Category Archives: Genome

Filling Gaps in the Spinach Genome with SMRT Sequencing
Allen Van Deynze from UC Davis presents the genome sequencing and assembly project for spinach, an organism of 980 Mbp. Results indicate a high-accuracy asse...

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Filling Gaps in the Spinach Genome with SMRT Sequencing - Video

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Newswise Although the time and cost of sequencing an entire human genome has plummeted, analyzing the resulting three billion base pairs of genetic information from a single genome can take many months.

In the journal Bioinformatics, however, a University of Chicago-based teamworking with Beagle, one of the worlds fastest supercomputers devoted to life sciencesreports that genome analysis can be radically accelerated. This computer, based at Argonne National Laboratory, is able to analyze 240 full genomes in about two days.

This is a resource that can change patient management and, over time, add depth to our understanding of the genetic causes of risk and disease, said study author Elizabeth McNally, MD, PhD, the A. J. Carlson Professor of Medicine and Human Genetics and director of the Cardiovascular Genetics Clinic at the University of Chicago Medicine.

The supercomputer can process many genomes simultaneously rather than one at a time, said first author Megan Puckelwartz, a graduate student in McNallys laboratory. It converts whole genome sequencing, which has primarily been used as a research tool, into something that is immediately valuable for patient care.

Because the genome is so vast, those involved in clinical genetics have turned to exome sequencing, which focuses on the two percent or less of the genome that codes for proteins. This approach is often useful. An estimated 85 percent of disease-causing mutations are located in coding regions. But the rest, about 15 percent of clinically significant mutations, come from non-coding regions, once referred to as junk DNA but now known to serve important functions. If not for the tremendous data-processing challenges of analysis, whole genome sequencing would be the method of choice.

To test the system, McNallys team used raw sequencing data from 61 human genomes and analyzed that data on Beagle. They used publicly available software packages and one quarter of the computers total capacity. They found that shifting to the supercomputer environment improved accuracy and dramatically accelerated speed.

Improving analysis through both speed and accuracy reduces the price per genome, McNally said. With this approach, the price for analyzing an entire genome is less than the cost of the looking at just a fraction of genome. New technology promises to bring the costs of sequencing down to around $1,000 per genome. Our goal is get the cost of analysis down into that range.

This work vividly demonstrates the benefits of dedicating a powerful supercomputer resource to biomedical research, said co-author Ian Foster, director of the Computation Institute and Arthur Holly Compton Distinguished Service Professor of Computer Science. The methods developed here will be instrumental in relieving the data analysis bottleneck that researchers face as genetic sequencing grows cheaper and faster.

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Whole Genome Analysis, STAT

Bravely Default Part 98 [~True Final Chapter~ Dimension #39;s Harp Genome Abilities]
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Bravely Default Part 98 [~True Final Chapter~ Dimension's Harp Genome Abilities] - Video

L 33 - Switchback [Genome Records]
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L 33 - Switchback [Genome Records] - Video

Better than Sanger: SMRT Sequencing for a High-GC Diploid Genome
Shane Brubaker from renewable oil manufacturer Solazyme reports using the PacBio system to sequence the genome of a GC-rich strain of algae that couldn #39;t be...

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Better than Sanger: SMRT Sequencing for a High-GC Diploid Genome - Video

Hatsune Miku Orange Genome CZ
Hatsune Miku Orange Genome CZ.

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Hatsune Miku Orange Genome sub ita
Salve! Eccoci qua con la mia prima traduzione su questo canale! *3* Tengo in maniera particolare a questa canzone; piuttosto triste e racconta una situazio...

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Newswise Led by biomedical engineer Justin Zook of the National Institute of Standards and Technology, a team of bioinformaticians from Harvard University and the Virginia Bioinformatics Institute of Virginia Tech has presented new methods to integrate data from different sequencing platforms, thus producing a highly reliable set of genotypes that will serve as a benchmark for human genome sequencing.

Understanding the human genome is an immensely complex task and we need great methods to guide this research, Zook says. By establishing reference materials and gold standard data sets, scientists are one step closer to bringing genome sequencing into clinical practice.

The methods put forth by the researchers make it increasingly possible to use an individuals genetic profile to guide medical decisions to prevent, diagnose, and treat diseases a priority of the National Institutes of Health. Their work was published this week in Nature Biotechnology.

We minimize biases toward any sequencing platform or data set by comparing and integrating 11 whole human genome and three exome data sets from five sequencing platforms, says Zook.

The National Institute of Standards and Technology organized the Genome in a Bottle Consortium to make well-characterized, whole-genome reference materials available to research, commercial, and clinical laboratories.

The team addressed the challenge with the expertise of David Mittelman, an associate professor of biological sciences at the Virginia Bioinformatics Institute, who creates tools that analyze vast amounts of genomic information.

The researchers created a metric to determine the accuracy of gene variations and understand biases and sources of error in sequencing and bioinformatics methods.

