Category Archives: Genome

October 2, 2013

The project will sequence the genome of a wild wheat relative responsible for the bread-making quality found in wheat.

An international effort, led by University of California, Davis, scientists is in progress, aimed at sequencing a wheat ancestors genome, which is 40 percent larger than the human genome.

The project, recently funded by a $9 million grant from the National Science Foundations Plant Genome Research project, is focused on better understanding the genetics of bread wheat, one of three cereals that provide most of the worlds food. Bread wheat also has the distinction of having a genome that consists of three genomes from separate species, each with a complexity and size that make genetic decoding exceptionally difficult.

The project will sequence the genome of the goatgrass Aegilops tauschii, a wild relative of common bread wheat that is responsible for the bread-making quality found in wheat. It also is highly tolerant of salt, drought, aluminum, frost, pests and many wheat diseases.

In studying the Ae. tauschii genome, scientists plan to identify the genes controlling the important environmental tolerance and resistance traits, and gain a finer understanding of the biological causes behind the enormous sizes of many plant genomes. The Ae. tauschii code also will provide geneticists with a badly needed reference for wheat genomics and sequence assembly.

The effort already has produced its first practical outcome: the discovery of a gene with a resistance to wheat stem rust, recently published as a cover article in the journal Science.

Geneticists previously had hoped to decode the wheat and Ae. tauschii genomes using the shotgun sequencing approach, which is like piecing together a book from millions of random sentence fragments. The team, instead, is using an approach known as ordered clone sequencing to generate a high-quality blueprint of the Ae. tauschii genome, along with nanomapping, which traps DNA molecules in nano-sized channels where their unique pattern is visualized and quantified.

This is really an exciting technology, said Jan Dvorak, a lead scientist on the team, as well as a UC Davis professor and geneticist. For the first time in genome sequencing, we have an independent means to check the accuracy of the genome sequence assembly and correct errors and fill gaps.

Ming-Cheng Luo, a co-investigator and UC Davis geneticist, worked with BioNano Genomics, the manufacturer of the sequencing instrument, to adapt the technology to ordered clone sequencing.

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Wheat geneticists to decode massive genome

Episode 5: The Trade-offs with Whole Genome Sequencing

By: Ridhi Tariyal

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Episode 5: The Trade-offs with Whole Genome Sequencing - Video

Dark matter makes up most of the universe and astronomers dont know what it is. Much like the universe, the human genome is mostly dark matter too, except scientists now know where this dark matter originates.

A Penn State research duo discovered where that dark matter non-coding RNA in the human genome originates from.

B. Franklin Pugh , the Penn State Willaman Chair in Molecular Biology and one of the two researchers, said this dark matter makes up more than 95 percent of the human genome.

The research, which was also conducted by Penn State postdoctoral scholar Bryan Venters , was published on Sept. 18 as an Advance Online Publication in Nature, according to a Penn State News release .

With dark matter making up a significant portion of the human genome, Venters, who is now an assistant professor at Vanderbilt University, said the researchers considered the question: Are the RNA transcripts regulated or randomly generated?

The origin of non-coding RNA is not that different from the origin of protein coding genes, Venters said.

[The researchers] discovered hundreds of thousands of sites in the human genome where molecular machinery is engaging with DNA to produce RNA, Shaun Mahony , assistant professor in the department of Biochemistry and Molecular Biology , said via email.

RNA, whether it codes for proteins or not, originates from initiation sites, sometimes called promoter sites, Pugh said.

In order to find these sites, the team narrowed their search space by developing a high-resolution method to figure out where a protein binds in the genomes and then applied it, Pugh said. Trying to just find these promoter sites would be like searching for a needle in a haystack, he added.

The technique allowed the team to see with a higher clarity and level of detail so they could see initiation sites that existed in dark matter, Venters said.

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Penn State Researchers discover ‘dark matter’ in human genome

DALLAS (CBS 11 NEWS) Bigfoot is realjust ask the researchers who have logged countless hours to prove their beliefs.

New photos and videos filled with never before seen images were released Tuesday by a group known as the Sasquatch Genome Project. They were in Dallas Tuesday to unveil its findings.

Dr. Melba Ketchum, a genetics scientist led the project. We want people to understand this is a serious study, said Ketchum.

The five-year study costs more than$500,000. It was funded by businessman Adrian Erickson.

Erikson says he has had numerous encounters with Sasquatch creaturesand says he has the images and science to back their existence. But he says he also understands the stigma and disbelief that comes with BigFoot.

People have chosen not to believe it. They cant find it in their minds to think these things exist.

So the group of researchers and scientists set out to track what they call the furry people.

The group says it followed a mother and daughter in Kentucky collecting thermal imagery, daytime and nighttime video, along with, photos of massive hand and footprints.

The group says there are thousands of these creatures in the United States including right here in North Texas.

But the strongest evidence the group says its has is DNA evidence. They say it is like nothing that has been seen before in mammals or humans.

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Sasquatch Genome Project Reveals Bigfoot Photos In Dallas

Bigfoot believers say there is scientific proof that Sasquatch exists.

A five-year DNA study conducted by the Sasquatch Genome Project along with new photos and videos of the alleged animal confirms Bigfoot is real. The group, which revealed its findings in Dallas on Tuesday, says Bigfoot is a human relative that has existed for 15,000 years, ABC News reports.

We want people to understand this is a serious study, Dr. Melba Ketchum, a genetics scientist led the project, told CBS Dallas. People have chosen not to believe it. They cant find it in their minds to think these things exist.

The five-year study funded by businessman Adrian Erickson cost more than $500,000. Ketchum led a team of experts in genetics, forensics, imaging and pathology sequenced three complete Sasquatch nuclear genomes and found that it is a human hybrid.

