inside - bio-it world · 9 january 2014 news and product briefs 10 genomoncology announces...
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An Essential Collection of Timely & Concise Reports Analyzing the Technologies, Markets, and Strategic Issues Driving R&D Productivity ….
About Our Sponsor6 Toby Bloom on the New York Genome Center’s Crystalizing Clinical Vision
9 January 2014 News and Product Briefs
10 GenomOncology Announces Collaborations, Partnerships Before AGBT
11 December 2013 News and Product Briefs
13 John Reynders on Building a Cloud-Based Biotech
15 Regeneron Partners with Clinical Network on Large Genetic Discovery
18 Collaborations & Partnership Survey, Conducted by Insight Pharma Reports
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Toby Bloom on the New York Genome Center’s Crystallizing Clinical VisionBY ALLISON PROFFITT | MARCH 26, 2014
Since its inception, the New York Genome Center has been evolving. The Center was legally incorporated in April of 2010, and was unveiled in a ceremony in November of 2011. In September 2013, NYGC moved into its Manhattan headquarters at its “official launch”. And last week, the Center announced its first founding technology member (as opposed to previously-named technology collaborators).
Now, three years after the legal incorporation, there’s the feeling that the Center is picking up momentum and crystallizing its identity. Since January, two faculty members have been hired—Tuuli Lappalainen and Joe Pickrell, both of whom also have appointments at Columbia Univer-sity—and a Chief Operating Officer and a Chief Communications Officer have joined the team.
The new hires make Toby Bloom, the Center’s Deputy Science Director, Informatics, look like an NYGC veteran with almost a year under her belt (she was hired in May 2013).
Though relatively new to New York, Bloom is a veteran of informatics and genomics. Bloom’s Ph.D. in computer science from MIT led her to IBM and Clinsoft after graduate school among other appointments, but before joining NYGC, she was back in Kendall Square managing busi-ness analytics and data warehousing at the Broad Institute for more than ten years.
With that expertise in hand, at the New York Genome Center she is responsible for the Central Computational Biology Group, all of the soft-ware engineering and informatics infrastructure needed for the sequencing center, and all of IT
and research computing: “Everything vaguely related to computers.”
In defining NYGC’s identity, Bloom is quick to clarify what the Center is not. “Initially the New York Genome Center looked to a lot of people like just a fee-for-service sequencing center. We are not that,” she says. “We are an academic research center with faculty members with joint appoint-ments at various New York institutions.”
The distinction is important to Bloom and NYGC. She stresses that NYGC is involved in research projects on its own and for its member organi-
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Partnerships are increasingly essential to the drug discovery process, with pharma pairing with biotechs and academia, academic groups spinning out closely-tied start-ups, CROs playing an ever-increasing role in clinical research, and large hospitals de-veloping working collaborations with several types of organizations.
Thanks to tight budgets, partnerships offer ways to expand reach, maximize impact, and explore new avenues of drug discovery and development that wouldn’t be acces-sible to organizations on their own.
For example, the New York Genome Center hopes to facilitate collaboration among its academic and hospital partner institutions and other groups that would to be in-volved. John Reynders at Moderna is relying on a host of cloud services partners to build a lightweight platform that can easily be connected to partners along the way. And the individual pairings across the industry are many.
Insight Pharma Reports’ recent survey asked 100 responders—nearly half of which represented pharma—about their current partners and the best business use cases for collaboration. Diagnostics was identified as the most common part of the pipeline to involve external partners, but more than 12 different aspects of research were chosen, emphasizing the diversity of collaborations across the life sciences.
Different partners are best suited for different tasks, the survey revealed, though tar-get identification was a common theme. Academia was identified as most useful for diagnostic assay and drug target identification; biotech was most commonly relied upon for device safety management and target identification; and pharma was almost exclusively tapped for help with target identification.
The findings are telling as the industry expands the current collaborative landscape. Finding the right partner to tackle the right problem is increasingly crucial for success.
Allison Proffitt Editorial Director
Collaborations and Partnerships Within Biotech and Pharma
Allison Proffitt
“Finding the right partner to tackle the right
problem is increasingly
crucial for success. ”
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which to focus.
The study is the first of its kind, said Robert Dar-nell, NYGC’s President, CEO, and Scientific Direc-tor, at the press conference held last week, and will, “connect the passion of the physician with the power of technology.”
Both projects are led by Darnell, who is also an attending neuro-oncologist at Memorial Sloan Kettering Cancer Center, and senior physician and professor of cancer biology at Rockefeller University.
“It’s hard to talk about whether they’re driven by the New York Genome Center or driven by Rockefeller because the President of the New York Genome Center is a Howard Hughes Medi-cal Investigator and Rockefeller Professor,” Bloom explains. “They’re being driven by Bob Darnell, which makes them driven by us on some level,” she says.
Clinical Culture
Darnell’s very hands-on leadership style shapes the Genome Center’s culture. “With the glioblas-toma project, Bob, I think, basically contacted every neurologist in the city he knew of,” Bloom says. To launch the IBM partnership, Darnell went to IBM and presented the vision for study himself, recalled John Kelly III, Senior Vice President and Director of IBM Research during the launch press conference.
The Center also has an active scientific and clini-cal steering committee made up of representa-tives from the member organizations that meet regularly to discuss projects and needs of the community.
The combined effect, Bloom says, is that the Center is “so much closer to clinical care” than other institutions. “There’s more of a sense that we have clinical projects that are associated with real patients.”
