Category Archives: Genome

Jim Kent: The UCSC Genome Browser
http://genomics.soe.ucsc.edu/

By: UC Santa Cruz

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Jim Kent: The UCSC Genome Browser - Video

Daidai genome Little Bit + VB download
So this is for my friends birthday, I hope you like it O: I never really made a "newcomer" video so here is a semi newcomer video xD her voicebank is up for ...

By: Yuusori Hinaku

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Daidai genome Little Bit + VB download - Video

NYU CHIBI Dr. Steven Shen: Reading and Interpreting Genome Activities 11.09.14
Sixty years after the discovery of the DNA double helix, genome study has advanced from identifying genome components to understanding how individual compone...

By: nyuinformatics

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NYU CHIBI Dr. Steven Shen: Reading and Interpreting Genome Activities 11.09.14 - Video

Our Global Human Genome
In order to create a comprehensive genomic cancer database, scientists have to reach out to the entire world. Starting with the underserved populations in South Chicago, oncologist Olufunmilayo...

By: World Science Festival

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Our Global Human Genome - Video

Stoke with Genome
Play with StokeNo Fumefx used.

By: Ling Sai

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Stoke with Genome - Video

YourGenome7505316702325174213jpg

A WEBSITE has been relaunched in a bid to take genetics to a wider audience and unravel the mysteries of DNA.

Relaunched last week to coincide with Association for Science Education's Annual Conference, yourgenome.org has been developed by public engagement professionals at the Wellcome Genome Campus at Hinxton.

The site aims to provide accessible, entertaining and thought-provoking guides to an area of science that is revolutionising diagnosis and treatment.

Genomics has been catapulted into the public conciousness in recent months, with the Government having pledged to understand the genomes of 100,000 people. In December, website 23andMe launched a UK version, enabling people in this country to to have their DNA screened for genes associated heridetary conditions such as cystic fibrosis or sickle cell anaemia. Regular readers of Ideas will also know that Cambridge is home to a number of firms specialising in genomics, such as start-up GeneAdviser which is aiming to provide accurate testing for patients with rare genetic diseases.

"Genomics is constantly in the news but, for many, DNA and its role in our biology is still something of a mystery," says Dr Julia Willingale-Theune, manager of public engagement at the Wellcome Genome Campus. "With yourgenome.org, we want to share what scientists know about the genome already and what they are trying to find out, helping everyone to understand and engage with a topic that's likely to have a huge impact on their future health."

The website provides key facts about genomics and bioinformatics with the help of videos and 3D animations. It also features posts by experts looking at advances in research and applications in healthcare. There are also debates that give readers a balanced view of the more controversial aspects of genomics, such as data security, animal research and gene therapy.

Content on the website is driven by an editorial board comprised of expert researchers and specialists in science education and communication from the Wellcome Genome Campus and beyond. This editorial board will ensure that the website remains up-to-date, relevant and accurate.

The Wellcome Genome Campus is home to the Wellcome Trust Sanger Institute, which made the greatest single contribution to the Human Genome Project in 2003 and has remained at the forefront of genetic research ever since. It is also home to the European Bioinformatics Institute, which goes by the catchy acronym of EMBL-EBI. This is a global leader in the storage, analysis and dissemination of large biological datasets, and helps scientists realise the potential of 'big data', enhancing their ability to exploit complex information to make discoveries that benefit mankind. Experts from both institutes have contributed to the site.

"During our lifetimes, the way we experience healthcare will change; in the next decade many aspects of care, from diagnosis to medication, and many lifestyle choices will depend on the information encoded in our genome," said Jon Kudlick, director of membership, marketing and communications at the Society of Biology.

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Yourgenome website from Wellcome Genome Campus to unravel mysteries of DNA

Simons Foundation awards up to $1 million to UC Santa Cruz Genomics Institute to develop a comprehensive Human Genome Variation Map for scientific and medical research

VIDEO:Benedict Paten discusses work on the Human Genome Variation Map at the University of California Santa Cruz Genomics Institute. view more

Researchers at the UC Santa Cruz Genomics Institute have received a grant for up to $1 million from the Simons Foundation to develop a comprehensive map of human genetic variation. The Human Genome Variation Map will be a critical new resource for both medical research and basic research in the life sciences.

The one-year pilot project aims to overcome the limitations of the current model for analyzing human genome data, which is based on the use of a single reference sequence for the human genome. Essentially, all novel sequencing data is analyzed by mapping new genome sequences to this one reference set of 24 human chromosomes to identify variants. But this approach leads to biases and mapping ambiguities, and some variants simply cannot be described with respect to the reference genome, according to David Haussler, professor of biomolecular engineering and director of the Genomics Institute at UC Santa Cruz.

"One exemplary human genome cannot represent humanity as a whole, and the scientific community has not been able to agree on a single precise method to refer to and represent human genome variants. There is a great deal we still don't know about human genetic variation because of these problems," said Haussler, who will lead the project with co-investigator Benedict Paten, a research scientist at the Genomics Institute.

According to Paten, the proliferation of different genomic databases has resulted in hundreds of specialized coordinate systems and nomenclatures for describing human genetic variation. UC Santa Cruz genomics researchers are intimately familiar with this "Tower of Babel" of databases through their work to display data from all these sources on the widely used UCSC Genome Browser. Launched in July 2000 shortly after UC Santa Cruz posted the first working draft of the human genome sequence on the Internet, the browser now serves 130,000 researchers around the world and gets more than 1 million web page requests per day.

