Category Archives: Genome

NEW YORK, Sept. 19, 2013 /PRNewswire/ --The New York Genome Center (NYGC) officially launched its scientific and clinical consortium of academic and industry leaders focused on harnessing genomics to advance the understanding and treatment of disease. The announcement was made at the start of NYGC's inaugural scientific symposium with New York City Mayor Michael Bloomberg speaking at a ribbon cutting ceremony.

The two-day scientific symposium kicks off the opening of NYGC's new 170,000 square foot research facility in Manhattan and brings together leaders of 16 member institutions to discuss the importance of genomics research for the detection, diagnosis, and treatment of human disease.

The symposium features a number of prominent speakers, including Dr. Harold Varmus, Director of the National Cancer Institute, Marc Tessier-Lavigne, President of The Rockefeller University, Nobel Laureate Dr. James Watson, Cold Spring Harbor Laboratory, and Dr. Tom Maniatis, Chairman of the Department of Biochemistry and Molecular Biophysics at Columbia University and Chair of NYGC's Scientific and Clinical Steering Committee, as well as panelists discussing Pharmacogenomics, Genomics, Quantified Health, and the Future of Big Data on Patient Care.

"The opening of the New York Genome Center is a major achievement in the City's ongoing efforts to advance the bioscience sector in New York City part of our commitment to diversify the city's economy and create jobs," said Mayor Bloomberg. "The Genome Center's new facility and its groundbreaking approach to collaboration will help solve some of medicine's most challenging problems by bringing together the city's best academic and clinical institutions."

"We applaud Mayor Bloomberg's longstanding support and unwavering commitment to the technology and science community here in New York City," said Dr. Robert Darnell, President and Scientific Director of NYGC. "Modern genomics has the power to transform medicine. NYGC will provide the leadership to change the standard of care of patients from day one. This new facility represents the intersection of the clinic and the lab--translational science. As a physician-scientist, I recognize the importance of uniting these two worlds. The collaboration we've formed with our member institutions will not simply just do great science but will work to save lives."

"Collaboration is essential for solving the most complex and difficult problems in biomedical science," said Dr. Tom Maniatis, Chair of NYGC's Scientific and Clinical Steering Committee. "I have been involved from the beginning in a city-wide effort to create a consortium that effectively marshals the resources, identifies the critical questions, and creates the environment to tackle problems that are too big for individual researchers or institutions to solve alone. By bringing together some of the best minds in science and the intellectual diversity represented in New York into the NYGC consortium, we believe that we can push forward the boundaries of biomedical science in an unprecedented manner."

"No other city in the world has the breadth of scientific talent, healthcare delivery systems, and demographically diverse population that can be found in New York," said Russ Carson, Co-Chair of NYGC's Board of Directors. "The New York Genome Center will be a catalyst to promote greater interaction and collaboration among the City's premier institutions and scientists by integrating basic research, diagnosis, and clinical care. Collectively this consortium has the potential to effectively change the paradigm in medicine by incorporating genomics across the spectrum of their activities."

About the New York Genome Center

The New York Genome Center (NYGC) is an independent non-profit organization that leverages the collaborative resources of leading academic medical centers, research universities, as well as pharmaceutical, biotech, and technology companies. The vision of NYGC is to transform medical research and clinical care in New York and beyond through the creation of one of the largest genomics research facilities in North America, integrating sequencing, bioinformatics, data management, and genomics research.

NYGC represents an unprecedented sharing of data and resources among premier institutions, which will dramatically increase the quality and speed of research outcomes to advance clinical care. The collaborative power of NYGC's members will help nurture scientific advances leading to accelerate the development of new diagnostics and treatments for human diseases, and provide an engine for life science commercialization in the region.

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New York Genome Center Launches Groundbreaking Consortium to Accelerate Scientific and Clinical Discoveries

Public release date: 19-Sep-2013 [ | E-mail | Share ]

Contact: Jia Liu liujia@genomics.cn BGI Shenzhen

September 20, 2013, Shenzhen, China An international team led by South Korea's Personal Genomics Institute and BGI unraveled the first whole genome of a 9-year-old male Amur tiger (Panthera tigris altaica), and compared it with the genomes of other big cats including the white Bengal tiger, lions, and snow leopards. The genomic data from this study provides an invaluable resource for the future studies of big cats and their whole family's conservation. The latest study was published online in Nature Communications.

