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Agilent Technologies, Broad Institute, Celera, ABI, Medical University of Graz, Digilab Genomic Solutions, Platypus, Pseudomonas stutzeri, Podospora anserina, Wellcome Trust Sanger Institute, University of Bristol, Stenotrophomonas maltophilia, Biogen Ide

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Agilent Licenses Genome Capture IP from Broad; Plans to Develop Kits
 
Agilent Technologies has licensed genome capture technology from the Broad Institute, the company said this week.
 
Agilent plans to use the method, which Broad researchers presented at a conference in February (see In Sequence 4/8/2008), to develop genome-partitioning kits that will incorporate the company’s Oligo Library Synthesis technology.
 
The Broad’s approach involves biotinylated long RNA probes. Agilent plans to offer kits containing custom mixtures of these probes that can efficiently capture 5 to 10 megabases of genomic DNA in a single tube.
 
The method is based on a combination of the Agilent SurePrint platform, which can synthesize high-quality oligo mixtures, and protocols developed by the Broad Institute to transform these into RNA probes.
 
Financial terms of the agreement were not released.
 

 
Celera, ABI to Split on July 1
 
Celera and Applied Biosystems will formally separate on July 1, subject to a number of conditions, parent Applera said last week.
 
Applera said that its board of directors approved the proposed separation, for which all of Celera’s outstanding shares will be redeemed. Each share of the current Celera tracking stock will be exchanged for one share of the independent Celera Corp.
 
Last month, Celera filed with the US Securities and Exchange Commission a preliminary prospectus to split off from Applera. Officials from both Celera and ABI have hinted for months that a split would be the likely outcome of a review begun in August by investment bank Morgan Stanley, which was hired to explore options for restructuring the groups.
 
Completion of the split is subject to a number of conditions including "an opinion from counsel to Applera regarding the tax consequences of the separation," as well as the SEC declaring effective Celera's registration statement on or prior to June 15.
 
Celera President Kathy Ordoñez will become CEO of the firm, which will retain its headquarters in Alameda, Calif. Celera will trade on the NASDAQ.
 
ABI will continue to trade on the New York Stock Exchange.
 

 
Medical University of Graz Purchases 454 GS FLX
 
The Medical University of Graz in Austria has purchased a 454 Genome Sequencer FLX, Roche said last week.
 
The instrument is housed at a core facility at the university’s Center for Medical Research. Scientists plan to use the instrument to study the composition of the intestinal flora in the human body and how it can help protect from disease. As a model, they want to study infection with Clostridium difficile, which mainly occurs after prolonged treatment with certain antibiotics and leads to severe infection of the large intestine and severe diarrhea.
 
According to Roche, this is the first purchase of a high-throughput sequencer by an Austrian university.
 

 
ABI to Sell Digilab's HydroShear with SOLiD System
 
Applied Biosystems will offer Digilab Genomic Solutions’ HydroShear DNA shearing device along with its SOLiD sequencing system, Digilab said last week.
 
The HydroShear uses hydrodynamic shearing forces to fragment DNA strands, Digilab said. According to the company, virtually any source of DNA at any concentration can be randomly fragmented to within two-fold size distribution.
 
Terms of the supply and reseller agreement were not disclosed.
 

 
Platypus Genome Sequenced; Provides Clues to Mammalian Evolution
 
An international team of scientists has sequenced the genome of one of the most unusual creatures on Earth: the platypus.
 
In a paper published online in Nature last week, the team described this feat — along with some of its conclusions about the evolution of this furry, egg-laying, duck-billed, milk-producing, toothless, and venomous animal. Five additional papers, published in the journal Genome Research last week, apply information discovered from the platypus genome to specific research on everything from venom production to RNA pathways to development.
 
The genome is expected to augment monotreme conservation efforts. And, researchers say, having the platypus genome on hand will also aid comparative mammalian studies.
 
With its apparent combination of mammalian, reptilian, avian, and unique features, the platypus, Ornithorhynchus anatinus, has long puzzled biologists. Along with other egg-laying mammals such as echidna, the platypus belongs to a taxonomic group called Monotremata, often considered a sub-class of mammals that branched off an estimated 160 to 210 million years before so-called therians — marsupials (Marsupialia) and placental mammals (Placentalia). It has 52 chromosomes, 10 of which are sex chromosomes.
 
