The New York Genome Center And IBM Watson Group Announce Collaboration To Advance Genomic Medicine

NEW YORK, March 19, 2014 /PRNewswire/ -- The New York Genome Center (NYGC) and IBM (NYSE: IBM) today announced an initiative to accelerate a new era of genomic medicine with the use of IBM's Watson cognitive system. IBM and NYGC will test a unique Watson prototype designed specifically for genomic research as a tool to help oncologists deliver more personalized care to cancer patients.

NYGC and its medical partner institutions plan to initially evaluate Watson's ability to help oncologists develop more personalized care to patients with glioblastoma, an aggressive and malignant brain cancer that kills more than 13,000 people in the U.S. each year. Despite groundbreaking discoveries into the genetic drivers of cancers like glioblastoma, few patients benefit from personalized treatment that is tailored to their individual cancer mutations. Clinicians lack the tools and time required to bring DNA-based treatment options to their patients and to do so, they must correlate data from genome sequencing to reams of medical journals, new studies and clinical records -- at a time when medical information is doubling every five years.

This joint NYGC Watson initiative aims to speed up this complex process, identifying patterns in genome sequencing and medical data to unlock insights that will help clinicians bring the promise of genomic medicine to their patients. The combination of NYGC's genomic and clinical expertise coupled with the power of IBM's Watson system will enable further development and refinement of the Watson tool with the shared goal of helping medical professionals develop personalized cancer care.

The new cloud-based Watson system will be designed to analyze genetic data along with comprehensive biomedical literature and drug databases. Watson can continually 'learn' as it encounters new patient scenarios, and as more information becomes available through new medical research, journal articles and clinical studies. Given the depth and speed of Watson's ability to review massive databases, the goal of the collaboration is to increase the number of patients who have access to care options tailored to their disease's DNA.

"Since the human genome was first mapped more than a decade ago, we've made tremendous progress in understanding the genetic drivers of disease. The real challenge before us is how to make sense of massive quantities of genetic data and translate that information into better treatments for patients," said Robert Darnell, M.D., Ph.D., CEO, President and Scientific Director of the New York Genome Center. "Applying the cognitive computing power of Watson is going to revolutionize genomics and accelerate the opportunity to improve outcomes for patients with deadly diseases by providing personalized treatment."

First Watson Application in Genomic Research
Watson will complement rapid genome sequencing and is expected to dramatically reduce the time it takes to correlate an individual's genetic mutations with reams of medical literature, study findings, and therapeutic indications that may be relevant. The intention is to provide comprehensive information to enable clinicians to consider a variety of treatment options that the clinician can tailor to their patient's genetic mutations. It will also help NYGC scientists understand the data detailing gene sequence variations between normal and cancerous biopsies of brain tumors.

"As genomic research progresses and information becomes more available, we aim to make the process of analysis much more practical and accessible through cloud-based, cognitive innovations like Watson," said Dr. John E. Kelly III, Senior Vice President and Director of IBM Research. "With this knowledge, doctors will be able to attack cancer and other devastating diseases with treatments that are tailored to the patient's and disease's own DNA profiles. If successful, this will be a major transformation that will help improve the lives of millions of patients around the world."

The goal is to have the Watson genomics prototype assist clinicians in providing personalized genomic analytics information as part of a NYGC clinical research study. The solution has been under development for the past decade in IBM's Computational Biology Center at IBM Research.

New York State's Investment in Genomic Medicine
New York State is at the forefront of advancing medical science and commercialization. Governor Andrew M. Cuomo recently proposed $105 million to fund a partnership between NYGC and the University at Buffalo's Center for Computational Research to advance genomics research. This investment to enhance the state's genomic medicine capabilities, together with NYGC's acquisition of Illumina's state-of-the-art HiSeq X Ten whole human genome sequencing system, will accelerate the availability of valuable genomic information in New York.

"New York State's investment in cutting-edge innovative industries is creating jobs and growing the economy in Western New York and across our state," said Governor Cuomo. "This collaboration between the New York Genome Center and IBM will help make the region a new hub for the growing bio-tech industry."

IBM is NYGC's Founding Technology Member and will advance the organization's goals of translating genomic research into clinical solutions for serious disease through the collaboration of medicine, science and technology. As biology increasingly becomes an information science, the promise of genomics is closer to reality with the help of data-driven analytics methods and more powerful computing systems. IBM and NYGC's computational biology experts are renowned for accelerating life sciences discoveries using deep analytical approaches and next generation information technologies.  

Learn more about this story at http://ibm.co/1cXTb6u.

To view a Flickr image gallery that illustrates today's news please click here.

For additional perspectives on this story, please watch this video.

To join the social conversation on Twitter use the hashtag #NYGCWatson. 

