The new coronavirus, SARS-CoV-2, causing a disease that has been called COVID-19, was first identified in Wuhan, China in December 2019, and has been transmitted widely across the globe. This article gives a general overview of what is currently known in a fast developing situation.
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Researchers at Rady Children’s Institute for Genomic Medicine (RCIGM) have utilized automated machine-learning and clinical natural language processing (CNLP) to diagnose rare genetic diseases in record time. This new method is speeding answers to physicians caring for infants in intensive care and opening the door to increased use of genome sequencing as a first-line diagnostic test for babies with cryptic conditions.
“Some people call this artificial intelligence, we call it augmented intelligence,” said Stephen Kingsmore, MD, DSc, President and CEO of RCIGM. “Patient care will always begin and end with the doctor. By harnessing the power of technology, we can quickly and accurately determine the root cause of genetic diseases. We rapidly provide this critical information to intensive care physicians so they can focus on personalizing care for babies who are struggling to survive.”
The workflow and research were led by the RCIGM team in collaboration with leading technology and data-science developers —Alexion, Clinithink, Diploid, Fabric Genomics and Illumina.
Dr. Kingsmore’s team has pioneered a rapid Whole Genome Sequencing process to deliver genetic test results to neonatal and paediatric intensive care (NICU/PICU) physicians to guide medical intervention. RCIGM is the research arm of Rady Children’s Hospital-San Diego.
By reducing the need for labour-intensive manual analysis of genomic data, the supervised automated pipeline provided significant time-savings. In February 2018, the same team achieved the Guinness World Record for fastest diagnosis through whole genome sequencing. Of the automated runs, the fastest times – averaging 19 hours – were achieved using augmented intelligence.
“This is truly pioneering work by the RCIGM team—saving the lives of very sick newborn babies by using AI to rapidly and accurately analyse their whole genome sequence “ says Eric Topol, MD, Professor of Molecular Medicine at Scripps Research and author of the new book Deep Medicine.
RCIGM has optimized and integrated several time-saving technologies into a rapid Whole Genome Sequencing (rWGS) process to screen a child’s entire genetic makeup for thousands of genetic anomalies from a blood sample.
Key components in the rWGS pipeline come from Illumina, the global leader in DNA sequencing, including Nextera DNA Flex library preparation, whole genome sequencing via the NovaSeq 6000 and the S1 flow cell format. Speed and accuracy are enhanced by Illumina’s DRAGEN (Dynamic Read Analysis for GENomics) Bio-IT Platform.
Other pipeline elements include Clinithink’s clinical natural language processing platform CliX ENRICH that quickly combs through a patient’s electronic medical record to automatically extract comprehensive patient phenotype information.
Another core element of the machine learning system is MOON by Diploid. The platform automates genome interpretation using AI to automatically filter and rank likely pathogenic variants. Deep phenotype integration, based on natural language processing of the medical literature, is one of the key features driving this automated interpretation. MOON takes five minutes to suggest the causal mutation out of the 4.5 million variants in a whole genome.
In addition, Alexion’s rare disease and data science expertise enabled the translation of clinical information into a computable format for guided variant interpretation.
As part of this study, the genetic sequencing data was fed into automated computational platforms under the supervision of researchers. For comparison and verification, clinical medical geneticists on the team used Fabric Genomics’ AI-based clinical decision support software, OPAL (now called Fabric Enterprise)—to confirm the output of the automated pipeline. Fabric software is part of RCIGM’s standard analysis and interpretation workflow.
The study titled “Diagnosis of genetic diseases in seriously ill children by rapid whole-genome sequencing and automated phenotyping and interpretation,” found that automated, retrospective diagnoses concurred with expert manual interpretation (97 percent recall, 99 percent precision in 95 children with 97 genetic diseases).
Researchers concluded that genome sequen-cing with automated phenotyping and interpretation—in a median 20:10 hours—may spur use in intensive care units, thereby enabling timely and precise medical care. “Using machine-learning platforms doesn’t replace human experts. Instead it augments their capabilities,” said Michelle Clark, PhD, statistical scientist at RCIGM and the first author of the study. “By informing timely targeted treatments, rapid genome sequencing can improve the outcomes of seriously ill children with genetic diseases.”
