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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

Burning bush plant promises low-cal vegetable oil, biofuels

May 21, 2010 By vani Leave a Comment

Washington, May 21 (ANI): New genetic discoveries from a shrub called the burning bush, known for its brilliant red fall foliage, could pave the way for new advances in biofuels and low-calorie food oils, found Michigan State University scientists.

New low-cost DNA sequencing technology applied to seeds of the species Euonymus alatus – a common ornamental planting – was crucial to identifying the gene responsible for its manufacture of a novel, high-quality oil.

However, despite its name, the burning bush is not a suitable oil crop.

Yet inserted into the mustard weed – well known to researchers as Arabidopsis and a cousin to commercial oilseed canola – the burning bush gene encodes an enzyme that produces a substantial yield of unusual compounds called acetyl glycerides, or acTAGs.

Related vegetable oils are the basis of the world’s oilseed industry for the food and biofuels markets, but the oil produced by the burning bush enzyme claims unique and valuable characteristics.

One is its lower viscosity, or thickness.

“The high viscosity of most plant oils prevents their direct use in diesel engines, so the oil must be converted to biodiesel. We demonstrated that acTAGs possess lower viscosity than regular plant oils. The lower viscosity acTAGs could therefore be useful as a direct-use biofuel for many diesel engines,” explained Timothy Durrett.

He said that its improved low-temperature characteristics could also make it suitable for diesel fuel.

And acTAGs boast lower calorie content than other vegetable oils,“thus they could be used as a reduced-calorie food oil substitute,” added Durrett.

The researchers now are working to improve the modified mustard weed seeds’ acTAGs yield and already report purity levels of up to 80 percent.

“It should now be possible to produce acetyl glycerides in transgenic oilseed crops or single cell production systems such as algae that are the focus of much current effort in biofuels research. With the basic genetics defined and thus one major technical risk greatly reduced, the way is open to produce and assess this novel oil in food and nonfood applications,” said Pollard.

The study was published in the latest issue of Proceedings of the National Academy of Sciences. (ANI)

Filed Under: International News Tagged With: Burning Bush Plant, calorie content, Dna Sequencing, Durrett, Euonymus Alatus, Fall Foliage, Food Oils, Genetic Discoveries, Glycerides, Low Calorie Food, Michigan State University, Mustard Weed, Oil Crop, Oil Substitute, Oilseed Crops, Oilseed Industry, Plant Oils, Temperature Characteristics, university scientists, Weed Seeds

New method to make DNA sequencing faster and cheaper

May 20, 2010 By vani Leave a Comment

Washington, May 20 (ANI): Boston University biomedical engineers have developed a new method to make DNA sequencing a lot faster and cheaper – and thus closer to routine use in clinical diagnostics.

The team has demonstrated the first use of solid state nanopores — tiny holes in silicon chips that detect DNA molecules as they pass through the pore — to read the identity of the four nucleotides that encode each DNA molecule.

“We have employed, for the first time, an optically-based method for DNA sequence readout combined with the nanopore system,” said Boston University biomedical engineer Amit Meller, who collaborated with other researchers at Boston University, and at the University of Massachusetts Medical School in Worcester. “This allows us to probe multiple pores simultaneously using a single fast digital camera. Thus our method can be scaled up vastly, allowing us to obtain unprecedented DNA sequencing throughput.”

The discovery could lead to major advances in drug development, preventative medicine and personalized medicine.

The new nanopore method does not rely on enzymes whose activity limits the rate at which DNA sequences can be read.

“This puts us in the unique advantageous position of being able to claim that our sequencing method is as fast as the rapidly evolving photographic technologies,” said Meller. “We currently have the capability of reading out about 200 bases per second, which is already much faster than other commercial third-generation methods. This is only the starting point for us, and we expect to increase this rate by up to a factor of four in the next year.”

“I believe that it will take three to five years to bring cheap DNA sequencing to the medical marketplace, assuming an aggressive research and development program is in place,” said Meller.

The research is detailed in Nano Letters. (ANI)

Filed Under: International News Tagged With: Advantageous Position, Aggressive Research, biomedical engineer, biomedical engineers, Boston University, dna molecule, Dna Molecules, dna sequence, dna sequences, Dna Sequencing, Generation Methods, Massachusetts Medical School, Medical Marketplace, Nano Letters, Photographic Technologies, preventative medicine, silicon chips, tiny holes, University Of Massachusetts Medical School, University Of Massachusetts Medical School In Worcester

New rat study may help understand genetic basis of human hypertension

April 29, 2010 By vani Leave a Comment

Washington, April 29 (ANI): Scientists have sequenced the genome of the spontaneously hypertensive rat, which could help understand causes of the disease in humans.