Journalists and bloggers can download broadcast video, b-roll and photos about the Watson and New York Genome Center collaboration at http://bit.ly/1dcWlZF. The video is available in HD, standard definition broadcast and streaming quality.

About the New York Genome Center
The New York Genome Center (NYGC) is an independent, nonprofit at the forefront of transforming biomedical research and clinical care with the mission of saving lives. As a consortium of renowned academic, medical and industry leaders across the globe, NYGC focuses on translating genomic research into clinical solutions for serious disease. Our member organizations and partners are united in this unprecedented collaboration of technology, science, and medicine. We harness the power of innovation and discoveries to improve people's lives - ethically, equitably, and urgently. Member institutions include: Albert Einstein College of Medicine, American Museum of Natural History, Cold Spring Harbor Laboratory, Columbia University, Cornell University/Weill Cornell Medical College, Hospital for Special Surgery, The Jackson Laboratory, Memorial Sloan-Kettering Cancer Center, Icahn School of Medicine at Mount Sinai, New York-Presbyterian Hospital, The New York Stem Cell Foundation, New York University, North Shore-LIJ, The Rockefeller University, Roswell Park Cancer Institute and Stony Brook University. For more information, visit: www.nygenome.org.

About IBM Watson
Named after IBM founder Thomas J. Watson, Watson was developed in IBM's Research labs and is now being accelerated into market by the new Watson Group. Watson represents a new class of software, services and apps that think, improve by learning, and discover answers and insights to complex questions from massive amounts of Big Data. Watson's ability to answer complex questions posed in natural language with speed, accuracy and confidence is transforming decision-making across a variety of industries, including health care, financial services and retail. IBM has advanced Watson from a game-playing innovation into a commercial technology. Using natural language processing and analytics, Watson processes information akin to how people think, representing a major shift in an organization's ability to quickly analyze, understand and respond to Big Data. Now delivered from the cloud and able to power new consumer and enterprise services and apps, Watson is 24 times faster, smarter with a 2,400 percent improvement in performance, and 90 percent smaller – IBM has shrunk Watson from the size of a master bedroom to three stacked pizza boxes. IBM is investing $1 billion to introduce a new class of cognitive computing services, software and apps, and investing $100 million to spur innovation for software application providers to develop a new generation of Watson-powered solutions. Learn more about IBM Watson at www.ibmwatson.com. Learn more about IBM Research at www.research.ibm.com.

Learn more about IBM healthcare at ibm.com/smarterhealthcare.

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Logo - http://photos.prnewswire.com/prnh/20090416/IBMLOGO

SOURCE IBM

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UC Davis Purchases Irys System From BioNano Genomics To Advance Genome Mapping And Assembly Of Wheat Relative

SAN DIEGO, Jan. 13, 2014 /PRNewswire/ -- BioNano Genomics announced today the purchase of an Irys™ System by UC Davis to assist, among other projects, in completing the genome assembly of Aegilops tauschii, one of three progenitors of today's bread wheat. The team of researchers at UC Davis, led by Dr. Jan Dvorak, will use the Irys System in their workflow as they determine the sequence, location, and orientation of all genes and transposable elements of the A. tauschii genome.  This information will be used to advance the assembly and analysis of the wheat genome sequence, which is known to be five times larger and significantly more complex than the human genome.

"Among the world's essential crops for human and animal food, the wheat genome has yet to be fully realized because of its complexity," said Erik Holmlin, president and CEO of BioNano Genomics. "The UC Davis team's research with A. tauschii will help determine how wheat genome is organized and contribute to the large international effort to decode the genome of one of the world's most important food crops."

"To date, very few high-quality assemblies are available for large and complex genomes, like wheat, because we have inaccurate, low-resolution physical maps on which to arrange DNA sequence information," stated Han Cao, Ph.D., founder and chief scientific officer of BioNano Genomics. "The Irys System provides a high-resolution genome map upon which DNA sequences can quickly and accurately be organized."

Ancestor Gives Clues to Today's Wheat

Bread wheat (Triticum aestivum L.) is a hexaploid species containing three different ancestral genomes (designated A, B, and D), each of which has seven pairs of chromosomes. In addition, approximately 90 percent of the wheat genome is made up of repetitive stretches of DNA, making the assembly of an accurate and complete genome map and genome sequence extremely difficult. As the progenitor to wheat's D genome, A. tauschii is a wild grass that spontaneously hybridized with cultivated tetraploid wheat 8,000 years ago, producing what we know today as bread wheat.

"In order to complete the sequence of a large genome, like that of wheat, we need to know how all the genes are organized within each chromosome and the length and location of the many long areas of repeats," said Ming-Cheng Luo, Ph.D., research geneticist in the Department of Plant Sciences at UC Davis and co-PI on the A. tauschii sequencing project. "Despite advances in high-throughput sequencing, accurate de novo assembly of a genome has previously been the weak link in genomics research."  