The New York refrain also runs deep in the Cen-ter’s identity. In the new faculty interviews posted on the NYGC blog, the second question asks why researchers wanted to move to New York City to practice science.
When discussing the glioblastoma study, Bloom points out the strengths of the New York City location. “One of the things about being in New York City is we have among the most diverse populations in the world, and if we’re looking at all of these hospitals—not just Rockefeller University or MSKCC—we’re going to get much
more diverse populations.”
But the Center is not limiting itself to collabora-tions or partnerships within New York City or State, Bloom says. Indeed, the Jackson Lab, headquartered in Maine, was one of the institu-tional founding members. Bloom says the Center is currently “talking to some institutions on the West Coast right now,” and that facilities are even open to non-members.
The environment was a draw for Bloom, she says. “The culture of a startup is just different… Moving fast and not having the grand plans but trying to build them day by day is just very different and very exciting and lots of fun.”
Database Love
Yet Bloom does have grand plans for the Center’s infrastructure.
“One of the first things I’m going to get done is that database [for the PCORI project] to hold the clinical data for all of those hospitals and to be able to answer queries for the PCORI network against that data,” she says.
Next on the to-do list has to do with the Illumina HiSeq X Ten system that’s on its way. NYGC pur-chased one of the systems a week after Illumina announced them, making it one of the first four X Ten customers.
Bloom expects the first of the ten instruments to arrive within the month. It will join 16 HiSeqs already in house in a sequencing facility that has the physical capacity for 80 instruments. But physical capacity and infrastructure are different animals.
“I’m looking at a brand new analysis pipeline management project to try to optimize all of the computation that we have to do to make sure that it will scale with the X Ten,” Bloom said. “I’m just making sure the computational infrastructure can scale.”
When NYGC completes a sequencing project, the Center stores all data for two years and analyzes as much of the data as the collaborators want analyzed—through interpretation if necessary. That will require a hefty infrastructure on its own, but Bloom says that the Center plans to provide space for data and compute capacity even to groups who haven’t done sequencing with the Center.
“We’re hoping to build that out as an informatics hub for the New York biomedical community,”
Bloom says. “Again, it’s a way to foster collabora-tion among all of those hospitals because if they can all get approval to exchange data, they have a place where they can easily share data.”
That’s the kind of project that Bloom loves.
“Building multimodal databases, multidimen-sional databases—whatever terminology you want to use—it’s not something we’ve done at this scale with this much data,” she says. “I want to build that database.”
And it seems that’s the kind of project the New York Genome Center loves as well.
“I’m an old data warehousing person from be-fore I was a genomics person. I want to build the be-all, end-all of multimodal databases that holds not only the genomics data but the clinical data you need, the personally-provided data you need, the information coming off devices—all of it,” Bloom says. “To bring all of that together in a way that you can look through cohorts you need, that you could answer the queries you need, that you could find the data you need, or the patients you need, or the other doctors who want to work with you on finding them.”
Editor’s Note: Toby Bloom will lead a panel discus-sion on the Big Data Storage and Security Maze: Balancing Collaboration and Privacy at the 2014 Bio-IT World Conference & Expo, May 1, in Boston.
zations—which currently number 17 including founding members, associate members, and technology members.
But the list of what the New York Genome Center does do is long. The center was a startup of six people when she joined, Bloom says (The NYGC has a staff of about 75 right now, and the website lists job openings for 20), serving a community of collaborators in New York and beyond. The Center is focused on clinical genomics, and using genomics to improve health in the short term, staying close to the patients and close to the doc-
tors who treat them. The Center provides pilot funding to researchers and maintains lab space for visiting researchers. The Center is not yet CLIA certified, though Bloom says that the CLIA audit has been completed, and NYGC is waiting on final approval. The Center organizes working groups on topics of interest and hosts a seminar series open to the community. Bloom says that the Center intends to be a trusted broker and neutral territory for data, and a facilitator of partnerships.
And it does some fee-for-service sequencing.
Pure Mix
The projects that NYGC takes on are a mix—“a pure mix”—of ones driven by the community and
ones driven by NYGC, Bloom says. For example, NYGC and six other large medical institutions in New York have a contract from PCORI, the Patient Centered Outcomes Research Institute, to merge all of the de-identified patient medical records from the hospitals. Bloom is expecting somewhere between 2.5 million and 6.5 million longitudinal medical records.
“That’s more data than any hospital can get on their own, and we are putting in place all the infrastructure, the regulations and security, data use agreements, and everything we need to be
able to do that to let researchers come to one place and get all of the clinical data they need,” she says.
The goal is to share the data with other PCORI sites around the country, Bloom says. Initially the collection should enable large retrospective studies of clinical data, but she hopes that ge-nomic data will one day be incorporated and that prospective studies can be done.
The PCORI project was driven by the partner in-stitutions, Bloom recalls, but the NYGC is driving two other large research projects.
The first is a project Bloom is very excited about: a large, 4-disease, autoimmune project. Though
in its early stages, Bloom expects to take early genome samples and then weekly blood samples from patients undergoing treatment for autoim-mune diseases. Microbiome samples will be gathered periodically, and possibly other data as well. In addition, the patients will see their doctors monthly and clinical measures of inflammation and other markers will be collected. Participants will be invited to download an app on their smart phones that will track their movement via GPS—information including how far they moved and how quickly—that will be relayed to the study.
The project is the future of clinical research, Bloom says.
“We’ve got five or six different kinds of data here. The multimodal nature of this data and the fact that it’s all longitudinal, that we’re taking it at different time points…makes it very challenging from the data analysis point of view, from the data storage point of view, from the data query-ing point of view.”
