Category Archives: Genome

The largest genome-wide association study (GWAS) to date, involving more than 300 institutions and more than 250,000 subjects, roughly doubles the number of known gene regions influencing height to more than 400. The study, from the international Genetic Investigation of Anthropometric Traits (GIANT) Consortium, provides a better glimpse at the biology of height and offers a model for investigating traits and diseases caused by many common gene changes acting together.

Findings were published online October 5 by Nature Genetics.

"Height is almost completely determined by genetics, but our earlier studies were only able to explain about 10 percent of this genetic influence," says Joel Hirschhorn, MD, PhD, of Boston Children's Hospital and the Broad Institute of MIT and Harvard, leader of the GIANT Consortium and co-senior investigator on the study. "Now, by doubling the number of people in our study, we have a much more complete picture of how common genetic variants affect height -- how many of them there are and how much they contribute."

The GIANT investigators, numbering in the hundreds, shared and analyzed data from the genomes of 253,288 people. They checked about two million common genetic variants (those that showed up in at least 5 percent of their subjects). From this pool, they pinned down 697 (in 424 gene regions) as being related to height, the largest number to date associated with any trait or disease.

"We can now explain about 20 percent of the heritability of height, up from about 12 percent where we were before," says co-first author Tonu Esko, PhD, of Boston Children's Hospital, the Broad Institute and the University of Tartu (Estonia).

"The study also narrows down the genomic regions that contain a substantial proportion of remaining variation -- to be discovered with even larger sample sizes," adds co-senior investigator Peter Visscher, PhD, of the University of Queensland, Australia.

Greater size, greater power

Height is a model trait for understanding how human genetics works -- especially for traits produced by not one gene, but many. Height is easy to measure, and an estimated 80 percent of variation in height is genetic.

Previous large-scale genome-wide association studies (GWAS) have indicated that a large number of genes influence height, and suggested that the majority of heritability comes from common genetic variants, not rare ones. Because sample sizes have not been large enough to draw definitive conclusions, the GIANT team built the largest sample to date.

"When you double the sample size and increase your statistical power, you can make new discoveries," says Hirschhorn. "Our results prioritize many genes and pathways as important in skeletal growth during childhood. Without a highly collaborative model, there's no way we could get this work done."

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Number of genes linked to height revealed by study

Alzheimer #39;s disease - Identified regions of the human genome that are altered over the life course
Alzheimer #39;s disease - Identified regions of the human genome that are altered over the life-course in a way. Subscribe this channel to watch more motivationa...

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Project Altered Beast (PS2): Story Cut Scene #46 - Acquired Genome Chip (Dragon)
This is the cut scene when you acquire the dragon genome chip. It #39;s from the video game, Project Altered Beast on the PlayStation 2. Ripped from the disc its...

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Project Altered Beast (PS2): Story Cut Scene #46 - Acquired Genome Chip (Dragon) - Video

By creating a global database an international consortium of scientists has increased the detailed knowledge of the variation in the cattle genome by several orders of magnitude. The first generation of the new data resource, which will be open access, forms an essential tool for scientists working with cattle genetics and livestock history. The results are published in an article in the scientific journal Nature Genetics.

"It's momentous," says one of the scientists behind the international effort, associate professor Bernt Guldbrandtsen from the Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University. Scientists from Aarhus University -- the only Danish university to participate -- have been part of the consortium from the start and have contributed 15 percent of the data.

Ancestral bulls

The data used in the huge database are derived from key ancestor bulls. These bulls have produced millions of descendants and have enormous influence on the genetic composition and characteristics of modern cattle breeds. For example, Holstein bulls in the database have fathered at least 6.3 million daughters worldwide.

The data consist of sequenced genomes for a number of bulls and are based on new sequencing techniques. The article in Nature Genetics describes data from 232 bulls and two cows of the breeds Angus, Holstein, Jersey and Fleckvieh. Since these animals are key ancestors, they carry most of the genetic variations present in the three races.

Currently, the database contains genomes of more than 1,200 animals of different cattle breeds, but as more scientists from other countries gradually join the project, there is a continual inflow of data. Key ancestor bulls have daughters all around the world, so it is a considerable strength of the project that such data are connected into one database.

High level of detail

What makes the database so special is the level of detail of the data. Where previously only the location of the genes on the genome and some of the gene variants were known, a large part of the total variation has now been identified and the genetic types carried by new offspring can be predicted. These data can be linked to data on key attributes such as health, calving, fertility, milk yield and growth allowing the identification of genetic variatiants that result in differences between animals.

"In the past we had only mapped approximately two percent of the variation. Now we have knowledge of it all for a great number of key ancestors. If you use the analogy of a road map, we previously only had sufficient information to see the mileposts on the chromosomal roadmap, but now we can see the entire roadmap," says Bernt Guldbrandtsen. He is supplemented by professor Mogens Sand Lund, director of the Center for Quantitative Genetics and Genomics at the Department of Molecular Biology and Genetics, Aarhus University: "Before we only knew about 700,000 markers. With the new and detailed database we have over 30 million markers to work with. We can predict the genotypes of all animals on the basis of the resource that we have created here."

