Category Archives: Genome

September 18, 2013

April Flowers for redOrbit.com Your Universe Online

In conservation efforts aimed at protecting endangered species, a group of international scientists has mapped the genome of the Siberian, or Amur, tiger. The findings, published in Nature Communications, reveal clues to how the big cat evolved to become a top predator with a carnivorous diet and superior muscle strength.

According to National Geographic, the Siberian tiger is the largest tiger subspecies. The animals weigh as much as 660 pounds and can grow up to ten feet in length. Currently only an approximate 450 Siberian tigers exist in the wild, with an estimated 4,000 tigers total remaining in their natural habitats.

We looked at this very large tiger first to see what made it distinctive from other cats, said genome expert Jong Bhak of South Koreas Personal Genomics Institute in Suwon. Bhak was part of the team lead by Yun Sung Cho at the Personal Genomics Institute, Genome Research Foundation that sequenced the genome of Taegeuk, a nine-year old male Siberian tiger from Everland Zoo in South Korea.

BBC News reports that the team also sequenced four other large cats the (African) lion, snow leopard, white (Bengal) tiger and white (African) lion enabling them to compare how the genes matched up in different members of the cat family.

Genetically all the cats are very close, so we need close genetic mapping to find the small differences that make them distinct, Bhak told Dan Vergano of National Geographic.

Beyond superior muscle strength and a need for lean meat, the genetic analysis gave clues to how the white lion gained its pale coat and how the snow leopard adapted to the snowy mountain ranges.

Across the study species, however, the cat family seems to rely on a narrow set of 1,376 genes linked to strong muscle fibers and digestion of protein. The study suggests that the genes likely originated in large part with the earliest common ancestor of big felines some 11 million years ago.

I take this to indicate that [big cats] have evolved to fill a very particular carnivorous niche in the environment that is predicated on the advantages in hunting these genes provide, Bhak told Vergano.

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Genome Sequencing Of Big Cats Complete

The first sequenced tiger genome shows that big cats evolved to kill.

Genes for strong muscle fibers and for meat-eating appear narrowly shared, researchers reported, among species as distinct as the African lion and Asia's snow leopard.

Scientists mapped the genes of the endangered Siberian tiger (or Amur tiger), both to understand the genes that make big cat species distinct from one another and to aid efforts to preserve genetic diversity in wild tiger populations. (Also see "Isolated Tigers Travel Surprising Lands to Find Mates.")

The largest tiger subspecies, Siberian tigers weigh as much as 660 pounds (300 kilograms) and grow to some ten feet (three meters) in length. Only about 450 Siberian tigers exist in the wild, and around 4,000 tigers total are thought to remain in their natural habitats. (See a National Geographic magazine interactive of big cats in danger.)

"We looked at this very large tiger first to see what made it distinctive from other cats," said genome expert Jong Bhak of South Korea's Personal Genomics Institute in Suwon, a co-author of the Nature Communications study reporting the mapping of the Siberian tiger genome.

Bhak and colleagues sampled genes from a nine-year-old male tiger at the Everland Zoo in Korea, and compared them with gene map information from the Bengal tiger, lion, and snow leopard. (See tiger pictures.)

Natural Born Killers

"Genetically all the cats are very close, so we need close genetic mapping to find the small differences that make them distinct," Bhak said.

Some gene differences are apparent in the mapping, such as two genes likely involved in adaptation to high altitudes and thin air in snow leopards and white fur in white African lions.

But overall, the cat family seems to rely on a narrow set of 1,376 genes linked to strong muscle fibers and digestion of protein, the study shows, seen widely across the study species. The genes likely originated in large part with the earliest common ancestor of big felines some 11 million years ago, the study authors suggest.

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Tiger Genome Sequenced, Shows Big Cats Evolved to Kill

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 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

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...

By: CBSNewsOnline

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Genome mapping for newborns to be government-funded - 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