Category Archives: Genome

The Joy Genome: Week 1
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The Joy Genome: Week 1 - Video

RESEARCH TRIANGLE PARK, N.C.--(BUSINESS WIRE)--

Precision BioSciences, Inc., a leader in the field of genome engineering, today announced that the United States Patent and Trademark Office has issued a Notice of Allowance for U.S. Patent Application 13/457,041 (the 041 Application). The allowed claims relate to materials and substitutions used for the creation of enzymes capable of modifying endogenous locations within a complex genome. These materials and substitutions constitute an important aspect of Precisions genome engineering technologies, known collectively as the Directed Nuclease Editor or DNE.

Precisions DNE technology allows for highly precise gene editing with engineered nucleases, a technique named Method of the Year by Nature Methods. The Notice of Allowance will further augment Precisions ability to protect and capitalize on this important biological tool. Upon issuance of the 041 Application, Precision will control a patent estate consisting of eleven foundational genome engineering patents in the U.S. and one in Europe. The 041 Application is expected to issue as U.S. Patent No. 8,304,222 on November 6, 2012.

We are pleased that the U.S. Patent Office continues to recognize our novel contributions to the genome engineering field, stated Derek Jantz, co-inventor and Precision BioSciences Vice President of Scientific Development. This patent will allow us to protect yet another valuable aspect of our nuclease technology.

About Precision BioSciences

Precision BioSciences mission is to continually provide, improve, and enable the worlds most powerful genome engineering technology. Precisions proprietary Directed Nuclease EditorTM (DNE) technology enables the production of genome editing enzymes that can insert, remove, modify, and regulate essentially any gene in mammalian or plant cells.

Precision BioSciences vision is to be the conduit through which the worlds greatest genome engineering challenges are solved. Precision has successfully utilized its DNE technology to create innovative products in partnerships with many of the worlds largest biopharmaceutical, agbiotech, and animal research firms. Internally, Precision is developing applications of DNE in biological production and human therapeutics. For additional information, please visit http://www.precisionbiosciences.com.

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Precision BioSciences Announces Allowance of Eleventh U.S. Patent Application Related to Genome Editing Nucleases

The blood tests may herald a new wave of noninvasive prenatal screening.

Expectant mothers are used to fuzzy images on ultrasound monitors and blood tests to screen for potential health problems in their unborn babies. But what if one of those blood tests came back with a readout of the baby's entire genome? What if a simple test gave parents every nuance of a baby's genetic makeup before birth?

Recent studies show that it's possible to decode an entire fetal genome from a sample of the mother's blood (see "Using Parents' Blood to Decode the Genome of a Fetus"). In the future, doctors may be able to divine a wealth of information about genetic diseases or other characteristics of a fetus from the pregnant mother's blood. Such tests will raise ethical questions about how to act on such information. But they could also lead to research on treating diseases before birth, and leave parents and their doctors better prepared to care for babies after birth.

It's been about 15 years since Dennis Lo, a chemical pathologist at the Chinese University of Hong Kong, first discovered that fragments of DNA from a fetus could be found in a pregnant woman's blood. The work was a breakthrough, since obtaining fetal DNA from the amniotic fluid, placenta, or directly from the fetus's blood requires an invasive procedure and carries a risk of miscarriage. A noninvasive test would make genetic testing safer and much more widely accessible.

Since then, several labs have worked to analyze this fetal DNA and exploit it for noninvasive prenatal tests. The field has progressed rapidly in the past couple of years as genetic sequencing technologies have become vastly cheaper and faster, and methods to analyze genetic data have improved (see "Analyzing the Unborn Genome").

One of the first tests to be developed is for RhD factor, a type of blood protein that can lead to fetal disease or death if the mother is RhD negative and her fetus is RhD positive. Sequenom, a San Diego, California-based company that licensed Lo's research, began offering a noninvasive RhD test in 2010 (prior tests required invasive procedures such as amniocentesis or chorionic villus sampling, which carry a small risk of miscarriage). Several companies have also offered tests for sex determination and paternity.