Rady Children’s Institutewww.radygenomics.org/category/news/pr/
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BIOHIT Healthcare is distributing test kits for the diagnosis of both current and past COVID-19 infections to help in the fight against coronavirus in the UK. The new product line includes the MutaPLEX® Coronavirus kit from Immundiagnostik AG (IDK) – a real-time RT-PCR assay to screen for infected individuals – and Epitope Diagnostics Inc’s (EDI’s) immunodiagnostic tests for IgM and IgG COVID-19 antibodies, to detect past infections.
The IDK MutaPLEX coronavirus screening assay allows the detection of SARS-CoV-2 viral RNA in a variety of biological specimens, especially nasal/throat swabs. This real time RT-PCR kit contains all the reagents, primers and dual-labelled probes required for the amplification and simultaneous differentiation of RNA from SARS-CoV-2 and other betacoronaviruses, as well as house-keeping genes designed to prevent false negative results due to insufficient sample collection or transport problems.
EDI’s Novel Coronavirus COVID-19 ELISA kits provide qualitative detection of antibodies in patient serum, indicating a past COVID-19 infection. The IgM assay provides the earliest immunodiagnostic indication of an infection, while the IgG test can be used to aid detection and provide an indication of long-term immunological response, making it particularly useful in cases where clustering is suspected or differential diagnosis is required.
These tests extend and complement BIOHIT’s repertoire of diagnostic kits for gastroenterology, aiding the evaluation of patients with both GI and upper respiratory complaints, as COVID-19 may include stomach and bowel symptoms in some cases. Inflammatory bowel disease patients being treated with immunosuppressive agents should also be considered at high risk for COVID-19, making differential diagnosis essential.
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BioCity, a life science incubator and business collective has released its biennial publication, the UK Life Science Start-Up Report, an in-depth analysis of emerging businesses within the life sciences across the UK.
The report looks at the prevalence of life science start-ups in the UK over the past five years and the broader landscape in which they operate to also asses the quality of UK life science start-ups.
The report documents an unprecedented period of growth for the life sciences, thanks in part to a change in the funding landscape, expressed in a four-fold increase to £2.8 billion of investment in early-stage ventures, compared to the previous five-year period.
Multiple factors are highlighted as driving this expansion, but of greatest impact was Industry news January 2020 11 | the emergence of a number of significant venture funds able and willing to make very large investments in early stage businesses. Also identified as a contributing factor is the increasing use of smaller companies and academia as sources of innovation by large pharma companies aiming to counteract falling R&D productivity. Simultaneously, many universities such as Bristol, Newcastle and Aberdeen introduced a gear change in spin-out formation.
Author of the report, Dr Glenn Crocker said: “Both the number of companies starting up and the amount invested in them has taken off. We have seen a 50% increase in the number of companies and a four-fold increase in investment going into them; this will likely result in a substantial increase in the demand for space. We estimate that this cohort of businesses alone could require 1.4 million sq ft of specialist facilities over the next five years. One consequence of this demand growth is that real estate investors are being increasingly attracted to the sector.”
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Olympus’ Image of the Year Award recognizes the best in life science imaging worldwide. Participants can win a CX43 microscope with a DP27 digital camera, X Line objectives, or an OM-D E-M5 Mark II camera. Those interested in participating can enter until 31 January 2020 by uploading images at www.olympus-lifescience.com/ioty. Winners will be selected by a jury panel and announced in March 2020. The jury consists of global representatives from both science and the arts, including photo- grapher Ron Caplain; Geoff Williams, a bioimaging facility manager at Brown University; Urs Ziegler, the head of a microscopy imaging facility at the University of Zurich; Stefan Terjung, the operational manager of an advanced light microscopy facility at EMBL Heidelberg; Hiroaki Misono, a graduate school professor of brain science at Doshisha University; Zhu Xueliang, a professor at the Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; Yalin Wang, Director of Biomedical Research Core Facilities at Westlake University, Hangzhou, China; and Wendy Salmon, a light microscopy specialist of a bioimaging facility at MIT. All entries will be evaluated based on artistic and visual aspects, scientific impact, and microscope proficiency. Regional prizes in Asia, Europe, and the Americas will be awarded in addition to the global prize. The Image of the Year European Life Science Light Microscopy Award began in 2017 to celebrate both the artistic and scientific value of microscopy images. Now on a global scale, the competition aims to encourage people to look at scientific images in a new way, appreciate their beauty, and share images with others. Participants may upload up to three microscopy images when submitting the online form. Images, accompanied by a brief explanation that notes the equipment used, can be uploaded until 31 January 2020. The jury will select and notify the winners in March 2020.
