Seven Bridges, Numerate, The Wellcome Trust Sanger Institute, And More: News From August 2017

August 30, 2017

August 30, 2017 | August featured exciting new, products, and partnerships from around the bio-IT community from innovating companies, organizations, and universities, including Seven Bridges, Numerate, the Wellcome Trust Sanger Institute, and more.

Interpretation and reporting of tumor variants identified by next-generation sequencing (NGS) can be challenging, especially as one scales up from panels of hundreds of genes to whole exome and, ultimately, whole genome sequencing. Variants need to be assessed for technical validity, and combinations of multiple variant types (SNVs, Indels, CNVs and SVs) can conspire to affect proper interpretation, which may also be affected by the tumor type of the case being reviewed. Aware of these challenges, Illumina and Genomics England entered a bioinformatics and interpretation partnership in early 2016 to collaborate on software that would enable variant interpretation that could support an operation the size of the 100K genome project. In little more than a year, the partnership has reached a significant milestone: the partners announced in late June that Illumina’s BaseSpace Variant Interpreter would be the primary interpretation and reporting software platform for tumor interpretation, supporting Genomics England. BaseSpace Variant Interpreter can be used to review results from targeted enrichment panels, whole exome and genome data. Following this milestone with Genomics England, Illumina will be launching BaseSpace Variant Interpreter as a commercial product to be generally available to the wider NGS community. The launched product also fully supports review of germline VCFs and family-based analysis, for research applications. Other key features include support for copy-number variant (CNV) and structural variant (SV) review with interactive visualization, an integrated genome browser, as well as availability of high-quality curated content from publicly available literature sources via the BaseSpace Knowledge Network. Press release

Seven Bridges announced that it has been selected to build a new data center in partnership with the Center for Data Driven Discovery in Biomedicine (D³b) at the Children’s Hospital of Philadelphia and a consortium of academic research institutions. This effort is funded by an award from the National Institute of Health Common Fund’s Gabriella Miller Kids First Pediatric Research Program (Kids First) and will establish the Kids First Data Resource Center.  The Kids First Data Resource Center will bring together harmonized, large-scale, pediatric cancer and structural birth defects data and provide researchers with access to multiple disease datasets in one location — a first for the pediatric community. Press release

Numerate announced that the National Heart, Lung, and Blood Institute (NHLBI) of the National Institutes of Health (NIH) has awarded Numerate a Small Business Innovation Research (SBIR) Phase I grant.  Numerate, working with members of the UCLA Cardiovascular Research Laboratory (CVRL), will use the funds to initiate a drug discovery program targeting cardiac arrhythmias. The project targets the discovery of small molecule drug candidates that address the need for a novel well-tolerated antiarrhythmic therapy for the treatment and prevention of ventricular tachycardias and fibrillation (VT/VF). Uwe Klein, Vice President, Biology at Numerate, will lead the discovery efforts and serve as Principal Investigator for the project titled, “Peripherally restricted α2/δ-1 subunit ligands that modulate CaV channel gating as novel antiarrhythmic drugs.” The project is funded under Grant Number 1R43HL139143-01. The co-investigators include esteemed members of the UCLA Cardiovascular Research Laboratory, including: Hrayr S. Karagueuzian, Professor of Medicine at the David Geffen School of Medicine at UCLA, Director of Translational Arrhythmias Research Section; Riccardo Olcese, Professor of Anesthesiology and Physiology at UCLA, Division of Molecular Medicine. Press release

"The Wellcome Trust Sanger Institute has recently re-evaluated its RNA-seq library preparation methods and has chosen to implement the NEBNext Ultra II Directional RNA Library Prep Kit," stated Mike Quail, Senior Staff Scientist, R & D Sequencing at the Sanger Institute, in a press release. "Our previous RNA-seq library preparation required a minimum input of 500 ng total RNA, but the high efficiency of the NEBNext Ultra II kit has allowed us to reduce this to either 100 ng for a standard pipeline, or down to just 5 ng for a low input option, enabling RNA-seq to be carried out from just 5,000-10,000 cells." "When processing a large number of samples, factors such as automation compatibility, workflow speed, input amount, and library quality become critical for efficient and successful sequencing runs. Further, library preparation ideally needs to be achieved with minimal optimization," stated Fiona Stewart, NEBNext Product Portfolio Manager at NEB. New England Biolabs (NEB) aimed to address these challenges when developing their recently launched NEBNext Ultra II RNA Library Prep kits for Illumina sequencing. "We know from many of our customers that RNA samples can be problematic for a variety of reasons. Library quality is often affected by low input amounts, RNA quality, and the presence of contaminants. Further, workflows must ideally be streamlined and optimized for a broad range of input amounts," continued Stewart. "We kept these needs in mind when developing the NEBNext Ultra II RNA Library Prep kits, and have been able to make dramatic improvements on all fronts. We are pleased that the Sanger Institute is having success with this kit for its samples and workflow needs, and look forward to working together." Press release

DNAstack announced the launch of a major update to its cloud-based genomics software platform. The update contains many new features, including a revolutionary application called Workflows that makes it easier and more affordable than ever for genome scientists to find, develop, share, and run bioinformatics workflows at scale. The app brings the most advanced technologies and standards for bioinformatics to market and positions DNAstack as a commercial leader in cloud genomics. Users of the Workflows App can choose from a growing selection of high quality, curated pipelines like Broad Institute's GATK Best Practices, a popular end-to-end genotyping toolkit, or author their own custom analyses. The Workflows App runs pipelines written in the Workflow Description Language (WDL), a language developed at the Broad Institute that is being adopted as a community standard. “WDL enables analysts to create and understand pipelines with as little friction as possible,” Jeff Gentry, Senior Principal Software Engineer at the Broad Institute and co-chair of the Containers & Workflows Task Team at GA4GH, said in a press release. “The ability to execute those pipelines in different environments, like DNAstack, is critical to the success of the whole ecosystem.” DNAstack’s application includes a WDL editor for authoring workflows that gives bioinformaticians and software developers a unified platform for developing, refining, and running their pipelines in the cloud. Press release