Despite big cats' reputation for ferocity, these majestic species face more danger than they pose: All are endangered, mainly due to habitat loss, poaching, and dwindling food supplies. As the largest felid species on earth, tiger has become one of the world's most endangered species. Understanding of tiger's genetic diversity and demography has been very limited without the whole-genome sequence of tiger, or any of the Panthera species.

In this study, researchers sequenced the whole genome of an Amur tiger, also known as the Siberian tiger, and assembled it using BGI self-developed software SOAPdenovo. The Amur tiger genome was predicted to contain 20,226 protein-coding genes and 2,935 non-coding RNAs, and was enriched in olfactory receptor sensitivity, amino-acid transport, and metabolic-related genes, among others. Additionally, researchers found that the Amur tiger genome showed more than 95 percent similarity to the genome of domestic cat.

Researchers also sequenced the genomes of other Panthera-a white Bengal tiger, an African lion, a white African lion, and a snow leopard-using next-gen sequencing technology, and aligned them using the genome sequences of tiger and domestic cat. They discovered a number of Panthera lineage-specific and felid-specific amino acid changes that may affect the metabolism pathways. These signals of amino-acid metabolism have been associated with an obligatory carnivorous diet.

Furthermore, the team revealed the evidence that the genes related to muscle strength as well as energy metabolism and sensory nerves, including olfactory receptor activity and visual perception, appeared to be undergoing rapid evolution in the tiger.

Previous studies showed that the human loci EGLN1 (Egl nine homologue 1) and EPAS1 (endothelial PAS domain-containing protein 1) are two key factors for mediating high-altitude adaptation. In this study, the team found that the snow leopard had unique amino-acid changes in both genes that may have contributed to snow leopard's acquisition of an alpine, high altitude ecological niche.

In addition, researchers found that white lions contain a variant in the TYR gene. Variants in TYR were previously reported to be related with white coat color in domestic cats as well as with a form of albinism in people. The white lion variant appeared to lead to an amino acid change that seems to affect the charge of the resulting protein.

When observing the species' genetic diversity, researchers found the genetic diversity of tiger and lion were similar to that of human. Interestingly, the diversity of snow leopard genome was nearly half that of the other Panthera species and slightly lower than that of the Tasmanian devil.

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Tiger, lion and leopard genomes revealed assisting big cats' conservation

Sep. 20, 2013 An international team led by South Korea's Personal Genomics Institute and BGI unraveled the first whole genome of a 9-year-old male Amur tiger (Panthera tigris altaica), and compared it with the genomes of other big cats including the white Bengal tiger, lions, and snow leopards. The genomic data from this study provides an invaluable resource for the future studies of big cats and their whole family's conservation.

The latest study was published online in Nature Communication.

Despite big cats' reputation for ferocity, these majestic species face more danger than they pose: All are endangered, mainly due to habitat loss, poaching, and dwindling food supplies. As the largest felid species on earth, tiger has become one of the world's most endangered species. Understanding of tiger's genetic diversity and demography has been very limited without the whole-genome sequence of tiger, or any of the Panthera species.

In this study, researchers sequenced the whole genome of an Amur tiger, also known as the Siberian tiger, and assembled it using BGI self-developed software SOAPdenovo. The Amur tiger genome was predicted to contain 20,226 protein-coding genes and 2,935 non-coding RNAs, and was enriched in olfactory receptor sensitivity, amino-acid transport, and metabolic-related genes, among others. Additionally, researchers found that the Amur tiger genome showed more than 95 percent similarity to the genome of domestic cat.

Researchers also sequenced the genomes of other Panthera-a white Bengal tiger, an African lion, a white African lion, and a snow leopard-using next-gen sequencing technology, and aligned them using the genome sequences of tiger and domestic cat. They discovered a number of Panthera lineage-specific and felid-specific amino acid changes that may affect the metabolism pathways. These signals of amino-acid metabolism have been associated with an obligatory carnivorous diet.

Furthermore, the team revealed the evidence that the genes related to muscle strength as well as energy metabolism and sensory nerves, including olfactory receptor activity and visual perception, appeared to be undergoing rapid evolution in the tiger.

Previous studies showed that the human loci EGLN1 (Egl nine homologue 1) and EPAS1 (endothelial PAS domain-containing protein 1) are two key factors for mediating high-altitude adaptation. In this study, the team found that the snow leopard had unique amino-acid changes in both genes that may have contributed to snow leopard's acquisition of an alpine, high altitude ecological niche.

