Daily Archives: April 11, 2013

NYC* 2013 - "How to analyze the human genome/DNA using Cassandra" by Sameer Farooqui
Speaker: Sameer Farooqui, Freelance Big Data Consultant and Trainer "How to Analyze the Human Genome/DNA Using Cassandra" SlideShare: http://www.slideshare.n...

By: PlanetCassandra

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NYC* 2013 - "How to analyze the human genome/DNA using Cassandra" by Sameer Farooqui - Video

SANTA CLARA, Calif.--(BUSINESS WIRE)--

Affymetrix, Inc. (AFFX) and BioDiscovery announce the availability of the Nexus for OncoScan Software for analysis of whole genome copy number data generated from formalin-fixed, paraffin-embedded (FFPE) solid tumor samples using the OncoScan FFPE Express 2.0 Service. Through a joint arrangement, this software, based on BioDiscoverys flagship Nexus Copy Number, is available to customers who are analyzing data generated using this service.

Obtaining high-quality copy number data using limited amounts of DNA from degraded FFPE samples is extremely challenging for cancer researchers. Utilizing Affymetrix unique Molecular Inversion Probe (MIP) technology, the OncoScan FFPE assay is capable of analyzing highly degraded DNA in FFPE tumor samples, even from less than 100 ng of starting DNA material, and is currently available as a service through Affymetrix Research Service Laboratory (ARSL) based in Santa Clara, California.

OncoScan FFPE Express 2.0 Service has been successfully used by more than 30 leading cancer research institutes, including M. D. Anderson Cancer Center, University of California San Francisco, and the Huntsman Cancer Institute at the University of Utah.

Cancer translational researchers have been able to quickly and easily analyze hundreds of degraded FFPE samples to correlate copy number aberrations with outcomes data, said Andy Last, Executive Vice President of the Genetic Analysis and Clinical Applications Business Unit at Affymetrix. Nexus for OncoScan Software is especially optimized for solid tumor copy number analysis and can generate whole genome copy number calls from raw data in minutes. We are very excited to continue to partner with BioDiscovery to bring this powerful and easy-to-use software to the cancer research community.

"The OncoScan FFPE assay is an amazing technology for cancer researchers allowing them to unlock DNA information from masses of archived FFPE samples to obtain high quality data," said Soheil Shams, President of BioDiscovery. Combining the powerful OncoScan FFPE technology with the proven power of Nexus Copy Number gives scientists a unique solution that is sure to accelerate cancer research, impact diagnosis, and ultimately lead to better patient care and treatment. We are very pleased to partner with Affymetrix in offering this powerful solution.

A next generation OncoScan FFPE product will be available in late 2013 enabling researchers to perform the assay and analysis in their own lab. Delivering results in about 48 hours, this new product will provide whole genome copy number coverage with high resolution in known cancer genes, loss of heterozygozity (LOH) as well as clinically relevant somatic mutation data - all from a single assay. An updated version of Nexus for OncoScan Software will be released in conjunction with the launch.

PLEASE NOTE: Affymetrix, the Affymetrix logo, and OncoScan trademarks are the property of Affymetrix, Inc. All other trademarks are the property of their respective owners.

Products mentioned in this release are for research use only. Not for diagnostic procedures.

Forward-looking statements

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Affymetrix and BioDiscovery Announce Software for Analysis of Whole Genome Copy Number Data Generated From FFPE Solid ...

Western Painted Turtle. Credit: 2006 Don VandeBergh, Oregon Department of Fish & Wildlife

Scientists have recently decoded the genome of the Western Painted Turtle, Chrysemys picta bellii, one of the most widespread, abundant and well-studied turtles in North America. This freshwater turtle is only the second reptile species for which complete genome sequences have been assembled and analyzed, behind the green anole lizard.

"Turtles are an exceptionally old group of organisms, and they're also evolving very slowly," said University of Hawai'i at Mnoa Assistant Professor of Biology Robert C. Thomson, who has worked on the Western Painted Turtle project since 2008. Turtle genomes evolve at about one-third the rate seen in humans, and roughly one-fifth the rate of other reptiles such as the python.

Thomson led the analysis of the turtle's rate of evolution and phylogenetic relationshipsthe pattern of evolutionary divergence between turtles and other groups of organisms. These analyses indicate that turtles' closest living relatives are crocodiles and birds, not snakes and lizards as some previous studies have suggested.

Western Painted Turtle Hatchlings. Credit: 2006 Don VandeBergh, Oregon Department of Fish & Wildlife

"In many respects, turtles are a very strange group of animals," Thomson said. "They have a number of novel traits that we can learn from." For the Western Painted Turtle, these novel traits include the ability to hibernate through long winters by burying themselves in near-freezing mud beneath streams and ponds, surviving with almost no oxygen for up to four monthslonger than any other known tetrapod.