Bloom hopes that by querying the data, research-ers will find patterns that can predict flares in Crohn’s Disease or rheumatoid arthritis.
“One of the things we’re trying to do here is see whether we can help patients better manage their own chronic diseases, at the same time that we’re trying to use genomics to figure out what the biological mechanism of those diseases is.”
Working with Watson
The second project being driven by NYGC is the collaboration with IBM announced last week. With nine other institutions, NYGC is leading a glioblastoma trial that currently involves over 20 neurologists and neuro-oncologists.
The Genome Center and its consortium members will sequence tumors of glioblastoma patients and combine that genomic data with RNA-seq data and clinical data. Watson’s role will be to take that sequencing and clinical data, and scan the available literature to try to identify what pathways are involved and which are the relevant mutations, so that the physicians can choose on
I want to build the be-all, end-all of multimodal databases that holds not only the genomics data but the clinical data you need, the personally-provided data you need, the information coming off devices—all of it-TOBY BLOOM, DEPUTY SCIENCE DIRECTOR, INFORMATICS AT THE NEW YORK GENOME CENTER
Toby Bloom, the Deputy Science Director, Informatics at the New York Genome Center
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GenomOncology Announces Collaborations, Partnerships Before AGBTBY BIO-IT WORLD STAFF | FEBRUARY 12, 2014
GenomOncology, based in Westlake, Ohio, has developed the GO Clinical Workbench, a decision support tool with a step-by-step workflow that takes raw data from the sequencer and translates the molecular profile of each patient’s tumor genome into an actionable clinical report. The research platform, GenomAnalytics, allows scientists to analyze one or hundreds of genomes simultaneously to look for causal variants.
The company’s Board of Directors includes Man-uel J. Glynias, President and CEO of GenomOncol-ogy, Bradley Wertz, former President and COO of Rosetta, John Doulis, CIO of a TriStar Technology Ventures partner fund, and Lee Zapis, principal of Zapis Capital Group.
The company will be attending and presenting at the AGBT meeting in Marco Island, Florida starting today and has primed the pump for their appearance with a string of press releases over the past two weeks.
The company announced a collaboration with Roswell Park Cancer Institute (RPCI) to develop an informatics solution that enables the asso-ciation of Next Generation Sequencing results with knowledge resources to define actionable mutations. GenomOncology and RPCI are work-
ing together to develop a software platform that integrates laboratory information management systems, electronic health records, information technology and bioinformatics and that provides a workflow enabling genomic analysts and pa-thologists to create actionable reports.
GenomOncology and Vanderbilt-Ingram Cancer Center (VICC) are working together on the exclu-sive commercial development of a decision sup-port tool based on My Cancer Genome, an online precision cancer medicine knowledge resource for physicians, patients, caregivers and research-ers. The MyCancerGenome.org website will remain free and open to the public. In addition, GenomOncology will develop a decision support tool based on My Cancer Genome data that will enable automated interpretation of mutations in the genome of a patient’s tumor, providing
actionable results in hours versus days. Accord-ing to the terms of the agreement, all commercial use of My Cancer Genome in any form will be licensed through GenomOncology.
The University of Pittsburgh has selected Ge-nomOncology’s GenomAnalytics platform and services to explore and mine the breadth of data that exists in The Cancer Genome Atlas (TCGA). The University of Pittsburg is one of the largest contributors to TCGA, and the GenomAnalytics platform will be used to investigate and visual-ize cancer genomic research data as a part of the University’s Personalized Medicine research initiative. The project is intended to engage the cancer research community and leverage the GenomAnlaytics platform to develop, validate and review scientific hypotheses associated with the unique drivers associated with cancer.
CompanionDx has selected GenomOncology’s GO Clinical Workbench to launch a series of next generation sequencing (NGS)-based assays related to cancer. CompanionDx will leverage GenomOncology’s GO Clinical Workbench to manage the entire workflow: from raw sequenc-ing data through delivery of an actionable clinical report to the client.
