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Roche and IBM Collaborate to Develop Nanopore-Based DNA Sequencing Technology

July 2, 2010 By vani Leave a Comment

Collaboration aims to accelerate human genome analysis and enable advancements
in personalized healthcare.
YORKTOWN HEIGHTS, N.Y. & BRANFORD, Conn.–(Business Wire)–
Roche (SWX:RO)(SWX:ROG)(Pink Sheets: RHHBY) and IBM (NYSE: IBM) announced today
an agreement to develop a nanopore-based sequencer that will directly read and
decode human DNA quickly and efficiently. Focused on advancing IBM`s recently
published “DNA Transistor” technology, the collaboration will take advantage of
IBM`s leadership in microelectronics, information technology and computational
biology and Roche`s expertise in medical diagnostics and genome sequencing.

The novel technology, developed by IBM Research, offers true single molecule
sequencing by decoding molecules of DNA as they are threaded through a
nanometer-sized pore in a silicon chip. The approach holds the promise of
significant advantages in cost, throughput, scalability, and speed compared to
sequencing technologies currently available or in development.

“By merging computational biology, biotechnology, and nanotechnology skills, we
are moving closer to producing a system that can quickly and accurately
translate DNA into medically-relevant genetic information,” said Ajay Royyuru,
Senior Manager of the Computational Biology Department at IBM Research. “The
challenge of all nanopore-based sequencing technologies is to slow and control
the motion of the DNA through the nanopore. We are developing the technology to
achieve this so that the reader can accurately decode the DNA sequence.”

Ultimately, the technology has the potential to improve throughput and reduce
costs to achieve the vision of whole human genome sequencing at a cost of $100
to $1,000. Having access to an individual`s personal genetic code could advance
the quality of medical care by identifying persons who will gain the greatest
benefit from a particular medicine and those who are at most risk of adverse
reaction.

“Sequencing is an increasingly critical tool for personalized healthcare. It can
provide the individual genetic information necessary for the effective diagnosis
and targeted treatment of diseases,” explained Manfred Baier, Head of Roche
Applied Science. “We are confident that this powerful technology – plus the
combined strengths of IBM and Roche – will make low-cost whole genome sequencing
and its benefits available to the marketplace faster than previously thought
possible.”

As part of the agreement, Roche will fund continued development of the
technology at IBM and provide additional resources and expertise through
collaboration with Roche`s sequencing subsidiary, 454 Life Sciences. Roche will
develop and market all products based on the technology.

Roche`s investment in future genomic technologies builds upon the strength of
its currently available 454 Sequencing Systems, which generate hundreds of
thousands of long, high quality sequencing reads in hours. The technology is
available for large-scale genomic analysis with the GS FLX System and for
benchtop sequencing with the GS Junior System. Shown to provide significant
medical value in targeted resequencing applications for virology and oncology
research, 454 Sequencing Systems are poised to be first next-generation
sequencing technology to move from the laboratory to the clinic.

For more information on 454 Sequencing Systems, visit www.454.com.

About Roche
Headquartered in Basel, Switzerland, Roche is a leader in research-focused
healthcare with combined strengths in pharmaceuticals and diagnostics. Roche is
the world`s largest biotech company with truly differentiated medicines in
oncology, virology, inflammation, metabolism and CNS. Roche is also the world
leader in in-vitro diagnostics, tissue-based cancer diagnostics and a pioneer in
diabetes management. Roche`s personalised healthcare strategy aims at providing
medicines and diagnostic tools that enable tangible improvements in the health,
quality of life and survival of patients. In 2009, Roche had over 80`000
employees worldwide and invested almost 10 billion Swiss francs in R&D. The
Group posted sales of 49.1 billion Swiss francs. Genentech, United States, is a
wholly owned member of the Roche Group. Roche has a majority stake in Chugai
Pharmaceutical, Japan. For more information: www.roche.com.

About IBM
For more information, visit www.ibm.com/smarterplanet

For life science research only. Not for use in diagnostic procedures.

454, 454 SEQUENCING, 454 LIFE SCIENCES, GS FLX and GS JUNIOR are trademarks of
Roche.

IBM is a registered trademark of International Business Machines Corporation in
the United States, other countries, or both.

