Pacific Biosciences, EPAM, Oxford Genetics, And More: News From May 2018

May 23, 2018 | May featured exciting new, products, and partnerships from around the bio-IT community from innovating companies, organizations, and universities, including Pacific Biosciences, EPAM, Oxford Genetics, and more.

Phase Genomics and Pacific Biosciences announced the release of the FALCON-Phase software as part of a new co-development effort to improve the FALCON-Unzip genome assembly method for providing high-quality, phased diploid genome assemblies. FALCON-Phase augments PacBio Single Molecule, Real-Time (SMRT) Sequencing-based assemblies with Hi-C proximity-ligation data to generate accurate phased diploid assemblies. Using Phase Genomics' genome scaffolding technologies and FALCON-Phase, maternal and paternal haplotypes can be separated or "phased" on a chromosomal scale. High-quality phased haplotypes provided by FALCON-Phase can, among many other use cases, facilitate the study of inherited disease and be leveraged to improve agricultural programs, such as increasing the efficacy of livestock and plant breeding. "SMRT Sequencing produces the most accurate and contiguous genome assemblies on the market, and the ultra-long range genomic connectivity of the in vivo Hi-C method serves as a perfect complement to SMRT Sequencing of large and complex genomes, helping to achieve full chromosome-level contiguity and phasing," stated Jonas Korlach, Chief Scientific Officer at Pacific Biosciences, in a press release. "Our collaboration with Phase Genomics has been truly synergistic and has yielded a method that enables researchers to get more value from long-read SMRT Sequencing and Hi-C technologies alone." FALCON-Phase is available as open source to scientists and also as a service through Phase Genomics. Scientists can utilize the new software to advance their current research and even revive historic genome projects with the addition of Hi-C data. Press Release

EPAM announced the launch of InfoNgen 7.0, an actionable insight engine that delivers ready-made, customized content from over 200,000 web sources in multiple languages, and includes sophisticated sentiment analysis. The addition of machine learning through neural networks significantly improves the fidelity of the signal over time, allowing users to find hidden patterns, trends and anomalies. InfoNgen customers can quickly find, analyze and share critical information to speed decision-making and stay competitive. “Actionable insights are increasingly valuable to businesses, especially when combined with structured and unstructured data analysis, allowing organizations to truly understand, identify and react to gaps in performance to achieve a competitive advantage,” said Jitin Agarwal, VP Enterprise Products, EPAM, in a press release. “The ability to quickly consolidate and analyze unstructured data is a necessary step towards true digital transformation, and InfoNgen is an easily customizable solution that allows business users to quickly aggregate and find patterns in the data for better decision-making.” “The global service provider landscape is dramatically changing, and our clients are demanding that we go beyond building platforms to orchestrating solutions from across a broader set of options,” Elaina Shekhter, CMO and Head of Strategy, EPAM, wrote in an official statement. “We are tackling this challenge head-on by incorporating partner solutions, EPAM platforms, open source components and our own products, like InfoNgen, into a holistic approach to solving our customers' most complex business problems.” Press Release

Oxford Genetics announced the launch of a new online customer portal designed to enable customers to better monitor project progress and track communications. This new portal provides customers with real-time updates through 24/7 access to the status of the projects they have underway with Oxford Genetics. The system collates project information from several sources, including bespoke Enterprise Resource Planning (ERP) systems and Laboratory Information Management (LIM) systems, to produce live Gannt charts. It also gives immediate access to all supporting documentation, such as order history, quality assurance/quality control (QA/QC) reports, and project progress reports. Ryan Cawood, CEO of Oxford Genetics said in a press release, “The primary reason for developing the tool was that by automating data collection and dissemination a lot of the traditional bottlenecks of managing projects by manual methods can be eliminated. The launch of this portal shows our commitment to providing a more valuable and simplified online environment for our customers. We are focused on delivering both innovative technologies and exceptional service, and the deployment of this online portal helps us enhance the overall experience our customers have with us. By providing customers with visibility of their projects, they can now choose how and when to interact with our team, streamlining their user experience and allowing Oxford Genetics to be more flexible and personally responsive to each customer. Added to this, the growth trajectory of Oxford Genetics fed the need to improve efficiencies and streamline operations to allow the company to continue providing a high quality-service to its customers. By implementing this tool across our customer projects, we can use resources more effectively and benefit from a scalable architecture that can support hundreds of concurrent projects.” The portal has taken around 12 months to build and was extensively tested with key customers to ensure it met the needs of all users. Press Release

SoftGenetics announced the inclusion of the capability to support performance metric reporting of the joint recommendations from the Association for Molecular Pathology (AMP) and the College of American Pathologists (CAP) for pipeline validation in its NextGENe and Geneticist Assistant Workbench softwares. This allows the combining of multiple reports containing all recommended performance metrics into a single comprehensive report. This reporting is highly beneficial for pipeline validation as well as performance monitoring over time. Geneticist Assistant Workbench allows the creation of custom quality metric profiles permitting users to determine which metrics are to be reported, to set thresholds for flagging variants, and to define where in the Geneticist Assistant input files the metrics can be found or can be calculated. Default profiles are built‐in based on the AMP/CAP recommendations. Metrics are reported in sample level and variant level tables with highlighting for metrics that are within the failure or warning range based on the user-defined thresholds. NextGENe outputs a separate PerformanceMetrics.txt file containing the quality metrics listed above. The metrics are also reported within the VCF files exported by NextGENe. Both files are automatically generated following the analysis. The VCF data can also be automatically imported to Geneticist Assistant to provide a seamless pipeline. Megan McCluskey, NextGENe Technical Product Manager, indicates in a press release that, “The ability to automatically capture, store and generate reports containing all CAP/AMP recommended quality metrics simplifies both in‐house monitoring of performance as well as demonstrating performance review procedures are in place for external audits.” Press Release

First Stop Health announced details of its 2017 annual results at the HLTH conference in Las Vegas. “In 2017 we realized triple-digit top-line revenue growth,” said Patrick Spain, CEO and Co-Founder. “As a leader in the telemedicine industry in utilization last year, we saw an average usage rate of 52% across our member base (52 calls per 100 enrolled employees). We believe our 2017 utilization was seven times the industry average for employer purchased programs,” Spain added. “In 2018 our utilization rate has continued to increase, outpacing that of competitors, while our triple-digit revenue growth is also continuing,” Spain said. Employers purchase First Stop Health’s telemedicine service through their brokers or benefit advisers for employees and their dependent family members. “Tracking the visits we divert from more expensive physical facilities, such as the ER or urgent care, allows us to provide detailed analyses to demonstrate the significant net healthcare cost savings we generate for employers,” Spain added. “First Stop Health is the only telemedicine provider to offer contractual guarantees of significant overall cost savings to its clients,” he said. Press Release