Category Archives: Genome

Public release date: 17-Sep-2013 [ | E-mail | Share ]

Contact: David McKeon dmckeon@nyscf.org 212-365-7440 New York Stem Cell Foundation

New York, NY (September 17, 2013) The New York Genome Center (NYGC) announced today that The New York Stem Cell Foundation (NYSCF) has become an Associate Member, joining NYGC's growing consortium of 16 research and clinical institutions, all working together in new ways to utilize genomic data for better detection, treatment, and prevention of disease.

"Biologists at the NYSCF working with the genomic scientists at NYGC will help address some of the critical roadblocks in stem cell research," said Dr. Robert B. Darnell, President and Scientific Director of NYGC. "Modern genomics has the potential to provide vital missing information to help us learn how to harness stem cells for use in clinical medicine. We've developed techniques and ideas here at NYGC that will greatly synergize with the beautiful and pioneering work ongoing at the NYSCF."

Stem cell biology and genomic analysis are both critical to the advancement of precision medicine. The collaboration between the Genome Center and NYSCF will merge cutting-edge capabilities in human biology with genomic research, creating an optimal environment for translating research into a better standard of care for patients.

"We are excited to work with NYGC as we continue to accelerate cures for the major diseases of our time. This will enable collaboration within the growing biotechnology community in New York," said Susan L. Solomon, CEO of The New York Stem Cell Foundation. "NYSCF has a number of current projects in which additional genomic analysis may play a critical role in better understanding disease susceptibility and risk factors. We hope to work with NYGC to integrate their genomic analysis into our research."

The New York Genome Center provides an "Integrated Genomics Solution", which includes (1) scientific consultation, (2) next-generation sequencing services for exomes, whole genomes, and RNA, (3) bioinformatic analysis of sequencing results using a high performance computing environment, and (4) data storage so that researchers and clinicians can readily access these results.

As an Associate Member, NYSCF will have priority access to these services. NYSCF will also become a member of the NYGC's Scientific and Clinical Steering Committee (SCSC), which provides guidance on research direction and oversees research collaborations and related funding.

NYSCF employs 45 full-time scientists and engineers in its laboratory who are engaged in the most advanced stem cell research and technology development, including creating NYSCF's Global Stem Cell Array, an automated technology platform that for the first time makes it possible to create identical stem cell lines from a large number of patients in a massively parallel process. This is a revolutionary tool that takes the vast amount of information we have learned from sequencing the human genome and puts it into a biological context to accelerate the development of safe and effective medicine. This robotic system creates induced pluripotent stem (iPS) cell lines and cell derivatives in a standardized manner from genetically diverse patients and patients with disease. This program will create an array of stem cell lines representing the full range of human genetics and the diversity of the world's population.

"This collaboration will expand our resources to analyze our stem cell samples at the genetic level, as we continue to bring the latest discoveries in genome science to our work to understand, prevent, and eventually cure diseases like diabetes, Alzheimer's, and multiple sclerosis among many others," said Scott Noggle, Director of the NYSCF Laboratory and the Charles Evans Senior Research Fellow for Alzheimer's Disease.

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New York Genome Center announces the New York Stem Cell Foundation as an Associate Member

Sep. 17, 2013 Numerous recent studies linked gut microbiota with various diseases such as obesity or diabetes. Little is known, however, on how gut and skin microbiota composition is controlled. In a recent study published in the journal Nature Communications on 17 September, John Baines, Saleh Ibrahim and their colleagues of the Inflammation Research Excellence Cluster show that composition of skin microbiota is controlled by the host genome and that skin bacteria may have a greater influence on inflammatory diseases than previously thought. Their landmark findings will open the door to identify gene variants controlling skin microbiota and to define their link to various diseases such as skin inflammatory disorders.

The human body contains more bacteria than human cells. Most of these bacteria comprise the normal gut and skin microbiota. Susceptibility to chronic inflammatory diseases is determined by immunogenetic and environmental risk factors that include resident microbial communities. Whether these differences are of primary etiological importance or secondary to the altered inflammatory environment remains largely unknown.

The inflammation cluster research groups led by Saleh Ibrahim of the University of Lbeck, and John Baines of the MPI and CAU, correlated the genomic variations of hundreds of mice that partially develop skin inflammatory diseases with skin microbiota. They showed evidence for host gene-microbiota interactions contributing to disease risk in a mouse model of autoantibody-induced inflammatory skin disease. Furthermore they identified genetic loci contributing to skin microbiota variability, susceptibility to skin inflammation and their overlap. The majority of the identified microbiotal communities are characterized by reduced abundance being associated with increased disease risk, providing evidence of a primary role in protection from disease.