Among its most notable features, the platypus has a sensitive electro-sensory system that it uses to capture invertebrate prey, and a unique defense system: Males are venomous during mating season, with venom being released from spurs in the animals’ hind legs.
 
Lead author Wes Warren, assistant director of Washington University School of Medicine’s Genome Center, and his colleagues used whole-genome shotgun Sanger sequencing to determine the 2.2 billion base pairs in the platypus genome to about six times coverage. This proved no small task, given that roughly half of the platypus genome is made up of repetitive sequence.
 
From the 1.84 gigabases of assembled sequence, they ordered 437 megabases onto 20 chromosomes, localizing sequences by fluorescence in situ hybridization. Not surprisingly, the authors found, “[t]he platypus genome, as well as the animal, is an amalgam of ancestral reptilian and derived mammalian characteristics.”
 
Even so, there were some unexpected finds. For example, the platypus genome contains an unanticipated number of small nucleolar RNAs — about 10 times as many as therian mammals. As for its other small RNA pathways, some are similar to mammals, while others are more similar to birds, specifically chickens. The researchers also found a group of some 183 new miRNAs that appear to be unique to platypus and echidna. The majority of these belonged to nine clusters, five of which are on the X1 chromosome.
 
Two of the accompanying papers in Genome Research describe these platypus RNA pathways in more detail. The first, by senior author Gregory Hannon, a Cold Spring Harbor Laboratory biologist, and his colleagues focuses on platypus small RNA. For that study, Hannon and his colleagues sequenced RNA from six platypus and echidna tissues deeply to better understand small RNA pathways and their tissue-specific expression.
 
The second, by University of Münster experimental pathologist Jurgen Brosius and his colleagues, deals specifically with the more than 200 platypus snoRNAs. By comparing them with those in other mammalian and vertebrate groups, Brosius and his team found new features in platypus snoRNAs that provide insights into snoRNA evolution.
 
Based on the Ensembl pipeline, Warren and his team predicted that the platypus genome contains 18,527 protein-coding genes — approximately the same number as humans and opossum. They also did whole-genome comparative alignments of the platypus sequence and sequence from human, dog, mouse, opossum, and chicken, and looked at the genetics behind characteristic platypus features.
 
“Of particular interest are families of genes involved in biology that links monotremes to reptiles, such as egg-laying, vision, and envenomation, as well as mammal-specific characters such as lactation, characters shared with marsupials such as antibacterial proteins, and platypus-specific characters such as venom delivery and underwater foraging,” the authors wrote.
 
In a separate paper in Genome Research, senior author Katherine Belov, a veterinary researcher at the University of Sydney, and her colleagues looked more closely at the evolution of genes related to the platypus’ venom and venom delivery system and to their defensin genes in general.
 
Meanwhile, senior author Jennifer Marshall Graves, a biologist at the Australian National University, and her team published a Genome Research paper comparing platypus sex chromosomes with those of other animals. They concluded that platypus sex chromosomes are distinct from those of therians and are more similar to those of birds.
 
Finally, senior author Sheau Teddy Hsu, an obstetrics and gynecology researcher at Stanford University, led a group of researchers who used information about platypus genetics to help them understand testicular descent in therian mammals. That work also appeared in Genome Research last week.
 
“The fascinating mix of features in the platypus genome provides many clues to the function and evolution of all mammals,” Richard Wilson, director of Washington University’s Genome Center and senior author of the Nature paper, said in a statement. “By comparing the platypus genome to other mammalian genomes, we’ll be able to study genes that have been conserved through evolution.”
 
The platypus genome sequence is available online from GenBank.
 

 
Nitrogen-Fixing Pseudomonas Species Sequenced
 
An international group of researchers has sequenced the genome of a nitrogen-fixing, root-associated bacterial species.
 
In a paper published online this week in the Proceedings of the National Academy of Sciences, Chinese and French researchers report sequencing the genome of a diazotrophic Pseudomonas stutzeri strain that lives in the soil in and around plant roots.
 