Ideagen has released the latest version of its popular collaborative document review, co-authoring and redaction software, PleaseReview. PleaseReview v6.2 brings several new features, including a collaborative co-authoring capability called PleaseReview OpenSpace, as well as @mentions and improved document handling. The OpenSpace enhancement enables collaborative co-authoring sessions in Microsoft SharePoint, bringing particular benefit to users during the pre-review stage. The added Mentions functionality notifies users of any comment where they have been mentioned and directs them to their specific review sections quickly and efficiently. Additional enhancements include improvements to the document upload process and the ability to attach files to Word and PDF reviews. The latest version also brings the addition of specified Standard, Multi-Phase and OpenSpace review types. Press release

PerkinElmer launched version 17 of its ChemDraw software with new capabilities that enable biomolecular researchers and chemists to advance their data analysis and accelerate their paths to discovery. The ChemDraw software is an industry-trusted chemical structure drawing application. Scientists across academia, government, pharmaceuticals, biotech, chemical processing, environmental, food & beverage, and oil production have utilized the software to support their research for more than 30 years. Press release

labfolder and the German Accelerator Life Sciences (GALS) announced the initiation of an extensive collaboration supporting the company’s expansion into the North American markets. With thousands of users and a growing number of customers in the U.S. already, the newly established Cambridge office will accelerate those efforts and support customer relations. labfolder digital lab notebook software was developed to support research teams in managing their vast amounts of data, and being more productive in the lab. The company is one of the world's leading electronic lab notebook (ELN) platforms with a strong user base within life sciences, biotech and pharma. “The Boston/Cambridge biotech hub is an important market for the laboratory supply industry with hundreds of top-tier biotech and pharmaceutical companies, the top 4 NIH-funded hospitals in the U.S., and 122 colleges and universities. Academic research institutions as well as industrial R&D giants worldwide are looking towards Boston as one of the most innovative regions. For us it is not only a great opportunity, but also an honor being able to support research teams with our software, and helping them to focus on making groundbreaking discoveries.”, said Simon Bungers, Co-founder and CEO of labfolder, in a press release. Press release

BioreclamationIVT announced that it has acquired Asterand Bioscience. Asterand Bioscience advances drug research by accelerating target identification and biomarker validation, and improving drug candidate selection to increase the likelihood of clinical success. “We are delighted that Asterand Bioscience’s talented staff is joining BioreclamationIVT. This is a great fit between two complementary companies,” said BioreclamationIVT Chief Executive Officer Jeff Gatz in a press release. This acquisition will expand BioreclamationIVT’s portfolio of highly-annotated disease-state biospecimens. After combining Asterand Bioscience’s first-rate oncology tissue sourcing network with our existing strength in procuring disease-state tissue and clinical biofluids, BioreclamationIVT will become the market leader in disease-state biospecimens and a top resource for researchers focused on precision medicine. The addition of Asterand Bioscience’s tissue services and PhaseZERO research services groups will allow the combined company to offer a full research workflow solution, ranging from specimen sourcing through experimental design to data collection. BioreclamationIVT’s new offerings will include target and biomarker validation using histology and molecular techniques, and compound evaluation using cell-based model systems.” Press release

Geneformics Data Systems announced Geneformics D, a distributed cloud compression solution for genomics data that increases the efficiency and speed of upload, download, storage and archiving by up to 10X and decreases cost by 90%. Geneformics D is integrated into the cloud infrastructure, providing seamless and truly scalable performance, unlike existing applications that are added to the genomic workflows. Based on lossless compression technology co-developed with the Weizmann Institute of Science, Geneformics D is an enterprise-grade Infrastructure as a Service (IaaS) for genomics cloud installations. With Geneformics D’s technology, precision medicine data from population sequencing, gene banks, hereditary, and rare disease, cancer, and genomics-based pharmaceutical efficacy research can be automatically and transparently compressed, saving time, bandwidth, and significant storage space. Press release

Medisafe announced the official launch of Medisafe Insights. Eclipsing 4 million users and 1 billion doses managed, Medisafe is turning its database of patient information, combining demographics, medication details, medical conditions and comorbidities, engagement with content and interventions, and other key information, into actionable insights for pharma. Medisafe Insights is a proprietary tool for market research (HIPAA compliant and ISO secure), which provides the pharmaceutical industry real-time information regarding patient behavioral trends impacting medication management. With a suite including a de-identified dashboard of high level trends, a targeted and context-aware survey tool and custom enterprise solutions, Medisafe Insights reveals obstacles throughout the patient journey and enables pharma to turn patient behaviors into aggregated actionable insights.  The launch of Medisafe Insights comes one year after announcing its commercial offering for pharma and life sciences companies and launching several successful pilot programs. Press release

Genomatica announced its latest innovation, the GENO BG process, a new biobased process technology to make a naturally sourced 1,3-butylene glycol. The GENO BG process has already produced biobased butylene glycol for sampling and Genomatica has transferred the process to 85,000 liter production fermentors. Press release