PetaGene, AstraZeneca, QIAGEN, and More: News From October 2019

October 31, 2019

October 31, 2019 | October featured exciting new, products, and partnerships from around the bio-IT community from innovating companies, organizations, and universities, including PetaGene, AstraZeneca, QIAGEN, and more.

PetaGene announced that their PetaSuite software has been selected to compress the genomics data sets for AstraZeneca’s Centre for Genomics Research (CGR). Using genomics data and state-of-the-art methods for genomic analysis, the CGR investigates underlying genetic causes of disease and aims to integrate genomics across the company’s drug discovery platform. PetaSuite accelerates data transfers for cloud computing and reduces storage costs for any research project involving genomics data. “Using genomic data for biopharmaceutical targets discovery requires large cohorts with massive multi-petabyte data sets. The time required to transfer these data from sequencers to compute clusters as well as the cost of storage can cripple these large initiatives,” said Vaughan Wittorff, Co-founder and Chief Commercial Officer of PetaGene, in a press release. “PetaSuite addresses the challenges caused by growing volumes of genomics data and achieves up to 10x reductions in storage costs and transfer times, while adhering to the industry-standard BAM and FASTQ genomics file formats.” To date, AstraZeneca’s CGR has processed more than 200,000 genomics datasets, generating over a petabyte of data. One petabyte of data is equivalent to streaming HD movies for 40 years without a break. At this volume of data, problems in processing time, data transfers and storage size can impact the ability to deliver at scale. PetaGene’s compression software will enable the CGR to compress over 200,000 BAM files in a 24-hour period and will add the compressed data to tiered cloud storage. “AstraZeneca’s Centre for Genomics Research has the bold ambition to analyze up to two million genomes by 2026. Minimizing the storage footprint and transfer time of genome data while maximizing data access and compute processing is a necessity to enable us to achieve our ambition,” said Slavé Petrovski, Vice President and Head of Genome Analytics and Bioinformatics, Discovery Sciences, R&D, AstraZeneca, in an official statement. PetaSuite will enable the CGR to achieve an average data reduction of 76% or a 4x expansion of storage capacity. PetaGene’s transparent, lossless compression of files reduces transfer times to less than a quarter, and PetaGene’s software allows unmodified analysis tools to run more quickly. Press release

Genomenon announced at the American Society of Human Genetics Annual Meeting (ASHG) a partnership with SOPHiA GENETICS that includes incorporating the Mastermind Genomic Search Engine into the SOPHiA Platform and the Alamut Suite. The partnership puts the most up-to-date genomic research at the fingertips of clinical researchers performing genomic analysis worldwide. The SOPHiA Platform is the technology of choice for streamlined Data-Driven Medicine, including clinical-grade genomic analysis, interpretation, and reporting. SOPHiA has been adopted by 1,000 healthcare institutions to date, and analyzed more than 420,000 genomic profiles – 16,000 new profiles processed each month. The Alamut Suite powered by SOPHiA is a decision-support software designed to explore and investigate variations of the human genome. Alamut helps clinical researchers in the complex tasks of genomic variants annotations, filtration and exploration. With the addition of Mastermind, users of both technologies will be able to quickly access the genomic evidence associated with human variants, shortening the search time required to interpret a variant and assess its pathogenicity. This partnership will allow SOPHiA’s users to see a wider picture of the detected variants. A key driver in the decision is the breadth and depth of Mastermind’s coverage of genomic variants and published literature. Mastermind has indexed over 7 million full text articles and 600,000 supplemental data sets and covers over 5.7 million variants found in the medical literature. Press release

