Category Archives: Genome

subaru forester 2.5T STI-Genome
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subaru forester 2.5T STI-Genome - Video

Peter #39;s Abundance Espresso Shot #18: Genome Sequencing in Your Pocket
For more Abundance Espresso Shots and Peter #39;s blogs, sign up at http://www.diamandis.com. Peter #39;s Abundance Espresso Shot is a new video series with author, ...

By: Peter Diamandis

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Peter's Abundance Espresso Shot #18: Genome Sequencing in Your Pocket - Video

XLDB 2013: 2012 Government Big Data Solutions Award: Analyzing Cancer-Genome Relationships
Speaker: Tom Plunkett (Oracle) XLDB-2013 website: http://xldb.org/2013 Copyright 2013 Stanford University This work is licensed under a Creative Commons Attr...

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XLDB 2013: 2012 Government Big Data Solutions Award: Analyzing Cancer-Genome Relationships - Video

Newswise DANVILLE, Pa. - Four Geisinger Health System researchers have taken center stage in the national arena of genomics thanks to new funding from the National Human Genome Research Institute (NHGRI), an arm of the U.S. National Institutes of Health (NIH). It recently awarded three grants totaling $25 million to initiate the Clinical Genome (ClinGen) Project.

Completed in April 2003, the Human Genome Project represents a landmark international research effort that mapped the genes making up human DNA. Today, the ClinGen Project is now harnessing data from hundreds of thousands of clinical genetics tests being performed each year and determining which variants are most relevant to improving patient care.

David Ledbetter, Ph.D., FACMG, executive vice president and chief scientific officer of Geisinger Health System; is principal investigator on two of the grants, one of which also includes Christa Lese Martin, Ph.D., FACMG, director of the Geisinger Autism & Developmental Medicine Institute, as a co-principal investigator. Andy Faucett, MS, CGC, director of policy and education, Geisinger Health System, is a key contributor to the ClinGen efforts, as is Marc S. Williams, M.D., FACMG, director, Geisinger Genomic Medicine Institute (http://www.geisinger.org/research/centers_departments/genomics/), who will lead efforts to make Geisinger the first institution in the nation to pilot the incorporation of this information into electronic health records.

Drs. Ledbetter and Martin founded the International Standards for Cytogenomic Arrays (ISCA) Consortium in 2007. Their initial effort has evolved into the ClinGen Project.

Because of the grant award and the major role Geisinger researchers played in securing it, Geisinger patients may now be among the first in the nation to bear witness to the benefits of advances in personalized medicine.

Technological advances are quickly allowing genome-wide analysis to become commonplace in the care of patients. However, the ability to detect DNA variants has greatly surpassed the ability to interpret their clinical impact, which has thus far limited the benefit of these technologies, said Dr. Ledbetter. Improving genomic interpretation will require a coordinated effort from both the clinical and research communities.

The ClinGen Project builds upon several years of work supporting data sharing of structural genomic variants among a large group of clinical cytogenetic laboratories through the ISCA Consortium, said Martin. By expanding our scope to include both structural and sequence variants, we will provide broader benefit to the community.

In 2012, Ledbetter and Martin, along with Joyce Mitchell, Ph.D. , University of Utah, Salt Lake City; Robert Nussbaum, M.D., University of California, San Francisco; and Heidi Rehm, Ph.D., Brigham and Womens Hospital and Harvard Medical School, Boston, Mass.; founded the International Collaboration for Clinical Genomics (ICCG), an organization of laboratories, clinicians and researchers dedicated to improving the quality of genomic testing through data sharing and collaboration.

As part of the ClinGen Project, the ICCG (www.iccg.org) has been awarded an $8.25 million U41 grant from the NHGRI and the Eunice Kennedy Shriver National Institute of Child Health and Human Development, divisions of NIH, to continue its work to develop a unified clinical genomics database from clinical laboratories. The ICCG will work closely with a team at the National Center for Biotechnology Information (NCBI), part of the National Library of Medicine, a division of the NIH, to develop a database to house the data, known as ClinVar

A unique aspect of this project is that it represents a strong public-private partnership that relies on the collaboration between academic and commercial genetic testing laboratories, many of which have not participated extensively in such an effort in the past. The project will result in improved patient care through data sharing that supports evidence-based curation of genes and variants.