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January 2014 News and Product BriefsNEWS BRIEFS
The Myelin Repair Foundation (MRF) and Bionure, Inc. entered a col-laborative partnership to advance therapeutics development for multiple sclerosis (MS). In this agreement, the Myelin Repair Foundation will work closely with Bionure to assess the neuroprotective capabilities of the com-pany’s proprietary MS therapeutic compound, BN201, which has shown promising results in promoting myelin repair. Bionure will collaborate with MRF researchers at the Myelin Repair Foundation’s Translational Medicine Center, an industry-standard laboratory facility dedicated to the evaluation of promising myelin repair candidates for MS. BN201 is a potential MS treat-ment for acute optic neuritis and severe MS relapses. EON
CTI Clinical Trial and Consulting Services (CTI), a global CRO, acquired Community Research, a dedicated, multi-specialty clinical research site with three locations throughout Greater Cincinnati, Ohio. Community Re-search conducts 40-60 phase I-IV clinical trials annually in a variety of thera-peutic indications, including internal medicine, dermatology, psychiatry, and sleep disorders, as well as trials in healthy volunteers. Community Research operates a hospital-based, residential phase I facility, which can accommo-date drug and device trials, and has a special emphasis on first-in-human studies in various patient populations. The team of over 50 employees from Community Research will also be joining CTI. Cincinnati Business Courier
ICON plc, a global provider of outsourced development services to the pharmaceutical, biotechnology and medical device industries, announced that its Chief Executive, Ciaran Murray, has been elected 2014 Chairman of the Association of Clinical Research Organizations (ACRO). ICON Legal Counsel, Diarmaid Cunningham, has also been elected as Secretary of ACRO for a second term. Press release
INC Research, a therapeutically-focused global CRO, announced the ap-pointment of two senior executives to its oncology team. Asli Turkes, PhD joined the Company as Vice President, Clinical Development, Oncology. Susan Timoney, PhD joined as Executive Director, Clinical Development, Oncology. The new executives will support global trials while also adding dedicated oncology leadership in Europe. Press release
The Center for Biotechnology (CeBiTec) at Bielefeld University added Tim-eLogic’s latest J-series Field Programmable Gate Array (FPGA) hardware to their computational tools platform. TimeLogic’s DeCypher systems are de-signed to increase the speed of sequence comparison by combining custom FPGA circuitry with optimized implementations of BLAST, Smith-Waterman, Hidden Markov Model and gene modeling algorithms. Press release
NEW PRODUCTS
Sapio Sciences announced the release of Exemplar NGS LIMS. Sapio’s NGS LIMS system will track multiple next-generation sequencing (NGS) plat-form workflows from request through processing and analysis. Sapio has worked with prominent NGS labs for over five years, resulting in a system that features: pre-built, CLIA standard workflows for leading NGS platforms; integration with robotic sample preparation platforms; and complete con-sumables management for reagents and other consumables with re-order alerts, in a 100% web based solution with no extra software required on the client. PR Newswire
Empiriko announced the availability of its Biomimiks technology, a bio-mimetic platform that mimics the in vivo metabolism mediated by liver enzymes (cytochrome P450) to enable pharmaceutical researchers to conduct rapid and iterative in vitro and ex vivo drug metabolism studies to predict the metabolic patterns, pathways and profiles of drugs. Empiriko’s chemistry-based solutions address the full drug development lifecycle, from lead generation to patient treatment, helping pharmaceutical companies improve safety testing and reduce later-stage attrition rates by predicting and preventing toxicity earlier in development. Press release
Oracle announced the latest release of Oracle Health Sciences Translational Research Center, a platform that enables secondary use of electronic health records and omics data to help accelerate biomarker identification for drug discovery, clinical development and translational medicine. The new release features expanded omics and clinical data models, new user interfaces and workflows for patient stratification and reporting, and analytical capabili-ties for the discovery of driver mutations. In addition, a new collaboration module lets users share patient stratification criteria and other research findings with another user or a user group, while supporting the safety of their data. Press release
Thermo Scientific released the new DXRxi Raman imaging microscope, designed to quickly reveal molecular structure, chemical composition and sample morphology. By employing the image-centric software interface, users can quickly profile materials through information-rich chemical im-ages. Instant visual feedback and instinctive image-driven control separates this instrument from other Raman microscopes. The DXRxi microscope offers new Thermo Scientific OMNICxi image-centric software to provide vi-sually driven data acquisition and intuitive sample targeting and parameter optimization; automated alignment and calibration; and near-instant visual chemical profiling that requires no spectroscopic expertise to interpret. Press release
IDBS has added key data visualization and data analysis capabilities to E-WorkBook 9.4. The new chemical drawing features enable users to capture a wider variety of molecular types and streamlines chemistry data input. Users can also define organometallic structures simply and efficiently, and a customizable chemical data lookup function speeds collaboration and data retrieval. The E-WorkBook Suite is a single platform solution with a suite of applications for data and sample management, analysis, reporting and IP retention. Press release
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NEW PRODUCTS
Earlier this fall, Quantum released version five of its StorNext appliances. It’s no longer easy to predict the type and amount of data, Skip Levens, direc-tor of technical marketing forQuantum, told Bio-IT World. Storage options need to be more flexible than ever before. When Quantum built StorNext 5, Levens says, the company started by building a completely new cache management technique with multicore processors. StorNext 5 was built to optimize performance, Levens says. “In building for performance, we saw up to 10x performance improvement… but scalability came along,” Levens says. “It turns out we can now address much larger number of files for larger and more diverse workgroups.” StorNext boasts a 5x scalability improvement. StorNext 5 will initially be available on StorNext appliances in 2013 and will be available as a software-only solution in the first half of 2014. Quantum
Agilent Technologies introduced MassHunter Profinder software, designed for batch processing of complex mass spectrometric data. MassHunter Pro-finder is powered by proprietary algorithms designed to identify differential compounds in highly complex data sets. The software reduces the noise as-sociated with data profiling by employing a new recursive feature extraction workflow, which eliminates additional manual editing tasks such as stacking, adding and deleting peaks. New user-defined peak re-integration capabili-ties return fewer false positives or false negatives. Press release