New basis for genetic work

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Global database: Cattle genome cracked in detail

A powerful scientific tool for editing the DNA instructions in a genome can now also be applied to RNA, the molecule that translates DNA's genetic instructions into the production of proteins. A team of researchers with Berkeley Lab and the University of California (UC) Berkeley has demonstrated a means by which the CRISPR/Cas9 protein complex can be programmed to recognize and cleave RNA at sequence-specific target sites. This finding has the potential to transform the study of RNA function by paving the way for direct RNA transcript detection, analysis and manipulation.

Schematic shows how RNA-guided Cas9 working with PAMmer can target ssRNA for programmable, sequence-specific cleavage.

Led by Jennifer Doudna, biochemist and leading authority on the CRISPR/Cas9 complex, the Berkeley team showed how the Cas9 enzyme can work with short DNA sequences known as "PAM," for protospacer adjacent motif, to identify and bind with specific site of single-stranded RNA (ssRNA). The team is designating this RNA-targeting CRISPR/Cas9 complex as RCas9.

"Using specially designed PAM-presenting oligonucleotides, or PAMmers, RCas9 can be specifically directed to bind or cut RNA targets while avoiding corresponding DNA sequences, or it can be used to isolate specific endogenous messenger RNA from cells," says Doudna, who holds joint appointments with Berkeley Lab's Physical Biosciences Division and UC Berkeley's Department of Molecular and Cell Biology and Department of Chemistry, and is also an investigator with the Howard Hughes Medical Institute (HHMI). "Our results reveal a fundamental connection between PAM binding and substrate selection by RCas9, and highlight the utility of RCas9 for programmable RNA transcript recognition without the need for genetically introduced tags."

From safer, more effective medicines and clean, green, renewable fuels, to the clean-up and restoration of our air, water and land, the potential is there for genetically engineered bacteria and other microbes to produce valuable goods and perform critical services. To exploit the vast potential of microbes, scientists must be able to precisely edit their genetic information.

In recent years, the CRISPR/Cas complex has emerged as one of the most effective tools for doing this. CRISPR, which stands for Clustered Regularly Interspaced Short Palindromic Repeats, is a central part of the bacterial immune system and handles sequence recognition. Cas9 -- Cas stands for CRISPR-assisted -- is an RNA-guided enzyme that handles the sniping of DNA strands at the specified sequence site.

Together, CRISPR and Cas9 can be used to precisely edit the DNA instructions in a targeted genome for making desired types of proteins. The DNA is cut at a specific location so that old DNA instructions can be removed and/or new instructions inserted.

Until now, it was thought that Cas9 could not be used on the RNA molecules that transcribe those DNA instructions into the desired proteins.

"Just as Cas9 can be used to cut or bind DNA in a sequence-specific manner, RCas9 can cut or bind RNA in a sequence-specific manner," says Mitchell O'Connell, a member of Doudna's research group and the lead author of a paper in Nature that describes this research titled "Programmable RNA recognition and cleavage by CRISPR/Cas9." Doudna is the corresponding author. Other co-authors are Benjamin Oakes, Samuel Sternberg, Alexandra East Seletsky and Matias Kaplan.

In an earlier study, Doudna and her group showed that the genome editing ability of Cas9 is made possible by presence of PAM, which marks where cutting is to commence and activates the enzyme's strand-cleaving activity. In this latest study, Doudna, Mitchell and their collaborators show that PAMmers, in a similar manner, can also stimulate site-specific endonucleolytic cleavage of ssRNA targets. They used Cas9 enzymes from the bacterium Streptococcus pyogenes to perform a variety of in vitro cleavage experiments using a panel of RNA and DNA targets.

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RCas9: A programmable RNA editing tool

BrianLehrer.tv: Soldier Debts; Bike Crash; Ashkenazi Genome; NY101
It #39;s deep debt and wage garnishment for soldiers who buy into deals at discount stores near military bases. Paul Kiel, an investigative reporter with ProPublica, explains. Then, following...

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PUBLIC RELEASE DATE:

1-Oct-2014

Contact: Guy Lasnier lasnier@ucsc.edu 831-459-2955 University of California - Santa Cruz @ucsc

The UC Santa Cruz Genomics Institute late Tuesday (September 30) released a new Ebola genome browser to assist global efforts to develop a vaccine and antiserum to help stop the spread of the Ebola virus.

The team led by University of California, Santa Cruz researcher Jim Kent worked around the clock for the past week, communicating with international partners to gather and present the most current data. The Ebola virus browser aligns five strains of Ebola with two strains of the related Marburg virus. Within these strains, Kent and other members of the UC Santa Cruz Genome Browser team have aligned 148 individual viral genomes, including 102 from the current West Africa outbreak.

UC Santa Cruz has established the UCSC Ebola Genome Portal, with links to the new Ebola genome browser as well as links to all the relevant scientific literature on the virus.

"Ebola has been one of my biggest fears ever since I learned about it in my first microbiology class in 1997," said Kent, who 14 years ago created the first working draft of the human genome. "We need a heroic worldwide effort to contain Ebola. Making an informatics resource like the genome browser for Ebola researchers is the least we could do."

