, as well as academic institutions. 

The TaqMan® OpenArray™ Genotyping Plates - these plates provide researchers with the flexibility to deploy TaqMan SNP Genotyping or Drug Metabolizing Enzyme (DME) Assays in many different configurations. Each TaqMan OpenArray Genotyping plate contains 3,072 through-holes arranged in 48 subarrays of 64 through-holes each.

 Among the types of studies that should benefit from the use of this system are those that associate genotypes with complex diseases, ethnic ancestry, drug-treatment response, and traits for breeding and quality control in agricultural studies.

This analysis system is based on the collaboration between Applied Biosystems and BioTrove,  to commercialize the OpenArray platform, under which Applied Biosystems has exclusive rights to develop, market and support custom-built OpenArray plates of TaqMan SNP Genotyping Assays.

Researchers using this integrated platform can experience an end-to-end genotyping workflow of less than eight hours, enabling them to analyze thousands to tens of thousands of samples in days, in contrast to weeks or months, on alternative genotyping platforms, outlines the company. Single nucleotide polymorphism (SNP) genotyping studies can also be performed in a cost-effective manner on this new platform, as the TaqMan OpenArray Genotyping System delivers a lower cost per genotype, compared to other commercially available platforms, coupled with a workflow requiring a minimal amount of user interaction.

“A faster, easier, more cost effective, high-sample-throughput genotyping solution that uses gold-standard TaqMan genotyping assays will be critical for advancing science in academic research, as well as industries such as health care, food, and agriculture ” said Peter Dansky, president for Applied Biosystems’ functional analysis division. “The TaqMan OpenArray Genotyping System will provide researchers and commercial organizations with a validation and screening tool that has the potential to dramatically improve genotyping efficiencies and simplify their workflows.”

The TaqMan OpenArray Genotyping System enables researchers to perform studies that investigate tens to hundreds of SNPs across thousands to tens of thousands of samples. This scale of genotyping study is often performed as part of breeding and quality control processes in the agricultural industry. In these applications, researchers investigate how SNPs from multiple genes contribute to measurable traits. These SNPs are then used as genetic markers for quality control testing, tracking, or selective breeding of crops and livestock.

Alternatively, large-scale population studies can involve tens of thousands of samples and also require high sample throughput technology to ensure efficient genotyping across candidate SNPs. For example, at the University of California, Davis School of Medicine, a team of researchers are using the TaqMan OpenArray Genotyping System for large-scale population studies aimed at assessing the role of ethnic ancestry in complex genetic disease. In collaboration with Applied Biosystems, Dr. Michael F. Seldin, a professor of biological chemistry and medicine has developed a panel of TaqMan SNP Genotyping Assays for determining continental origin and admixture proportions in common populations in America. During the past year, as an early access user of the system, Dr. Seldin has been able to perform more cost-effective genotyping projects that involve SNPs from these panels—64, 96 or 128—in large numbers of biological samples.

For example, his team is currently genotyping approximately 20,000 samples from participants in the Women’s Health Initiative, a long-term national health study that focuses on strategies for preventing heart disease, breast and colorectal cancer and fracture in postmenopausal women, in order to examine ancestry association with various phenotypes in admixed subject groups including African Americans and Hispanic Americans.

“The TaqMan OpenArray Genotyping System enables a cost and labour efficient genotyping method for projects using tens to hundreds of defined SNPs and large numbers of samples,” said Dr. Seldin. “This platform increases the speed, simplicity, and efficiency of our studies. It also enables a high quantity of sample throughput with similar genotyping quality to that achieved by conventional TaqMan SNP Genotyping Assays.”

Additionally, the flexible format of this new system allows researchers to perform genotyping studies using a range of SNPs and samples in each experiment.
 
The TaqMan OpenArray Genotyping Plates provide researchers with the flexibility to deploy assays in many different configurations. Each TaqMan OpenArray Genotyping plate contains 3,072 through-holes arranged in 48 subarrays of 64 through-holes each. The TaqMan OpenArray Genotyping System validates or screens up to 256 SNPs across more than 1500 samples per day with minimal user interaction. Alternative platforms require more than a day to obtain results from sample analysis and often involve the need for extensive user interaction.

