Category Archives: Genome

Jan. 23, 2013 A retrovirus called HERV-H, which inserted itself into the human genome millions of years ago, may play an important role in pluripotent stem cells, according to a new study published in the journal Retrovirology by scientists at UMass Medical School. Pluripotent stem cells are capable of generating all tissue types, including blood cells, brain cells and heart cells. The discovery, which may help explain how these cells maintain a state of pluripotency and are able to differentiate into many types of cells, could have profound implications for therapies that would use pluripotent stem cells to treat a range of human diseases.

"What we've observed is that a group of endogenous retroviruses called HERV-H is extremely busy in human embryonic stem cells," said Jeremy Luban, MD, the David L. Freelander Memorial Professor in HIV/AIDS Research, professor of molecular medicine and lead author of the study. "In fact, HERV-H is one of the most abundantly expressed genes in pluripotent stem cells and it isn't found in any other cell types."

In the study, Dr. Luban and colleagues describe how RNA from the HERV-H sequence makes up as much as 2 percent of the total RNA found in pluripotent stem cells. The HERV-H sequence is controlled by the same factors that are used to reprogram skin cells into induced pluripotent stem (iPS) cells, a discovery that garnered the 2012 Nobel Prize in Physiology or Medicine. "In other words, HERV-H is a new marker for pluripotency in humans that has the potential to aid in the development of iPS cells and transform current stem cell technology," said Luban.

When a retrovirus infects a cell, it inserts its own genes into the chromosomal DNA of the host cell. As a result, the host cell treats the viral genome as part of its own DNA sequence and begins making the proteins required to assemble new copies of the virus. And because the retrovirus is now part of the host cell's genome, when the cell divides, the virus is inherited by all daughter cells.

In rare cases, it's believed that retroviruses can infect human sperm or egg cells. If this happens, and if the resulting embryo survives, the retrovirus can become a permanent part of the human genome, and be passed down from generation to generation. Scientists estimate that as much as 8 percent of the human genome may be composed of extinct retroviruses left over from infections that occurred millions of years ago. Yet these sequences of fossilized retrovirus were thought to have no discernible functional value.

"The human genome is filled with retrovirus DNA thought to be no more than fossilized junk," said Luban. "Increasingly, there are indications that these sequences might not be junk. They might play a role in gene expression after all."

An expert in HIV and other retroviruses, Luban and his colleagues were seeking to understand if there was a rationale behind where, in the expansive human genome, retroviruses inserted themselves. Knowing where along the chromosomal DNA retroviruses might attack could potentially lead to the development of drugs that protect against infection; better gene therapy treatments; or novel biomarkers that would predict where a retrovirus would insert itself in the genome, said Luban.

Turning these same techniques on the retrovirus sequences already in the human genome, they discovered a sequence, HERV-H, that appeared to be active. "The sequences weren't making proteins because they had been so disrupted over millions of years, but they were making these long, noncoding RNAs," said Luban.

Specifically, the HERV-H sequence was making abundant amounts of RNA in human embryonic stem cells -- and only stem cells. In total, there are more than 1,000 HERV-H retrovirus genomes scattered throughout the human genome. The Luban lab also found high levels of HERV-H RNA in some iPS cells. Other iPS cells, perhaps those lines that were not sufficiently reprogrammed to pluripotency, had lower levels of the HERV-H RNA, another indication that HERV-H may be an important marker for pluripotency.

Interestingly, the HERV-H genes that were expressed in human pluripotent stem cells are only found in the human and chimpanzee genomes, indicating that HERV-H infected a relatively recent ancestor to humans, said Luban.

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Retrovirus in the human genome is active in pluripotent stem cells

Genome and Clinic in the Care of Renal Cell Carcinoma - by W. Kimryn Rathmell, MD, PhD
Uniting the Genome and Clinic to Advance the Science and Care of Renal Cell Carcinoma Lecture by W. Kimryn Rathmell, MD, PhD Associate Professor of Medicine and Genetics, UNC School of Medicine

By: TheOncologistJournal

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Genome and Clinic in the Care of Renal Cell Carcinoma - by W. Kimryn Rathmell, MD, PhD - Video

Public release date: 22-Jan-2013 [ | E-mail | Share ]

Contact: Sam Smith newsbureau@mayo.edu 507-284-5005 Mayo Clinic

ROCHESTER, Minn. and FOSTER CITY, Calif. -- Mayo Clinic and Silicon Valley Biosystems (SV Bio) today announced a strategic collaboration for whole genome diagnostics and interpretation at the Mayo Clinic Center for Individualized Medicine and Mayo Medical Laboratories. This strategic collaboration unites SV Bio's proprietary genome interpretation solution with Mayo Clinic's growing genome reference library and its commitment to individualized medicine, and will increase accessibility and clinical utility of next-generation sequencing for patients. SV Bio will provide clinical genome interpretation services and clinical decision support interfaces to Mayo Clinic, and Mayo's Center for Individualized Medicine will contribute clinical and laboratory expertise and support. Financial details of the agreement were not disclosed.