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Geisinger Genomics Researchers Take Leading Role in Clinical Genome Project

Genome Browser demonstration
Genome Browser demonstration.

By: Hakon Gudbjartsson

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Genome Browser demonstration - Video

AARHUS, Denmark--(BUSINESS WIRE)--

This week, collaborating researchers at CLC bio and Queen Mary University of London have released a genome assembly of the European ash tree, Fraxinus excelsior, as part of the British Ash Tree Genome project.

The release comes as populations of ash trees across Europe have been devastated by the ash dieback fungus, which spread to Denmark and to the UK in 2003 and 2012, respectively. Fortunately, a small number of ash trees appear to have low susceptibility to the disease. It is hoped that by releasing the genome sequence publicly, scientists around the world can use it to determine the genetic or epigenetic causes of the variation in susceptibility.

Senior Lecturer at QMUL, Dr. Richard Buggs, states, We were very fortunate to sequence a tree that was the progeny of a self-pollination, produced ten years ago by David Boshier from the University of Oxford. The tree is now an invaluable resource, because its low heterozygosity enables a higher quality genome assembly than would have been possible in a more heterozygous tree.

PhD student at CLC bio, Lizzy Sollars, continues, "Using CLC bios de novo assembler, along with the open-source scaffolding tool SSPACE, we produced our best de novo assembly so far. The current version consists of 142,000 scaffolds, with an N50 of almost 69,000, and hits 97% of 248 conserved eukaryotic genes. Although several plant species have now been sequenced, there is still no closely related reference sequence for the ash. We hope that the new reference genome can lay the foundations of research into the ash dieback disease, as well as enable other forestry researchers to use genomic approaches in their studies."

The British Ash Tree Genome project, funded by an urgency grant from NERC, started in January 2013. Samples were taken from the selfed tree, owned by The Earth Trust, Oxfordshire, UK, and DNA was extracted from the sample by QMUL PhD student Jasmin Zohren. Samples were then sent to Eurofins, Germany, for sequencing on Illumina and Roche 454 platforms, and the resulting data was assembled into contigs using the CLC bio de novo assembler and open-source software.

The latest assemblies are available for download on the BATG website:

http://www.ashgenome.org

About CLC bio

http://www.clcbio.com/about

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CLC bio and UK scientists assemble ash tree genome

Iban Device - Genome app + Ableton + Nord Lead2

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Iban Device - Genome app + Ableton + Nord Lead2 - Video

The Philippine Genome Center (PGC) DNA Sequencing Core Facility (DSCF) has found a temporary home on the second floor of the National Institute of Molecular Biology in UP Diliman, but is already opening its doors to research projects that will directly impact the nation's economy.

The PGC will temporarily be housed here until the completion of the first PGC building in 2016, also located in the UP Science Complex.

The DSCF, which officially opened Tuesday, makes available sequencing and genotyping services to academic research groups in the country.

Don't copy other countries

This is where genomic studies on agriculture, health, biodiversity, forensics, and ethnicity will be done that cater specifically to the Filipino people.

We cannot copy Singapore, Hong Kong, Taiwan, or even the US because the Philippines has its unique needs, said Dr. Carmencita Padilla, Executive Director of PGC.

The PGC now operates two core facilities DNA Sequencing and Bioinformatics. PGC has yet to find space for its third core facility, the Biobank a repository for DNA samples.

The Department of Science and Technology (DOST) has granted PGC a total of P800 million, of which P520 million was released this year, according to Padilla.

The center already has a string of projects underway for the agricultural and medical sectors.

Separating bad from good sugarcane

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PHL Genome Center opens new DNA sequencing facility to local researchers

ST. LOUIS, Sept. 24, 2013 /PRNewswire/ --SAGE Labs, Inc., a leading provider of in vivo products, services and technologies in the field of genome engineering, announced today that it has entered into a partnership and licensing agreement with Caribou Biosciences, Inc. (Caribou Bio) for key intellectual property related to the CRISPR/Cas9 genome editing system.

Under the agreement, SAGE Labs will gain exclusive rights to Caribou Bio's intellectual property to produce and sell genetically engineered rats, and will gain non-exclusive rights for mouse and rabbit models. The Cas9 system will complement SAGE's Zinc Finger Nuclease (ZFN) technology, allowing SAGE to offer customers access to novel animal models of human disease, as well as reduced turnaround times for its custom model creation platform, SAGEspeed.