QIAGEN announced the launch of innovative new technologies for faster, simpler library preparation for next-generation sequencing (NGS) in the growing field of RNA research. “These new QIAseq FastSelect solutions add to our innovative portfolio addressing critical bottlenecks in next-generation sequencing, allowing scientists to quickly remove unwanted RNA types from samples, gaining time and cost savings and maximizing their research insights,” said Dr. Thomas Schweins, Senior Vice President of QIAGEN’s Life Sciences Business Area, in a press release. “Our novel QIAseq FastSelect technologies remove unwanted RNA with a single 10-second pipetting step and 14 minutes of incubation. We are pleased to offer these valuable additions to our universal NGS portfolio to meet the growing need for reliable, efficient preparation of RNA libraries in search of deeper insights for the life sciences.” Press release

iSpecimen today announced it has partnered with new providers of diseased and healthy hematologic tissue to offer one of the industry’s largest, most integrated networks of donors and collection sites available while addressing proliferating demand for hematopoietic stem and immune cell products. Now, researchers can readily access cells with highly specific characteristics through the iSpecimen Marketplace, an online platform that increases access to human biospecimens from specific patients and healthy donors that can provide them. Using the iSpecimen Marketplace, researchers gain centralized, single-source access to a vast and growing population of healthy donors and patients (e.g., solid and liquid tumors, autoimmune, and numerous other diseases) with hematopoietic and immune cell phenotypes that match their particular research study criteria. Moreover, the Specimen Marketplace enables researchers to conveniently select from a comprehensive list of donor attributes, specify exclusion criteria, request a quote, and order banked or prospectively collected specimens online. By centralizing specimen procurement through the Marketplace, researchers can save precious time and human resources via a single source of procurement, order management, contracting, compliance and data access. iSpecimen also announced it has upgraded the iSpecimen Marketplace experience for hematopoietic and immune cell customers, enabling a uniquely convenient and customizable online product selection experience. Now, researchers can easily refine their specimen selections involving numerous parameters such as HLA type (low and high resolution), blood type, body mass index, ethnicity, race, age, and gender. The iSpecimen Marketplace also offers the industry’s most comprehensive donor screening capability, permitting researchers to select the required scope of infectious disease testing such as CMV, hepatitis (B&C), HIV, West Nile Virus, syphilis, Chagas, and more. Press release

AODocs released AODocs for Life Sciences, a modern, intelligent Quality Management System (QMS) to address FDA and GxP compliance in Life Sciences organizations. “We have designed and built our content services platform to be applicable to numerous use cases in a wide range of vertical industries,” Stéphane Donzé, CEO of AODocs, said in a press release. “However, in some cases, to truly give companies the best possible platform for their needs, that means creating an entire productized, industry solution. Companies in the life sciences space have long been seeking a more effective way to use technology to manage and validate their quality control systems and we believe that AODocs for Life Sciences addresses that need.” With AODocs for Life Sciences, organizations can easily manage all aspects of quality operations, including document control, change management and user training, with automated and continuous validation. “Compliance and efficiency are two things that regulated industries, such as life sciences, place great emphasis on as the success of their business is directly tied to them,” said Mike Hansen, Product Solutions Manager at AODocs, in an official statement. “Enabling companies to automatically show compliance with regulations such as FDA CFR21 part 11 is one thing, but combining that with a 10 to 20-day implementation process, versus the many months it typically takes to do this, is a game-changer.” AODocs partnered with xLM to bring continuous validation to the AODocs for Life Sciences platform. xLM offers agile and continuous validation life cycle management rigorous enough to meet FDA regulations while remaining cost-effective. This partnership allows AODocs for Life Sciences to execute compliance tests in a fraction of the time it would take to conduct manually or through other vendors. Press release

The European Investment Bank (EIB) and Univercells have signed a EUR 20 million loan agreement to support the development of a portfolio of four essential and undersupplied vaccines to be delivered at an affordable price. The portfolio – including polio, measles and rubella, and rabies vaccines – requires significant investment in process development through to clinical and regulatory validation. In funding Univercells, the EIB is aiming to promote the delivery of such vaccines, increasing their availability for diseases with high unmet medical needs. The fight against infectious diseases is of high policy relevance for the European Union and for the EIB, its financing arm. While infectious diseases are already amongst the leading causes of death worldwide, the emergence of resistant pathogens is on the rise and anti-microbial resistance is therefore expected to become the leading cause of death by the middle of this century. At the same time there is little investment in drugs and vaccines to fight infectious diseases and a limited number of players in the field. Univercells, a Belgian biotech company founded in 2013, is committed to acting on technology to deliver essential biologics at low costs, thereby promoting their dissemination in currently undersupplied regions. Univercells recently introduced its NevoLine biomanufacturing platform capable of delivering large quantities of vaccines at a fraction of the traditional cost. With the support of the EIB, the company will leverage the technology to pursue its mission and make four global health vaccines more available and affordable to all. “Supporting innovation is a key priority for the European Union’s bank, and helping innovative European SMEs and mid-cap companies fill the funding gap for their R&D is of the utmost importance,” EIB Director General Jean-Christophe Laloux said. “This financing, with its specific terms adapted to the company’s needs, shows our commitment to creating optimal conditions for R&D including in the field of pharmaceutical research. The fight against infectious diseases ranks high on our policy agenda. These diseases pose an increasing threat to humanity, yet the field remains under-invested. It will be a major war and the battle has just begun. We are proud to join Univercells and be able to support its pioneering research into such essential vaccines and its efforts to make them available to those countries with high needs.” Press release