These findings offer a promising potential for using those probiotic species for preventative and therapeutic treatment development. John Baines: "It appears that the skin flora is a phenotype that is partially controlled by the host genome variations. This in turn predisposes to the development of disease. The more we learn about these interactions, the more possibilities there will be for a better and more individualized treatment and prevention of skin inflammatory diseases.

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The above story is based on materials provided by Christian-Albrechts-Universitaet zu Kiel.

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Host genome controls skin microbiota and inflammation

Kimberly Strong - In sickness and in health variables effecting genome sequencing ethical issues
Watch on LabRoots at: http://labroots.com/user/webinars/details/id/43 In addition to the exciting promise that genome sequencing holds, concerns are also oft...

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Kimberly Strong - In sickness and in health variables effecting genome sequencing ethical issues - Video

Yaniv Erlich - Genome Hacking
Watch on LabRoots at: http://labroots.com/user/webinars/details/id/41 Sharing sequencing datasets without identifiers has become a common practice in genomic...

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Yaniv Erlich - Genome Hacking - Video

Ethical, Legal, and Social Issues in Whole Exome and Whole Genome Sequencing
Whole exome and whole genome sequencing are two very new testing techniques that are poised to change the current paradigm of clinical genetic testing. To get ready for these up-and-coming...

By: TheWSGSC

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Ethical, Legal, and Social Issues in Whole Exome and Whole Genome Sequencing - Video

Kansas City, Mo. (PRWEB) September 16, 2013

What are the fastest growing start-ups in my city? Which of them are hiring? Who are the founders and investors in my industry that I should meet given the stage Im at in my entrepreneurial journey?

These are the questions local entrepreneurs and city leaders often ask, and finding the correct answers can be time-consuming, if not impossible. The Ewing Marion Kauffman Foundation today announced a grant to an organization that has a tool to help them find the answers. Startup Genome is a worldwide network of volunteer curators who create up-to-date and accurate maps of the entrepreneurial communities in which they live and work. Kauffmans grant will support and accelerate Startup Genomes ability to build its database and collect and evaluate data.

Mapping local start-up ecosystems not only provides an important tool to communities, but it will create a treasure trove of rare data on local start-ups, said Dane Stangler, director of Research and Policy at the Kauffman Foundation. Our plans include studying how start-up communities develop and identify action steps that cities can take to grow their entrepreneurial community and measure their progress.

Startup Genome enables entrepreneurs and investors to plug into their city's start-up scene, which has untold benefits to them and their local economies, said Thom Ruhe, vice president of Entrepreneurship at the Kauffman Foundation. So everyone wins when communities gain a better understanding of their city's entrepreneurial climate.

Startup Genomes goal is to recruit 1,000 local curators who will populate start-up community data in their citys maps. Currently, 332 curators are curating maps in 271 cities and 57 countries. So far they've collected data on more than 26,000 founders, 84,000 startups, 5,800 investors and more than 18,000 deals. Curators can be entrepreneurs, investors, accelerator program managers, Startup Weekend organizers, community builders, students, journalists and more.

Working with the Kauffman Foundation will help us toward our long-term vision to build the deepest, most accurate database of start-up companies and entrepreneurs in the world, said Shane Reiser, founder of Startup Genome. Kauffmans research team will enable us to leverage that data to help organizations and cities measure their impact and identify ways to grow, and to share the data openly so that anyone can use it to build useful tools for entrepreneurs.

Startup Genome launched a new website last week at http://www.startupgenome.com with improved searches, speed, curator tools; updated statistics and industry pages; and responsive design for mobile phones. The site will continue to develop data automation tools, integrations and partnerships with other online sources such as CrunchBase, Angel List and LinkedIn.

About the Kauffman Foundation

The Ewing Marion Kauffman Foundation is a private, nonpartisan foundation that aims to foster economic independence by advancing educational achievement and entrepreneurial success. Founded by late entrepreneur and philanthropist Ewing Marion Kauffman, the Foundation is based in Kansas City, Mo., and has approximately $2 billion in assets. For more information, visit http://www.kauffman.org, and follow the Foundation on http://www.twitter.com/kauffmanfdn and http://www.facebook.com/kauffmanfdn.

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Kauffman Foundation Announces Grant to Startup Genome to Grow and Study World’s Largest Maps of Local Entrepreneur ...

Marcel Dinger - Lighting up the dark matter of the genome Unravelling the roles of noncoding DNA ...
Watch on LabRoots at: http://labroots.com/user/webinars/details/id/51 Approximately 98% of the human genome comprises noncoding DNA, the function of which is...

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Marcel Dinger - Lighting up the dark matter of the genome Unravelling the roles of noncoding DNA ... - Video

Genome mapping for newborns to be government-funded
The government is launching a $25 million program to map a newborn baby #39;s DNA to allow doctors to screen for thousands of conditions. Professor of medicine o...

