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Pharmaco-Kinesis Corporation and the Ohio Clinical Trials Collaborative Consider Strategic Partnership to Develop Cloud-Linked Biosensors

Pharmaco-Kinesis Corporation (PKC) and the Ohio Clinical Trials Collaborative (OCTC) recently announced that they have agreed to explore the potential of a partnership aimed at the development of technology that provides physicians real-time patient information that once required days to secure.

IBM, Coriell Life Sciences and CareKinesis Deliver Personalized Medicine to the Elderly Via the Cloud

IBM (NYSE: IBM) recently announced a collaboration with Coriell Life Sciences, a provider of genetic analysis at point of care, and CareKinesis, Inc., a Medication Risk Mitigation® pharmacy services firm, to bring personalized medicine to the elderly based on analyzing and storing genetic data in a secure cloud environment.

Big Data From Alzheimer’s Disease Whole Genome Sequencing Will Be Available to Researchers Due to Novel Global Research Database

The Alzheimer’s Association and the Brin Wojcicki Foundation announced recently that massive amounts of new data have been generated by the first “Big Data” project for Alzheimer’s disease. The data will be made freely available to researchers worldwide to quickly advance Alzheimer’s science.

Discussed recently at the Alzheimer’s Association International Conference (AAIC) 2013 in Boston, the project obtained whole genome sequences on the largest cohort of individuals related to a single disease – more than 800 people enrolled in the Alzheimer’s Disease Neuroimaging Initiative (ADNI).

The genome sequencing data – estimated to be 200 terabytes – will be housed in and available through the Global Alzheimer’s Association Interactive Network (GAAIN), a planned massive network of Alzheimer’s disease research data made available by the world’s foremost Alzheimer’s researchers from their own laboratories, and which also is being publicly announced today at AAIC 2013. GAAIN is funded by an initial $5 million dollar investment by the Alzheimer’s Association, made possible due to the generous support of donors.

“The Alzheimer’s Association is committed to creating open access to research data, and we believe GAAIN will transform how neuroscience data is shared and accessed by scientists throughout the world,” said Maria Carrillo, Ph.D., Alzheimer’s Association vice president of Medical and Scientific Relations. “By fostering a higher level of global data sharing, GAAIN will accelerate investigation and discovery in Alzheimer’s through a system comparable to a search engine like Google or Bing for relevant data.”

“With the addition of more than 800 whole genomes on ADNI subjects that can be linked to the current rich dataset, ADNI data will be even more useful to scientists who are seeking new approaches to treatment and prevention of Alzheimer’s disease,” said Robert C. Green, M.D., M.P.H., of Brigham and Women’s Hospital and Harvard Medical School, who led the ADNI sequencing project. “ADNI is a leader in open data sharing, having provided clinical, imaging and biomarker data to over 4,000 qualified scientists around the world, which has generated over 700 scientific manuscripts.

First, Massive Whole Genome Sequencing Project in Alzheimer’s Disease

Whole genome sequencing determines all six billion letters in an individual’s DNA in one comprehensive analysis. The raw data from the ADNI project is being made available to qualified scientists around the globe to mine for novel targets for risk assessment, new therapies, and much-needed insight into the causes of the fatal brain disease. The new data may enable scientists to better understand how our genes cause and are affected by bodily changes associated with Alzheimer’s disease.

ADNI enrolls people with Alzheimer’s disease, mild cognitive impairment, and normal cognition who have agreed to be studied in great detail over time. The goal is to identify and understand markers of the disease in body fluids, structural changes in the brain, and measures of memory; the hope is to improve early diagnosis and accelerate the discovery of new treatments. ADNI is led by Principal Investigator Michael W. Weiner, M.D., of the University of California San Francisco and the San Francisco VA Medical Center. Dr. Green collaborated on managing the sequencing efforts with Arthur Toga, Ph.D., of UCLA and Andrew J. Saykin, Psy.D., of Indiana University. The actual genome sequencing was performed at Illumina, Inc.

ADNI is a public-private research project led by the National Institutes of Health (NIH) with private sector support through the Foundation for NIH. Launched in 2004, ADNI’s public-private funding consortium includes pharmaceutical companies, science-related businesses, and nonprofit organizations including the Alzheimer’s Association and the Northern California Institute for Research and Education.

The Global Alzheimer’s Association Interactive Network (GAAIN)

Data-sharing has already greatly benefitted scientific disciplines such as genetics, molecular biology, and the physical sciences. Data-sharing in genetics has led to dramatic advances in understanding the risk factors underlying complex diseases. The Alzheimer’s Disease Neuroimaging Initiative (ADNI) is a compelling example of dozens of geographically-dispersed researchers working together to share their data while making it freely available to others for analysis and publication.