Bright Computing announced that the University of North Dakota (UND) has chosen Bright Cluster Manager for HPC, Bright Cluster Manager for Data Science, and Bright OpenStack to unify its newly designed clustered infrastructure giving them more versatility, access to the cloud and to deep learning resources. The supercomputer at UND runs on the HPE Apollo 6500 Gen10 system, purpose-built for HPC and a leading platform for deep learning. The project was overseen by Core Technology Services (CTS) of the North Dakota University System, with input from Bright partner, Data in Science. UND is a public research university in Grand Forks, North Dakota. The Computational Research Center (CRC) provides project support as well as user training, education, and onboarding services for Talon, the University’s Bright-based private research computing cloud. Systems administration, network services, and storage support are contracted out to the North Dakota University System Core Technology Services (NDUS CTS) team. Press release

Ginkgo Bioworks and Berkeley Lights announced a $150MM collaboration. Through a multi-year, non-exclusive agreement, Ginkgo will incorporate Berkeley Lights' optofluidic platform into its automated genetic engineering foundries. Leveraging the intersection of microfluidic, optical, and semiconductor technology, Berkeley Lights' platform captures, manipulates, and characterizes individual cells on a massively parallel basis, dramatically increasing the potential throughput and speed of life science R&D and cutting down the time it takes to complete biological experiments from weeks or months to days. Incorporating the Berkeley Lights platform into core workflows of Ginkgo's automated foundries will enable scientists to observe and manipulate thousands of individual cells, providing unprecedented control over cells that are too small to see by eye. The collaboration will drive continued growth in output and efficiency of Ginkgo's foundries and enable new innovation in synthetic biology and its application across numerous industries from food to fragrances. The infusion of new technology from Berkeley Lights is expected to more than triple Ginkgo's capacity to measure the performance of cells, increasing the overall speed and efficiency of product delivery to its customers. The ability to measure and visually observe the performance of individual cells at a microscopic scale on the Berkeley Lights platform will significantly reduce the time needed for data collection. Further, the Berkeley Lights platform will provide the data richness from single cell analysis that is currently unavailable in data from conventional bulk measurements. Together, the two companies will also expand the application of Berkeley Lights' optofluidic platforms through the expansion of workflows available beyond those already released for the biopharmaceutical market. Existing workflows on the Berkeley Lights platform are primarily focused on mammalian cells for drug discovery and development. The Ginkgo/Berkeley Lights collaboration will generate a number of new workflows, leveraging the Berkeley platform, for several organisms including yeast, bacterial and fungal cells that will enable the development of a broad range of synthetic biology products. Press release