"At Mayo Clinic, we are committed to integrating genomic medicine into the continuum of care for all of our patients," says Gianrico Farrugia, M.D., director of the Mayo Clinic Center for Individualized Medicine. "The Individualized Medicine Clinic represents one of Mayo's bold steps toward realizing the promise of these game-changing technologies and offering new hope to patients, including those with cancer and diagnostic dilemmas."

While the rapidly declining cost of sequencing has been widely heralded and has led to varying degrees of clinical implementation at a handful of health care organizations, managing the sheer volume of data remains a bottleneck to widespread application of personalized medicine.

"Every human disease has a genetic component but, to date, medical providers have not been able to fully utilize this information to improve clinical outcomes," says Dietrich Stephan, Ph.D., founder, president and CEO of SV Bio. "With the SV Bio platform, we've made the translation to a single assay a full human genome with the diagnostics rapidly and precisely happening in silico." The SV Bio process is fully computerized and automated and reduces the time needed for clinically actionable genome interpretation from several weeks to a few minutes and puts the results in the provider's hands at the point of care.

The goal of the collaboration is to unlock the full potential of next-generation sequencing and open these technologies to every patient. SV Bio's turnkey genomics interpretation solutions query a patient's genome at the point of care and distill the biological data into a concise, actionable report that physicians can use to make faster, more informed decisions. Mayo Clinic will provide medical and scientific expertise to help ensure patients receive the maximum benefit.

"We are now able to take data from any next-generation sequencer and determine with clinical grade sensitivity and specificity which variants within a patient's DNA sequence are influencing a disease or condition, and rapidly provide a report for the clinician that is clear and actionable," Dr. Stephan says. "This level of speed, accuracy and integration into the clinical work flow is not only a first for molecular testing, but also a sea change in the application of next-generation sequencing with no compromise of quality in clinical diagnostics."

As part of the collaboration, Mayo Medical Laboratories, the reference laboratory that provides services worldwide, and SV Bio will work together to refine approaches to clinical genome interpretation.

"In our laboratories, we are rapidly adopting and implementing next-generation sequencing as a platform upon which we will be providing cutting-edge genome-based testing," says Franklin Cockerill, M.D., president of Mayo Medical Laboratories. "This collaboration with SV Bio furthers our mission of bringing the latest diagnostic technologies to health care providers around the world."

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Mayo Clinic and SV Bio enter strategic relationship on genome diagnostics and interpretation

By mapping the genome of the diamondback moth, scientists have uncovered some of the genes that make it such a destructive agricultural pest. The discovery may lead to new ways to protect crops.

Two Australian scientists have helped reveal the "evolutionary trick" which makes the diamondback moth one of the world's worst agricultural pests.

University of Adelaide Ramsay research fellow Dr Simon Baxter and Charles Sturt University Professor Geoff Gurr, from the EH Graham Centre for Agricultural Innovation, were part of an international consortium which today revealed the genetic blueprint of the moth in a paper in the international journal Nature Genetics.

Diamondback moth wreaks billions of dollars worth of damage to crops around the world each year, costing producers $4-5 billion in crop loss and control measures, and has caused major problems for the Australian canola industry.

The caterpillars feed on cabbage and related plants and are difficult to control because they can quickly develop resistance to all types of insecticide.

Dr Baxter said the moth had spread throughout the world and could be found in vegetable gardens and farms across Australia.

"They have an incredible ability to migrate long distances and to quickly adapt to the environments they encounter, making outbreaks of these insects difficult to predict and control," Dr Baxter said.

"This project has helped identify the genes that make diamondback moth such a successful pest and will enable new insecticide resistance monitoring techniques and pest management strategies to be developed."

Professor Gurr said the successful sequencing of the moth's genome revealed the moth's "evolutionary trick"; its ability to detoxify the defence compounds produced by plants in the cabbage family.

"These are the same compounds that make mustard so pungent and cabbage so smelly," Professor Gurr said.

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Genome reveals how moths detoxify pesticides

NOKOMIS, Fla.--(BUSINESS WIRE)--

Since the new year began, Rainbow Coral Corp. (RBCC) has wasted no time in searching for new targets to add to its portfolio of projects for commercialization. Last week, the Companys executive leadership accepted an invitation to tour a genome-mapping facility in Houston with which RBCC could soon partner.

New healthcare innovations related to the human genome represent a target-rich area of interest for RBCC.The Texas company currently being reviewed performs tests to identify genetic markers in patients that can potentially boost or nullify the effects of certain medications.

Such testing could dramatically change the way medications are prescribed, potentially fostering a significant reduction in global health care costs.