Roche Diagnostics
Dr. Burkhard Ziebolz
Phone: +49 8856 604830
Email: burkhard.ziebolz@roche.com
or
454 Life Sciences Corporation, a Roche Company
Dr. Ulrich Schwoerer
Phone: +1 203 871 2300
Email: ulrich.schwoerer@roche.com
or
IBM
Michael Loughran
Phone: +1 914 945 1613
Email: mloughra@us.ibm.com

Filed Under: International News Tagged With: adverse reaction, biology department, computational biology, dna sequence, Dna Sequencing, genetic code, genetic information, human dna, Human Genome Analysis, Human Genome Sequencing, medical diagnostics, novel technology, Nyse, pink sheets, Rhhby, Silicon Chip, Swx, Technology Collaboration, Transistor Technology, Yorktown Heights

Dingoes may be world’s oldest dog breed

March 19, 2010 By vani Leave a Comment

A new study has found the Australian dingo may be the oldest breed of dog in the world.

An international study has found that the dingo, along with the new guinea singing dog, are most like the dogs domesticated in Asia and the Middle East thousands of years ago.

Dr Alan Wilton, from the University of New South Wales, says the two breeds are also the most closely related to wolves.

“There are a lot of physical and behavioural traits that are different between ancient dogs like the dingo and modern European dogs,” he said.

“Dingoes don’t bark, they howl; the new guinea singing dog sings or howls. What this study is doing is supporting that information with genetic information.

“One of the interesting parts of the study is that it shows just how unique dingoes are and how very different they are from other breeds of dogs, particularly the European domestic dogs.”

Filed Under: International News Tagged With: animals, asia, Australia, Australian Dingo, Behavioural Traits, breeds of dogs, Dingo Dogs, Dingoes, dog breed, Domestic Dogs, dr alan, genetic information, Human Interest, lot, mammals, Middle East, New Guinea Singing Dog, New South Wales, science and technology, University of New South Wales, Wilton, wolves

Scientists discover active genes in the developing mammal brain

July 14, 2009 By admin Leave a Comment

Washington, July 14 (ANI): Penn State scientists claim that they have for the first time used high-throughput sequencing to uncover active genes in developing brains.

The researchers believe that their work provides what is likely the best evidence thus far for the activity in the brain of such a large number of genes.

They say that the significance of their study lies in the fact that it provides new insights into the genes that are involved in a mammal’s early brain development, including those that contribute to neurological disorders.

They hope that their findings may one day lead to the development of drugs or gene therapies that treat neurological disorders, such as autism and mental retardation.

Led by Distinguished Professor of Biology Hong Ma and Associate Professor of Biology Gong Chen, the research team used a high-throughput technique to sequence millions of messenger-RNA molecules, which carry genetic information from DNA molecules to protein molecules.

The researchers obtained the RNA from the brains of mice, which are an important model system for studying human biology.

They found that over 16,000 genes-more than half of the mouse’s entire set of known genes-are involved in the brain’s development and functions.

“The brain represents one of the most, if not the most, complex organs in a mammal’s body. So we weren’t surprised to find that the number of genes that are active in the brain is so high,” said Ma.

The researchers focused on two critical times during the development of a mouse’s brain: embryonic day 18 (E18) and post-natal day 7 (P7).

“These two time points represent major milestones during brain formation. Brain development in an 18-day-old embryo involves a significant amount of brain cells, or neurons. In contrast, brain development in a seven-day-old infant involves the formation of numerous connections between these neurons. Our goal was to determine which genes are active during these two critical times,” said Ma.

The scientists examined genes that correspond to the RNA molecules from the cortex of a mouse.

“The cortex is the surface portion of the large brain that is responsible for most cognitive and sensory abilities,” said Ma.

According to the researchers, more than 3,700 of the 16,000 genes identified by them have different levels of activity between the E18 and P7 time points.

“This differential activity tells us about the differences in the brain at these two stages. For example, the genes that are active at E18, but not at P7, probably are important during E18. We get some support for this notion when we see that certain genes that already are known to be involved in cell division are actively expressed during E18, while other genes that are known to play a role in building the connections between neurons are much more active at P7,” said Ma.

What makes their findings even more interesting is the fact that some of the genes identified in mice are known to be matched to the human genes that are involved in neurological disorders, such as Alzheimer’s disease, autism, and some forms of mental retardation.