“GAAIN is similar in spirit and goals to other ‘big data’ initiatives that seek to greatly improve the tools and techniques needed to access, organize, and make discoveries from huge volumes of digital data,” Carrillo said. “The advent of cloud computing makes it possible to link databases throughout the world and expand their data processing capability significantly to benefit the research community.”

Carrillo will supervise the development of GAAIN in conjunction with co-principal investigators Art Toga, Ph.D., of the Laboratory of Neuro Imaging (LONI) at the University of Southern California and Giovanni Frisoni, M.D., of the National Center for Alzheimer’s Disease Research and Care and the Instituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Fatebenefratelli Hospital, Italy. Enrique Castro-Leon, Ph.D., who will serve as a consultant, is an enterprise and data center architect for strategic partner Intel Digital Enterprise Group.

GAAIN is built on an international database framework already in use by thousands of scientists and local computational facilities in North America and Europe. The network makes research data available free-of-charge for searching, downloading, and processing across a cloud-based, grid-network infrastructure accessible anywhere through Internet access.

The key to GAAIN’s innovation is its federation of data, which is unprecedented for such a system. GAAIN leadership will invite scientists conducting qualified studies to become partners by permitting GAAIN to link directly to their databases. This will enable researchers to add continually to their data sets and keep all data in GAAIN current and dynamic. It also will enable the scientists to retain control over access to their data, which the Association believes will be important to encouraging participation.

“This is unprecedented and of the utmost importance in brain research, where sometimes thousands of examples are required to observe even the smallest change in the brain,” said Giovanni Frisoni, M.D., neurologist and deputy scientific director at the National Center for Alzheimer’s Disease Research and Care at the IRCCS. He will lead the work of GAAIN in Europe.

“Through GAAIN we envision combining massive amounts of data from multiple sources across many subjects participating in numerous studies,” said Art Toga, Ph.D., professor of neurology at UCLA and director of LONI. “This will provide more statistical power than ever before.”

Source: Alzheimer’s Association

Genophen Taps NextBio Clinical to Incorporate Genomic Data into Disease Risk Software

NextBio recently announced that it has formed a partnership with Genophen, a Stanford University spinout, which will focus on generating personalized disease prevention and wellness plans for patients based on a combination of genomic, clinical, environmental, and behavioral data.

Specifically, Genophen is partnering with NextBio so that it can use the NextBio Clinical platform to analyze genetic variants from whole genome sequence data and combine these with information on things like diet, family history, and exercise to create bespoke disease prevention plans for patients.

Genophen’s President and CEO Hossein Fakhrai-Rad told BioInform that the company tapped NextBio’s platform because it offered access to a curated database of genomic variants that are associated with various disease conditions, and because it expands Genophen’s own internally built repository. The arrangement also lets Genophen focus its efforts on disease risk assessment rather than spend time going through the literature and linking variants and diseases, he said.

Founded in 2008 at the Stanford Genome Technology Center, Genophen has developed a software system dubbed ‘the Genophen platform’ that uses a series of proprietary algorithms to assess patients’ risk of developing complex or multi-factorial diseases such as type II diabetes based on genetic, clinical, environmental, and behavioral information. The platform then provides personalized recommendations to help patients minimize their risk. The platform also prioritizes factors that increase patients’ risk based on their health profiles, and calculates how lifestyle changes could help reduce risk.

Genophen plans to launch its platform publicly in a few weeks, and it will include new features such as a new user interface, Fakhrai-Rad said. He added that in the last year his company has been putting the platform through its paces with a select group of physicians and patients via a pilot project and a currently ongoing beta test program.

The company has also partnered with Illumina’s CLIA laboratory to handle the whole-genome sequencing aspect of its business, Fakhrai-Rad said. Also, it is finalizing arrangements with a second CLIA lab that will offer genotyping services, which are less comprehensive than NGS but much cheaper, Fakhrai-Rad said.

In addition, Fakhrai-Rad stressed that the company will not offer a direct-to-consumer service, but will work in concert with physicians and genetic counselors who will be responsible for discussing a recommended course of action with patients and helping them make decisions about next steps.

For NextBio, the partnership with Genophen reflects a growing demand for its tools from healthcare providers who are looking to make it easier to use whole-genome and targeted sequencing data, NextBio CEO Saeid Akhtari told BioInform.