Accelrys released the Accelrys Materials Studio 7.0 modeling and simula-tion environment for chemists, polymer scientists and other materials sci-entists. The latest release contains enhancements in quantum mechanics, classical simulation, visualization, and collaboration, enabling scientists to engineer better performing and more cost-effective materials across a wide range of applications including pharmaceuticals, catalysts, polymers, com-posites, metals, alloys, batteries, fuel cells and more. PR Newswire
Media Cybernetics released Image-Pro Premier 9.1, designed for scientific and industrial image analysis and image processing. This new version pro-vides tools to capture, process, measure, share, visualize and compare im-
ages. New life science features include colocalization of multiple fluorescent images or channels; learning classification of tissues or cells using multiple parameters for pathologists; automated wound healing analysis; and ad-vanced ring analysis for otoliths, scales, and trees. Press release
ArrayFire released ArrayFire v2.0, adding full commercial support for OpenCL devices including all AMD APUs and AMD FireProTM graphics, Intel Xeon Phi coprocessors, CUDA GPUs from NVIDIA, and other OpenCL devices from Imagination, Freescale, ARM, Altera, and Apple. ArrayFire is a CUDA and OpenCL library designed to bypass the need to write CUDA and OpenCL device code. The library contains hundreds of functions for math, signal processing, image processing, and algorithms. Product page
Aspera announced the beta availability of Aspera Drive, a new unified shar-ing and collaboration platform for big data. The platform can be deployed on-premise, in the cloud, or in a hybrid model. Aspera Drive brings remote file browsing, transfer, synchronization, and package sending and receiving to the desktop, browser and mobile device. An innovative backend archi-tecture and API allows for centralized control over content access, security, and bandwidth. Press release
Clinovo will release an exclusive preview of two new features to its open source Electronic Data Capture (EDC) system ClinCapture at the 2014 Outsourcing in Clinical Trials West Coast conference in January. The new features are Medical Coding, enabling users to appropriately categorize medical terms entered in ClinCapture; and Risk-based Monitoring, allowing ClinCapture to integrate with Patient Profiles to create individual reports for each subject. Patient Profiles automatically runs algorithms to mine clinical data and identify data that is unusual. PRWeb
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December 2013 News and Product BriefsNEWS BRIEFS
Insight Genetics launched a new CLIA-certified laboratory, Insight Mo-lecular Labs. The new lab offers diagnostic tests that identify specific cancer biomarkers. It provides clinical trial support services for targeted thera-peutics, assisting in the identification of appropriate patients for trials, and specializes in the detection and monitoring of drug resistance in patients being treated with specific cancer therapies. Press release
Linguamatics announced that Huntsman Cancer Institute (HCI) at the University of Utah has deployed its natural language processing based I2E software platform to transform the immense stores of unstructured text in electronic health records into actionable information to drive improve-ments in cancer research, treatments and outcomes. HCI is using I2E with its in-house clinical informatics infrastructure to extract data from the un-structured text contained in surgical, pathology, radiology, and clinical notes related to hematology oncology disease areas. Press release
Life Technologies’ Austin manufacturing facility received the 2013 Presidential Green Chemistry Challenge Award in the category of Greener Synthetic Pathways. The award was presented at a ceremony at the Envi-ronmental Protection Agency (EPA) in Washington, D.C., and recognized the facility’s novel methods for developing Deoxyribonucleotide triphosphates (dNTPs) – the individual building blocks for DNA that are made during PCR. Conventional syntheses of dNTPs are inefficient, involve multiple steps that require isolation and purification of intermediates, and use excessive vol-umes of toxic or hazardous solvents and reagents. Press release
YarcData, a Cray company, entered a collaborative effort with Selventa, a leading provider of systems diagnostics for personalized medicine. Selventa will have access to YarcData’s big data analytics appliance, Urika, to help pharmaceutical organizations better target drugs and accelerate market delivery. Because data loaded into Urika does not need to be partitioned by disease area, the collaboration will enable analysis to be performed
across larger or combined data sets, making it possible to find previously unknown relationships between genes and proteins, treatments and disease mechanisms, human and animal biology, diseased tissue and blood, as well as identification of biomarkers representative of predictive and prognostic indications. Press release
Arsenal Capital Partners, a New York-based private equity firm, acquired Certara, the leading provider of model-based drug development and data analytics software and consulting services to the biopharmaceuti-cal research and development market. Certara provides computer-based models supported by scientific consulting services, spanning the discovery, pre-clinical and clinical stages of drug development, enabling data-driven decisions to reduce the time and expense of bringing new drugs to market. Press release
Myriad Genetics announced it will present data from four clinical stud-ies with Prolaris at the 14th Annual Meeting of the Society for Urologic Oncology (SUO) in Bethesda, MD. Prolaris is a prognostic test that predicts cancer-specific disease progression and mortality based on an analysis of 46 cell cycle progression genes. Myriad’s data will demonstrate the ability of the Prolaris test to accurately stratify a prostate cancer patient’s risk of having an aggressive form of the disease. Another new study in renal cell carcinoma also will be presented at the SUO meeting, demonstrating that Myriad’s cell cycle progression gene panel predicts metastatic progression in patients with this cancer. Press release
Pareto Biotechnologies was selected for funding by Breakout Labs, a philanthropic revolving fund. Pareto is a San Francisco-based startup that utilizes polyketide pathways in a synthetic biology platform to develop “designer molecules.” Pareto seeks to create molecules with commercial applicability in pharmaceuticals, nutraceuticals, and industrial commodities, such as plastics, resins, and adhesives. Press release
InsightPharmaReports.com
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365 for all of our collaboration communications technology, whether it’s Lync or SharePoint. And then we’re also looking at a variety of bespoke, or specialized cloud solutions. We’re deploying SilkRoad Heartbeat as an HRIS (human resources information system), Greenlight for eLearning, and RedCarpet for onboarding—all cloud-based solutions. And we have also decided on our fi-nancial platform which will be NetSuite—again, a cloud based solution. We’re also architecting to ensure all these cloud solutions are able to inte-
grate on top of one another. There’re some very strong platforms that are best-in-class. I wouldn’t propose to put everything on say Google or Force.com or Amazon, but I think each is able to serve a solution in the ecosystem very effectively and to complement each other very well. One of the things about the overall cloud architecture, is pulling all the pieces together.