But what has gained more attention in the United States is a recent wave of tests that detect Down syndrome, which is caused by an extra copy of chromosome 21. Because women in the United States are routinely offered testing for Down syndrome, the market for such a test is large.

The test for Down syndrome could, in particular, have an enormous beneficial impact. Typically, a pregnant woman receives an initial screening test for substances in her blood associated with Down syndrome. Jacob Canick, a professor of pathology and laboratory medicine at Brown University, explains that the tests will detect 90 percent of Down syndrome cases, but have a false positive rate of 2 to 5 percent. That may sound small, but given that Down syndrome affects only one in 500 pregnancies, the number of women with a false positive is much higher than those who are truly carrying an affected fetus. The only definitive diagnosis is through amniocentesis or chorionic villus sampling. "That means that 19 out of 20 women that undergo an invasive procedure will find out that they don't have the genetic abnormality," Canick says.

With those low odds, many women choose not to undergo an invasive procedure at all. But new noninvasive tests could make screening much more widespread. "It looks, from our data and other data, that these tests are very, very good," says Canick, who led a trial, funded by Sequenom, on one these tests. They are still not definitive, but could ensure that far fewer women unnecessarily undergo invasive tests.

A number of startups have begun offering fetal tests for Down syndrome and other health problems caused by extra copies or missing chromosomes. Diana Bianchi, executive director of the Mother Infant Research Institute at Tufts Medical Center, who is on the advisory board of a startup called Verinata Health that is developing such fetal tests, says it's been surprising how quickly the tests have made their way into the clinic.

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New Tests Could Divine a Baby's Genome Before Birth

Public release date: 24-Oct-2012 [ | E-mail | Share ]

Contact: Glenna Picton picton@bcm.edu 713-798-4710 Baylor College of Medicine

HOUSTON -- (October 24, 2012) , said a Baylor College of Medicine physician-scientist who was part of the local team that took part in the international effort. A report appears online in the journal Nature.

"We now know every gene involved in pancreatic cancer," said Dr. William Fisher, professor of surgery and director of the Elkins Pancreas Center at BCM. "This study ushers in a whole new era of taking care of patients with pancreatic cancer. We will look back on this as a turning point in understanding and treating this disease."

The study follows a five-year collaboration between the Michael E. DeBakey Department of Surgery and the Baylor College of Medicine Human Genome Sequencing Center, said Fisher.

The Baylor College of Medicine Human Genome Sequencing Center was one of three sequencing centers worldwide that analyzed the genomes of pancreatic tumors and normal tissues taken from 142 patients with the disease. The BCM center, along with the Australian Pancreatic Center Genome Initiative and the Ontario Institute for Cancer Research Pancreatic Cancer Genome Study carried out detailed studies on 99 of the tumors, identifying 1982 mutations that resulted in a change to a protein and 1,628 significant copy number variations events in which the structure of the chromosomes themselves are changed, either deleting or duplicating genetic information.

The multi-institution, international consortium of researchers discovered mutations in genes involved in chromatin modification (changes that affect the way DNA is packaged inside the cell) and axon guidance (the process by which the axon a long threadlike project that carries impulses away from the neuron is guided to grow to its proper target).

"This is a category of genes not previously linked to pancreatic cancer," said Fisher. "We are poised to jump on this gene list and do some exciting things."

New information is much welcome in the field of pancreatic cancer, which is the fourth leading cause of cancer death with an overall five-year survival rate of less than 5 percent. The figures have not changed substantially in the past 50 years.

The study is the first to report findings from primary tumors in the disease. Previously only cell lines or tumors transplanted into mice had been used because the tumors are so small. "Therefore it required new techniques to sensitively identify mutations that were important to the development of cancer," said Dr. David Wheeler, associate professor in the BCM Human Genome Sequencing Center who oversees the center's cancer projects. Wheeler and Fisher are also members of the NCI-designated Dan L. Duncan Cancer Center at BCM.