Pharmaceutical and biopharmaceutical manufacturers can now verify the identity of ionic salts in the warehouse in a matter of seconds with a new portable X-ray fluorescence (XRF) analyzer. The technology helps save time and money spent on conventional analysis techniques by putting laboratory-grade capabilities directly into the hands of raw material and quality control managers anywhere in the manufacturing plant. The Thermo Scientific IonicX portable XRF analyzer is designed to identify and authenticate the top five salts used in biopharmaceutical and pharmaceutical manufacturing – sodium chloride (NaCl), potassium chloride (KCl), magnesium chloride (MgCl2), calcium chloride (CaCl2) and sodium hydroxide (NaOH). This capability can reduce the time and cost of pharmaceutical materials testing while helping to maintain regulatory compliance and rigorous quality standards. The IonicX meets good manufacturing practices (GMP) and the 21 CFR Part 11 requirements. Designed specifically for the pharmaceutical industry, the IonicX XRF analyzer is easy-to-use, portable, fast, and requires minimal sample prep. "Compliance and efficiency are top concerns for raw materials managers, but thoroughly analyzing all incoming materials takes time and resources," said Kyle Dumke, product manager, Thermo Fisher Scientific, in a press release. "Pharmaceutical companies purchase these salts in large amounts and are required to test each container to meet strict regulatory requirements. That's a tedious and costly process when using standard wet chemistry lab or near-infrared (NIR) benchtop testing. With a portable XRF analyzer, testing can be done right on the warehouse floor in seconds." Press release

Thermo Fisher Scientific also announced it has entered into a co-marketing agreement with Genialis, a data science company leading the industry in RNA-based discovery. The agreement will create an analysis workflow integrating the Invitrogen Collibri Stranded RNA Library Prep Kit for Illumina Systems with Genialis Expressions analysis software to support the data analysis needs of Thermo Fisher Collibri customers. When researchers initiate their NGS research, the library preparation kit provides a short, automation-friendly workflow, converting mRNA to sequencing-ready library in as little as four and a half hours. Once sequencing is completed, the software eases analysis bottlenecks associated with scalable computation, pipeline optimization and downstream data interpretation. “With our RNA library prep kits, we strive to make library preparation for high-throughput genome sequencing as efficient as possible. Genialis is a leader in providing industrial-strength analytics to pharma, biopharma and large sequencing centers. Through our collaboration, data analysis will now be as rapid as the library preparation, easing the barriers to high-throughput sequencing to advance science for all,” said Raymond Mercier, vice president and general manager of molecular biology for Thermo Fisher Scientific, in a press release. “With an accelerated analysis process, our customers can dedicate more time to deriving meaningful results from the data. This collaboration, leveraging Thermo Fisher’s innovative library prep kits, is yet another example of how we are developing solutions that enable our customers to make the world healthier.” The Collibri Stranded RNA Library Prep Kits for Illumina Systems enable clean gene expression analysis, with successful projects involving both human and plant samples. The Genialis software will allow for more streamlined processing of Collibri RNA-Seq data sets for applications such as biomarker discovery. Press release

Discovery Life Sciences announced its substantial investment in long-read genomic sequencing technology from Pacific Biosciences (PacBio). The instrumentation will complement the existing infrastructure of HudsonAlpha Discovery, Discovery's genomic sequencing and bioinformatics division. HudsonAlpha Discovery will continue to scale sequencing over a range of technologies, creating the most comprehensive infrastructure to support the most accurate and complete analysis of complex genomic and transcriptomic projects possible. This investment creates a PacBio Center of Excellence for long-read sequencing. Existing short-read sequencing is like a complex jigsaw puzzle. Researchers align and merge many short DNA sequences to reconstruct a representation of the reference genome, but the alignment and assembly from short reads has limitations. Long-read sequencing provides additional power and context; recent studies show that it detects structural variants in disease genes that are missed by previous methods. Combining short- and long-read sequencing creates a depth and breadth to comprehensively understand the complex genomics driving cancer and other diseases. The multiple PacBio Sequel II Systems that Discovery is acquiring provide highly accurate long reads and supplement HudsonAlpha Discovery's existing short-read platforms to add resolution across both DNA and RNA applications. In addition to whole genome sequencing for variant detection, the Sequel II Systems will provide high-volume capacity for long-read RNA sequencing of gene isoforms. These sequencing services, combined with the HudsonAlpha Discovery proprietary methods for long-fragment RNA isolation from FFPE and access to millions of FFPE biospecimens, deliver a novel set of applications to the entire genomics community. Press release