In addition, researchers found that white lions contain a variant in the TYR gene. Variants in TYR were previously reported to be related with white coat color in domestic cats as well as with a form of albinism in people. The white lion variant appeared to lead to an amino acid change that seems to affect the charge of the resulting protein.

When observing the species' genetic diversity, researchers found the genetic diversity of tiger and lion were similar to that of human. Interestingly, the diversity of snow leopard genome was nearly half that of the other Panthera species and slightly lower than that of the Tasmanian devil.

The Amur tiger genome is the first reference genome sequenced from the Panthera lineage and the second from the Felidae species. The data from tigers, lions and snow leopards provides a rich and diverse genome resource that could be used in future studies of conservation and population genomics. Genetics underpins the local adaptation and potential inbreeding and/or outbreeding in wild and captive populations can be illuminated and thereby help ensure the future survival of these majestic species.

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Tiger genome sequenced: Tiger, lion and leopard genomes compared

Published: Sept. 18, 2013 at 2:44 PM

STATE COLLEGE, Pa., Sept. 18 (UPI) -- Two U.S. scientists said they discovered more on origin of genomic dark matter, non-coding RNA, which comprises more than 95 percent of the human genome.

B. Franklin Pugh, the Willaman chair in Molecular Biology at Penn State University, and Bryan Venters, who is on faculty at Vanderbilt University, discovered essentially all coding and non-coding RNA originates at the same types of locations along the human genome, Penn State said Wednesday in a release.

The scientists said their findings could help pinpoint exactly where complex-disease traits reside, since genetic origins of many diseases are outside of the coding region of the genome.

Pugh and Venters set out to identify the precise location of the beginnings of transcription, the first step in the expression of genes into proteins but they determined where proteins that initiate transcription of non-coding RNA were located along human chromosomes.

"So rather than look for the RNA product of transcription we looked for the 'initiation machine' that makes the RNA," Pugh said. "This 'machine' assembles RNA polymerase, which goes on to make RNA, which goes on to make a protein."

Pugh and Venters determined non-coding initiation machines recognized the same DNA sequences as the ones at coding genes, indicating they have a specific origin and their production is regulated, Pugh said.

"These non-coding RNAs have been called the 'dark matter' of the genome because, just like the dark matter of the universe, they are massive in terms of coverage ... . However, they are difficult to detect and no one knows exactly what they all are doing or why they are there," Pugh said. "Now at least we know that they are real, and not just 'noise' or 'junk.'"

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Scientists uncover milestone in genome's 'dark matter'

Public release date: 18-Sep-2013 [ | E-mail | Share ]

Contact: Craig Boerner craig.boerner@vanderbilt.edu 615-322-4747 Vanderbilt University Medical Center

Using technology he helped develop, Vanderbilt University scientist Bryan Venters, Ph.D., has shed new light on the "dark matter" of the genome and has begun to explore a possible new approach to treating cancer.

"Clarity is everything," said Venters, assistant professor of Molecular Physiology and Biophysics who further developed the high-resolution technology as a postdoctoral fellow in the lab of Frank Pugh, Ph.D., at Pennsylvania State University before moving to Vanderbilt in January.

Venters and Pugh are co-authors of a paper published this week in the journal Nature that describes their finding.

Much of the DNA of the human genome has been called "dark matter" because only a tiny fraction, about 3 percent, makes up the approximately 20,000 protein-coding genes that are transcribed into RNA copies, and then translated into proteins.

Other parts of the genome are transcribed into non-coding RNA, presumably to perform other functions, but until recently the origin of this non-coding RNA was unknown.

Now, with a technique called ChIP-exo developed at Penn State that identifies protein-DNA interactions at near base-pair resolution, Venters and Pugh have shown that so-called transcription initiation complexes drive much of the non-coding transcription occurring throughout the genome.

In a model leukemia cell line, they discovered about 150,000 complexes along non-coding stretches of the DNA the most ever discovered. This suggests, they concluded, that "pervasive non-coding transcription is promoter-specific, regulated, and not that much different from coding transcription (of genes)."

Venters compared the technique to the highly sensitive satellite cameras that enable web-based map applications to zoom in from a continental view to street level, "and tell house from house."