Comparative genomic information about animal species is often valuable for scientists working on certain human health-related problems. Understanding how turtles protect their vital organs during periods of oxygen deprivation may one day improve treatment for human victims of heart attack or strokes, researchers say. This majority of the turtle gene sequencing effort was completed at Washington University's Genome Institute, which is one of three National Institutes of Health (NIH)-funded sequencing centers in the United States.

No freshwater turtles are native to Hawai'i, although three species have been introduced, from the pet trade and for food. Five types of sea turtles occur in the Pacific waters off Hawai'i's coasts.

More information: Shaffer, H. et al. 2013. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biology 14:R28 doi:10.1186/gb-2013-14-3-r28

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Western Painted Turtle genome decoded: Scientist uncover evolutionary history behind common turtle's novel traits

Apr. 10, 2013 The "holy grail" for understanding how and why koalas respond to infectious diseases has been uncovered in an Australian-led, world-first genome mapping project.

The joint undertaking between QUT and The Australian Museum has unearthed a wealth of data, including the koala interferon gamma (IFN-g) gene -- a chemical messenger that plays a key role in the iconic marsupial's defence against cancer, viruses and intracellular bacteria.

Professor Peter Timms, from QUT's Institue of Health and Biomedical Innovation (IHBI), said the IFN-g gene was the key to finding a cure for diseases such as Chlamydia and Koala Retrovirus (KoRV), currently threatening the vulnerable species.

"We know koalas are infected with various strains of Chlamydia, but we do not know why some animals go on to get severe clinical disease and some do not," Professor Timms said.

"We also know that genes such as IFN-g are very important for controlling chlamydial infections in humans and other animals. Identifying these in the koala will be a major step forward in understanding and controlling diseases in this species. "

The research team -- made up of Professor Timms, Dr Adam Polkinghorne, Dr Ana Pavasovic and Dr Peter Prentis from QUT; The Australian Museum; veterinarians from Australia Zoo and the Port Macquarie Koala Hospital; and bioinformaticians from Ramaciotti Centre and UNSW -- have sequenced the complete transcriptome from several koala tissues.

Dr Polkinghorne from QUT's School of Biomedical Sciences said data sets from immune-related tissues of Birke, a koala who was euthanized following a dog attack, have revealed a wealth of information about the species' immune system including the sequences of at least 390 immune-related genes.

"Virtually nothing is known about the immune system of the koala and the absence of information has been a major hinderance to our efforts to understand how Chlamydia and KoRV infections lead to such debilitating disease in this native species," he said

Since finding the 'holy grail' the QUT team has developed a molecular test to measure IFN-g expression in the blood of healthy and diseased koalas, which has already been applied to a small group of wild koalas taken to the Australia Zoo Wildlife Hospital suffering ocular and reproductive tract disease.

The results will allow researchers to pull apart the complex immune response to better understand how to successfully treat and immunise the vulnerable koala population.

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Genome mapping of koalas is promising start for understanding how koalas respond to infectious diseases

Source: The HAND Foundation

Since PARSA Community Foundation granted $250,000 to Stanford Universitys Iranian Genome Project in 2010, the project has grown significantly. The Iranian Genome Project aims to provide knowledge to both the scientific and Iranian community by studying and understanding the genetic background of Iranians representing all ethnicities in Iran, including Armenians, Kurds, and Turks. Based on the emerging field of genomics, where scientists map the genetic code, this project allows for research on how variations in the genetic code lead to differences in health and disease across and within populations.

The Iranian Genome Project believes that furthering the knowledge of the Iranian genetic code will enable the community to gain a better understanding of how certain Iranian genes affect health in the population. This may one day allow for the creation of tailored treatments and drugs. This is important as most genetic research has been conducted on people of European descent. As the age of personalized medicine begins, knowledge of genetic variation will be key in making sure that everyones unique needs are met.

The research is being done by the Department of Bioengineering at Stanford University, lead by the Principal Investigator Russ Altman, Chairman of Department and Director of Biomedical Informatics Training Program. The lead researcher is Roxana Daneshjou, a medical student at Stanford University School of Medicine and a Ph.D. candidate in Genetics. The team also has two consultants who are leaders in the field of genentics: Mostafa Ronaghi, Chief Technology Officer and Senior Vice President at Illumina and a former principal investigator and senior research associate at the Stanford Genome Technology Center; and Pardis Sabeti, Assistant Professor at the Center for Systems Biology at Harvard, Department of Organismic and Evolutionary Biology, and Senior Associate Member of the Broad Institute of Harvard.

