Complete Genomics Service Targets $1000 Genome by 2009

Complete Genomics emerged from stealth mode today brandishing an audacious service model for wholesale next-generation sequencing, with its first human genome already assembled and the CEO’s pledge to reach the magical “$1000 genome” price point as early as spring 2009.

Based in Mountain View, Calif., Complete Genomics has raised $46 million in three rounds of financing since its incorporation in 2006. Unlike its commercial next-gen sequencing rivals – Roche/454, Illumina, Applied Biosystems (ABI) and Helicos – Complete Genomics will not be selling individual instruments, but rather offer a service aimed initially at big pharma and major genome institutes.

“Our mission is to be the global leader in complete human genome sequencing,” chairman, president and CEO Clifford Reid in a briefing last week. “We are setting out to completely change the economics of genome sequencing so that we can do diagnostic quality human genome sequencing at a medically affordable price. Essentially, [we’ll] transition this genome sequencing world from a scientific and academic endeavor into a pharmaceutical and medical endeavor.”

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International Project Launched to Sequence Human Microbiome, Share Data

In Heidelberg, Germany, today researchers from eight countries and the European Commission announced the formation of a new research enterprise, the International Human Microbiome Consortium (IHMC), which will sequence the genomes of tens of thousands of microorganisms that live in and on the human body and that influence human health.

Initial funding of more than US$200 million is being provided by the U.S. National Human Genome Research Institute (NHGRI) and the European Commission (EC).

Jane Peterson, associate director of extramural research at the NHGRI, said international collaboration is very important in advancing science, and that “the sum is more than the parts.” Participants in the IHMC have agreed in principle to the free and open release of data and resources, and the coordination of research plans, as well as to sharing innovative developments, she reported. Data from microbiome research already being conducted by the NIH Human Microbiome Project and the EC Metagenomics of the Human Intestinal Tract (MetaHIT) project will contribute an initial set of microbial genomes to the IHMC. Because the field is so young – less than three years old – there is much to be gained by collaboration, Peterson said.

Christian Desaintes, from the Research Directorate of the European Commission, said the IHMC’s goal for five years hence is to be sequencing 1000 microbiome genomes from over 1000 individuals’ body parts. The parts in question are the skin, mouth, nasal passages, gastro-intestinal tract, and urogenital tract.

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Computational tool to help us better understand how microbes govern human, environmental health

We all understand that even the tiniest changes in the environment can create big opportunities and challenges for plants, animals and humans, but rarely do we consider what’s happening on a microscopic level and what those changes could mean for the infinite varieties of life on Earth or how mankind’s day-to-day experiences could be affected.

But University of Houston researchers Yuriy Fofanov and Lennart Johnsson understand that what we don’t see often carries big-picture implications. They’ve recently garnered international recognition for applying such vision while creating technologies to help monitor the sizes and genomic diversity of microbial communities.

“The computational tools will pave the way to less expensive and more reliable tests that can be used across the globe. The sheer number of microbial communities presents great commercial potential,” said Johnsson, Cullen distinguished professor of computer science, mathematics, and electrical and computer engineering and head of UH’s TLC2 and the Advanced Computing Research Laboratory (ACRL).

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New antibiotic beats superbugs…

The problem with antibiotics is that, eventually, bacteria outsmart them and become resistant. But by targeting the gene that confers such resistance, a new drug may be able to finally outwit them. Rockefeller University scientists tested the new drug, called Ceftobiprole, against some of the deadliest strains of multidrug-resistant Staphylococcus aureus (MRSA) bacteria, which are responsible for the great majority of staphylococcal infections worldwide, both in hospitals and in the community. The research, to be published in the August 2008 issue of the journal Antimicrobial Agents and Chemotherapy, looked at how well Ceftobiprole worked against bacterial clones that had already developed resistance to other drugs. In every case, Ceftobiprole won. “It just knocked out the cells 100 percent,” says the study’s lead investigator, Alexander Tomasz, head of the Laboratory of Microbiology at Rockefeller.

Previous research had already shown that — in general — Ceftobiprole was highly effective against most clinical isolates of S. aureus. “Instead, we looked more carefully at the highly resistant cells that already occur in such clinical isolates at very low frequency — maybe in one bacterium in every 1,000,” says Tomasz. Ceftobiprole was able to kill these resistant cells. Never before has an antibiotic been tested this way. “In the history of antibiotic development, an antibiotic arrives on the scene, and sooner or later resistant bacteria emerge,” Tomasz says. “We sought to test in advance which would win this particular chess game: the new drug, or the bacteria that now cause human deaths.”