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Study helps bring genome's 'dark matter' into light

Public release date: 18-Sep-2013 [ | E-mail | Share ]

Contact: Leah Ramsay lramsay@jhu.edu 202-642-9640 Johns Hopkins Medicine

The National Human Genome Research Institute has selected the Johns Hopkins Berman Institute of Bioethics to establish a "Center of Excellence" to study the ethical, legal and social implications (ELSI) of genomic research. The Berman Institute will receive three years of funding to build on its multidisciplinary expertise in the ethics of human genomics and public health, bringing the fields together in the largely unexplored but crucial study of genomics as applied to infectious disease. The center will be known as GUIDE: Genomic Uses in Infectious Disease & Epidemics.

Pandemic scares in recent years, from SARS to influenza to MERS, necessitate this research, says Gail Geller, a co-principal investigator for GUIDE and faculty member at the Berman Institute. "Infectious diseases account for a significant proportion of illness and death worldwide, across all aspects of society," Geller notes. Recent research has suggested that a person's genes can play a significant role in the severity of viral infection, and even a predisposition to death from flu.

"It is important to begin to map out and address the ELSI issues involved in the use of genomic information for major public health areas like infectious disease, as the science in this area is moving quickly," says Jeffrey Kahn, co-principal investigator with Geller and deputy director at the Berman Institute.

As an exploratory Center for Excellence in ELSI Research (CEER), the GUIDE Center will bring together a multidisciplinary team of Hopkins' global leaders in diverse fields including genomics, immunology and infectious disease, bioethics, epidemiology, public health preparedness, education, and health policy, in keeping with the intention that CEERs create opportunities for trans-disciplinary research. This team will initially explore public health genomics in two case studies of human-to-human infectious disease: pandemic influenza and Hepatitis C.

The research team will examine how the genome affects a person's response to a flu vaccine as well as to the virus. "Although vaccinations are generally safe and highly effective interventions for disease prevention, understanding more about the genetics of an individual's response may help us design vaccines that maximize protective efficacy while minimizing the potential for adverse events," says Ruth Karron, a co-investigator in the CEER and director of the Johns Hopkins Center for Immunization Research. She says that in the future, genomic information could result in the production and use of vaccines with more refined understanding of effects on particular subpopulations, which will necessitate decisions about prioritization, privacy, opt-out policies and genotyping for flu-resistant first responders.

The project will also assess the ELSI issues arising from recent Hepatitis C studies, including research conducted by GUIDE co-investigators Chloe Thio and Priya Duggal, showing that individuals with a specific variation of the gene IFNl3 had five times better response to treatment and three times better chance of clearing the virus spontaneously, without treatment. These discoveries raise important questions about disclosure of genetic status as well as the use of expensive therapies in those individuals carrying the mutation. Currently Hepatitis C is found in virtually every region of the world, with an estimated 123 million people chronically infected.

"Hepatitis C is a timely and crucial case study in the necessity of clear ethical guidance for rapidly advancing public health genomics," says Geller. "Should individuals with the IFNl3 variation receive different treatments and priority? Should reporting the IFNl3 variation be mandatory?" Kahn adds that "These are among the questions the Berman Institute's CEER will address in our Hepatitis C case study, with the goal of producing an ethical framework that can apply more widely to genomics in the context of infectious disease."

At the conclusion of the three-year grant period, GUIDE will apply to transition from an exploratory to a specialized CEER, a designation that would come with an additional five years of funding from the National Human Genome Research Institute.

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Personal genome, public health

US Human Genome News 2003
An international consortium of scientists announced Monday that it has completed the map of the human genetic code to an accuracy of 99.99 percent and said the accomplishment opens a new era...

By: tastatura wovessf

Excerpt from:
US Human Genome News 2003 - Video

September 18, 2013

April Flowers for redOrbit.com Your Universe Online

In conservation efforts aimed at protecting endangered species, a group of international scientists has mapped the genome of the Siberian, or Amur, tiger. The findings, published in Nature Communications, reveal clues to how the big cat evolved to become a top predator with a carnivorous diet and superior muscle strength.

According to National Geographic, the Siberian tiger is the largest tiger subspecies. The animals weigh as much as 660 pounds and can grow up to ten feet in length. Currently only an approximate 450 Siberian tigers exist in the wild, with an estimated 4,000 tigers total remaining in their natural habitats.