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Genome analysis of pancreas tumors reveals new pathway

SANTA CLARA, CA--(Marketwire - Oct 31, 2012) - NVIDIA Tesla GPU accelerators are enabling Life Technologies Corporation's new Ion Proton System to accelerate primary genome-sequence analysis -- the computation that generates DNA base pairs -- by over 16 times. This will dramatically reduce the cost to sequence an entire human genome from about $1 billion a decade ago to $1,000 in the near future.

"GPU acceleration and other advanced Ion Proton features enable every laboratory in the world to take advantage of human genome sequencing quickly and easily, without costly IT investments," said Alan Williams, vice president of software and engineering in the Ion Torrent unit at Life Technologies Corporation. "By democratizing genome sequencing, we expect to see an unprecedented wave of innovation in life sciences and the advancement of clinical research."

The Ion Proton System's technology builds on the rapid advances in increasing throughput, accuracy and read-length achieved with the Life Technologies Ion Personal Genome Machine (PGM) Sequencer, which also uses GPUs to accelerate primary analysis. The Ion PGM sequencer was the first to decode the deadly 2011 E. coli bacteria outbreak in Germany because of its exceptional speed.

Setting new standards for performance, ease of use and affordability, the Ion Proton System enables researchers to rapidly go from multiplex sample sequencing to genome-scale sequencing on a single platform. At one-fifth the cost of light-based genome-scale sequencing systems, it can save researchers hundreds of thousands of dollars.

"GPU acceleration has become pervasive in all aspects of computing for life science applications and will enable research to push the envelope of scientific discovery," said Sumit Gupta, general manager of the Tesla accelerated computing business unit at NVIDIA. "The pace of research has fundamentally been accelerated by the use of GPUs for everything from gene sequencers and sequence analysis to molecular modeling and diagnostic imaging."

About NVIDIA Tesla GPUs NVIDIA Tesla GPUs are massively parallel accelerators based on the NVIDIA CUDA parallel computing platform and programming model. Tesla GPUs are designed from the ground up for power-efficient, high performance computing, computational science, and supercomputing, delivering dramatically higher application acceleration for a range of scientific and commercial applications than a CPU-only approach.

More information about NVIDIA Tesla GPUs is available at the Tesla website. To learn more about CUDA or download the latest version, visit the CUDA website. More NVIDIA news, company and product information, videos, images and other information is available at the NVIDIA newsroom. Follow us on Twitter at @NVIDIATesla.

About NVIDIA NVIDIA ( NASDAQ : NVDA ) awakened the world to computer graphics when it invented the GPU in 1999. Today, its processors power a broad range of products from smartphones to supercomputers. NVIDIA's mobile processors are used in cell phones, tablets and auto infotainment systems. PC gamers rely on GPUs to enjoy spectacularly immersive worlds. Professionals use them to create 3D graphics and visual effects in movies and to design everything from golf clubs to jumbo jets. And researchers utilize GPUs to advance the frontiers of science with high performance computing. The company has more than 5,000 patents issued, allowed or filed, including ones covering ideas essential to modern computing. For more information, see http://www.nvidia.com.

Certain statements in this press release including, but not limited to, statements as to: the impact and benefits of NVIDIA Tesla GPUs and the effects of the company's patents on modern computing are forward-looking statements that are subject to risks and uncertainties that could cause results to be materially different than expectations. Important factors that could cause actual results to differ materially include: global economic conditions; our reliance on third parties to manufacture, assemble, package and test our products; the impact of technological development and competition; development of new products and technologies or enhancements to our existing product and technologies; market acceptance of our products or our partners products; design, manufacturing or software defects; changes in consumer preferences or demands; changes in industry standards and interfaces; unexpected loss of performance of our products or technologies when integrated into systems; as well as other factors detailed from time to time in the reports NVIDIA files with the Securities and Exchange Commission, or SEC, including its Form 10-Q for the fiscal period ended July 29, 2012. Copies of reports filed with the SEC are posted on the company's website and are available from NVIDIA without charge. These forward-looking statements are not guarantees of future performance and speak only as of the date hereof, and, except as required by law, NVIDIA disclaims any obligation to update these forward-looking statements to reflect future events or circumstances.