In an ominous new “move” in this chess game, S. aureus strains with resistance to vancomycin (VRSA), a different class of antibiotics, also began to appear in hospitals in the United States. Ceftobiprole was also able to kill these new resistant VRSA strains. The drug is effective because the chemists who developed Ceftobiprole managed to outwit the bacteria at their own game, Tomasz says. The broad-spectrum antibiotic was discovered by Basilea Pharmaceuticals, based in Basel, Switzerland, and is being developed in the U.S. and worldwide by Johnson & Johnson. The research was supported by Johnson & Johnson along with a grant from the U.S. Public Health Service.

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Researchers Develop Tool To Study Genes

Two Texas A&M University researchers have developed a computational tool that will help scientists more accurately study complex units of clustered genes, called operons, in bacteria. The tool, which allows scientists to analyze many bacterial genomes at once, is more accurate than previous methods because it starts from experimentally validated data instead of from statistical predictions, they say. The researchers hope their tool will lead to a better understanding of the complex genetic mechanisms involved in a cell’s functioning. “Eventually, we want to try to improve our tool to make it better and more accurate,” Sze said. “Although our tool can analyze a lot of bacteria at the same time, it compares each bacterium to E. coli separately. So the ultimate goal would be to develop a tool that will analyze them all together.”

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Genome Viewers/Editors – Three of the Best

A number of online and offline genome are viewers available, each with it’s own set of pros and cons. Here is an overview three.

Artemis

Artemis is a genome viewer available from Sanger Institute. Its a java based tool with a 3-paned interface window that depicts the genome at various resolutions. Alternating between the different resolutions is a bit tricky but once you get a hold of it shouldn’t be difficult. There is a also search tool that allows your to track down the particular feature that you’re looking for.

A great feature of Artemis is that it allows you to edit the sequence annotations and features. Although the tool isn’t perfect and is a bit finicky at times, it gets the job done.

Artemis supports the most common filetypes -EMBL, GENBANK, FASTA or raw format. Extra sequence features can be added in in EMBL, GENBANK or GFF format.

The best thing I like about Artemis is that there is a web version as well as an offline version, which means once you get used to it you can run it on or offline on any computer anywhere that has java.

Apollo

Apollo genome viewer is another java based genome viewer and annotation tool. It is a part of the Gmod project which runs most of the online genome viewers. The tool came out of a collaboration between the Berkeley Drosophila Genome Project and The Sanger Institute.

Apollo has a similar set of features to Artemis provides, but I found the interface to be less user-friendly. But that’s just a personal opinion so you would be best to have a go at using both Artemis and Apollo and decide for yourself which is best. Again, the user guide will help you make best use of Apollo.

The NCBI Genome Workbench

The NCBI Genome Workbench is far more than just a genome viewer. As the name suggests, it is a complete and customizable workbench of tools that allow you to organize sequence data, which you can retrieve from NCBI databases or from your own files, for a project then view and manipulate them in a variety of ways. There is no online version available but downloading and installing NCBI genome workbench is quite simple.

The software allows you to view sequences as flat sequence files, phylogenetic trees, alignments and more.

The excellent zoomable graphics mode is the real strength of this package. It allows you to easily explore your sequence data at different levels of detail – individual genes can be viewed alone or in their genomic context and can be BLASTed straight from the graphical view. A nice set of alignment analysis tools is also available and BLAST and analysis results can be saved to your project making this a great way to keep track of your sequence data and analyses.

The tool supports quite a number of file formats, and I had no problems working with FASTA and most other file formats however when I tried to import the complete 1st chromosome of Dicyostelium which is in a GFF3 format the program kept crashing repeatedly, so clearly some bugs still need to be ironed out.

The NCBI genome workbench is a great idea, and provides a number of useful tools that make the program a must-have but the interface is a bit clunky and takes some getting used to. However, the site has a comprehensive set of instructions/tutorials to help you get up the learning curve quickly.

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The good news in our DNA: Defects you can fix with vitamins and minerals

As the cost of sequencing a single human genome drops rapidly, with one company predicting a price of $100 per person in five years, soon the only reason not to look at your “personal genome” will be fear of what bad news lies in your genes.

University of California, Berkeley, scientists, however, have found a welcome reason to delve into your genetic heritage: to find the slight genetic flaws that can be fixed with remedies as simple as vitamin or mineral supplements.

“There are over 600 human enzymes that use vitamins or minerals as cofactors, and this study reports just what we found by studying one of them,” Rine said. “What this means is that, even if the odds of an individual having a defect in one gene is low, with 600 genes, we are all likely to have some mutations that limit one or more of our enzymes.”

The subtle effects of variation in enzyme activity may well account for conflicting results of some clinical trials, including the confusing data on the effect of vitamin supplements, he noted. In the future, the enzyme profile of research subjects will have to be taken into account in analyzing the outcome of clinical trials.