The system includes an instrument platform, reagents, and consumables, with the main components consisting of the TaqMan OpenArray Genotyping Instrument Platform and TaqMan OpenArray Genotyping Plates that are pre-loaded with pre-designed or custom TaqMan SNP Genotyping or Drug Metabolizing Enzyme (DME) Assays. Researchers will be able to select genotyping assays from Applied Biosystems’ comprehensive line of more than 4.5 million individual pre-designed TaqMan SNP Genotyping Assays, Custom TaqMan SNP Genotyping Assays, or TaqMan DME Genotyping Assays for detecting polymorphisms in the drug metabolism enzyme genes. Once customers receive their assays pre-loaded on TaqMan OpenArray plates, they will then use an automated sample loader to introduce their DNA samples into the arrays. After a short processing time, the OpenArray plates are read by the accompanying imaging system and analysis software to determine sample genotype.

The TaqMan Open Array Genotyping System is available in limited release from Applied Biosystems until January 2009, when global commercialization is expected to begin.
 
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Georgetown University Medical Center and Oak Ridge National Laboratory Announce Partnership

Georgetown University Medical Center and Oak Ridge National Laboratory Announce Partnership

Washington, DC (OBBeC) - Georgetown University Medical Center (GUMC) and Oak Ridge National Laboratory (ORNL) have announced an agreement between the institutions that formalizes their research relationship and will help facilitate additional biomedical research—particularly in the areas of structural biology, systems genetics, biomarkers, computational biology, and radiation biology.


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The European Biosimilars Market: Trends and Key Success Factors

The European Biosimilars Market: Trends and Key Success Factors

The European biopharmaceuticals market currently accounts for approximately 45% of the global market, and is expected to grow at over 10% during the forecast period. According to figures by the European generic association (EGA), generic medicines have made a major contribution to affordable and accessible healthcare for over 20 years, saving the European Union (EU) alone an estimated €20 billion annually.
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Researchers Trace Origins of Genes that Trigger the Body's Immune Response to Viral Infection

Researchers Trace Origins of Genes that Trigger the Body's Immune Response to Viral Infection

Richmond, VA (OBBeC) - According to a report from  the Virginia Commonwealth University Institute of Molecular Medicine, researchers at the institute have traced the evolutionary origin of two genes that serve as primary cellular sensors of infection with RNA viruses, such as influenza, poliovirus, West Nile virus, and HIV, which may ultimately provide researchers with insight into a possible new pathway for the development of innate immunity.
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Engineers Build Multi-Input "Plug-and-Play" Synthetic RNA Device

Engineers Build Multi-Input "Plug-and-Play" Synthetic RNA Device

Pasadena, CA (OBBeC) – According to a report from the California Institute of Technology (Caltech),  Engineers from the institute have created a "plug-and-play" synthetic RNA device--a sort of eminently customizable biological computer--that is capable of taking in and responding to more than one biological or environmental signal at a time.
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Pennate Diatom Genome Sequenced

Pennate Diatom Genome Sequenced

La Jolla, CA (OBBeC) - An international team of researchers led by U.S. Department of Energy Joint Genome Institute (DOE JGI) and the Ecole Normale Supérieure of Paris, as well as  scientists from the J. Craig Venter Institute have sequenced and analyzed the genome of Phaeodactylum tricornutum. The results were published in October 15 edition of Nature. This is only the second diatom and the first of the pennate class to be sequenced and published.

Diatoms are eukaryotes that have a unique cell wall made from silica. They are keys to better understanding the environmental health of the marine ecosystems since they are the major residents in the world’s waters and are responsible for most of the regulation of carbon and production of oxygen in these waters.

Researchers compared the P. pseudonana genome to the previously sequenced diatom, Thalassiosira pseudonana to further understand diatom evolution, function and prevalence. P. tricornutum has 27.4 million base pairs of DNA, and 10,402 genes making it slightly smaller than T. pseudonana.