www.olympus-lifescience.com/ioty
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The ReactoMate DATUM from Asynt is a high quality, dual-rod stainless steel and aluminium support system built to ensure the stability and safety of your lab reactor. Sturdy, yet compact, the ReactoMate DATUM support system can accommodate a wide range of reaction vessels from 100 mL up to 5000 mL.
Designed with user-friendliness in mind, the ReactoMate DATUM support system incorporates a suite of innovative features.
Changing a vessel supported by the ReactoMate DATUM is as simple as “Clip & Click”. The novel neck clamp allows fast changeover between reactor vessel sizes thereby enabling simple reaction scale-up, whilst the ingenious mounting mechanism ensures excellent stability and alignment every time.
The Reactomate DATUM support system is fully compatible with all leading brands of overhead stirrers and circulator heating/cooling systems. Designed by chemists for chemists, low-friction polymer bearings line both the overhead stirrer alignment chuck and the neck support to ensure smooth and easy operation.
Ideally suited for use within a benchtop fume hood, adjustable feet allow you to level the ReactoMate DATUM support system ensuring stability and security while you work. Each DATUM system is also supplied with a moulded drip tray that fits perfectly within the base of the support, for safely catching any drips and spills from the reaction vessel during draining.
With a wide range of accessories and upgrades available, including drain manifolds and automation packages, the ReactoMate DATUM support system is the perfect all-rounder for laboratory scale reactions.
For more information, visit: www.asynt.com/product/reactomate-datum
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As the COVID-19 pandemic progresses in countries around the globe, there is an urgent need for rapid and reliable point-of-need detection testing. Dolomite Microfluidics and Mologic are working together to accelerate the development and launch of these tests.
UK-based Mologic is a leading developer of rapid response diagnostic tests for diseases such as malaria and Ebola virus disease. Clients include the Bill & Melinda Gates Foundation, where Mologic is leveraging its core technology through its Centre for Advanced Rapid Diagnostics (CARD) to develop the next generation of ultra-sensitive point-of-care diagnostics which are easy to use andinexpensive to manufacture – critical to the success of many global health programmes. Most recently, Mologic has received UK Government funding to develop and manufacture a high sensitivity test for COVID-19 that generates results within minutes – rather than hours or days – without the need for a laboratory or specialist equipment.
The technology behind these tests involves the use of precisely manufactured nanoparticles. Dolomite specialises in equipment that allows the development and scale-up of precision nanoparticles. This is achieved by using microfluidic technology to retain advanced control of production conditions. Dolomite is working with Mologic to combine ground-breaking diagnostic technology with continuous flow microfluidic manufacturing processes to accelerate the validation and release of Mologic’s COVID-19 diagnostic test.
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GAMBICA is the Trade Association for Instrumentation, Control, Automation and Laboratory Technology in the UK. Our insight and influence help our members to be more competitive by increasing their knowledge and impact. Together we remove barriers and maximise the market potential in our industry. GAMBICA members are active in the following sectors: • Industrial automation products and systems • Process instrumentation and control • Laboratory technology • Test and measurement equipment for electrical and electronics industries
www.gambica.org.uk
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A City of Hope scientist and his colleagues have developed a user-friendly approach to creating “theranostics” – therapy combined with diagnostics – that target specific tumours and diseases.
Key to the process are molecules called metallocorroles, which serve as versatile platforms for the development of drugs and imaging agents. City of Hope’s John Termini, Ph.D., and his colleagues at the California Institute of Technology and the Israel Institute of Technology developed a novel method to prepare cell-penetrating nanoparticles called “metallocorrole/protein nanoparticles.” The theranostics could both survive longer in the body and better snipe disease targets.
The study details a unique way the researchers prepared the theranostics that may be generalizable to many similar molecules.
