Monthly Archives: May 2013

Future of Me: Your Accessible Genome
Advances in gene sequencing technologies plus increased computer capacity for information analysis means we are on the verge of being able to access and unde...

By: TheBridge8

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Future of Me: Your Accessible Genome - Video

The population of Ireland has yet to rebound from the deaths and migrations caused by the famine of mid-19th-century.

James Mahony/Wikimedia Commons

The great potato famine of the 1840s was a defining event in Irelands recent history. An Gorta Mr the Great Hunger in the Irish language caused millions to starve or emigrate and helped catalyse the countrys bloody war of independence from Great Britain.

Working from 150-year-old dried leaves, two competing teams have now sequenced the genome of the single-celled organism that wreaked havoc on the Irish potato crop. It is the first ancient plant pathogen to have its genome decoded. (In 2011, scientists reported the sequence of the plague-causing bacteria responsible for the Black Death of the 1340s.)

Phytophthora infestans, which causes potato late blight, is an oomycete a type of single-celled organism related to brown algae. Carried by infected potatoes, the disease probably arrived at the port of Antwerp in Belgium in the summer of 1845, before quickly spreading through the Low Countries and much of western Europe.

Irelands dependence on potatoes was the reason the epidemic exacted a far greater toll there than it did on the rest of the continent. Irish peasants working plots owned by absentee British landlords relied on potatoes for most of their calories, says Detlef Weigel, a plant geneticist at the Max Planck Institute for Developmental Biology in Tbingen, Germany, who co-led a study published today in the journal eLIFE1. The potato is really an amazing staple crop. If you have a diet of potato and milk, you dont need anything else.

The disappearance of that staple had devastating consequences, including 1 million deaths and still more emigrations. Irelands population of 4.5 million is still less than three-quarters of its pre-famine level. The perception that Britain did little to intervene in the catastrophe helped foment Irish nationalism, eventually resulting in the Irish War of Independence in 1919.

Long before it hit Europe, P. infestans probably circulated in the Toluca Valley in central Mexico, where it infected wild relatives of the potato. Until recently, only a single strain of P. infestans, dubbed US-1, plagued potatoes outside Mexico and South America. So it came as a surprise when, in 2001, scientists suggested that a different strain was responsible for the famine, after analysing a short stretch of P. infestans DNA from herbarium archives2.

Weigels team went to herbaria in Kew Gardens, outside of London, and at Germanys Botanische Staatssammlung in Munich and sequenced DNA preserved from the dried leaves of infected plants dating between 1845 and 1896.

Mitochondrial genomes from the famine strains showed they were more closely related to the US-1 strain than the earlier research suggested, and that the two strains diverged only in the early 1800s. Weigel says the split probably occurred in the United States, before the strain responsible for the famine was imported to Europe. That strain now appears to be extinct, or perhaps restricted to small pockets of the world.

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Pathogen genome tracks Irish potato famine back to its roots

Striking a blow at foodborne diseases, the 100K Pathogen Genome Project at UC Davis Tuesday announced that it has sequenced the genomes of its first 10 infectious microorganisms, including strains of Salmonella and Listeria.

"We are creating a free, online encyclopedia or reference database of genomes so that during a foodborne disease outbreak, scientists and public health professionals can quickly identify the responsible microorganism and track its source in the food supply using automated information-handling methods," said Professor Bart Weimer, director of the 100K Genome Project and co-director of BGI@UC Davis, the Sacramento facility where the sequencing is carried out.

Weimer estimates that the availability of this genomic information will cut in half the time necessary to diagnose and treat foodborne illnesses, and will enable scientists to make discoveries that can be used to develop new methods for controlling disease-causing microorganisms in the food chain.

The project is dedicated to sequencing the genomes of 100,000 bacteria and viruses that cause serious foodborne illnesses in people around the world.

In the United States alone, foodborne diseases annually sicken 48 million people and kill 3,000, according to the Centers for Disease Control and Prevention.

The initial 10 genome sequences mark the first in a series that the

"This initial release validates the entire process, from start to finish, of acquiring the bacterium, producing the genome sequence, and making automated public releases," Weimer said.

A genome is the complete collection of an organism's hereditary information.

Weimer said that the 100K Genome Project currently is sequencing a second set of 1,500 microbial genomes, with an anticipated release in the fall of 2013.

The 100K Genome Project was launched in March 2012 as a collaborative effort between UC Davis, Agilent Technologies, and the U.S. Food and Drug Administration. Since then, the U.S. Centers for Disease Control and Prevention, Department of Agriculture, and National Institutes of Health, as well as seven corporate partners, have joined the worldwide effort. For more information visit http://100kgenome.vetmed.ucdavis.edu.

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100K Pathogen Genome Project maps first genomes at UC Davis

DAVIS Striking a blow at foodborne diseases, the 100K Pathogen Genome Project at the University of California, Davis, today announced that it has sequenced the genomes of its first 10 infectious microorganisms, including strains of Salmonella and Listeria.

We are creating a free, online encyclopedia or reference database of genomes so that during a foodborne disease outbreak, scientists and public health professionals can quickly identify the responsible microorganism and track its source in the food supply using automated information-handling methods, said professor Bart Weimer, director of the 100K Genome Project and co-director of BGI@UC Davis, the Sacramento facility where the sequencing is carried out.