BITW: You mentioned that for big pharma it would be hard for everything to go on the cloud because you can do it around the edges, but generally you’re so established, entrenched. What are the other differences you’re seeing as you come away from J&J and Lilly and AstraZeneca to this organization?
Reynders: I guess some of the differences are, you’re able to from the beginning think about how would you design a data architecture, an application architecture where the pieces can talk to one another. Something that I think has been challenging for large pharma is, either you have geographic separation, you have functional separation and whether it’s on-prem or off-prem, you always are trying to ask these integrated questions.
The harder problem is you have a lot of diversity of data in imaging data, genetic data, clinical data. The kinds of critical questions we’re asking of that data, the translational questions for ex-ample, you have to pull together lots of different
kinds of data to ask these questions. And you have these perennial sort of silo-to-silo challeng-es that can exist in big pharma or big biotech.
Something we spent a lot of time on here at Moderna, is designing from the start. Here is what the entire data architecture needs to look like. Here’s the chemistry system, here’s the mRNA science and sequencing system, here’s production. We thought about ontologies, we’ve thought about the data architecture. When all of
this is assembled, we can ask those integrated questions. So it’s very hard to integrate on the backend. You hear about all the silos and how it’s time to take a wrecking ball through them to make them talk to one another, so that’s one thing I’d say is very different. We’re in a position to architect from the get-go, here’s how all these important pieces of the puzzle need to talk to each other at once. And I think if you chat with any informatics or IT colleagues in big pharma, one of the top challenges you’ll typically find on the list is, how do we get our data to talk to each other?
Bio-IT World: What are some of the pitfalls you are protecting against as you build your system from the beginning?
Reynders: If you look at one of the pitfalls we have, it’s this big data myopia where you’re look-ing only at your class of data, but no matter how deep and sophisticated we become in under-standing genotypes unless we also connect that to understanding genomics and pathways, it has limited value. Any silo by itself, no matter how deep, is not able to solve many of the complex heterogeneous data questions that we have. So it really starts by having hypothesis-driven questions that pull together the right data, rather than emerging questions where we go down one data silo or pull it together and hope something emerges.
Bio-IT World: What’s your end goal?
Reynders: At the end of the day, this is all about, “How do you enable effective decisions?” Of all the systems that we’re producing here, the front door is trying to understand, say, the key ques-tion in a nucleotide chemistry. Or a colleague is trying to understand the dynamics of a sequence. It’s all about solving very specific questions and making, frankly, what’s happening under the hood transparent. When [researchers] are asking
those questions, here’s everything that’s happen-ing to actually connect that piece of data to that piece of data so it never becomes a roadblock. So a scientist can follow as rapidly as possible their path and intuition to ask one question which leads to another question and leads to another question. You never want the informatics system or the IT system to say, “Oh, wait a second, now you need to go jump to this other environment and ask these other questions because of this other query.” It all starts with a question and a scientific path of inquiry and making sure that whether someone is trying to pull up a terabyte of data or you’re trying to combine all sorts of stuff that’s from different classes of data, they aren’t seeing that—they can just concentrate on their question.
That’s the beauty of, I would say, doing big data right. If you’re doing it right, then you never know what’s happening under the hood—and can just focus on pursuing your scientific insight.
That’s the beauty of, I would say, doing big data right. If you’re doing it right, then you never know what’s happening under the hood—and can just focus on pursuing your scientific insight. -JORDAN STOCKTON, CHIEF INFORMATION OFFICER, MODERNA
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John Reynders on Building a Cloud-Based BiotechBY ALLISON PROFFITT | JANUARY 10, 2014
John Reynders has quite the pharma pedigree, having held roles at AstraZeneca, Johnson and Johnson, and Eli Lilly spanning informatics to companion diagnostics to neuroscience biomarkers. Before his turn in pharma, he was part of the team building informatics capability at Celera after the genome was assembled, and before that spent about eight years at Los Alamos National Laboratory.
Last fall, he traded his big pharma hat for the CIO position at Moderna, a privately held biotech based in Cambridge, Ma., focusing on messenger RNA therapeutics. Before the holidays, Reynders sat down with Bio-IT World Editor Allison Proffitt to talk about his vision for the three-year-old company. One that depends heavily on the cloud.
Bio-IT World: John, can you give me an over-view of what you’re doing at Moderna?
John Reynders: Yeah, sure. So my role here at Moderna I’m Chief Information Officer, respon-sible for informatics, IT, and automation. I’ve been here about three months [as of November 2013]… One of the things I find really exciting about the opportunity here at Moderna is not only is it a transformative scientific platform—in terms of messenger RNA serving as a therapeutic and helping the body to make its own medi-cines—but the informatics that support actually designing these constructs. mRNA, in a sense, is a piece of software that’s telling the body, the hardware, how to program to make therapeutics and proteins that are its own medicine. There’s quite a bit of modeling, quite a bit of informatics, quite a bit of automation to bring that to light. So it’s an exciting challenge. Great to be part of it.
BITW: In March 2013, while you were still at AstraZeneca, the pharma announced a major agreement with Moderna starting with an up-front $240 million payment. Was your move a part of that deal?
Reynders: Oh, no. Basically, Stéphane [Bancel, Moderna’s President and Founding Chief Ex-ecutive Officer] and I know each other from Eli Lilly and we sort of go back, and Stéphane had reached out to me well before the AstraZeneca deal was announced. As exciting as it was at As-traZeneca with all the technology opportunities there, what we were doing with big data, as I learned more about what Moderna was trying to do, it became very exciting, the opportunity. And actually, I had made my decision to join Moderna
and it wasn’t until then that I learned about the deal and I thought, oh, okay, well, that’s really nice to know and sort of confirming evidence. But no, I was in discussions with Stéphane well before I knew about the agreement.