“Our results can help to pinpoint the specific time during brain development when the genes related to certain diseases are active. This knowledge may help other scientists to develop drugs or gene therapies that can treat the diseases. For example, if a particular gene defect causes poorly constructed connections between certain neurons, a drug might be developed that enhances those connections to compensate for the gene defect,” said Ma.

Ma has revealed that his future studies will look at some of the genes to see whether they are important for the brain to be formed properly.

The researchers also plan to study how genes function in development disorders of the brain.

A research article on their study has been published in the online edition of the Proceedings of the National Academy of Sciences. (ANI)

Filed Under: Uncategorized Tagged With: best evidence, brain cells, Critical Times, Dna Molecules, E18, Early Brain Development, gene therapies, genetic information, high throughput, human biology, mammal, Messenger Rna, model system, Natal Day, Neurological Disorders, new insights, penn state scientists, protein molecules, rna molecules, Time Points

Scientists use genetic engineering to make virus-resistant grapevines

July 3, 2009 By admin Leave a Comment

Washington, July 3 (ANI): Scientists are making certain plants resistant to the “Grapevine fanleaf virus” GFLV by genetic engineering.

Extremely hot or rainy periods can destroy entire crops, not to mention the wide variety of pests that can appear on the scene.

Bugs such as the vine louse or the rust mite, fungi such as mildew, or viruses such as the GFLV can give the vines a hard time.
he GFLV infects the grapevine and causes fanleaf disease, resulting in deformed and very yellowed leaves, smaller grapes and crop loss.

Now, with the help of genetic engineering, researchers at the Fraunhofer Institute for Molecular Biology and Applied Ecology IME in Aachen in Germany, are making certain plants resistant to GFLV.

“Our modified plants produce antibodies,” explained Dr. Stefan Schillberg, head of department at the IME. “These antibodies ‘recognize’ the viruses and prevent them from spreading in the plant and causing damage,” she added.

To enable the plant to produce the antibodies, the scientists have to modify its genotype and channel genetic information for the antibodies into it.

This task is performed by tiny helpers called agrobacteria, which genetic engineers have been using for over twenty years.

These are soil bacteria that inherently transfer parts of their own genome to that of the plant.

Using simple routine processes, the researchers introduce the antibody gene into the bacteria, which then act as a transport vehicle and carry it over to the vine.

The researchers are still testing this process on model plants, and the first results show that their modified versions are up to 100 percent resistant to the virus.
“The antibody is produced very effectively inside the plants,” said Schillberg. “The next step on the agenda is to test the method on actual grapevines and then to carry out field tests,” he added. (ANI)

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Genetic map of widespread infection-causing parasite constructed

June 29, 2009 By admin Leave a Comment

Washington, June 29 (ANI): In a major achievement, scientists at the Southwest Foundation for Biomedical Research (SFBR) in San Antonio have constructed a genetic map of the parasite that causes schistosomiasis.

Schistosomiasis is a chronic intestinal infection that can damage internal organs and, in children, impair growth and cognitive development.

Schistosome parasites are flatworms that infect more than 200 million people a year worldwide.

“A genetic map is the essential tool needed for finding the genes that are responsible for drug resistance and pathogenesis in this parasite. In the case of drug resistance, identification of underlying mutations is critical for management of this disease,” said Dr. Timothy Anderson, of SFBR’s department of genetics.

He added: “First, identification of mutations allows us to better understand the mechanism of action of the drugs used, and to redesign drugs to restore treatment efficacy. Second, identification of mutations involved allows us to efficiently monitor the spread of resistance in parasite populations using simple molecular methods.”

For the study, the researchers used two adult flatworms to breed 88 S. mansoni offspring.

They then compared the genetic information of the offspring to the parents, and generated a genetic map of chromosomes of the pathogen.

These parasites have a complex lifecycle. Adult male and female worms measuring around half an inch, live in pairs in the blood vessels, and eggs are expelled in the faeces or urine.

The larval parasites initially develop in water snails and human infection occurs when parasite larvae burrow through the skin of people entering the water.

The researchers are planning further research using the genetic map to understand why some parasites cause more pathology than others.