To assemble a genome de novo (from scratch), scientists must determine how the small lengths of DNA sequences generated from short-read next generation sequencing (NGS) methods are organized in the whole genome. BioNano's Irys System is a genome mapping technology that fills a void in de novo assemblies by providing a high-resolution physical genome map to anchor and organize DNA sequence information to dramatically improve the fidelity of the final genome assembly. 

"Last year, we worked with BioNano to generate Irys data that allowed us to quickly create and publish a high-resolution genome map of a particularly complex region of Aegilops tauschii genome," said Dr. Luo. "Based on the success of that collaboration, we have decided to acquire our own Irys system, and we will build upon that research to create an accurate draft of the entire D genome sequence. Once completed, the high-quality draft of A. tauschii D genome can be used by the global research community to predict gene locations and accelerate genome sequencing and assembly of wheat and its relatives."

New Technologies Are Reducing the Costs of Genome Research

Assembling a genome to completion has previously been an intractable problem because researchers have not been able to easily visualize repetitive elements and structural variations. All genomes contain structural variations, which include large sections of repeats, deletions, duplications, insertions, inversions, translocations, and copy-number variants.  

BioNano's Irys System is an automated, long-read technology that allows for precise and accurate visualization of the underlying organization and structural variation of extended stretches of DNA.

"NGS methods, where the DNA is cut into smaller pieces to be sequenced, loses structural information making genome assembly an inaccurate, labor-intensive and costly task," said Dr. Luo. "With BioNano's Irys System, we can actually retain the long-range contiguity of the DNA, which allows us to accurately assemble and finish genomes as well as compare the structural variations that exist among different genomes to learn how an organism has genetically adapted to changing environments."

Dr. Cao added, "The hidden costs in sequencing are assembly, analysis, and annotation of the genome.  Rapid and accurate de novo map assembly with BioNano's technology makes sequencing projects less expensive by streamlining the process and providing a genome map with unprecedented quality and accurate structural variation information.  Our technology actually reduces backend analysis costs so that researchers can expand the number of genomes that can be studied, thus supporting more comprehensive surveys and comparisons among genomes."

Safeguarding Wheat's Future

The United Nations has said that harvest yield of wheat will need to increase by 60 percent by 2050 to meet the dietary needs for our expected population growth. However, wheat output has recently plateaued causing alarm in the wheat research and production community. A more complete genomic map of wheat and ultimately genome sequence could provide important information on how wheat adapts to drought, disease, and temperature changes.

Dr. Luo concluded, "With our recent grant from the National Science Foundation and the integration of the Irys System and the new high-throughput V2 chips into our workflow, we will be able to quickly complete a high-quality draft of the A. tauschii genome. By decoding the sequences of all genes and determining their locations and orientations relative to each other, wheat geneticists will be able to identify changes in the wheat genome that are responsible for the high productivity of modern cultivars. This knowledge and more efficient breeding techniques based on an accurate wheat genome sequence will accelerate breeding of new, more productive varieties."

To learn more: BioNano Genomics will be hosting a workshop at the upcoming International Plant and Animal Genomes Conference held in San Diego on Tuesday, January 14, at 1:30PM. Presentations will include results generated with the Irys System on wheat and other crop plants.

About Irys

Irys makes it possible to routinely and accurately detect genomic structural variation and to finish genome assemblies. The fully automated Irys benchtop instrument uses the IrysChip to uncoil and confine long DNA molecules in proprietary Nanochannel Arrays™ where they are uniformly linearized in a highly parallel display for high-resolution, single-molecule imaging. Irys does not employ DNA fragmentation or amplification, which are typical with next-generation sequencing. The result is sequence information over extremely long "reads" ranging from hundreds of kilobases to a megabase, where the sample's valuable structural information is preserved. Irys makes it possible for researchers to directly observe structural variants including replications, deletions, translocations and inversions.

About BioNano Genomics

Headquartered in San Diego, BioNano Genomics is delivering an altogether better way of gaining a fully informed understanding of genomes. The Company's platform provides researchers and clinicians the most comprehensive, organized and actionable picture of a genome with unprecedented insights into how the individual components of genomes are ordered, arranged, and interact with each other. BioNano Genomics works with institutions in life science, translational research, molecular diagnostics and personalized medicine. The Company is supported by private investors and grant funding from genomics programs at federal agencies, including the NIH and NIST-ATP.

www.BioNanoGenomics.com

Notes: BioNano Genomics is a trademark of BioNano Genomics, Inc. Any other names of actual companies, organizations, entities, products or services may be the trademarks of their respective owners.

SOURCE BioNano Genomics

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