There it uses nitrogenase enzymes to convert dinitrogen to ammonia, which can be used by plants. The team also started teasing apart genes that were shared with other Pseudomonas species and those that were unique to P. stutzeri.
 
The team sequenced the 46-megabase P. stutzeri A1501 genome to about seven-fold coverage using whole-genome shotgun sequencing. The genome contains an estimated 4,146 protein coding genes. About half of these, some 1,977, are similar to genes found in five other Pseudomonas species, suggesting this may represent the core Pseudomonas genome. Interestingly, genes related to nitrogenase function are located on a so-called nitrogen-fixation island that is about 49 kilobases in size and houses 59 genes.
They also used microarrays to gauge transcription status across the A1501 genome. For instance, most of the genes found in the nitrogen-fixation island were up-regulated in response to nitrogen fixation conditions, but down-regulated when excess nitrogen was available.
 
The bug contained hundreds of genes coding transporters along with several suspected to mediate osmotolerance. The team also found genes that may be help P. stutzeri survive in soil and colonize plant roots, though they noted that more work is necessary to pinpoint the exact role of these genes.
 

 
Researchers Publish Draft Genome of Model Fungus P. anserina
 
A team of researchers from France and the Netherlands has sequenced the model fungus Podospora anserina and published a draft version of its genome.
 
P. anserina is a dung-inhabiting, saprophytic fungus used by biologists to study, for example, ageing and sexual development.
 
The researchers, from the Institute of Genetics and Microbiology in Paris and other institutions, used whole genome shotgun sequencing to produce a 10x draft sequence of the fungus. They published their analysis of the genome last week in Genome Biology.
 
The genome of P. anserina, which is closely related to Neurospora crassa, contains a set of genes that are potentially involved in the breakdown of complex carbon sources such as cellulose and lignin, making them potentially useful for biotechnology applications.
 
The researchers found evidence of extensive gene loss and gene shuffling, as well as substantial gene duplication in the fungus. The transcription machinery of P. anserina, they found, produces a large number of RNAs that could potentially have regulatory roles.
 

 
Sanger, U. of Bristol Sequence Resistance-Prone Steno
 
Scientists from the Wellcome Trust Sanger Institute and the University of Bristol have sequenced Stenotrophomonas maltophilia, commonly known as Steno, a pathogen that frequently develops drug resistance and causes hospital-acquired infections.
 
The analysis of the 4.8-megabase GC-rich genome was published online in Genome Biology last month. The sequence reveals “remarkable capacity for drug and heavy metal resistance,” according to the paper.
 
Steno flourishes in moist environments, such as around taps and shower heads, but it can only enter the body through devices such as catheters or ventilation tubes, where it forms biofilms.
 
About 1,000 cases of Steno blood poisoning are reported in the UK each year, with a mortality rate of about 30 percent. While Steno infections are still relatively uncommon, they are on the rise, according to the authors.
 
“This is the latest in an ever-increasing list of antibiotic-resistant hospital superbugs,” Matthew Avison, a researcher at the University of Bristol and senior author of the paper, said in a statement. “The degree of resistance it shows is very worrying. Strains are now emerging that are resistant to all available antibiotics, and no new drugs capable of combating these ‘pan-resistant’ strains are currently in development.”
 

 
Biogen Idec to Use Almac Technology to Extract Genetic Material from Samples
 
Biogen Idec has tapped Almac Diagnostics to help it extract genetic information from formalin-fixed paraffin-embedded tissue, Almac said last week.
 
Craigavon, Northern Ireland-based Almac said that Biogen Idec would use the process for SNP analysis in a phase II study of a drug for treating gastrointestinal stromal tumors. The firm’s process enables researchers to use FFPE samples in qPCR and microarray SNP-genotyping and gene-expression studies.
 

 
Consumer Genomics Leaders Talk Ethics and More at CSHL Meeting
 
Scientific leaders from three personalized genomics companies joined ethics and policy experts last week to discuss the ethical, legal, and social implications of direct-to-consumer genomic testing.
 