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Genome mapping for newborns to be government-funded - Video

Genome as a program. Part 1 #39;
The start of "Digital Genetics". Presentation on BarCamp Sarasota, Spring 2013. Originally recorded May 5, 2013.

By: Victor Sumskoy

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Genome as a program. Part 1' - Video

Public release date: 12-Sep-2013 [ | E-mail | Share ]

Contact: Jia Liu liujia@genomics.cn BGI Shenzhen

Cambridge, MA, San Antonio, TX and Shenzhen, China, September 12, 2013BGI Tech Solutions Co., LTD, (BGI Tech), a subsidiary of BGI, the world's largest genomics research organization, and South Texas Accelerated Research Therapeutics (START), announced today that they are collaborating on the San Antonio 1000 Cancer Genome Project, a groundbreaking cancer genome study designed to link genetic alterations that underlie different cancers to detailed clinical outcomes. Such findings could enable scientists to pursue the development of targeted, personalized cancer treatments. All data generated from SA1kCGP will be made available publicly and freely to researchers and others worldwide.

The San Antonio 1000 Cancer Genome Project (SA1kCGP) is presently conducting whole genome sequencing of cancerous and normal tissue and blood samples from patients with one of 10 cancers. Under the collaboration, BGI Tech will provide next-generation high-throughput genomic sequencing to identify mutations associated with specific cancers, as well as gathering, analyzing and archiving at BGI all genetic and clinical data generated through the tumor sequencing and clinical analyses. START, which initiated SA1kCGP, will conduct patient recruitment, tumor sample acquisition, and collection of clinical patient information.

SA1kCGP is unique relative to other major cancer genome research projects, given the project's direct linkage of genomic and clinical information, including both treatment and survival data, using START's electronic medical records and proprietary Clinical Synchrony software technology, so that the relationship of genomic alterations and clinical outcome can be realized. This cannot be done with data from other major cancer genome research projects that only collect minimal clinical information, such as The Cancer Genome Atlas, a research program conducted by the National Institutes of Health at a cost to date of more than $375 million.

"We are excited to be collaborating with START on this extremely important, fundamentally different cancer genomic research," stated Yingrui Li, Chief Executive Officer of BGI Tech. "With SA1kCGP's world-class team of physicians and researchers, the leadership of START's Dr. Tony Tolcher, and the scope and size of the project, we expect SA1kCGP to accelerate the development of new cancer diagnostics and therapies. SA1kCGP is unique as a privately funded project strategically structured to generate correlated, useful, and accessible clinical and genomic cancer data that could lead to beneficial, targeted cancer treatments," he continued.

"Teaming with BGI Tech, with its broad array of sequencing technologies, deep bioinformatics expertise, and extensive throughput capacity, will advance SA1kCGP to a whole new level," stated Dr. Anthony W. Tolcher, clinical director for START. "As a privately funded effort, SA1kCGP depends upon the shared vision and commitment of community-based donors, and the profound role BGI will play in the project further elevates the potential benefits that can be achieved for cancer patients through these generous contributions," he added.

SA1kCGP, launched in 2012, has already exceeded its initial goal of collecting samples from 1,000 patients. With a 90 percent consent rate and growing pace of enrollment, 1,200 patients have agreed to date to have their tumor tissues sampled and to allow for the transplantation of their tumors to mouse models in order to target genetic mutations for drug selection and development. SA1kCGP plans to sequence the cancer genomes of 10,000 patients at a fraction of the cost of other major cancer genome projects. The budget for SA1kCGP currently stands at $5 million, with approximately $1 million raised to date exclusively through community contributions.

SA1kCGP has assembled a world-class team of more than 200 San Antonio area cancer surgeons, pathologists, researchers and oncologists from numerous hospitals, most of which are local providers at community-based facilities where 90 percent of cancer care and where clinical studies occur. These hospitals are enrolling cancer patients into the research project, and collecting the tissue samples to be sequenced and analyzed. By working through this community network, referral bias (influence of disparate data source) will be avoided since the patient population will be typical of the representative cancer patient in the community, as opposed to patients in tertiary cancer centers. This increases the ability to generate large enough data sets for analysis through predicative algorithms that could ultimately explain underlying biological causes of cancer.

In contrast to past research, where sample preservation was formaldehyde based for 30 years, hematology and oncology researchers involved in SA1kCGP have agreed to change the paradigm for genomic oncology by using fresh tissue for this analysis. The logistics of obtaining fresh tissue is a major hurdle to large scale genomic research in oncology, a barrier that START has addressed by targeting community treatment centers, where 90 percent of cancer care occurs. These samples will also be available for further research in areas of RNA and protein analysis to complement the DNA sequencing.

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BGI and START initiate collaboration to advance unique San Antonio 1000 Cancer Genome Project