At Bio-IT 2015 Big Data via Integration Platforms for Data Analysis, Patient Monitoring, and Collaboration

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Last week’s Bio-IT World Conference and Expo in Boston was attended by more than 3,000 scientists, members of the pharmaceutical industry, and subject matter experts to discuss latest requirements in data analysis, management, and storage, and in the context of all of that, cloud computing and data integration.

For me the conference started out with an excellent keynote session by Chris Sander from Memorial Sloan-Kettering Cancer Center discussing on how to deliver Precision Medicine in cancer while touching upon the fantastic insights into the molecular diversity of tumors as provided in the Cancer Genome Atlas. He finished up with describing the cBioPortal which organizes data for over 20,000 tumor samples from 89 cancer studies. Following Chris’ talk, I enjoyed seeing Owen White, Institute for Genome Sciences at the University of Maryland School of Medicine, receiving the Benjamin Franklin Award for Open Access in the Life Sciences. In his award talk, he emphasized the role of metadata and how much it matters, while annotations remains a huge challenge across the field. Better data mining requires well annotated data to enable intelligent data mining with confidence.

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Here below a list of the major announcements coinciding with the conference:

Best Practices Award

  • National Institutes of Health Undiagnosed Diseases Program Named “Best Practices” Research System by Bio-IT World The Undiagnosed Diseases Program Integrated Collaboration System (UDPICS) was developed over a two-year span at the NIH UDP. Initially developed to meet tactical needs such as tracking patient samples and coordinating research activities, the system now provides a strategic environment that makes all project data accessible and allows project team members to effectively collaborate on the development of innovative hypotheses and project plans. To date, UDPICS has helped the NIH UDP recruit outside collaborators for more than 300 patients, develop and apply a unique genomics analysis pipeline to more than 250 patient samples, fulfill its mandate to deposit data in the public domain, and uphold its commitment to deliver high-quality, ethical care to its patients by giving the program more control over and visibility into all of its research practices. The commercial version of the UDPICS, CloudDx Translational, is available as a hosted solution for Clinical Research through Appistry.

Data management, analysis, and interpretation

  • Lab7 Systems Releases Clinical Annotation Manager for Lab7 ESP and Two Acceleration Programs to encourage broader adoption of NGS technologies in academia and clinical practice. The Clinical Annotation Manager (CAM) module is a complete data management and visualization tool that ties together third-party variant annotation databases with in-house annotations and allows clinicians to quickly build ACMG-style reports from their VCF files. The CAM augments the functionality of the Lab7 ESP, a software platform that gives users control over their laboratory operations, from sample submission, through instrument runs, analyses, and actionable reports.
  • BGI launched new cloud-computing platform for genomic data analysis, called BGI Online, which will provide an online computational environment managing NGS projects and enables users to create and run complex data analysis pipelines. BGI Online is advertising its services for not only large genomics centers, but also genetic testing companies and the pharmaceutical industry. BGI Online is designed to address the common challenges associated with time and cost that researchers face when analyzing, storing, and sharing tremendous volumes of next-generation sequencing (NGS) data. With a robust and reliable infrastructure tailored toward large genomics data analysis projects and best-in-class safety and security, BGI Online provides easier and more effective solutions to institutions of all types and sizes, for jobs ranging from data storage, automated analysis, and data delivery to project collaboration, bioinformatics methods development, and community sharing.
  • Launch of Genedata Profiler[TM], an open, interoperable enterprise software platform designed to facilitate efficient patient and compound profiling processes. Genedata Profiler supports the integrative analysis of NGS and other omics data with clinical patient data, ensuring the highest data security and quality standards.