Our study has sequenced 20 whole mitochondrial genomes and utilized next generation sequencing to obtain 3 whole nuclear genomes from purported Sasquatch samples. The genome sequencing shows that Sasquatch mtDNA is identical to modern Homo sapiens, but Sasquatch nuDNA is a novel, unknown hominin related to Homo sapiens and other primate species, the group wrote in a press release.

A five-year DNA study conducted by the Sasquatch Genome Project along with new photos and videos of the alleged animal confirms Bigfoot is real. Sasquatch Genome Project

A five-year DNA study conducted by the Sasquatch Genome Project along with new photos and videos of the alleged animal confirms Bigfoot is real. Sasquatch Genome Project

The team used 111 specimens taken from alleged Sasquatches hair, blood, skin and other tissue type that came from 34 different hominin research sites in 14 U.S. states and two Canadian provinces.

Ketchum, a veterinarian by profession, was initially a skeptic. When she began testing DNA samples five years ago, she set strict protocols when extracting collected samples. "This creature does not follow general rule. What it does do is very different. We think it is human hybrid. That is our theory," she said.

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Bigfoot Existence Confirmed? Sasquatch Genome Project Releases DNA Evidence, New Footage [PHOTOS]

MOUNTAIN VIEW, Calif., Sept. 30, 2013 (GLOBE NEWSWIRE) -- Complete Genomics, Inc. (formerly NASDAQ: GNOM) ("Complete"), a wholly-owned subsidiary of BGI-Shenzhen, a leading international genomics organization based in Shenzhen, China, today announced that its highly-accurate whole genome sequencing technology played a pivotal role in identifying a point mutation that causes Prader-Willi Syndrome (PWS). That discovery helped resolve a diagnostic conundrum for four young male patients. These data were published today in Nature Genetics.

A photo accompanying this release is available at http://www.globenewswire.com/newsroom/prs/?pkgid=21224

PWS is a rare genetic disorder that causes poor muscle tone, low levels of sex hormones, and a constant feeling of hunger, according to the Eunice Kennedy Shriver National Institute of Child Health and Human Development. As a result, people with this condition tend to overeat, leading to obesity.

The first patient in this study was tested for PWS when he was one year old, but the result was negative. Over the next 12 years, he began to manifest some, but not all, of the typical PWS symptoms.

Then the patient met with paper author Dr. C. Thomas Caskey, who was director and chief executive officer of the Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, part of the University of Texas Health Science Center at Houston. Dr. Caskey has since joined Baylor College of Medicine as professor of molecular and human genetics.

It was Dr.Caskey who referred the patient to Dr. Christian Schaaf, an assistant professor of molecular and human genetics at Baylor College of Medicine, and faculty member at the Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, a co-lead author on the paper. Dr. Schaaf evaluated the patient and confirmed the earlier findings. Dr. Schaaf then used Complete's highly-accurate whole genome sequencing service to determine the genetic basis of his patient's symptoms.

Those sequencing results were reviewed by fellow co-lead author Dr. Manuel L. Gonzalez-Garay, an assistant professor and a bioinformatics expert at the University of Texas Health Science Center at Houston's Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases. Dr. Gonzalez-Garay identified a single mutation, a base deletion, on the protein-coding MAGEL2 gene in a section of chromosome 15 that had been previously linked to PWS. It proved to be a frame-shift deletion mutation in a difficult to sequence GC rich region, which disrupts the activity of the MAGEL2 protein product.

As MAGEL2 is only expressed on the paternal gene, it was important to determine whether the mutation was on the maternal or paternal version of chromosome 15. In this case, the MAGEL2 mutation was confirmed to be on the paternal gene using a modified version of Complete Genomics' Long Fragment Read technology.

To investigate MAGEL2's role in this disease further, the researchers reviewed more than 1,200 exome sequencing reports from the Baylor Whole Genome Sequencing Laboratory, searching for other patients with point mutations on that gene. They identified three additional patients -- one had classic PWS and the other two had PWS-like symptoms. However, they all had negative PWS tests as infants. All four patients were also diagnosed with autism spectrum disorder and intellectual disability.

"This is the first study to show that point mutations can cause Prader-Willi Syndrome," said Dr. Schaaf. "This is an important development that increases our understanding of this complex disorder, and also gives four boys a diagnosis, which they and their parents have sought for many years."

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Photo Release -- Complete Genomics Whole Genome Sequencing Enables Discovery of Point Mutation Responsible for Prader ...

Howard Jacob - Use of Whole Genome Sequencing in Clinical Practice
Watch on LabRoots at: http://labroots.com/user/webinars/details/id/68 Learning Objectives: Know what personalized medicine is Understand how big data will im...

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Howard Jacob - Use of Whole Genome Sequencing in Clinical Practice - Video

Startup Genome, Mapping Communities | Top of Mind Episode 34
http://www.entrepreneurship.org/e360tv/top-of-mind.aspx This week on Top of Mind, we talk about mapping startup communities with Startup Genome founder, Shan...

By: KauffmanTopOfMind

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Startup Genome, Mapping Communities | Top of Mind Episode 34 - Video

Genome British Columbia Intro Video
Genome British Columbia is a catalyst for the life sciences cluster on Canada #39;s West Coast, and manages a cumulative portfolio of over $625M in 180 genomics ...

By: genomicseducation

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Genome British Columbia Intro Video - Video

Cinnamon Bloss - Return of Genome Sequencing Results to Physicians and Patients
Watch on LabRoots at: http://labroots.com/user/webinars/details/id/63 There has been considerable debate in the scientific and clinical communities regarding...

By: LabRoots

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Cinnamon Bloss - Return of Genome Sequencing Results to Physicians and Patients - Video