"SAGE Labs is the leader in creation of next-generation research models. As such, it is important to have access to key technologies needed to perform complex genome engineering projects," commented Dr. David Smoller, CEO of SAGE Labs. "Using Cas9 allows us to provide our customers with enhanced models that provide the most translational value for their research."

"We believe the Cas9 system will become very important in the creation of new models of human disease, both in vitro and in vivo," commented Dr. Rachel Haurwitz, CEO of Caribou Bio. "SAGE Labs' track record as a market leader in commercializingin vivotechnologies will enable them to useCas9-based engineering to bring innovative, high-quality engineered research modelsto the marketplace."

Please see http://www.sageresearchlabs.com for further details.

About SAGE Labs

SAGE Labs is a world-class provider of next-generation research models and transgenic support services. Using proprietary platform technologies, such as Zinc Finger Nucleases (ZFN) and the CRISPR/Cas9 system for genome engineering, SAGE produces complex in vivo research models in half the time as models produced using conventional technologies. For more information, visit http://www.sageresearchlabs.com.

About Caribou Bio

Caribou Bio specializes in the research and development of technologies for cellular engineering and analysis. Caribou Bio's technologies are based on the unique capabilities of Cas enzymes from the CRISPR prokaryotic immune system. Caribou Bio's lead technology is the Cas9 enzyme, a highly efficient and easy to use genome editing platform that does not require unique protein development.

Media Contact: Phil Simmons (314) 313-7847 Phil.Simmons@sageresearchlabs.com

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SAGE Labs, Inc. Licenses CRISPR/Cas9 genome engineering technology from Caribou Biosciences, Inc.

Google wants to extend human life through science, but what should we get out of it?

Do you want to live as long as a Vulcan, sea turtle, or Time Lord? If Google has its way, maybe you will in the not-too-distant future.

Last week, Google CEO Larry Page announced the launch of Calico, an effort to tackle humankind's most pesky ailments: aging and death. On the surface, it sounds like the plot of countless science-fiction and James Bond movies, in which immortality and world domination are mutually exclusive. On a more practical level, Calico is one of Google's more realistic "moonshots" because it's going to be driven by what Google is really good at: collecting and disseminating gobs and gobs of data. It's already been able to predict flu outbreaks based on our searches, so it stands to reason that Calico will eventually figure out this whole aging thing and be able to slow it down to the point where some of us might actually live long enough to ride on the Hyperloop.

Calico's announcement did not reveal much about the company's day-to-day operations but it seems the venture will initially focus solely on research and non-profits. However, you have to assume at some point Calico will spawn a consumer-facing product or service. But while the Calico news, anchored by a TIME cover story, is currently a hot topic in the tech space, projects like this often quickly transform into bubble fodder and ultimately become victim to our ever-shrinking news cycle.

For once, I'd like that to change. And given Calico's lofty goals aimed at benefitting the human race, I think Google needs to think about pivoting from its pledge to be a research-only venture to start and instead offer a service to the public that has the potential to benefit both Calico's data machine and the individual. How? In a word: DNA.

The cost of getting a human genome mapped has dropped drastically in the past few years. For a few thousand dollars, you can now unlock your body's genetic code and perhaps get insights into whether you might be susceptible to certain diseases like cancer. Is a few thousand dollars out of your budget? Unfortunately, you'd be hard-pressed to find an insurance company that would pay for it, but soon that may not be necessary. Earlier this year, a CNNMoney article declared the race to the $100 genome is underway as a handful of genetic science startups are offering inexpensive genome mapping services.

As the article points out however, we're still a few years away from that magical $100 price tag to unlock your body's deepest, darkest secrets. So to expedite the process, what if Google and Calico forge partnerships with companies already offering genome mapping? They could subsidize the costs to the point where anyone could get his or her genome mapped cheaply, or even for free. Google, Calico, and the partnering companies get the data they need to advance their research, and we get the gift that keeps on giving as scientific research advances over the course of our lives: a copy of our living code.

Might this be something Google is already thinking about? Are you eager to have your DNA mapped, either for your own edification or for the benefit of humanity? And perhaps most importantly, do you want Google to be the one handling your genetic business?

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How Google's Calico Can Win Us Over, One Genome at a Time