The new study has been published in the journal Genome Biology. (ANI)

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Genetic variations could predict ovarian cancer risk, survival prospects

April 20, 2009 By admin Leave a Comment

Washington, Apr 20 (ANI): Genetic variations in the micro-RNA (miRNA) processing pathway genes and miRNA binding sites could predict a woman’s risk of developing ovarian cancer and her prospects for survival, according to a new study.

The study by researchers from The University of Texas M. D. Anderson Cancer Centre was the first to examine the association of genetic variants related to miRNA with ovarian cancer risk, overall survival for ovarian cancer patients, and platinum-based chemotherapy response.

“We found a gene dosage effect, the more unfavourable variations a woman has, the greater her ovarian cancer risk and the shorter her survival time,” said senior author Xifeng Wu, M.D., Ph.D., professor in M. D. Anderson’s Department of Epidemiology.

They found that median survival, for example, ranged from 151 months for women with fewest unfavourable variations to 24 months for those with the most.

It was also found that many of the variations indicated likely response to platinum-based chemotherapy.

“Our findings have the potential clinical application of indicating a patient’s prognosis and showing who will respond to different therapies by analysing a single blood sample. We also will incorporate this genetic information with epidemiological information to build a comprehensive model to predict susceptibility to ovarian cancer,” said Wu.

Researchers focussed on the miRNA-processing pathway because it is crucial to production of miRNAs, the small molecules that regulate between one third and half of all genes.

Also, they chose the binding sites on host genes where miRNAs exert their effects on gene expression.

The study examined genetic information from 417 cancer patients and 417 healthy controls.

For the study, they analysed 219 potential functional single nucleotide polymorphisms (SNPs) – variations of a single DNA building block in a gene – in eight genes that process miRNA and at the miRNA binding sites of 129 cancer-relevant genes.

And it was found that 12 SNPs were significantly linked with ovarian cancer risk.

Also, the risk of developing ovarian cancer was 4.5 times more in women with five or fewer unfavourable genotypes as compared to those with eight or more of these unfavourable genotypes.

Women with six to eight unfavourable SNPs were at twice the risk.

The team also found that 21 SNPs were significantly associated with overall survival.

The findings of the study were presented at the 100th annual meeting of the American Association for Cancer Research. (ANI)

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Groundbreaking study sheds light on intermediary steps of genetic encoding

March 29, 2009 By admin Leave a Comment

Washington, March 29 (ANI): A breakthrough study by researchers at Brandeis University and the MRC Laboratory of Molecular Biology (Cambridge, U.K.) has for the first time provided significant insights into a crucial step in the process whereby human genetic information is transmitted to action in the human cell, and frequently at which point genetic disease develops in humans.

The researchers say that they have been successful in crystallizing a very large complex of a macromolecular “machine” in the human cell, in determining what it actually looks like, and thereby in zeroing in on the process of genetic encoding.

Importantly, 15 to 20 percent of all human genetic disorders, including muscular dystrophy, are caused by defects in this genetic encoding process known as RNA splicing.

The scientists used x-ray crystallography to create a three-dimensional structure of an integral complex of the human spliceosome, which consists of specialized RNA and protein subunits.

The spliceosome’s job is to modify the message relayed from DNA by clipping genetic bits in such a manner that they are acceptable for translation into protein.

Brandeis biochemist Daniel Pomeranz Krummel says that it also rearranges the genetic bits of the message in such a way that it can generate multiple and varied proteins which can and do have dramatic effects on human development.

“The process of RNA splicing is vital to human cell development and survival. In this process, the regions of our DNA encoding for protein are removed from non-encoding regions and brought together-quite often in alternative arrangements. Defects in this process can have disasterous repercussions in the form of genetic disorders,” said Pomeranz Krummel, adding that neuronal development can be particularly affected when things go awry.

Recent studies have implicated defects in this process in various human neurological disorders, including epilepsy.

This macromolecular machine clips gene sequences transcribed as part of a precursor to the mRNA, removing them before the final mRNA product is translated into protein.

The spliceosome must clip these sequences, known as introns, at the right place in the precursor mRNA.

“In human cells one gene can be made into a variety of proteins, so if the process just goes slightly wrong, the genetic alteration can lead to incredible disaster; yet on the other hand, this incredible complexity has led to our amazing evolutionary progress,” said Pomeranz Krummel.