Weimer estimates that the availability of this genomic information will cut in half the time necessary to diagnose and treat foodborne illnesses, and will enable scientists to make discoveries that can be used to develop new methods for controlling disease-causing microorganisms in the food chain.

The project is dedicated to sequencing the genomes of 100,000 bacteria and viruses that cause serious foodborne illnesses in people around the world.

In the United States alone, foodborne diseases annually sicken 48 million people and kill 3,000, according to the Centers for Disease Control and Prevention.

The initial 10 genome sequences mark the first in a series that the project will enter into a publicly available database at the National Center for Biotechnology Information of the National Institutes of Health.

This initial release validates the entire process, from start to finish, of acquiring the bacterium, producing the genome sequence, and making automated public releases, Weimer said.

A genome is the complete collection of an organisms hereditary information.

Weimer said that the 100K Genome Project currently is sequencing a second set of 1,500 microbial genomes, with an anticipated release in the fall of 2013.

The 100K Genome Project was launched in March 2012 as a collaborative effort between UC Davis, Agilent Technologies, and the U.S. Food and Drug Administration. Since then, the U.S. Centers for Disease Control and Prevention, Department of Agriculture, and National Institutes of Health, as well as seven corporate partners, have joined the worldwide effort. For more information visit http://100kgenome.vetmed.ucdavis.edu.

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100K Pathogen Genome Project maps first genomes

BALTIMORE, May 21, 2013 /PRNewswire/ --Personal Genome Diagnostics Inc. (PGDx), today announced that it will use its proprietary methodologies and expertise in genomic analysis of defined cancer subtypes to identify novel kinase targets in collaboration with Blueprint Medicines. PGDx is an innovator in conducting patient-specific analyses aimed at identifying genomic alterations in tumors, and Blueprint Medicines is an expert in developing highly selective kinase inhibitors for a genetically defined patient population.

"This collaboration brings together two companies that are at the forefront of applying advanced genomics to improve cancer therapy," said Antony Newton, chief commercial officer of PGDx. "Blueprint is a leader in identifying novel targets and developing highly selective kinase inhibitors for specific genomically-defined patient populations, and PGDx has unique capabilities to identify kinase and other tumor-specific alterations."

PGDx leverages the deep expertise of its scientific founders, who are internationally recognized leaders in cancer genomics at Johns Hopkins University, and its proprietary technologies to provide advanced genome-mapping services and analyses to oncology researchers, drug developers and clinicians. The founders of PGDx were the first to analyze the entire set of kinase genes in tumors, the "kinome", and have identified alterations in a variety of protein and lipid kinases, including the discovery of alterations in PIK3CA, one of the most frequently mutated genes in human cancer. PGDx has also been a pioneer in enabling scientists and clinicians to comprehensively analyze entire exomes and genomes to identify novel cancer alterations.

"We are assessing a series of cancer subtypes that have not been examined before and look forward to working with PGDx to identify new and important aberrations," commented Dr. Christoph Lengauer, chief scientific officer of Blueprint Medicines. "Our goal of identifying key genomic drivers of cancer and leveraging these insights to develop the next generation of highly selective and tailored kinase inhibitors aligns well with PGDx's focus."

Blueprint Medicines is building a pipeline of next-generation kinase inhibitors against specific genetic abnormalities. Using their significant expertise in cancer genomics and biology, Blueprint has built a proprietary genomics platform to rapidly identify novel targets and potential combination therapies. Blueprint is able to rapidly execute on newly-identified targets using their broad and exquisitely selective chemical library of novel kinase inhibitor compounds.

As part of the collaboration, PGDx will employ a number of technologies including cancer exome analysis to capture and selectively analyze tumor sequences. These approaches, when combined with other patented PGDx technologies and computational methods, enable comprehensive analysis and unbiased detection of novel cancer-related mutations.

About Personal Genome Diagnostics

Personal Genome Diagnostics (PGDx) provides advanced genome-mapping services and analyses to oncology researchers, clinicians and patients. The company was founded in 2010 by international leaders in cancer genetics at Johns Hopkins University. PGDx conducts patient-specific analyses aimed at identifying the unique genomic alterations in tumors and linking them to the underlying biology. PGDx employs cancer exome analysis, which enables comprehensive and reliable genome-wide identification of cancer-related mutations. The company's proprietary methods for genome sequencing and analysis are complemented by its deep expertise in cancer genomics. PGDx's CLIA-certified facility provides personalized cancer genome analyses to patients and their physicians. For more information, visit http://www.personalgenome.com.

About Blueprint Medicines

Blueprint Medicines is a patient-driven company building a pipeline of exquisitely selective and tailored next-generation kinase drugs against genetic abnormalities. Using the molecular blueprint of genetically-defined patient populations and a proprietary genomics platform, Blueprint is rapidly identifying novel targets and combinations. Blueprint deploys a chemical library of novel compounds that covers a majority of the human kinome, as highly selective starting points for drug development programs as well as tool compounds. Blueprint Medicines was founded by a proven team, including the developers of Gleevec, and is backed by leading venture firms, Third Rock Ventures and Fidelity Biosciences. For more information, please visit the company's website at http://www.blueprintmedicines.com.

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Personal Genome Diagnostics And Blueprint Medicines Form Collaboration to Identify Novel Kinase Targets