2012 NVIDIA Corporation. All rights reserved. NVIDIA, the NVIDIA logo, CUDA and Tesla are trademarks and/or registered trademarks of NVIDIA Corporation in the U.S. and other countries. Other company and product names may be trademarks of the respective companies with which they are associated. Features, pricing, availability and specifications are subject to change without notice.

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New Gene Sequencer to Break $1,000 Cost Barrier With NVIDIA Tesla GPU Acceleration

J. Craig Venter may have just started a race to discover alien life on the Red Planet.

Hot place: Some biologists want to send a DNA sequencing machine to Mars to search for life.

Two high-profile entrepreneurs say they want to put a DNA sequencing machine on the surface of Mars in a bid to prove the existence of extraterrestrial life.

In what could become a race for the first extraterrestrial genome, researcher J. Craig Venter said Tuesday that his Maryland academic institute and his company, Synthetic Genomics, would develop a machine capable of sequencing and beaming back DNA data from the planet.

Separately, Jonathan Rothberg, founder of Ion Torrent, a DNA sequencing company, is collaborating on an effort to equip his company's "Personal Genome Machine" for a similar task.

"We want to make sure an Ion Torrent goes to Mars," Rothberg told Technology Review.

Although neither team yet has a berth on a Mars rocket, their plans reflect the belief that the simplest way to prove there is life on Mars is to send a DNA sequencing machine.

"There will be DNA life forms there," Venter predicted Tuesday in New York, where he was speaking at the Wired Health Conference.

Venter said researchers working with him have already begun tests at a Mars-like site in the Mojave Desert. Their goal, he said, is to demonstrate a machine capable of autonomously isolating microbes from soil, sequencing their DNA, and then transmitting the information to a remote computer, as would be required on an unmanned Mars mission. (Hear his comments in this video, starting at 00:11:01.) Heather Kowalski, a spokeswoman for Venter, confirmed the existence of the project but said the prototype system was "not yet 100 percent robotic."

Meanwhile, Rothberg's Personal Genome Machine is being adapted for Martian conditions as part of a NASA-funded project at Harvard and MIT called SET-G, or "the search for extraterrestrial genomes."

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Genome Hunters Go After Martian DNA

The microbial communities in people's mouths are more closely tied to environmental exposures than to genetics, according to a study published online in Genome Research. A University of Colorado, Boulder, team performed 16S ribosomal RNA sequencing on spit samples from more than 100 individuals, each of whom was tested up to three times over the course of a decade. Among the participants were 27 identical- and 18 non-identical twin pairs. Although the investigators saw similarities between younger twins' mouth microbiomes, that was less often the case for older twins, who were more apt to live apart. And while all of the individuals tested shared a core set of mouth microbiome components, the mouth microbiomes in non-identical twins were as similar to one another as those in identical twins.

The Tufts University School of Medicine's Tim van Opijnen and Andrew Camilli delve into relationships between genotype and phenotype for the bacterial pathogen Streptococcus pneumoniae. Using a high-throughput screening method that's based on transposon insertion sequencing, or Tn-seq, the researchers screened S. pneumoniae in 17 different carriage (in vitro) or infection (in vivo) situations that involved a range of carbon sources, stressors, and so on. In the process, they created a genotype-phenotype map representing more than 1,800 interactions. "We have generated a resource that provides detailed insight into the biology and virulence of S. pneumoniae," the pair writes, "and provided a road map for similar discovery in other microorganisms."

Finally, a study led by investigators at Kansas State University and Iowa State University takes a look at quantitative trait loci distribution in the maize genome. The team tallied up trait-associated SNPs in maize and looked at whether these tended to fall in genic or non-genic bits of the genome. Although variants affecting gene expression often turned up in non-genic parts of the maize genome, they were typically concentrated within a few thousand bases upstream of protein-coding genes. From these and other findings, the group concludes that "efficient, cost-effective genome-wide association studies in species with complex genomes can focus on genic and promoter regions."

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This Week in Genome Research

Impact of genome size on guard cell size. Paris japonica (A) and Quercus robur (B) differ 170-fold in genome size and this is reflected in the size of the guard cells. Both pictures are taken at the same magnification. Credit: Peter Franks

Using the size of guard cells in fossil plants to predict how much DNA each cell contained (the genome size), researchers have discovered that variations in genome sizes over geological time correlate with atmospheric carbon dioxide levels.