You can sign up to be a participant in the research at the Iranian Genome Project website. Follow the work of The Iranian Genome Project via Twitter @irangenes.

... Payvand News - 04/10/13 ... --

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Mapping the Iranian Genome

Public release date: 10-Apr-2013 [ | E-mail | Share ]

Contact: Alison Hewitt ahewitt@support.ucla.edu 310-206-5461 University of California - Los Angeles

Humans could learn a thing or two from turtles, and scientists who have just sequenced the first turtle genome uncovered clues about how people can benefit from the shelled creatures' remarkable longevity and ability to survive for months without breathing.

Understanding the natural mechanisms turtles use to protect their heart and brain from oxygen deprivation may one day improve treatments for heart attack and stroke, the researchers said.

UCLA conservation biologist and lead author Brad Shaffer collaborated with the Genome Institute at Washington University in St. Louis and 58 co-authors on the multi-year research project. Their paper, which appears in the journal Genome Biology, describes the genome of the western painted turtle, one of the most widespread and well-studied turtles in the world.

Researchers were somewhat surprised to find that the painted turtle's extraordinary adaptations were not the result of previously unknown genes but of gene networks that are common in vertebrates including humans, said Shaffer, a professor at UCLA's Institute of the Environment and Sustainability (IoES) and UCLA's Department of Ecology and Evolutionary Biology.

"They're the same genes we have, and the turtles are just using them in different ways and really cranking up their activity in most cases," said Shaffer, who also directs the La Kretz Center for California Conservation Science at the IoES.

"Given how extreme their adaptations are, I imagined we would see weird new genes, so I was surprised," he added. "But the fact that they're common means they may have direct relevance to human health conditions, especially those related to oxygen deprivation, hypothermia and possibly longevity."

Inside the turtle genome, the researchers found 19 genes in the brain and 23 in the heart that became more active in low-oxygen conditions, including one that became 130 times more active. These genes, all of which are present in humans, may be important candidates for exploring oxygen-deprivation treatment in humans, the researchers noted.

Many of the extreme adaptations the researchers studied, such as the ability to survive months of anoxia total oxygen depletion are primarily seen in painted turtles, and the western painted turtle is the most anoxia-tolerant terrestrial vertebrate known. At low temperatures, such as in the ice-covered ponds where they hibernate, painted turtles can survive for four months underwater without coming up for air. Turtles are also famous for their extreme longevity, with some species even continuing to reproduce into their second century of life.

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Scientists decode genome of painted turtle, revealing clues to extraordinary adaptations

Scientists have for the first time decoded the genome of a turtle, unlocking clues to their longevity and ability to survive without oxygen, an attribute that could someday be used to help humans.

The research team included scientists from Washington University School of Medicine and St. Louis University as well as the University of California at Los Angeles. Their analysis is available online in the journal Genome Biology.

In science, turtles are a bit of an enigma. Their distinctive body design with a sharp beak instead of teeth and protective hard shell has changed very little over the past 210 million years. They can live up to four months with no oxygen while hibernating in ice-covered ponds. And while most small animals have short lifespans, a box turtle roaming your backyard can live more than 100 years.

They may be slowly evolving, but turtles have developed an array of enviable features, said senior author Richard Wilson, director of Washington Universitys Genome Institute. They resist growing old, can reproduce even at advanced ages, and their bodies can freeze solid, thaw and survive without damaging delicate organs and tissues. We can learn a lot from them.

Researchers sequenced the genome of the western painted turtle, which lives in freshwater ponds and streams and is the most widespread turtle in North America. What they found was that the creatures unique physiological adaptations are not from novel genes; but from activating genes common to most vertebrates, including humans.

This is a back-door route for turtles to evolve, said co-author Patrick Minx at he genome institute. Rather than evolve new genes, they adapted existing genes for new uses.

The scientists identified 19 genes in the brain and 23 in the heart that are activated in low-oxygen conditions, including one gene that increased nearly 130-fold. These genes are also present in humans and could be important in treatments to protect the heart and brain from oxygen deprivation during a heart attack or stroke.

Their study also showed just how slowly turtles evolve about one-third the rate of humans and one-fifth the rate of the fast-evolving python. The sequencing also puts to rest the argument over where turtles fall in the tree of life. Scientists found they are most closely related to crocodiles and birds, and not lizards and snakes.

Scientists will next try to better understand how the genes work together to protect organs during oxygen deprivation. They can also use the genome information to study other traits such as longevity.

How can their tissue and their cells survive so much longer? said co-author Wesley Warren, also at the genome institute. Thats why this genome is important, for scientists to have access to the entire sequence, so we can start understanding these mechanisms.

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Turtle genome offers clues to longevity, surviving without oxygen