JCVI researchers, Dr. Andrew Allen, and Dr. Jonathan Badger, developed novel phylogenomic profiling techniques to identify the origins of the diatom genes. They found that more than 300 of these genes were of bacterial origin. This finding has significant implications in understanding diatom evolution and should enable better understanding of how diatoms utilize nutrients found in their environments.

First author Dr. Chris Bowler of the Ecole Normale Supérieure and his colleagues are also trying to understand the role that iron plays in the Phaeodactylum’s development. Iron is even more precious than nitrogen in the ocean and its absence in the southern hemisphere is likely a major cause of oceanic deserts of photosynthesis there. Bowler’s team has demonstrated that when iron deficiency occurs processes such as photosynthesis and nitrogen assimilation are suppressed.

Recently, Allen, Bowler and colleagues published a paper in the journal PNAS describing how diatoms metabolize iron and how they adapt to low iron environments. In this study, the team determined that some of the genes responsible for the diatoms’ abilities to survive in low iron availability are bacterial and that diatoms appear to have a bacterial-like iron binding protein.
JCVI researchers are funded by NSF grants in the Biological Oceanography and Microbial Genome Sequencing programs.
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Scientists Generate Digital Zebrafish Embryo Featured

Scientists Generate Digital Zebrafish Embryo

According to a report from the European Molecular Biology Laboratory (EMBL), researchers at the institute have generated a digital zebrafish embryo - the first complete developmental blueprint of a vertebrate.
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deSciner  and Gene Logic Enter into a Partnership to Create 'Genomics Gateway'

deSciner and Gene Logic Enter into a Partnership to Create 'Genomics Gateway'

Leicester, UK and  Gaithersburg, Md. (OBBeC) - deSciner Business Network and Gene Logic have announced that they have entered into a Strategic Alliance  to create an interactive genomics information resource.

Both organizations will work together to create a unique knowledge resource in genomics called 'Genomics Gateway'. The vision of this partnership is to present applications of genomics in pursuit of improved and affordable healthcare and therapeutics. The Gateway will feature leading scientists, developments and progress in this area through webinars, interactive interviews, and blogs amongst other vehicles.

The Gateway will be featured as new sections on the OBBeC Biotech portal powered by deSciner and Gene Logic's thought leadership forum.

“We are extremely delighted to be working with Gene Logic to incorporate such rich knowledge resource into OBBeC Portal,” says Tim El-Sheikh, Managing Director and CEO of deSciner Business Network. “We always strive to provide our worldwide readers with high quality and informative content from leading scientists and businesses from around the globe, discussing strategic issues and best practices in biotechnology, Bio-IT and healthcare sectors, all through a single online interface.”

Anu Acharya, CEO, Gene Logic says, “We have a very strong corporate social responsibility program through which we reach out to our community. Genomics over the years has been defined and re-defined and we are now seeing exciting applications of genomics in the biotech sector. As a leader in the genomics space, we are pleased to partner with deSciner to present the latest in the genomics and discovery space through various programs we have planned.”

Dr. Ashwin Sivakumar, Director Marketing & Alliances, Gene Logic says, “State-of-the-art technologies like Genotyping, Differential Gene Expression, Genome Wide Association, SNPs et cetera have contributed immensely to global biomarker discovery programs as we all continue our pursuit for improved and affordable therapeutics. This alliance with deSciner is a first of its kind partnership where we have broken traditional barriers to feature pioneering work of the genomics community and present news relating to advancements in this sector.”
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Genome of a Monkey Human-Malaria Parasite Sequenced Featured

Genome of a Monkey Human-Malaria Parasite Sequenced

According to an announcement from Wellcome Trust Sanger Institute, a team of researchers at the institute have decoded the genome of a malaria parasite that has a host range from monkeys to man. Identified originally in monkeys, the parasite was first reported in a human infection just over 40 years ago.

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FDA Awards up to $2.5 Billion to Modernize Information Technology over Ten Years

FDA Awards up to $2.5 Billion to Modernize Information Technology over Ten Years

Rockville, MD (OBBeC) - The U.S. Food and Drug Administration has announced the selection of ten contractors to receive up to a total of $2.5 billion for information technology (IT) and data centre management services over the next ten years. The contract is the cornerstone of the FDA’s Information Technology for the 21st Century (ICT21) bioinformatics initiative, an extensive IT modernization program encompassing data management, data warehousing, IT infrastructure and IT security.