Scientists around the world can access the open-source browser to compare genetic changes in the virus genome and areas where it remains the same. The browser allows scientists and researchers from drug companies, other universities, and governments to study the virus and its genomic changes as they seek a solution to halt the epidemic.

The release of the new Ebola genome browser comes as the U.S. Centers for Disease Control and Prevention Tuesday confirmed the first case of Ebola in the United States.

The Ebola browser was started shortly after a phone conversation between Kent and his sister, an epidemiologist at the CDC, who spoke of how she and her staff were consumed with Ebola research in the face of the escalating crisis. UC Santa Cruz Professor Phil Berman, an HIV specialist, had also asked Kent for help with his efforts in developing a vaccine for Ebola.

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Ebola genome browser now online to aid researchers' response to crisis

The UC Santa Cruz Genomics Institute has released a new Ebola genome browser to assist global efforts to develop a vaccine and antiserum to help stop the spread of the Ebola virus.

The team led by University of California, Santa Cruz researcher Jim Kent worked around the clock for the past week, communicating with international partners to gather and present the most current data. The Ebola virus browser aligns five strains of Ebola with two strains of the related Marburg virus. Within these strains, Kent and other members of the UC Santa Cruz Genome Browser team have aligned 148 individual viral genomes, including 102 from the current West Africa outbreak.

UC Santa Cruz has established the UCSC Ebola Genome Portal, with links to the new Ebola genome browser as well as links to all the relevant scientific literature on the virus.

Ebola has been one of my biggest fears ever since I learned about it in my first microbiology class in 1997," said Kent, who 14 years ago created the first working draft of the human genome. "We need a heroic worldwide effort to contain Ebola. Making an informatics resource like the genome browser for Ebola researchers is the least we could do.

Scientists around the world can access the open-source browser to compare genetic changes in the virus genome and areas where it remains the same. The browser allows scientists and researchers from drug companies, other universities, and governments to study the virus and its genomic changes as they seek a solution to halt the epidemic.

The release of the new Ebola genome browser comes as the U.S. Centers for Disease Control and Prevention Tuesday confirmed the first case of Ebola in the United States.

The Ebola browser was started shortly after a phone conversation between Kent and his sister, an epidemiologist at the CDC, who spoke of how she and her staff were consumed with Ebola research in the face of the escalating crisis. UC Santa Cruz Professor Phil Berman, an HIV specialist, had also asked Kent for help with his efforts in developing a vaccine for Ebola.

Kent asked his supervisor, UC Santa Cruz bioinformatics researcher David Haussler, if he could divert his team to Ebola work. Haussler replied with an enthusiastic affirmative, and they pulled together a team of UC Santa Cruz bioinformatics scientists that, within a week, was able to create a fully functional Ebola genome browser.

"The incredible speed with which this group was able to assemble all the genetic information about Ebola and make it available to the world shows what a great team Jim Kent has assembled," Haussler said.

In June 2000, Kent and Haussler released the first working draft of the human genome sequence on the web. Two months later, Kent developed the UCSC Genome Browser, which has become an essential resource to biomedical science.

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Ebola genome browser now online

DEFINITION of 'Genomics'

The study of the genome, which is the complete set of the genetic material or DNA present in an organism. Genomics studies all genes and their inter relationships in an organism, so as to identify their combined influence on its growth and development. The field of genomics attracted worldwide attention in the late 1990s with the race to map the human genome. The Human Genome Project (HGP), completed in April 2003, made available for the first time the complete genetic blueprint of a human being. Genomics has already made huge strides in better health care by enabling researchers to develop improved diagnostics and more effective therapies, while providing better decision-making tools for patients and health care providers.

The human genome is a very complex entity containing huge amounts of information. DNA molecules are made of two twisting, paired strands often called a double helix and each strand consists of four chemical units called nucleotide bases adenine (A), thymine (T), guanine (G) and cytosine (C). Bases on opposite strands pair in a very specific manner for example, an A always pairs with a T, and a C always pairs with a G. The order of this genetic alphabet determines the meaning of the information encoded in that part of the DNA molecule.

The human genome contains about 3 billion of these base pairs. Genome sequencing involved figuring out the exact order of all 3 billion of these DNA nucleotides, a feat which would not have been possible without massive amounts of computing power.

The Human Genome Project, which was formally initiated by the U.S. Department of Energy and National Institutes of Health in 1988, was successfully completed in April 2003. It was designed to create a resource that could be used for extensive biomedical studies, such as looking for the genetic variations that increase the risk of specific diseases. A study released in June 2013 reported that the $14.5-billion investment in HGP by the U.S. had paid off more than 60-fold in new jobs, drugs and a booming genetics industry, with a total economic impact of $966 billion.

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Genomics

What Is The Definition Of Drosophila genome - Medical Dictionary Free Online
Visit our website for text version of this Definition and app download. http://www.medicaldictionaryapps.com Subjects: medical terminology, medical dictionar...

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What Is The Definition Of Drosophila genome - Medical Dictionary Free Online - Video