Georgetown University, 10x Genomics, Jackson Laboratory, And More: News From March 2017

March 30, 2017 | News, products, and partnerships from around the bio-IT community including news from Georgetown University, 10x Genomics, Jackson Laboratory, and more. 

Researchers from Georgetown University used an Oxford Nanopore MK1B MinION device to sequence environmental DNA in Antarctica. They reported their findings in the April issue of The Journal of Biomolecular Techniques. (doi:10.7171/jbt.17-2801-009) The researchers measured performance characteristics of the MinION without internet or a laboratory facility, using only local battery power supplied by the laptop through a USB 3.0 cable connection, to determine the feasibility for in situ genomic sequencing in extreme environments. By adequately insulating the sequencer and laptop, it was possible to run the sequencing protocol for up to two and a half hours under arduous conditions. Researchers used an offline version of the MinKNOW software. In all sequencing runs, there were more fail reads than high-quality pass reads. However, the pass/fail ratio dramatically increased with increased ambient temperature. Researchers were unsure whether the decline was due to slowing in software or the sequencer. “Although the duration of our field-sequencing runs was shorter than typical for most laboratory runs, these proof-of-principle concept results demonstrate that preparing and sequencing DNA libraries are feasible on future sampling expeditions, particularly ones requiring prolonged stays in the field,” the authors wrote. “The preservation of battery power in the extreme cold remains a challenge, but longer sequencing runs can be enabled by switching among laptops with fully charged batteries and/or using an electrical generator.”

10x Genomics announced the commercial availability of the first high-throughput solution for profiling paired V(D)J transcripts from hundreds to millions of lymphocytes. The ability to more completely identify and characterize the body’s immune agents (T and B cells) at the single-cell level will impact our understanding and development of more effective and durable immunotherapies, including immuno-oncology (I/O) drugs for targeted cancer therapy. “The field of immuno-oncology has been hampered by insufficient resolution of complex molecular biological mechanisms at the cellular level. High-definition V(D)J sequencing has the potential to accelerate and improve the development of immuno-oncology therapies and bring about new powerful ways to track patient response,” said Serge Saxonov, CEO and co-founder of 10x Genomics, in a statement. “Our robust high-throughput paired gene solution for V(D)J sequencing is now available to the research community without restrictions. We see vast potential for enabling a wave of discovery in translational research and immunotherapy development. The commercial launch of this ground-breaking product is an exciting milestone for our single-cell portfolio and paves the way for additional applications that will be introduced later this year.” Press release

Jackson Laboratory (JAX) Professor Yijun Ruan has received a three-year grant totaling $1,050,000 from the international Human Frontier Science Program (HFSP) to explore the fundamental mechanics involved in memory and learning as well as epilepsy. This year, HFSP funded 21 proposals from a total of 858 applications. The Ruan team proposal was ranked sixth in the overall evaluation. The funding, Ruan said in a statement, “will help us to expand the concept and technologies we developed at JAX in 3D genome organization, or genome topology, into neural science, to uncover potential topological codes in memory and learning. It will also specifically support us to investigate the topological mechanisms in epilepsy, a devastating neurological disorder.” Ruan will be a keynote speaker at this year’s Bio-IT World Conference & Expo. Press release

GENALICE and Bio-Discovery have announced a co-marketing partnership to offer their products together as a turn-key end-to-end solution for the use of next-generation sequencing (NGS) data to interpret genomes. GENALICE provides an ultra-fast and highly accurate secondary analysis suite that seamlessly connects to BioDiscovery’s tertiary informatics and genomics interpretation system, N_xClinical. “The GENALICE and BioDiscovery co-marketing partnership is a response to the rapidly growing volumes and usage of NGS data, which highlights the urgent need for faster processing and interpretation technologies. Only few solutions are on the market that truly speed up read mapping, variant calling and interpretation. Our partnership offers a new reality in which large volumes can be analyzed close to real time, enabling truly important data interpretation and data mining of genomic variants of interest in a cost-effective manner. This game-changing solution in big data processing will have a significant positive impact in clinics towards the goal of achieving precision medicine in complex DNA disease areas, for instance in oncology” GENALICE’s Commercial Director Michelle Meijer said in a written statement. Press release