"This contract sets the stage for the FDA to have IT to acquire, analyze and act on data critical for import protection, food protection and medical product safety plans," said Dr. Andrew C. von Eschenbach, Commissioner of Food and Drugs. "We are creating a high-tech, efficient, data management system designed to meet the needs of those who must accomplish our mission -- protecting and promoting the health of the American public."

The contracts, with a minimum value of $25,000 in orders per contractor, were awarded to: Buccaneer, of Warrenton, Va.; Computer Sciences Corporation, Rockville, Md.; Dynanet, of Elkridge, Md.; Electronic Data Systems, Herndon, Va.; General Dynamics, Fairfax, Va.; Human Touch, McLean, Va.; IDL-Pragmatics, Vienna, Va.; Interactive Technology Solutions, Silver Spring, Md.; Telesis, Rockville, Md.; and Unisys, Reston, Va.

According to the announcement, the ten contractors will compete for data information technology task orders through this contract. The FDA has awarded three task orders under the ICT 21 contract for the design and migration of all systems applications to two new data centres, which will be the cornerstone of the FDA IT infrastructure and bioinformatics modernization for the next decade. The three task orders were awarded to:

IT Solutions (Task Order 1 - funded initially at $3,000,000) provides the design and implementation as well as migration of existing FDA applications to the newly configured White Oak Data Centre, which will support all FDA test and development applications.

Buccaneer (Task Order 2 - funded initially at $3,000,000) provides the operations and maintenance of the White Oak Data Centre.

EDS (Task Order 3 - funded initially at $12,000,000) provides the design, implementation, migration and operations and maintenance of existing FDA applications to a Contractor Owned Contractor Operated hosted data centre for FDA production operations.

All FDA software applications and hosting operations will transition to the new data centres over a two-year period. The resulting enhanced computing power and greater responsiveness will provide the FDA with the tools it needs to ensure that all products reaching the American public are safer and more effective.
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Sequence Your Genome for Only $5,000

Sequence Your Genome for Only $5,000

Mountain View, CA (OBBeC) - Complete Genomics, a third-generation human genome sequencing company, has announced its launch as the world's first provider of large-scale human genome sequencing services.

The company is building, what it claims to be, the world's largest commercial human genome sequencing centre.

Starting next spring the company will be offering a complete human genome sequencing services to pharmaceutical and biotechnology companies as well as other medical researchers that were previously priced out of the market. By offering a sequencing service instead of following the traditional instrument sales model, Complete Genomics is relieving its customers of operational, computational and capital purchase burdens, allowing them to focus their resources on scientific discovery.

"We will be the first company to sequence complete human genomes for less than $1,000 in material costs," said Dr. Clifford Reid, chairman, president and chief executive officer of Complete Genomics. "This breakthrough materials cost, combined with our low per-genome instrument, labour and overhead costs, will allow us to offer complete human genomes for just $5,000 in Q2 2009."

"This $5,000 price point, combined with the scale of our sequencing centre, will dramatically increase the availability and affordability of human genome sequencing. For the first time, our customers can conduct systematic studies of the genetic basis of disease and drug response. Our sequencing services will be one of the core enablers of the impending revolution in personalized medicine," Reid added.

"Many chronic and life-threatening human diseases have a genetic basis, and Complete Genomics' sequencing service will allow medical researchers to study disease pathways comprehensively and cost-effectively in a large number of individuals. The ability to compare a significant number of genomes of people with a disease against those without the disease is central to enabling drug discovery and the development of new diagnostics," added Dr. George M. Church, professor of genetics at Harvard Medical School, director of the Center for Computational Genetics and member of Complete Genomics' Scientific Advisory Board.

According to the announcement, after the company launches its third-generation human DNA sequencing service in Q2 2009, it plans to sequence 1,000 genomes in the same year. The company will then sequence 20,000 genomes in 2010.

The company also, in conjunction with partners, intends to open additional genome sequencing centres across the U.S. and abroad. Over the next five years, the company projects that 10 such centres will be able to sequence 1 million complete human genomes.