Knowing specifics about an individuals genetic make-up can greatly assist a patients doctor in determining correct doses of medications as well as ruling out medications that could prove harmful, said RBCC CEO Patrick Brown. Genome mapping opens up a host of new possibilities for doctors and patients alike, and were very interested in the technologys economic potential.

As the company searches for its next partner, RBCCs biotech subsidiary Rainbow Biosciences remains close to a joint venture deal with Amarantus Bioscience, makers of exciting new diagnostic tools and therapies for neurological diseases such as Parkinsons.

Amarantus recently announced highly promising results in new animal trials of its forthcoming Parkinsons therapeutic, known as MANF.

For more information on RBCC and its biotechnology targets, please visitwww.rainbowbiosciences.com/investors.

Rainbow BioSciences is dedicated to developing new medical and research technology innovations to compete alongside companies such as Amgen Inc. (AMGN), Cell Therapeutics, Inc. (CTIC) and Abbott Laboratories (ABT).

Follow us on Twitter atwww.twitter.com/RBCCinfo.

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RBCC Visits Texas Genome-Mapping Target

IranBiotech 2013 Genome data interpretation
Marianna Ivanova, Oftalmic CEO speech

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IranBiotech 2013 Genome data interpretation - Video

Featured Article Academic Journal Main Category: Cancer / Oncology Also Included In: Biology / Biochemistry;Genetics Article Date: 21 Jan 2013 - 3:00 PST

Current ratings for: Quadruple Helix DNA Exists In Human Genome

Lead investigator Shankar Balasubramanian, a professor at Cambridge University's Department of Chemistry and Cambridge Research Institute, says in a statement:

"We are seeing links between trapping the quadruplexes with molecules and the ability to stop cells dividing, which is hugely exciting."

"The quadruple helix DNA structure may well be the key to new ways of selectively inhibiting the proliferation of cancer cells. The confirmation of its existence in human cells is a real landmark," he adds.

Balasubramanian and colleagues write about their findings in the 20 January online issue of Nature Chemistry.

They are called G-quadruplexes because they form in regions of DNA rich in Guanine, one of the four chemical bases or building blocks that encode genetic information (the other three are Adenine, Cytosine, and Thymine).

The team started with hypothetical computer models of the quadruplexes, then made synthetic versions in test tubes, and then proved, using fluorescent biomarkers, that the structures exist in real life in human cancer cells.

Although there is evidence that G-quadruplexes occur in single-celled organisms called ciliates, this is the first time they have been seen in human cells.

Balasubramanian says this suggests targeting the quadruplexes could form the basis of new personalized treatments.

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Quadruple Helix DNA Exists In Human Genome

GenomeMark (Bookmarks for Genome Browser)
Generate GenomeMarks for the genome browser, to easily jump between features, filter by values, and more.

By: OmicsoftCorporation

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GenomeMark (Bookmarks for Genome Browser) - Video

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Genome - Video

A former "white hat" hacker hired by banks to test their computer security has been able to discover the names of individuals who volunteered to take part in genome studies on the condition of anonymity.

Nearly 50 people who had agreed to have their genomes sequenced and placed on scientific databases provided that their names would not be used were identified by Yaniv Erlich as part of an exercise to test the vulnerability of personal data held in DNA libraries.

The revelation will prove embarrassing for organisations who have promoted the widespread use of genome sequencing in medical research. Last month, the Government announced a plan to sequence the genomes of 100,000 Britons to boost the discovery of new drugs and treatments.

Dr Erlich used computer algorithms to link DNA sequences, particularly of the male Y chromosome, with surnames and other personal data held on genealogy databases as part of a deliberate attempt to test the security of the anonymised information held on genome databases.

This is an important result that points out the potential for breaches of privacy in genomic studies, said Dr Erlich, a fellow of the Whitehead Institute for Biomedical Research in Cambridge, Massachusetts, whose hacking study is published in the journal Science.

Our aim is to better illuminate the current status of identifiability of genetic data. More knowledge empowers participants to weigh the risk and benefits and make more informed decisions when considering whether to share their own data, Dr Erlich said.

We also hope that this study will eventually result in better security algorithms, better policy guidelines, and better legislation to help mitigate some of the risks, he said.

The number of people having their full genomes sequenced has risen rapidly in recent years as the cost of DNA sequencing has come down. Scientists around the world are collaborating on a number of international projects to sequence thousands of genomes, often with the guarantee of anonymity to the volunteers who take part.

However, using little more than an internet connection and some clever software, Dr Erlich and his colleagues were able to match specific DNA sequences in publicly-accessible genome databases with items of personal information from other public sources, which led to the positive identifications,

Civil liberties groups have raised concerns that DNA data gathered for scientific or medical reasons under conditions of confidentiality could be used to identify individuals and even to link peoples names to genetic disorders or medical predispositions hidden within the DNA sequences of their genomes.

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'White hat' hacker discovers names of 'anonymous' volunteers of genome study in security drill