If one considers not just vitamin-dependent enzymes but all the 30,000 human proteins in the genome, “every individual would harbor approximately 250 deleterious substitutions considering only the low-frequency variants. These numbers suggest that the aggregate incidence of low-frequency variants could have a significant physiological impact,” the researchers wrote in their paper.

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A brief history of the platypus!

Blogging earlier on the platypus What’s Our Connection to the Platypus? here is some think i came across, a very interesting compilation on the history of the mystery mammal. I have always thought and fancied a platypus in the place of TUX the Linux mascot, every time i see tux i don’t think of a penguin but a platypus! may be tux to me looks more like a platypus than a penguin!

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A nice item, a brief history of the platypus, in 5 parts that’s just brilliant. Further interesting is the foot note “Further reading” don’t miss it. This is a wonderful historical account and should be made more widely available. For Quick reach here :

• Genome analysis of the platypus reveals unique signatures of evolution. Nature 453: 175-183. Abstract | Full text
• Relevant abstracts from Genome Research Platypus Genome Special
• Hall, B.K. (1999). The Paradoxical Platypus. BioScience 49(3): 211-218. JSTOR link

This is a wonderful historical account and should be made more widely available.

• Platypus biology at the Australian Platypus Conservancy

23andMe and The Parkinson’s Institute Announce Initiative to Advance Parkinson’s Disease Research

23andMe, a privately-held personal genetics company, and The Parkinson’s Institute and Clinical Center (“Parkinson’s Institute”) today announced a research initiative under which Parkinson’s Institute patients, with financial support from The Michael J. Fox Foundation, will enroll in the 23andMe Personal Genome Service™ to support the development of advanced methods for clinical and epidemiologic research for Parkinson’s disease.

The new research initiative is designed to improve current methods of collecting information for Parkinson’s research by leveraging the internet to dramatically expand the involvement of Parkinson’s patients in clinical research and increase the frequency and quality of patient data collection. Specifically:

• Together, 23andMe and the Parkinson’s Institute will design and validate web-based clinical assessment tools that can be administered to online communities.
• 23andMe will establish a social networking platform to facilitate the development of communities and research projects based on common traits of Parkinson’s disease patients.
• All participating Parkinson’s Institute patients will be enrolled in the 23andMe Personal Genome Service™ and will provide a saliva sample for a comprehensive genome scan generating more than 580,000 data points per patient.
• Parkinson’s Institute patients will provide specific information and insights that will include their individual environmental exposures, family history, disease progression and treatment response.
• Patients’ risk factor and clinical data collected through the newly developed and validated web-based tools will then be merged with their genetic data to conduct research on Parkinson’s disease.
• New surveys will be developed and administered to the growing cohort of patients, generating new risk factor and clinical data for comparison with the existing genetic data.
• Through the deployment of an innovative approach to clinical research information gathering utilizing web-based tools, the initiative will help to expand the involvement of Parkinson’s disease patients in clinical research and increase the frequency and uniformity of patient data collection.

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What’s Our Connection to the Platypus?

The platypus (Ornithorhynchus anatinus ) is endemic to Australia and one of nature’s oddest creatures, seemingly assembled from the spare parts of other animals. The semi-aquatic monotreme is a venomous, duck-billed mammal that lays eggs, nurses its young and occupies a lonely twig at the end of a sparse branch of the vertebrate evolutionary tree.

The ancient, patchworked platypus is a relatively unchanged animal that may be a scientific boon for researchers, who are learning a lot from its recently decoded genome about mammalian gene regulation and immune systems, which could have huge implications for human disease susceptibility research.

Professor Jenny Graves, at Australian National University (ANU), Canberra explains the findings, in an interview with Anna Buckley from BBC World Service’s Science in Action programme.

This mix-and-match animal is more than just an oddity, though. Researchers report in Nature that its genome provides important clues into how mammals, birds and reptiles evolved from a common ancestor some 315 million years ago. And researchers at Stanford University School of Medicine report in Genome Research that they linked the evolution of a gene in the old platypus to a mutated version in humans responsible for moving the testes outside of the body and into an external pouch, or scrotum.

An international team of researchers that sequenced and analyzed the genome of a wild female platypus named Glennie, which lives in southeastern Australia. Among its findings: The platypus’ genome is two thirds the size of the human genome and contains 18,500 genes. (The human genome comprises 20,000 to 25,000 genes.) Eighty-two percent of the animal’s genes are found in other mammals. The genome is organized into 52 chromosomes (tightly packed structures of DNA stored in a cell’s nucleus), 10 of which determine the animal’s sex. (In humans, there are 46 chromosomes—23 pairs—and only two (X and Y) are sex-determining.)

Genome analysis of the platypus reveals unique signatures of evolution

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