The spontaneously hypertensive rat (SHR) strain is the most widely studied animal model of human hypertension. Research on this strain has identified many genomic regions that likely harbour genetic variants that are responsible for the hypertension phenotype, however without a complete sequence of the hypertensive rat genome, it has been difficult to resolve many of these genomic changes and explore their molecular consequences.

Taking advantage of new technologies that are rapidly driving down the cost of DNA sequencing, an international team of researchers led by Timothy Aitman of the MRC Clinical Sciences Centre and Imperial College London have sequenced the first genome of a mammalian disease model with second-generation sequencing technology.

By comparing the SHR genome sequence with that of the rat reference genome sequence, Aitman and colleagues generated a nearly complete catalog of SHR genomic variants that could contribute to hypertension and other phenotypes.

They also found that genes known to be abnormally expressed in SHR are especially enriched for sequence variants.

The group expected that the genome sequence would reveal mutations disrupting a number of genes in the SHR strain, however the number of mutated genes they found was quite surprising – 788 genes are mutated in SHR compared to the reference genome, including 60 that are deleted altogether.

“So many major differences in protein sequence were unexpected because of the previous belief that differences in a small number of genes and proteins would be responsible for the phenotypic differences between such rat strains,” said Aitman.

Of the 788 mutated genes identified in the SHR genome, many are related to cellular functions such as ion transport and plasma membrane localization, as well as immunological and neurological processes.

The authors suggest that defects in these functional categories may be causally associated with the known phenotypes of this strain.

Aitman said that their characterization of genetic variation in the hypertensive rat would be invaluable for complete elucidation of the causes of hypertension and related traits at the molecular level in hypertensive rat.

“This in turn will pave the way for greater understanding of the genetic basis of hypertension in humans,” Aitman said.

The study has been published online in Genome Research. (ANI)

Filed Under: International News Tagged With: clinical sciences centre, disease model, Dna Sequencing, genes and proteins, genetic variants, genome sequence, genomic regions, Human Hypertension, Hypertension Research, Hypertensive Rat, Imperial College London, Molecular Consequences, mrc clinical sciences centre, Phenotypic Differences, plasma membrane, protein sequence, Rat Genome, Rat Strains, Rat Study, Sequence Variants

Discovery of millions of new microbes opens ”huge frontier” in science

April 20, 2010 By vani Leave a Comment

London, April 19 (ANI): Scientists have discovered millions of tiny microbes, hitherto unknown to science, at the bottom of the sea.

These organisms include microbes of bacteria, worms and ocean insects less than 1mm long.

Scientists made the path-breaking discovery using technology such as DNA sequencing, that allows researchers to differentiate between different species, and submarines that can be operated thousands of feet under the sea.

A survey was conducted as part of a 10-year international project to find out more about the oceans, the Census of Marine Life.

For one study, ocean samples were gathered from over 1,200 sites around the world to find out more about microbial life.

It discovered microbes with 18 million different DNA sequences, suggesting the presence of millions of yet unknown species.

Another project found 7,000 new genus of bacteria in the Western English Channel alone.

Nearly 3,000 types of bacteria were found in a sponge from Australia”s Great Barrier Reef.

The findings of the survey have led scientists to believe that there could be a billion microbial cells in every litre of seawater.

A separate study of holozooplankton, that look like tiny transparent insects, increased the number of known species to 14,000 from 7,000.

A study into roundworms found 500,0000 in a single square metre of ocean floor, while currently there are 16,000 known species of seaworms.

John Baross of the University of Washington, a contributor to the census, said the findings would open up new doors in science that could help understand changes in the food chain, weather patterns and carbon cycles.

“Marine animals alone may account for hundreds of millions microbial species. This is a huge frontier for next decade,” the Telegraph quoted him as saying. (ANI)

Filed Under: International News Tagged With: Bottom Of The Sea, Carbon Cycles, dna sequences, Dna Sequencing, great barrier reef, John Baross, Marine Animals, microbial cells, microbial life, microbial species, ocean floor, Ocean Samples, Roundworms, seawater, square metre, tiny microbes, types of bacteria, unknown species, using technology, weather patterns

Discovery of millions of new microbes opens ”huge frontier” in science

April 19, 2010 By vani Leave a Comment