Their findings are available to the public on the Genome Comparison and Analytic Testing website, known as GCAT, to enable real-time benchmarking of any DNA-sequencing method. The collaborative, free online resource compares multiple analysis tools across a variety of crowd-sourced metrics and data sets.

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Researchers Establish Benchmark Set of Genotypes for Human Genome Sequencing

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14-Feb-2014

Contact: Clifford Beall Beall.3@osu.edu 614-292-9306 Ohio State University

COLUMBUS, Ohio Scientists have pieced together sections of DNA from 12 individual cells to sequence the genome of a bacterium known to live in healthy human mouths.

With this new data about a part of the body considered "biological dark matter," the researchers were able to reinforce a theory that genes in a closely related bacterium could be culprits in its ability to cause severe gum disease.

Why the dark matter reference? More than 60 percent of bacteria in the human mouth refuse to grow in a laboratory dish, meaning they have never been classified, named or studied. The newly sequenced bacterium, Tannerella BU063, is among those that to date have not successfully been grown in culture and its genome is identified as "most wanted" by the Human Microbiome Project.

The federal Human Microbiome Project aims to improve research about the microbes that play a role in health and disease. Those 12 cells of BU063 are a good example of the complexity of life in the mouth: They came from a single healthy person but represented eight different strains of the bacterium.

BU063 is closely related to the pathogen Tannerella forsythia, a bacterium linked to the gum disease periodontitis. Despite being "cousins," this research revealed that they have clear differences in their genetic makeup.

Those genes lacking in BU063 but present in forsythia meaning they are a likely secret behind forsythia's virulence are now identified as good targets for further study, researchers say.

"One of the tantalizing things about this study was the ability to do random searches of other bacteria whose levels are higher in periodontitis," said Clifford Beall, research assistant professor of oral biology at The Ohio State University and lead author of the study. "We looked for genes that were present in these bacteria and forsythia and not in BU063. There is one particular gene complex in a whole list of these periodontitis-related bacteria that could be involved with virulence."

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Scientists chip away at the mystery of what lives in our mouths

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19-Feb-2014

Contact: David Gilbert degilbert@lbl.gov 925-296-5643 DOE/Joint Genome Institute

Duckweed is a tiny floating plant that's been known to drive people daffy. It's one of the smallest and fastest-growing flowering plants that often becomes a hard-to-control weed in ponds and small lakes. But it's also been exploited to clean contaminated water and as a source to produce pharmaceuticals. Now, the genome of Greater Duckweed (Spirodela polyrhiza) has given this miniscule plant's potential as a biofuel source a big boost. In a paper published February 19, 2014 in the journal Nature Communications, researchers from Rutgers University, the Department of Energy Joint Genome Institute and several other facilities detailed the complete genome of S. polyrhiza and analyzed it in comparison to several other plants, including rice and tomatoes.

Simple and primitive, a duckweed plant consists of a single small kidney-shaped leaf about the size of a pencil-top eraser that floats on the surface of the water with a few thin roots underwater. It grows in almost all geographic areas, at nearly any altitude. Although it's a flowering plant, it only rarely forms small indistinct flowers on the underside of its floating leaves. Most of the time, it reproduces by budding off small leaves that are clones of the parent leaf. It often forms thick mats on the edges of ponds, quiet inlets of lakes and in marshes. It's among the fastest growing plants, able to double its population in a couple of days under ideal conditions.

These and other properties make it an ideal candidate as a biofuel feedstock a raw source for biofuel production. For example, unlike plants on land, duckweeds don't need to hold themselves upright or transport water from distant roots to their leaves, so they're a relatively soft and pliable plant, containing tiny amounts of woody material such as lignin and cellulose. Removing these woody materials from feedstock has been a major challenge in biofuel production. Also, although they are small enough to grow in many environments, unlike biofuel-producing microbes, duckweed plants are large enough to harvest easily.

S. polyrhiza turns out to have one of the smallest known plant genomes, at about 158 million base pairs and fewer than 20,000 protein-encoding genes. That's 27 percent fewer than Arabidopsis thaliana which, until recently, was believed to be the smallest plant genome and nearly half as many as rice plants.

"The most surprising find was insight into the molecular basis for genes involved in maturation a forever-young lifestyle," said senior author Joachim Messing, director of the Waksman Institute of Microbiology at Rutgers University.

S. polyrhiza leaves resemble cotyledons, embryonic leaves inside plant seeds that become the first leaves after germination. But where other plants develop other kinds of leaves as they mature, S. polyrhiza's never progresses and continuously produces cotyledon leaves. This prolonging of juvenile traits is called "neoteny." S. polyrhiza had fewer genes to promote and more genes to repress the switch from juvenile to mature growth.

"Because of the reduction in neoteny, there is an arrest in development and differentiation of organs. So this arrest allowed us to uncover regulatory networks that are required for differentiation and development," Messing said.

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Pond-dwelling powerhouse's genome points to its biofuel potential