"One million genomes represent 1,000 people each in 1,000 disease studies," Reid said. "Our customers will conduct these studies to reveal the genetic basis of all major human diseases including cancer, psychiatric and neurological diseases, metabolic and cardiovascular diseases, autoimmune diseases, and many other poorly understood multifactorial diseases."

A key component of Complete Genomics' sequencing centre is its data centre, purpose-built to manage and analyze the staggering amount of genetic data that will be generated by sequencing thousands of human genomes. Because the data generated by a single human genome would fill 1,000 laptop computers, each with 100 GB of disk storage, data management for Complete Genomics' genome centre will be a massive undertaking. The company plans to have 10,000 processors with five petabytes (5 million gigabytes) of disk storage in 2009 and will further increase its capacity to 60,000 processors with 30 petabytes of disk storage in 2010. Complete Genomics expects to sequence 200 genomes per day by the end of 2010, making it the world's highest-throughput human genome sequencing centre. To put this in context, fewer than 20 complete human genomes have been sequenced in the world to date.
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Wall Street Journal Selects PhyloChip Array as a Top Technology Innovation

Wall Street Journal Selects PhyloChip Array as a Top Technology Innovation

Santa Clara, CA (OBBeC) - Affymetrix has announced today that the PhyloChip, a custom Affymetrix microarray developed by Lawrence Berkeley National Laboratory, has won the bronze prize in the 2008 Wall Street Journal Technology Innovation Awards. The PhyloChip helps researchers identify dangerous pathogens before they can affect humans.

The custom array PhyloChip was developed to simultaneously identify and quantify up to 8,900 distinctive environmental and pathogenic microbial species in a single experiment, in less than nine hours. The PhyloChip is unprecedented in its ability to accurately test any clinical or environmental sample without the need for culturing. The chip has been used by the Department of Homeland Security for bioterror detection, the Japanese Defence Force, the U.S. Department of Energy in bioremediation of contaminated soils to detoxify the earth and the State of California Water Quality Board for monitoring contaminated beaches.

"The speed with which we can now carry out our research far outpaces serial cloning. We offer the potential for numerous applications, including human health assessment, water quality and environmental cleanup, enabling complete evaluation of numerous samples on a daily basis," said Dr Gary Andersen, project leader at Berkeley Lab. "Affymetrix has allowed us to replace expensive and time-consuming cloning and sequencing with a method that will offer a competitive advantage to anyone wanting to detect bacteria in soil, air, water or clinical samples."

In July the PhyloChip won an R&D Magazine award for technology advancement. It was recognized for its ability to quickly, comprehensively and accurately identify species within microbial samples from any environmental source, without any culturing required. The PhyloChip is not yet commercially available. For more information please contact Dr. Andersen at the Lawrence Berkeley National Laboratory.
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MPI Signs Powered by Affymetrix Agreement

MPI Signs Powered by Affymetrix Agreement

Santa Clara, CA (OBBeC) - Affymetrix and Medical Prognosis Institute A/S (MPI), a cancer diagnostic development company based in Denmark, have announced that they have signed a Powered by Affymetrix (PbA) agreement. With this agreement, MPI gains non-exclusive access to Affymetrix microarray technology to develop and commercialize drug sensitivity prediction and prognostic products for patients with cancer.

Based on Affymetrix microarray technology, MPI aims to market its own proprietary products targeted at individual cancer prognosis and prediction of anti-cancer treatment response.

"Our partnership with Affymetrix enables us to translate our discoveries into robust tools with broad clinical utility to greatly improve the prognosis and treatment of millions of people living with cancer. It also boosts the probability of successful anti-cancer drug development in partnership with drug companies," said Jesper Drejet, president and CEO of Medical Prognosis Institute.

"MPI's cancer prognosis tools have the potential to customize treatment schemes, revolutionize the control of this disease and the chances of recovery," said Kevin King, president of Affymetrix. "Agreements such as this continue to validate the need for microarrays for complex signatures for reproducibility and accuracy. We are proud to help MPI advance its ambitions to improve drug therapy choices and provide hope for those struggling with this destructive disease."
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