“The human genome is not terribly different from the earthworm’s with regards to its size, but the process of RNA splicing that occurs in our cells is different. The fundamental difference between us and the earthworm is that our cells have evolved to utilize this process of RNA splicing to generate a whole other dimension to the transmission of genetic information,” the researcher added.

Pomeranz Krummel’s team will continue studying how this complex interacts with other macromolecular machines in the human cell. (ANI)

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Immune cells in rheumatoid arthritis patients have prematurely aged chromosomes

March 5, 2009 By admin 1 Comment

Washington, Mar 5 (ANI): Scientists at Emory University School of Medicine have discovered that T cells, or white blood cells, from patients with the autoimmune disease rheumatoid arthritis have prematurely aged chromosomes due to lack of structures called telomeres.

elomeres are structures that cap the ends of cells’ chromosomes, grow shorter with each round of cell division unless a specialized enzyme replenishes them.

It is important to maintain telomeres as they are thought to be important for healthy aging and cancer prevention.

T cells from patients with rheumatoid arthritis were found to have trouble turning on the enzyme that replenishes telomeres, when compared with cells from healthy people.

Reversing this defect could possibly help people prone to the disease maintain a balanced immune system.

Senior author Cornelia Weyand, MD, PhD said that in rheumatoid arthritis, T cells are chronically over-stimulated, invading the tissue of the joints and causing painful inflammation.

She claimed that in childhood, new T cells are continually produced in the thymus, but after about age 40, the thymus “involutes” – or shrinks and ceases to function. After that, the immune system has to make do with the pool of T cells it already has.

“What we see in rheumatoid arthritis is an aged and more restricted T cell repertoire. This biases the immune system toward autoimmunity,” she said.

Intrigued by earlier studies claiming that in rheumatoid arthritis, T cells tend to shift the molecules on their surface and function differently, the researchers wanted to study the mechanisms of T cells’ premature aging.

They found the answer in telomerase, the enzyme that renews telomeres and is necessary to prevent loss of genetic information after repeated cell division.

Telomerase adds short repeated DNA sequences to the ends of chromosomes to protect them. The enzyme is active in embryonic development but is usually switched off in adult cells. Many cancer cells reactivate it to enable runaway growth.

T cells are some of the very few cells in adults that can turn on telomerase when stimulated, probably because they have to divide many times and stay alive for decades.

Researchers found that T cells from patients with rheumatoid arthritis make 40 percent less telomerase enzyme when stimulated.

The cells came from 69 patients, 92 percent female, with an average age of 50, and were compared with cells from healthy people with similar demographics.

By shutting off a gene encoding part of the enzyme normal T cells were made vulnerable to programmed cell death, and transferring telomerase into patients’ T cells rescued them from dying.

Scientists said that the finding suggests that restoring defective telomerase to T cells could possibly help “reset” the immune system in rheumatoid arthritis.

The results are published online in Proceedings of the National Academy of Sciences. (ANI)

Filed Under: Science News Tagged With: adult cells, autoimmune disease, autoimmunity, cancer cells, Cancer Prevention, cell repertoire, chromosomes, dna sequences, embryonic development, emory university school, emory university school of medicine, genetic information, involutes, md phd, painful inflammation, patients with rheumatoid arthritis, rheumatoid arthritis, school of medicine, t-cells, white blood cells

Now, a statistical model to predict stroke risk with 86pct accuracy

February 26, 2009 By admin Leave a Comment

Washington, February 26 (ANI): Experts at the Children’s Hospital Informatics Program (CHIP) say that an individual’s lifetime risk of stroke can now be predicted with the aid of a new statistical model.

During a study, they used genetic information from 569 hospital patients, and showed that their predictive model could estimate an individual’s overall risk of cardioembolic stroke – the most common form of stroke – with 86 percent accuracy.

“For complex diseases like stroke, it’s not just a single mutation that will kill you. More likely it is an interaction of many factors,” explains CHIP researcher Dr. Marco Ramoni, an Associate Professor at Harvard Medical School and senior author of the study reported in the journal Stroke.