The total amount of DNA in the nucleus of an organism is known as the genome size. In plants this character varies nearly 2400-fold between species, with many having up to 50 times more DNA than is found in our own genome.

Fossil guard cells reveal genome size evolution

Understanding the biological significance of this variation has been an ongoing research theme at Kew for nearly 30 years. One area of focus has been the study of genome size evolution and great progress has been made by superimposing genome size data onto the phylogenetic trees of plants. Nevertheless, we have had no idea of how genome size has varied over geological time as it is impossible to measure this from fossils.

Given that the size of genomes and guard cells (which form the stomata) are closely linked (see picture), researchers at the universities of Sheffield (UK) and Yale (USA), in collaboration with Kew scientists, used the size of fossil guard cells as a proxy for genome size to track how this has changed over the past 400 million years (spanning the full geological history of vascular plants). The results suggest that genome size evolution has been dynamic with both increases and decreases taking place during plant evolution.

Genome sizes correlate with carbon dioxide levels

Coupling this information with knowledge of how atmospheric carbon dioxide levels have fluctuated over the same time period revealed a good correlation between these parameters, with larger guard cells and inferred genome sizes found when levels of carbon dioxide were high. Of course, the observed correlation does not mean that carbon dioxide levels are directly driving changes in guard cell size and genome size. Nevertheless, because guard cells play a key role in optimising gas exchange in plants, the results hint at the possibility that carbon dioxide might be one of the selective forces responsible for generating the diversity of guard cell and genome sizes encountered in today's flora.

Given that the particular genome size of a plant can have a considerable influence on where, when and how a plant lives, understanding the nature of the relationship between carbon dioxide levels and genome size will become increasingly important as the level of atmospheric carbon dioxide continues to rise.

More information: Franks, P. J., Leitch, I. J., Ruszala,E. M., Hetherington, A. M. & Beerling, D. J. (2012). Physiological framework for adaptation of stomata to CO2 from glacial to future concentrations. Philosophical Transactions of the Royal Society B 367: 537-546. Franks, P. J., Freckleton, R. P., Beaulieu, J. M., Leitch, I. J. & Beerling, D. L. (2012). Megacycles of atmospheric carbon dioxide concentration correlate with fossil plant genome size. Philosophical Transactions of the Royal Society B 367: 556-564

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Genome evolution and carbon dioxide dynamics

ScienceDaily (Oct. 31, 2012) By decoding the genomes of more than 1,000 people whose homelands stretch from Africa and Asia to Europe and the Americas, scientists have compiled the largest and most detailed catalog yet of human genetic variation. The massive resource will help medical researchers find the genetic roots of rare and common diseases in populations worldwide.

The 1000 Genomes Project involved some 200 scientists at Washington University School of Medicine in St. Louis and other institutions. Results detailing the DNA variations of individuals from 14 ethnic groups are published Oct. 31 in the journal Nature. Eventually, the initiative will involve 2,500 individuals from 26 populations.

"With this resource, researchers have a roadmap to search for the genetic origins of diseases in populations around the globe," says one of the study's co-principal investigators, Elaine Mardis, PhD, co-director of The Genome Institute at Washington University. "We estimate that each person carries up to several hundred rare DNA variants that could potentially contribute to disease. Now, scientists can investigate how detrimental particular rare variants are in different ethnic groups."

At the genetic level, any two people are more than 99 percent alike. But rare variants -- those that occur with a frequency of 1 percent or less in a population -- are thought to contribute to rare diseases as well as common conditions like cancer, heart disease and diabetes. Rare variants may also explain why some medications are not effective in certain people or cause side effects such as nausea, vomiting, insomnia and sometimes even heart problems or death.

Identifying rare variants across different populations is a major goal of the project. During the pilot phase of the effort, the researchers found that most rare variants differed from one population to another, and that they developed recently in human evolutionary history, after populations in Europe, Africa, Asia and the Americas diverged from a single group. The current study bears this out.