"For now, all our browser staff can do is to serve the data from these disparate sources in their native, mutually incompatible formats," Paten said. "This lack of comprehensive integration, coupled with the over-simplicity of the reference model, seriously impedes progress in the science of genomics and its use in medicine."

Recently, with funding from the Simons Foundation, researchers David Reich and Nick Patterson at the Broad Institute of MIT and Harvard have amassed more than 300 complete human genome sequences representing a range of ethnicities. Haussler and Paten plan to use this set of human genomes, which they say is deeper and more completely organized than any prior human data set, to build a new graph-based human reference genome structure.

"This unique data set of genome diversity gives us an opportunity to define a comprehensive reference genome structure that can be truly representative of human variation. Eventually, we will want to expand it to include many more genomes, but this pilot project will focus on building a map structure based on the Reich-Patterson data set," Paten said.

The new Human Genome Variation Map will replace the current snarl of isolated, incompatible databases of human genetic variation with a single, fundamental representation formalized as a very large mathematical graph. The clean mathematical formulation is a major strength of this new approach, Paten said.

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UC Santa Cruz to lead effort to build a new map of human genetic variation

Evaluating and ranking genome assemblers by Michael Barton
Scientific results are shared as manuscripts which researchers read and interpret in their own work. Based in the field of genomics, this talk will show how ...

By: Docker

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Evaluating and ranking genome assemblers by Michael Barton - Video

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Michelle Leis

OPB | Jan. 12, 2015 12:06 p.m. | Updated: Jan. 12, 2015 1:41 p.m.

In 2003, the first human genome wassequenced through the collaborative effort of 20 research centers. It cost nearly $3billion.

Almost 12 years later, the cost ofsequencing has come down faster than Moores law. We can now sequence an entire genome for $2,000 to $3,ooo in a fraction of the time it took to sequence that first humangenome.

In the first part of a new series on genomics, we examine the ways in which genetic data is used to personalize medicine, and take a look at whats being done in the clinical setting. Specifically, well address how this technology has changedwhat we know about cancer and discuss some of the limitations of what we can accomplish through genomeanalysis.

GUESTS:

In the next part of our series, well look into some of the legal and ethical concerns surrounding geneticresearch.

Rose E. Tucker Charitable Trust

James F. and Marion L. Miller Foundation

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Genomics: The Slow Revolution

The Association for Molecular Pathology (AMP), the premier global, non-profit organization serving molecular testing professionals, announced the release of an important white paper addressing the consequences of regulatory and reimbursement forces directed against molecular diagnostic testing that threaten patient care. The paper, titled, "A Molecular Diagnostic Perfect Storm: The Convergence of Regulatory & Reimbursement Forces that Threaten Patient Access to Innovations in Genomic Medicine" is now available online at http://bit.ly/1yGlghJ.

"The breakthroughs made possible by mapping the human genome -- a multi-billion dollar project that took more than a decade to complete -- are being threatened by government regulations, which in turn are threatening patient access to truly revolutionary treatments," said Victoria M. Pratt, PhD, Indiana University School of Medicine, active AMP Member, and lead author of the paper. "We hope that this manuscript further enlightens regulatory and reimbursement stakeholders about the storm brewing in Washington that could dismantle the development and coverage of important molecular diagnostic tests."

Medical professionals in universities, cancer centers, clinical laboratories, and pharmaceutical/manufacturing companies across the country have honored the public trust in the Human Genome Project by developing hundreds of innovative diagnostic tests and therapies that are advancing modern medicine in ways that would have been impossible without this breakthrough. By eliminating the barriers outlined in "The Perfect Storm" paper, genome-based research will continue to play a critical role in the development of more powerful tools to treat complex diseases such as cancer, diabetes, and cardiovascular disease.

Threats stemming from efforts by the U.S. Food and Drug Administration (FDA) and the Centers for Medicare and Medicaid Services (CMS), the two federal agencies that oversee molecular diagnostic testing, are the cause of this "Perfect Storm."

The FDA's new policies will effectively reformulate existing medical device regulations and consider medical professionals as manufacturers which will impose substantially new and duplicative requirements on clinical laboratories and hospitals. Meanwhile, CMS, who runs Medicare, the nation's largest insurer and whose actions are frequently mimicked in the private sector, has taken a heavy handed approach in denying coverage or reducing payment for several medically necessary molecular pathology tests. Unfortunately, health care providers -- those developing and delivering innovative diagnostic tests -along with patients, who are the ultimate intended beneficiaries, are caught in the middle.

"AMP is addressing the consequences of this gathering perfect storm of regulatory and reimbursement challenges directed against molecular diagnostic testing with recommendations designed to preserve patient access to these essential medical services" said AMP President, Janina Longtine, MD. "We are greatly concerned that these forces are coalescing to bring about consolidation of laboratory testing, to the detriment of local testing. This would have far-reaching negative effects on the healthcare system. As such, AMP is committed to working with the regulatory and reimbursement bodies to find a resolution that optimizes patient safety and offers access to important medical tests."

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The above story is based on materials provided by Association for Molecular Pathology. Note: Materials may be edited for content and length.

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Convergence of regulatory, reimbursement forces threaten patient care, experts say