BITW: You’ve characterized your job at Mod-erna as, “creating a fully cloud-based biotech.” Can you tell me a little bit about what your goal is there? How does the cloud-based bio-tech fit in with RNA therapeutics?
Reynders: Sure. I mean one of the things that was really exciting about joining Moderna was the opportunity from kind of de novo—from scratch—to design informatics, a technology platform for a next-generation biotech. And one of the things that was very clear is there’s no way you’d be building up your own datacenters, building up your own internal on-premise appli-cations. What you’re able to do in the cloud now is rather impressive. A lot of folks get distracted and think, oh, the cloud is all about saving money and doing IT cost-effectively. That’s certainly part of it. But the most valuable part of it is how fast you can move, the speed with which you can deploy new capabilities, the agility or you can change things and entire huge components of applications that are out there that can be readily and quickly assembled. So it’s challenging for an established firm or biotech because there’s a lot of legacy and moving to cloud, it’s something you can do around the edges. But for us, we made the commitment to doing everything in the cloud and other than some specific systems onsite to support labs, basically, we have all of our calcula-tions, all of our production systems, our ERP [en-terprise resource planning] and G&A systems, all
served out of a variety of cloud solutions that are serving us very well.
BITW: But Moderna has a wet lab. You can’t do that in a cloud.
Reynders: Well, no, no. We’re designing and making messenger RNA therapeutics. So we cer-tainly have laboratories. There is a strong compo-nent of lab systems, there’s a strong component of informatics that’s required for design, so all the in silico components whether it’s to design the mRNA at the beginning, whether it’s understand-ing how the mRNA construct is flowing through production, whether it’s tracking all of these piec-es and parts as they’re coming together. That’s all done through the cloud, so everything to do with designing, tracking, and analytics. Other than a few systems that need to be directly bolted onto an instrument (to, for example, analyze certain imaging features), everything else pretty much we’ve taken up into the cloud. But indeed, no, we’re fully integrated in terms of being able to do everything from chemistries, to mRNA science, production, QC, screening, in vitro, in vivo, we have all those capabilities end-to-end in-house.
BITW: Who are you using for the cloud? Is this a private cloud, or are you using a commercial vendor?
Reynders: Oh, we’re using a constellation of part-ners. So I’ve been very impressed with Amazon. We set up a virtual private cloud with Amazon. They’ve done quite a bit to make sure their solu-tions are HIPAA compliant, recently, they have secured FedRAMP certification. We use Office
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Regeneron Partners with Clinical Network on Large Genetic StudyBY BIO-IT WORLD STAFF | JANUARY 10, 2014
There was a time, not too long ago, when the genetics community could be wowed by sufficient volumes of genetic information: the 1,000 Genomes Project, the Personal Genome Project with its 100,000 genomes, the Million Veteran Program. But in 2014, the most noteworthy thing about the 100,000 whole exomes Regeneron plans to sequence in a new genomic initiative is how quickly and comprehensively the pharmaceutical company should be able to match genetic data to individuals’ medical histories.
That’s because Regeneron is partnering with Geisinger Health Systems, a Pennsylvania health care network that serves a population of 3 million in the state’s rural northeast and center. Geis-
inger has already made a big push into electronic health records, not only connecting all its clinics in a single health record database, but also imple-menting the MyGeisinger tool where patients can
access their medical information and communi-cate with their physicians online. That reliance on electronic records gives this new genomic project an important head start in linking genetic infor-mation to data on health outcomes and a range of phenotypic variables – and tracking that data over a long period of time.
Under the terms of the project, Geisinger will inform patients of the study, obtain informed consent from volunteers, and provide both serum samples and anonymized health records for each enrollee. Regeneron will bear Geisinger’s costs, and will perform whole-exome sequencing on each participant’s samples at its genetic lab in Tarrytown, NY. The genetic sequences will be de-
identified, but tagged to the appropriate health records, allowing Regeneron to seek out disease associations and changes in health outcomes tied to even very rare genetic variants. The company hopes this information will lead to publications and new pharmaceutical targets. Regeneron has had some success in this arena before, bringing a cholesterol drug to late stage development based on gene-phenotype association studies, but has never before relied on internal genetic research on this scale.
The project, which over its 5-year initial term will attempt to sequence 100,000 participants, is not as extensive as the Million Veteran Project, which has already collected more than twice that
number of volunteers – but Regeneron has the resources to obtain whole exomes of each par-ticipant, rather than relying on narrowly targeted sequencing. It is also not as ambitious as the Per-sonal Genome Project, which collects whole ge-nomes and a truly monumental amount of health data – but with the cooperation of Geisinger, Regeneron should be able to acquire a huge dataset much more quickly, and track changes in participants’ health more easily over time. For those waiting for a gold standard genomic study, which ties genes to health over a long timeframe and wide spectrum of outcomes, this partnership is a promising candidate to deliver early results.
It may also have a direct impact on some pa-
tients’ lives right away. As Regeneron sequences samples, it will report any actionable findings – genetic variants that are known with high confidence to be tied to a treatable or prevent-able disease – to Geisinger, who will be able to re-identify the samples and find the patients concerned. Volunteers will therefore have free and early access to important genetic informa-tion about their health.