BioIVT announced that it has acquired PPA Research Group, a human hematologic product provider, based in Gray, TN. This acquisition will significantly expand BioIVT's immunology and disease-state product portfolios, enhancing its ability to support immuno-oncology and cell therapy researchers. PPA Research Group operates full-service donor centers in Johnson City, TN and Berkeley, CA focused primarily on producing leukopaks. Leukopaks contain concentrated leukocytes together with high levels of peripheral blood mononuclear cells. Leukopaks are used during drug development for target discovery, validation, lead optimization, and toxicity assays as well as for stem cell and gene therapy research. In addition to having its own healthy donor collection sites, PPA Research Group has the largest nationwide diseased hematologic tissue collection network with the largest repository of donor profiles in the nation. "With the addition of PPA Research Group, BioIVT gains greater access to disease-state and control leukopaks, plasma and sera, and extra immune cell processing capabilities, which will allow us to meet growing client demand, particularly in the areas of immuno-oncology and cell therapy," BioIVT Chief Executive Officer Jeffrey Gatz said in a press release. "This acquisition, which is BioIVT's eighth since 2017, furthers our mission of becoming the partner of choice for biopharmaceutical clients and industry experts in specialty application areas." Press release

Synthego announced the launch of genome engineering for induced pluripotent stem (iPS) cells. The new offering expands Synthego’s automated cell editing to achieve unprecedented editing efficiency of iPS cells at an industrial scale. The company simultaneously announced the National Institute on Aging (NIA) at the National Institutes of Health (NIH) has awarded Synthego a contract to create panels of mutations in a variety of genetic backgrounds to study Alzheimer's disease and related dementias (ADRD). Synthego also announced the addition of Dr. Bill Skarnes, a pioneer in stem cell research, to the company’s advisory board. A fundamental challenge in research and therapeutic development is the lack of high quality, physiologically relevant biological models for translational medicine. iPS cells are reprogrammed human adult cells reverted to a stem cell state, and can provide one of the most reliable and accurate models for disease due to the ability to create patient-specific variations, but have traditionally been difficult to handle and modify genetically. By overcoming these challenges, scientists gain access to creating models for thousands of disorders ranging from inherited conditions such as Cystic Fibrosis to neurodegenerative diseases such as Alzheimer’s, and even organ-specific ocular diseases. Synthego’s proprietary cell editing platform removes the difficulty of editing, cloning, and maintaining high pluripotency in clinically-relevant iPS cells, with editing rates as high as 90% prior to cloning and 100% in clones. The new offering of iPS cells includes modification by removal of gene function (knockout), single nucleotide variation, protein tagging, and other knock-ins, enabling scientists to generate edits at a massive scale to accelerate research and disease modeling. Synthego also announced it has been selected as one of NIH’s partners for a multi-million dollar effort to better understand neurodegenerative diseases. Synthego’s genome-edited iPS cells will introduce mutations relating to ADRD. These edited cells will then be characterized functionally by NIA researchers to better understand these insidious diseases and identify new ways to treat them. Press release

TYAN announced support for the NVIDIA EGX platform on TYAN’s NGC-Ready Thunder SX TN76-B7102 server, providing AI computing for the edge networks. “AI has transformed every industry by enabling more accurate decisions to be made based on the massive amounts of streaming data being processed. Now we see the next opportunity for AI is erupting at the edge,” said Danny Hsu, Vice President of MiTAC Computing Technology Corporation’s TYAN Business Unit, in a press release. “TYAN’s NVIDIA GPU server platforms are now NGC-Ready for Edge validated and with NVIDIA’s EGX stack and hybrid cloud partners, enables enterprises to securely and rapidly deploy and manage AI workloads from the edge to the cloud.” TYAN’s TN76-B7102 server is optimized to offer scalable and accelerated features that can help customers best move, store and process data at the edge, driving decisions locally in real time. The server platform is NVIDIA NGC-Ready for Edge validated and capable of running today’s most demanding AI workloads across a wide range of industries, including retail stores, manufacturing, healthcare, and smart cities. The TN76-B7102 is a 2U dual-socket 2nd gen Intel Xeon Scalable processor-based server platform. With support for up to 4 NVIDIA T4 GPUs, 24 DDR4 DIMM slots and an OCP mezzanine slot for dual-port 25GbE LAN card deployment, the TN76-B7102 is an EGX platform with optimal performance and scale-out support. Press release