“Through collaborative brainpower, we were able to create something that has huge chemotherapeutic potential,” Termini said. “Down the road, theranostics such as this could shorten treatment duration and diminish the dreaded side effects so many cancer patients fear.”
City of Hope
https://tinyurl.com/y67c26em
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by Dr Tolga Durak Around the world, organizations are building next-generation research facilities intended to encourage communication, collaboration and creativity. However, these new spaces must overcome a wide range of complex challenges to meet the needs of researchers today and in the future. This article explores five important questions that should be considered in order to build an innovation space that is safe, successful and productive.
Fundamental questions for good design
Research facility design and construction is evolving rapidly, as organizations around the world strive to create work environments that meet the needs of today’s scientists. Whether these new spaces are relatively small-scale makerspaces, large pharmaceutical manufacturing plants, or tightly regulated high-containment laboratories, they are being built to foster communication, collaboration, and innovation, often in ways that depart significantly from the traditional R&D rubric. As a result, every stage of the process – from initial site assessment, architectural design, and construction and continuing all the way through to ongoing maintenance and operation – must be approached with fresh eyes. To get started, design and construction teams must consider the following five fundamental questions. 1. Who is going to work in the facility and what will they need to be successful? Most research projects now span multiple disciplines, and laboratory spaces often need to accommodate the varied needs of biologists, chemists, engineers, physicists and/or others – all working together but with different methods. Research facility design must accommodate each specialty’s unique requirements across a wide spectrum that includes equipment, infrastructure (electrical, ventilation, etc), information technology (IT), workflow and compliance. In addition, designers must factor in flexibility, so workspaces can adapt as the research advances and needs change. 2. What is required for compliance? Navigating regulatory boards and obtaining approvals can be a complex, time-consuming, and expensive process, especially for clinical research facilities. Typically, these structures must be constructed in compliance with Good Laboratory Practice (GLP) regulations, Good Manufacturing Practice (GMP) regulations, and other guidelines and mandates from local, state and federal jurisdictions. In addition, laboratories that research or use infectious agents or other biological hazards must comply with regulations based on the degree of the health-related risk associated with the work being conducted. The four biosafety levels (BSLs) of containment – BSL-1, BSL-2, BSL-3, and BSL-4 – aim to safeguard against the accidental release of pathogenic organisms and other biohazards and may involve airflow systems, containment rooms, sealed container storage, waste management, decontamination procedures, and security capabilities. Clearly, the challenges of compliance need to be tackled early in the design process because meeting all of the requirements can take years, which increases the risk that research priorities change and/or that key staff moves on to other projects. 3. How sustainably can we build it? When people think about sustainable research facility design, they usually focus on power and water consumption. Granted, researchers typically use lots of heat-generating equipment (which then require complementary cooling solutions). Their labs also generally need extensive ventilation, sophisticated sensor networks, uninterrupted power supplies – as well as back-up redundancies for all of these systems. However, in a broader sense, sustainable research facility design also addresses the health and well-being of the workforce. That means air quality, natural light, workflow and productivity considerations, material selection, and all related aesthetics can drive design and construction processes as well. 4. How will the needs of this facility change? Science is constantly evolving, and research priorities will shift over time. Likewise, technology, regulations and workforce needs will change too. Flexibility and adaptability need to be key considerations of every plan, and designers and developers have to strike a balance between short- and long-term needs. In some cases, permanent or portable modular components may be the most efficient and cost-effective options. 5. Is building the best business decision? For some organizations, the best business decision may be to share laboratory space, rather than to build their own. Entering into a partnership, collaboration or lease agreement with an organization that is already operating a facility can expedite research results, reduce costs, ease the burden of meeting compliance requirements and even stimulate innovation. Of course, benefits like those must be weighed against potential disadvantages, such as the lack of customization, loss of control and the risks associated with failure to protect intellectual property.
Summary
Thoughtful consideration of these five key questions will help you create an innovation space that will meet your research needs today and for years to come. As you work through your answers to each one, be sure to solicit input from architects, engineers, builders and others who have the experience and expertise to guide you in the process. Adopting a team approach is essential to building a next-generation innovation space that is that is safe, successful and productive. The author Tolga Durak PhD Environment, Health and Safety Office, Professional Education, MIT, Cambridge, MA 02139, USA E-mail: tdurak@mit.edu
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