Historically, the company’s products have been patronized by customers in the pharmaceutical and biotechnology industries involved in drug research and development. However, since the launch of NextBio Clinical last April (BI 4/27/2012), it has begun to receive business from clients in the clinical market including cancer centers, hospitals, and diagnostic companies, Akhtari said.

For instance, last June the company announced that the Cancer Care Institute had licensed its product portfolio — which also includes the NextBio Research software — to analyze oncology patient data for research studies and to select appropriate treatments for patients based on their molecular profiles (BI 6/29/2012).

Earlier this year, Emory University’s Winship Cancer Institute and the Aflac Cancer Center of Children’s Healthcare of Atlanta tapped NextBio Clinical to support their partnership, which is focused on identifying biomarkers that can predict brain cancer metastasis in children in order to help clinicians determine which patients should receive radiation therapy (BI 1/25/2013).

And NextBio expects that the demand for its clinical software to continue to grow and even surpass demand from the pharma/biotech market over the next few years as more clinicians and patients continue to avail themselves of sequencing and molecular profiling technologies, Akhtari said.

The software is also holding its own, Akhtari said, against competing products such as KnomeClinic, a software suite launched by Knome for interpreting and annotating human genomes(BI 6/15/2012).

NextBio believes customers prefer its offering, according to Akhtari, because it provides access to analytic capabilities on private cloud infrastructure so that customers don’t have to purchase their own hardware; offers comprehensive curated content; and comes with an adaptive learning knowledgebase that uses newly incorporated information from patients to improve correlations between variants and disease. The company also updates its software and database content regularly in response to customers’ requests, he said.

Akhtari said that NextBio has potential deals currently going through an “approval process” with other companies besides Genophen, but declined to disclose who those new clients are.

Source: Genophen

Bina Technologies Launches Platform Today, Delivering Breakthrough Big Data Solution for Genomic Analysis

Bina Technologies, the genomic big data science platform accelerating personalized medicine, today announced the commercial launch of the Bina Genomic Analysis Platform. The platform is a linearly scalable end-to-end solution for genomic analysis that is uniquely built to deliver improved data accuracy, reducing the time and improving the cost-effectiveness of processing raw genetic data and generating new insights.

With the Bina Platform, research institutions, universities and health organizations are now equipped to analyze and manage the increasing volume of sequenced DNA data available for variant analysis, which has quickly become a big data problem and bottleneck across the genomic industry. Instead of analyzing a single genome which takes days to complete, the Bina Genomic Analysis Platform can analyze a whole human genome in 4 hours or less.

“One of the main barriers in making personalized medicine a reality is the ever growing challenges around data analysis and data management as more genomic data is generated each day,” said Narges Bani Asadi, founder and CEO of Bina Technologies. “We at Bina are excited to help solve these challenges and deliver scalable genetic analysis, enabling clinicians and scientists to uncover entirely new medical insights.”

Over the past several months, Bina has been conducting an ambitious pilot program with organizations including the Stanford Genetics Department and the Veteran Affairs (VA) Hospital of Palo Alto who have been using the Bina Platform to ingest and analyze genomic data with increased speed and accuracy. Each pilot is experiencing record-breaking results in both speed and accuracy, analyzing several hundred whole human genomes, each in under 4 hours at 40x coverage—or an effective acceleration factor of 100x. Increasingly, scientific researchers and clinicians performing genomic analysis at scale are relying on improvements in both speed and accuracy, while expecting reductions in cost.

Historically, the delivery of data between upstream sequencing companies and downstream health and research organizations has been limited due to the lack of streamlined and affordable data analysis and delivery. The Bina Platform integrates elegantly as a much-needed pipeline between both the sequencing and analysis, and applied health and research segments of the market, enabling vast improvements in patient care due to timely and greater insight into diseases at the molecular level, such as cancer and other genetic disorders.

Moreover, most of today’s genomic analysis tools within research organizations have been too reliant on open source pipelines that are not practical or accurate enough at true scale, as well as clinics who have become too dependent on homegrown technologies. The Bina Platform performs mission critical analysis at scale, more accurately and for less than the cost of doing it with open source or legacy solutions, speeding analysis by weeks and months.

The platform is offered as a massively scalable and extensible on-premise and hybrid cloud solution available on a monthly subscription basis, offering a high-performance computing and big data system for large-scale genomic analysis that organizations can trust. The on-premise solution, or the Bina Box, provides secure and dependable, private cloud storage for clinical organizations requiring even greater data security. Customers can also add Bina Boxes to rapidly increase their ability to analyze whole genomes at scale.

The new platform offering is the first formal technology product from the Silicon Valley based startup.

Source: Bina Technologies