Working in collaboration with Dr. Karen Furie, the director of the stroke unit at Massachusetts General Hospital (MGH), and Rachel Ramoni, of the Harvard School of Dental Medicine, Ramoni identified 569 patients that had presented to MGH’s emergency department and outpatient neurology clinics between 2002 and 2005 with symptoms of suspected stroke.

The researchers gathered information from the 146 patients with confirmed cardioembolic stroke, and 423 controls who were followed and found not to have stroke.

The team looked for 1,313 genetic variants, called single nucleotide polymorphisms or SNPs, known to correlate with stroke.

The SNPs that each patient had were then entered into the model, known as a Bayesian network, which not only helped the researchers identify the genetic variants that correlated with stroke, but also enabled them to determine how such factors interplayed and what was the strength of such interactions.

“The model looks for factors, combines them and finds out which are the best predictive factors. It’s never one factor at a time, it’s always more than one factor. What this technology allows you to do is to generate a network of factors that contribute to stroke,” says Ramoni.

According to the researcher, the model was able to predict an individual’s risk of cardioembolic stroke with an accuracy of 86 percent.

“It sounds like magic. But it’s just a piece of technology. It gives hope that we will be able to predict early on whether someone is at risk of getting stroke, and allow you to convince them to make life changes,” says Ramoni.

“The next step is to get more SNPs. These analyses looked at only 1,313 out of 3.3 million known SNPs. Even a million SNPs would cover the vast majority of the genome. We would get much better predictions,” the researcher adds.

Ramoni also says that by identifying all the genetic variants that modulate the risk of stroke, it could provide insight into its mechanisms and provide targets for future drugs.

He is currently refining the model and believes that this technology could be used to predict inherited risk of many other conditions. (ANI)

Filed Under: Health News Tagged With: bayesian network, dr karen, emergency department, genetic information, genetic variants, harvard medical school, harvard school of dental medicine, hospital patients, informatics program, journal stroke, lifetime risk, massachusetts general hospital, mgh, predictive factors, predictive model, s hospital, single nucleotide polymorphisms, snps, statistical model, stroke unit

Scientists uncover new genetic markers linked to increased heart attack risk

February 18, 2009 By admin Leave a Comment

Washington, February 18 (ANI): Scientists have identified new gene variants associated with an increased risk for heart attack.

The international team of researchers behind this work say that the identified genes and their underlying mechanisms provide new starting points for understanding genetic patterns in heart attack, and for developing new treatment options.

One of their findings is that the heart attack risk is more than twice as great in individuals who carry not only one but several of the genetic markers.

The team, including researchers from Germany’s University of Lubeck and Helmholtz Zentrum Munchen, performed a genome-wide scan of thousands of patients with hundreds of thousands of genetic markers.

The researchers included in their studies heart attack patients from the KORA study as well as healthy control persons from the population.

“The future challenge for us will be to integrate the insights we have gained about genetic factors and lifestyle factors in order to provide effective preventive measures for the population,” said Prof. Dr. Annette Peters, research group leader at Helmholtz Zentrum M|nchen.

The first of the three studies investigated a million genetic markers in 1,200 MI patients and the same number of healthy test persons, while subsequent control studies on an additional 25,000 patients and healthy persons confirmed the initial suspicion: Culprit genes for MI are located on chromosomes 3 and 12. Scientists suspect that one of these genes, the MRAS gene, plays an important role in cardiovascular biology.

The second gene, the HNF1A gene, is closely associated with cholesterol metabolism.

The researchers not only studied individual genetic markers as to their influence on the risk of heart attack, but they also investigated combinations of up to ten neighbouring markers, believing that the approach could enable them to derive additional genetic information.

Thus, they were able to identify another region, this time localized on chromosome 6, which is associated with heart attack risk. The LPA gene at this locus regulates the concentration of a specific lipoprotein (Lp(a)), a particle which transports lipids in the blood. This finding, too, may be useful in the future for developing new therapeutic interventions.

The third study was able to identify three further, previously unknown MI genes on chromosomes 2, 6 and 21. It also showed that in individuals with not just one but several genetic markers, the heart attack risk was more than double.

The higher the number of disease genes now identified, the higher the disease risk.

The researchers say that the newly gained knowledge will aid in assessing the risk for heart attack in order to develop preventive and early intervention strategies.

They say that their findings suggest that there may be many mechanisms involved in heart attack that are still to be discovered. (ANI)

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