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Partnerships and collaborations are nothing new to research and development. This strategic method expedites diagnostic and therapeutic development by overcoming challenges re-lated to the breadth of innovative knowledge and financial provisions. In a recent survey sent out by Insight Pharma Reports, 100 responders report their experience with partnerships and competitive strategies. This survey analysis will address several distinct areas of partnerships, including reasons for collaboration, company genre of choice, advantages, and challenges.
Interestingly, 87% of partnerships occur with North American companies and institutions. According to the survey, external partners are most commonly involved with diagnostic assay development and therapeutic development. This was identified by 34% and 38% of participants, respectively. The data illustrate overall benefits of collaborating with a variety of industries including academia, pharmaceutical, and biotechnology, which make up 74% of external partnerships in R&D, with the majority of partnerships being with pharmaceuti-cal companies (occurring 34% of the time). This is followed by biotechnology and academic partnerships, which respectively occur 23% and 17% of the time.
With regard to the benefits, 49% of participants highlight access to knowledge and innova-tion as the greatest advantage to external collaborations. Respondents further elaborated on this speaking to the benefits of partner with specific company genres. According to the results, product validation was identified by 44% of participants as the as the most substantial benefit of collaborating with academia; while product development was identified by 42% and 72% of participants as the greatest advantage to partnering with biotechnology and pharmaceutical companies, respectively. Furthermore, 44% of collaborations with academia, 25% of collaborations with biotechnology companies, and 72% of collaborations with phar-maceutical companies were pursued for drug target identification. Even more so, 60% of participants expect their collaboration with external partners to increase over the next three years, while only 4% expect a decrease. This illustrates the dramatic, positive effects specific partnerships have had on a number of institutions.
Although collaborations have greatly influenced R&D and increased efficiency in the devel-opment of diagnostics and therapeutics, participants identify several areas that are in dire need of improvement, including financial limitations (identified by 28% of participants) and developing projects in a rapid manner (identified by 21% of participants). The latter improve-ment is no doubt due to legal issues concerning patents, stipulations, and contracts between collaborating companies. Because things can easily snowball out of effect and /or inhibit projects and deadlines, it comes as no surprise that the majority of the participants’ partner-ships are with academia; this allows them a little more leeway with regard to licensing and copyright laws. Further, academia stands as more of a neutral zone in a very polar market; this keeps the competition high between major players in the R&D space.
Partnerships & CollaborationsSurvey Data
How do you expect the number of projects with your external partner to change over the next three years?
Increase 60%
Stay the same 25%
Decrease 4%
Unsure 11%
How would you categorize the organization you are in?
Academia 4%
Government 0%
Pharmaceutical 45%
Biotechnology 36%
Hospital/Clinic 4%
Other 11%
Target Identification
Drug target validation
Drug target development
Diagnostic assay development
Lead Discovery or Lead Optimization Chemistry
Lead Discovery or Lead Optimization Assay
Device safety and management
Safety Assessment Testing
Instrument validation
Therapeutic identification
Therapeutic validation
Therapeutic development
Other
13%
21%
19%
38%
26%
17%
11%
25%
25%
15%
25%
34%
13%
In which aspect(s) of your drug discovery research do you typically involve external partners?
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What percentage of your partnerships is with academia?
None 0%
Less than 10% 11%
10% 11%
20% 0%
30% 22%
40% 0%
50% 11%
More than 50% 44%
Which organizations have you partnered with the most?
Biotechnology 23%
Pharmaceutical 34%
Academia 17%
Hospital/clinics 9%
Government institution 2%
I haven’t had a history of collaborations 6%
Other 9%
North America
Western Europe
Eastern Europe
Asia
Other
87%
53%
11%
38%
4%
In which geographic region(s) do you have external collaborators?
What is the benefit of partnering with academia?
Product identification 22%
Product development 33%
Product validation 44%
Product safety and management 0%
Other 0%
Which aspects of your drug discovery research typically involve partnering with academia?
Drug target identification 44%
Device safety and management 11%
Instrument validation 0%
Diagnostic assay development 33%
Other 11%
What is the benefit of partnering with biotechnology companies?
Product identification 25%
Product development 42%
Product validation 25%
Product safety and management 8%
Other 0%
What percentage of your partnerships is with biotechnology companies?
None 0%
Less than 10% 8%
10% 33%
20% 0%
30% 17%
40% 8%
50% 17%
More than 50% 17%
Which aspects of your drug discovery research typically involve partnering with biotechnology companies?
Drug target identification 25%
Device safety and management 25%
Instrument validation 17%
Diagnostic assay development 17%
Other 17%
What is the benefit of partnering with pharmaceutical companies?
Product identification 6%
Product development 72%
Product validation 17%
Product safety and management 0%
Other 6%
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What is the greatest challenge to seeking external collaborators?
Undertaking cultural change 8%
Financial limitations 28%
Meeting project deadlines 19%
Developing projects in a rapid manner 21%
Maximizing return on investment 19%
Other 6%
Less than 10%
10%
20%
30%
40%
50%
More than 50%
11%
6%
11%
17%
6%
28%
22%
What percentage of your partnerships is with pharmaceutical companies?
Which aspects of your drug discovery research typically involve partnering with pharmaceutical companies?
Drug target identification 72%
Device safety and management 0%
Instrument validation 0%
Diagnostic assay development 22%
Other 6%
What is the greatest advantage to seeking external collaborators?
Access to knowledge and innovation 49%
Developing extensive networks 13%
Developing projects in a rapid manner 15%
Delivery of projects in a rapid manner 15%
Maximization of return on investment 4%
Other 4%
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