"This information is crucial and will improve our interpretation of individual genomes," says another of the study's co-principal investigators, Richard K. Wilson, PhD, director of The Genome Institute and a pioneer in cancer genome sequencing. "Now, if we want to study cancer in Mexican Americans or Japanese Americans, for example, we can do so in the context of their diverse geographic or ancestry-based genetic backgrounds."

Results of the new study are based on DNA sequencing of the following populations: Yoruba in Nigeria; Han Chinese in Beijing; Japanese in Tokyo; Utah residents with ancestry from northern and western Europe; Luhya in Kenya; people of African ancestry in the southwestern United States; Toscani in Italy; people of Mexican ancestry in Los Angeles; Southern Han Chinese in China; Iberian from Spain; British in England and Scotland; Finnish from Finland; Colombians in Columbia; and Puerto Rican in Puerto Rico.

All study participants submitted anonymous DNA samples and agreed to have their genetic data included in an online database. To catalog the variants, the researchers first sequenced the entire genome -- all the DNA -- of each individual in the study about five times. Surveying the genome in this way finds common DNA changes but misses many rare variants.

Then, to find rare variants, they repeatedly sequenced the small portion of the genome that contains genes -- about 80 times for each participant to ensure accuracy -- and they looked closely for single letter changes in the DNA sequence called SNPs (for single-nucleotide polymorphisms).

Using special tools developed to analyze and integrate the data, the researchers discovered a total of 38 million SNPs, including more than 99 percent of the variants with at frequency of at least one percent in the participants' DNA samples. They also found numerous structural variations, including 1.4 million short stretches of insertions or deletions and 14,000 large DNA deletions.

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Global genome effort seeks genetic roots of disease

By Carolyn Y. Johnson, Globe Staff

A massive consortium of researchers, led in part by local scientists, has taken the next step after researchers mapped the human genome, compiling an encyclopedia that illuminates how the vast majority of the 3 billion building blocks of human DNA works.

When the genome, the blueprint of a person, was first deciphered 11 years ago, scientists were faced with a conundrum: only a tiny fraction was made up of genes, the stretches that carried instructions to make proteins that gave rise to inherited traits, such as having blue eyes or black hair. The rest was called junk DNA.

The raft of publications being released in top scientific journals Wednesday should permanently change the meaning of junk. Hundreds of scientists from 30 institutions elucidated the functions of 80 percent of the genome, finding regulatory elements that act like switches, determining which genes are on or turning their volume up or down.

The information, gained through more than 1,600 experiments on cells from 147 types of tissue could help explain the causes of human disease, because many studies that scan the genome for changes associated with common illnesses such as diabetes or cardiovascular disease have highlighted areas that have no genes, but may be important in regulating genes.

This is Google Maps, said Eric Lander, director of the Broad Institute, a genomic research center in Cambridge that participated in the new project, called ENCODE for Encyclopedia of DNA Elements. The human genome project gave us the picture of the whole human genome like a satellite image, but its not immediately obvious: where are the cities, where are the pizzerias, where are the coffee shops, where are the highways, what has traffic.

The new data, he said, give scientists the ability to understand how the genome works and begin to unravel human disease.

The effort does not have a single, simple finding, but provides a resource that will be useful in making sense of genetic information. It also helps solve a puzzle that first emerged when the human genome was sequenced: why so few genes?

When the genome was published, people had all kinds of speculations about how many genes there are in the human genome -- the number thrown around was 100,000 genes, said Zhiping Weng, director of the program in bioinformatics and integrative biology at the University of Massachusetts Medical School, who will play a leading role in the next phase of the project. When it became clear it was 25 to 30,000 genes, a lot of people are very upset, and why? Because the fly has 20,000 genes, the worm has 20,0000 genes, and are we just bigger? What exactly makes us us? Its how our genes are regulated.

Weng will lead a four-year, $8 million grant to continue the analysis and integration of the vast amounts of information as scientists continue to understand the function of the remainder of the genome and apply the techniques developed to understand the genome more broadly.

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Massive encyclopedia helps explain how the human genome works