SCIEX announced the latest additions to its growing line of solutions for pharmaceutical drug discovery and development. The Routine Biotransform Solution and the Advanced Biotransform Solution are powered by SCIEX’s new MetabolitePilot Software 2.0. The new solutions will accelerate and automate small molecule metabolism and biologics catabolism studies. Both solutions provide intuitive metabolism data processing with automated structural interpretation, advanced processing options, and templates for analysis of antibody-drug conjugate (ADC) catabolism, improving efficiency and cost savings for both routine and comprehensive Metabolite ID studies. Press release

Linguamatics announced a partnership with premium news content provider Dow Jones. The agreement allows pharmaceutical companies to extract key insights from Dow Jones Factiva utilizing Linguamatics I2E text mining technology. The Linguamatics I2E platform is currently used by 18 of the top 20 global pharmaceutical companies. The Linguamatics-Dow Jones partnership helps users to derive key insights from Factiva content by leveraging advanced NLP to identify and extract critical concepts in a structured format for review and quick analysis. I2E eliminates the need for users to manually read through large quantities of documents to search for critical information. Instead, I2E rapidly connects relevant facts and relationships in a way that synthesizes knowledge and creates actionable insights. Press release

Genomenon announces the launch of Mastermind Panel Design Service, a novel approach to finding genes and variants associated with a particular disease in the medical literature. Genomenon uses its Mastermind literature-driven knowledge-base to deliver a candidate gene list for any disease supported by medical literature citations and customized around customers’ specific requirements. "Mastermind Panel Design was born from customer demand” wrote Mike Klein, CEO of Genomenon. “Labs were using Mastermind to find all the disease-associated genes and were looking to further accelerate their panel design process.  By mining the Mastermind database backend, we have been able to deliver a turnkey gene panel in just a matter of days."
Genomenon provides a more scientific, reproducible method to deliver the primary evidence required to build a gene panel to screen for a specific disease. Mastermind Panel Design not only drastically cuts the time it takes to create a new panel, it provides literature citations for each and every candidate variant, gene and exon selected to go on the panel.  Reference citations are important for clinical labs to provide a rationale for the diagnostic tests they are asking insurers to reimburse. Press release

Synthego, who recently announced a $41 million Series B financing, announced the availability of chemically modified synthetic guide RNA in the CRISPR evolution product family, including modified full length 100-mer synthetic single guide RNA (sgRNA). Critical for editing challenging cell types such as primary and stem cells, modified guide RNAs provide protection against intracellular immune responses present in primary cells, such as stem cells. Additionally, chemically modified RNA improves in vivo stability by protecting RNA molecules against exonuclease attack - allowing it to persist longer in certain cell types and regions of genomic DNA that can be challenging to edit using conventional guide RNAs. Synthego’s modified sgRNA are synthesized with 2’-O-methyl analogs and 3’ phosphorothioate internucleotide linkages in the first three nucleotides at both the 5’ and 3’ end of the RNA molecule. It’s currently impossible to make chemical modifications to plasmid or in vitro transcription (IVT) based guide RNAs. Press release

Eurofins Genomics announced the U.S. commercial launch of a unique DNA synthesis service based on the company's revolutionary next-generation synthesis platform. The service, which is designed to supply small quantities of high-quality oligos for use in molecular biology and synthetic biology, among other applications, allows users to receive high-fidelity, QC-verified oligos for low cost and with industry-leading turnaround. Standard approaches to synthesizing oligonucleotides—commonly used as primers for PCR, qPCR, and next-generation sequencing-based workflows—produce much more DNA than scientists need, forcing them to pay for excess material that will never be used. The new Eurofins Genomics synthesis platform was engineered for scalability, producing both small synthesis scale (down to 0.5 nanomoles) to very large orders of DNA. By allowing scientists to choose how much DNA to buy, this service will reduce costs and enable users to perform more experiments on the same budget. Press release