Partnerships and collaborations

  • Quest Diagnostics and France’s national health agency announced the launch of a data sharing initiative to help improve knowledge of patients’ genetic risks of developing ovarian or breast cancer. The initiative, called BRCA Share, aims to better analyze the link between the BRCA1 and BRCA2 genes and cancer risk by creating a larger pool of data. The initiative will build upon the French National Institute of Health and Medical Research Institution’s database, which contains the BRCA1 and BRCA2 genetic testing data from 16 labs that are part of the Unicancer Genetic Group.
  • IDBS announces a strategic technology partnership which sees ChemAxon’s industry-leading chemical sciences software integrated into IDBS’ E-WorkBook and ActivityBase. The addition of these advanced chemical indexing and web rendering capabilities from ChemAxon complements IDBS’ deep-domain biology expertise and bolsters its single, cross-domain platform.
  • WuXi NextCODE Genomics and DNAnexus formed strategic alliance. WuXi NextCODE’s genomic database model and clinical and research interfaces directly available on the DNAnexus cloud, allows users to store and interpret their sequence data and collaborate with colleagues around the world through one platform. The companies will also provide and host the same platform and capabilities within China, in full compliance with local regulations. Users will be able to use their genomic data seamlessly in tandem with the open-access capability and technology platform that WuXi offers to the global pharmaceutical, biopharmaceutical, and medical device industry.
  • Bina Technologies and AstraZeneca announce collaborative agreement for global deployment of Bina’s Genomic Management Solution. With this announcement AstraZeneca becomes the first member to join the Bina Alliance Program and to further develop the Bina Genomic Management Solution (GMS) AstraZeneca will utilize the Bina GMS as an enterprise platform to support its development work across three main therapeutic areas: oncology, cardiovascular, and metabolic disease and respiratory inflammation and autoimmunity. Bina’s proprietary technology enables translational and academic researchers to perform fast and scalable analyses. Under the terms of the agreement, AstraZeneca will adopt Bina GMS globally to support enterprise genomic data analysis and management. Bina in turn will provide AstraZeneca with direct access to its scientific and engineering teams to further develop the Bina GMS for pharmaceutical applications.
  • Intel-Edico partnership aims to break a medical logjam: This partnership pairs Edico Genome’s Dragen high-speed DNA sequence analyzer with Intel’s high-powered Xeon processors to accelerate the speed at which genomic sequences can be analyzed. The companies estimated that Dragen and Xeon, working together, would be able to analyze a patient’s entire genome in real time – until recently, it typically took 10 to 20 hours to analyze data from a single genome, and in practice, backlogs and other delays can mean a long wait between sequencing and diagnosis. Edico Genome rolled out the Dragen processor chip in 2014.

Fundraising

  • DNAnexus Raises $15M to Expand Cloud-Database Service to China: Wuxi PharmaTech has provided DNAnexus with $15 million in Series D funding. DNAnexus, which has been backed by Goolge Ventures and other investors, has technology that allows scientists to stream DNA sequencing data to the cloud, where researchers in various locations can view and analyze the information.

Other

  • UConn Health has selected Qumulo as they design and build out their large scale high-performance computing datacenter, which is used for a wide range of life science research, including genomics, personalized medicine, complex systems modeling, and big data.

Some other news releases, not directly associated with the Bio-IT World Conference, but released within the same time frame and of relevance to the same audience

  • GenomeWeb survey finds High Interest in Long-Range Genome Data, Nanopore Tech While Illumina Rules NGS Market: Illumina continues to have a dominant presence in labs performing next-generation sequencing, and the majority of users planning to purchase a new NGS instrument are considering a platform from the company. Interest in technologies that provide long-range genome information, which Illumina’s short-read technology cannot provide on its own, is high. Pacific Biosciences’ PacBio RS II has been the instrument of choice for those operating a platform for long-range genomics. Looking forward, most users consider purchasing an Oxford Nanopore sequencer for long-read applications, a system that continues to generate excitement among the user base.
  • BaseHealth announced a new integrated enterprise offering for health organizations which combines genomic insights and a wide variety of health data to deliver personalized wellbeing recommendations to individuals. The cloud based, HIPAA-compliant enterprise offering creates personalized health assessments and detailed action plans incorporating a user’s environmental factors, genetics, lifestyle, and medical records. LABCO, the largest European medical diagnostics group, has already implemented BaseHealth inside its existing platform, and will roll the new capability out to its network of 50,000 referent physicians over the next 5 years.
  • Roche plans to integrate CAPP Medical, the Stanford University spinout it acquired earlier this month for an undisclosed amount, into its sequencing unit: CAPP Medical, which is based in Palo Alto, had been operating in stealth mode and had disclosed few details about its funding and research prior to the acquisition. However, a year ago, Diehn’s and Alizadeh’s groups published a paper in Nature Medicine in which they presented CAPP-Seq, short for Cancer Personalized Profiling by deep Sequencing, a sensitive and inexpensive method for detecting and profiling ctDNA from cancer patients. The Roche spokesperson confirmed that CAPP Medical was developing the CAPP-Seq method. The method relies on identifying highly mutated genomic regions for specific cancer types in silico based on existing data, capturing those regions in patient blood samples, and sequencing them with high coverage.
  • Color Genomics raises $15 million to make medical testing cheaper: For a fraction of the cost of current genetic testing, $249, Color offers comprehensive genetic testing with a “spit kit” ordered online and sent to recipients by mail. After the kits are returned, Color analyzes 19 genes—including BRCA1 and BRCA2, the two gene mutations related to breast and ovarian cancer. After receiving results, testers will be able to get in touch with board-certified genetic counselors at Color about the next steps based on results and a screening prevention plan.