We looked at this very large tiger first to see what made it distinctive from other cats, said genome expert Jong Bhak of South Koreas Personal Genomics Institute in Suwon. Bhak was part of the team lead by Yun Sung Cho at the Personal Genomics Institute, Genome Research Foundation that sequenced the genome of Taegeuk, a nine-year old male Siberian tiger from Everland Zoo in South Korea.

BBC News reports that the team also sequenced four other large cats the (African) lion, snow leopard, white (Bengal) tiger and white (African) lion enabling them to compare how the genes matched up in different members of the cat family.

Genetically all the cats are very close, so we need close genetic mapping to find the small differences that make them distinct, Bhak told Dan Vergano of National Geographic.

Beyond superior muscle strength and a need for lean meat, the genetic analysis gave clues to how the white lion gained its pale coat and how the snow leopard adapted to the snowy mountain ranges.

Across the study species, however, the cat family seems to rely on a narrow set of 1,376 genes linked to strong muscle fibers and digestion of protein. The study suggests that the genes likely originated in large part with the earliest common ancestor of big felines some 11 million years ago.

I take this to indicate that [big cats] have evolved to fill a very particular carnivorous niche in the environment that is predicated on the advantages in hunting these genes provide, Bhak told Vergano.

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Genome Sequencing Of Big Cats Complete

The first sequenced tiger genome shows that big cats evolved to kill.

Genes for strong muscle fibers and for meat-eating appear narrowly shared, researchers reported, among species as distinct as the African lion and Asia's snow leopard.

Scientists mapped the genes of the endangered Siberian tiger (or Amur tiger), both to understand the genes that make big cat species distinct from one another and to aid efforts to preserve genetic diversity in wild tiger populations. (Also see "Isolated Tigers Travel Surprising Lands to Find Mates.")

The largest tiger subspecies, Siberian tigers weigh as much as 660 pounds (300 kilograms) and grow to some ten feet (three meters) in length. Only about 450 Siberian tigers exist in the wild, and around 4,000 tigers total are thought to remain in their natural habitats. (See a National Geographic magazine interactive of big cats in danger.)

"We looked at this very large tiger first to see what made it distinctive from other cats," said genome expert Jong Bhak of South Korea's Personal Genomics Institute in Suwon, a co-author of the Nature Communications study reporting the mapping of the Siberian tiger genome.

Bhak and colleagues sampled genes from a nine-year-old male tiger at the Everland Zoo in Korea, and compared them with gene map information from the Bengal tiger, lion, and snow leopard. (See tiger pictures.)

Natural Born Killers

"Genetically all the cats are very close, so we need close genetic mapping to find the small differences that make them distinct," Bhak said.

Some gene differences are apparent in the mapping, such as two genes likely involved in adaptation to high altitudes and thin air in snow leopards and white fur in white African lions.

But overall, the cat family seems to rely on a narrow set of 1,376 genes linked to strong muscle fibers and digestion of protein, the study shows, seen widely across the study species. The genes likely originated in large part with the earliest common ancestor of big felines some 11 million years ago, the study authors suggest.

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Tiger Genome Sequenced, Shows Big Cats Evolved to Kill

Published: Sept. 17, 2013 at 7:43 PM

SUWON, South Korea, Sept. 17 (UPI) -- International scientists say they've mapped the genomes of the tiger, lion and snow leopard, hoping to bolster efforts to protect the endangered species.

The team led by Yun Sung Cho at the Genome Research Foundation in Suwon, South Korea, sequenced the genome of a female Siberian tiger at the Everland Zoo in South Korea.

Writing in the journal Nature Communications, the researchers said the sequencing revealed tigers share 96 percent of their genes with domestic cats.

The team then went on to sequence the DNA of four other big cat species -- the African lion, snow leopard, white Bengal tiger and white African lion.

The genomes show how big cats gained their superior muscle strength, the ability to digest large amounts of meat and a keen sense of smell, and also yielded genetic clues to how the white lion gained its pale coat and how the snow leopard adapted to the snowy mountain ranges, the researchers said.

The tiger genome map will be an important resource for looking at genetic diversity, they said, as the preservation of diminishing wild tiger populations is a major concern of animal conservationists.

"Our tiger reference genome can be used as the basis for comparing all the tigers in the world, so that we know the genetic diversity of tigers," researcher Jong Bhak told the BBC.

"And we can actually have a plan of how we can breed tigers effectively [in zoos] to save the genetic diversity."

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Scientists decode the genome of the world's big cats