Developed for use in conjunction with the new Bluetooth-enabled Thermo Scientific E1-ClipTip electronic pipettes, My Pipette Creator is the first cloud-based application designed to enable efficient, centralized programming of connected pipettes, as well as secure storage and sharing of protocols between pipettes and colleagues within the lab. Offering a library of pre-programmed protocols for the E1-ClipTip pipettes and Thermo Fisher Scientific reagent kits, the My Pipette Creator application allows users to save time, enhance consistency and minimize programming errors to help achieve reproducible, reliable and traceable results. The new application has been ergonomically constructed to reduce the strain on the user’s eyes and hands commonly experienced with repeated operation of individual pipettes. In addition to Bluetooth, connectivity with the E1-ClipTip pipettes can also be achieved using a micro USB cable, depending on the user’s preference. Press release

Bionano Genomics announced results from a first-of-its-kind study demonstrating that next-generation mapping (NGM) accurately identified potentially clinically-relevant oncogenes and pathogenic driver mutations never before detected by next-generation sequencing (NGS). The study, “Next-generation mapping reveals novel large genomic rearrangements in prostate cancer,” was published in the March 1, 2017 online issue of the peer-reviewed journal Oncotarget (DOI: 10.18632/oncotarget.15802). The study was led by Vanessa Hayes, Lab Head of Human Comparative and Prostate Cancer Genomics at the Garvan Institute of Medical Research in Sydney, Australia. Hayes and her team demonstrate the significance of physical genome mapping as an essential tool to identify large structural variations (SVs) implicated in the progression of prostate cancer. The study found that NGM using Bionano’s Irys System at 35x genome coverage identified 10 times more SVs larger than 1,000 base pairs than the Illumina X10 platform at 60x genome coverage. Of those novel SV calls otherwise missed by NGS, 94% were validated using a combination of analysis tools. Importantly, of the large SVs detected on the Bionano system, half were in or near genes with oncogenic potential. Of the sequence variants detected with NGS, only 0.5 percent were in or near such genes. Press release

Thermo Fisher Scientific announced a line-up of new products at the 2017 Pittcon Conference and Exhibition that enable application-specific workflows for pharma/biopharma, materials science, and environmental and food safety markets. The announcement included introducing the new Thermo Scientific iCAP Triple-Quadrupole Inductively Coupled Plasma Mass Spectrometry (iCAP TQ ICP-MS) system, which features powerful identification capabilities designed for analytical accuracy in a range of applications, including clinical research and pharmaceutical QA/QC. An extension of the company’s highly successful iCAP line, the new-generation iCAP TQ ICP-MS system is expected to redefine triple quadrupole mass spectrometry by combining increased power with simplified operation. Pharmaceutical and biopharmaceutical laboratories performing qualitative and quantitative liquid chromatography (LC) or LC-MS analysis can now rely on a single-vendor solution for sample characterization. The Thermo Scientific Q Exactive Biopharma workflow consists of a specially designed selection of instruments, consumables, columns and software for rapid, high-quality analysis. Press release

Patheon announced that the company was selected as the winner of the “Supply Chain Resiliency Partner of the Year” award by the Global Supply Chain Resiliency Council. The awards program is designed to recognize organizations and individuals that serve as role models and leaders in driving supply chain resiliency strategy success within their company, supply chain network, and across industries. The awards committee considered nominations from across the industry, including its general membership of over 1,000 members worldwide comprised of OEMs/brand owners, suppliers, and experts from the Council’s technical advisor, Resilinc. Press release

WuXi NextCODE announced that the company's chief operating officer Hannes Smarason has been appointed as the company's chief executive officer, and WuXi AppTec senior vice presidents John Long and Alex Fowkes have been named chief financial officer and chief operating officer, respectively. "WuXi NextCODE is executing on its vision to enable anyone to use the genome to advance health and wellness worldwide," said Ge Li, founder and chairman of WuXi AppTec group and chairman of WuXi NextCODE, in a statement. "It is also positioning itself as the data management platform at the heart of the genomics revolution and what may become the world's largest data ecosystem. Hannes, John and Alex have the breadth of vision and proven executive capabilities to carry out this strategy and advance the company to the next level." Press release