The event, part of Cold Spring Harbor Laboratory’s Biology of Genomes meeting, highlighted the current state of such tests and their implications for medicine and society. Dietrich Stephan, co-founder and CSO of Navigenics; 23andMe
Co-founder Linda Avey; and Decode President, CEO, and Director Kari Stefansson each presented an overview of their companies’ consumer genomics services before participating in the panel discussion and taking questions from researchers in attendance.
          
Francis Collins, director of the National Human Genome Research Institute, moderated the session. Also participating were Kathy Hudson, founder and director of the Genetics and Public Policy Center at Johns Hopkins University, and Joseph McInerney, executive director of the National Coalition for Health Professional Education in Genetics. Hudson presented information related to the oversight of genetic tests, while McInerney focused on physician education related to the tests.
 
As he kicked off the session, Collins lauded the recent passage of the Genetic Information and Non-discrimination Act, noting that it puts the field of genomic research “on much firmer footing.”
 
Still, the debate continues over whether direct-to-consumer genomic tests are a boon to society — providing individuals with a glimpse into their genetics — or a bane, representing a premature application of genetic data.
 
Not surprisingly, at last week’s session, representatives of companies offering genomic tests were quick to point out the potential societal value of their services. For instance, citing factors such as rising healthcare costs, an aging population, and a surge in diseases such as diabetes, Navigenics’ Stephan highlighted the role of personalized genomics in preventative medicine. He proposed that the tests could increase early disease detection and decrease health burdens.
 
Stephan’s presentation also touched on issues that Navigenics has stressed in the past with respect to its Health Compass genomic testing service, such as its commitment to privacy, stringent curation of genetic associations, and guidelines related to test validity.
 
For her part, Avey presented the 23andMe genetic tests as a product with applications for healthcare and beyond. “23andMe looks at genetics very holistically,” she said.
 
She touched not only on the promise of genomic tests for diagnosing and treating diseases, but also on 23andMe’s pop culture applications. For example, Avey said, 23andMe provides "ancestry chromosome painting" to capitalize on the public’s appetite for genealogy. She also envisions links between genomic testing and social and/or health networking.
 
Stefansson, meanwhile, presented personalized genomic testing — such as Decode’s DecodeMe service — as a logical extension of the way healthcare has been developing over the past few years. As more and more patients seek answers online and elsewhere before seeing their physician, he noted, direct-to-consumer genomic tests could “empower people” by giving them more control over their healthcare. And, he said, the tests could become a jumping-off point for doctor-patient dialogues.
 
Like Stephan, Stefansson touted genomic tests as a tool for shifting away from conventional medicine and towards preventative medicine. He also highlighted his company’s commitment to operating with high specificity, accuracy, and consistency under strict standards.
 
But despite the individual companies’ voluntary standards and guidelines, Hudson said, the field in general could benefit from better regulation and oversight. Touching on many of the same concerns she and others have expressed in the past regarding regulatory oversight, privacy, and clinical validity, Hudson argued that more research is necessary to determine how the public will respond to genetic information.
 
For instance, she noted that although some companies voluntarily conform to standards such as the Health Insurance Portability and Accountability Act, they are not required to do so. That means the current oversight of genetic testing does not guarantee that appropriate standards are put in place.
 
To overcome such potential problems, Hudson suggested that the public and policymakers demand transparency from genomic testing companies, require third-party review of tests, take action against false claims, and modernize views and regulations of genetic tests.
 
Even so, Hudson expressed optimism over voluntary standards presented by company leaders at the session. “I’m happy to hear that the companies are supportive of raising the bar here,” Hudson said. She added, “In the absence of demonstrative harm,” individuals should have the option of getting their genetic information.
 
“There are a lot of reasons to be optimistic and hopeful [about personalized medicine],” Hudson said. “There’s a really, really strong appetite for health information, including genetic information.”
 
A great deal of discussion also centered on the role of primary care physicians and other healthcare professionals for applying information from genomic tests. The NCHPEG’s McInerney discussed the main challenges to genetics education for primary care physicians and the subsequent integration of genetics into primary care. He also introduced GeneFacts, an NCHPEG database aimed at providing a genetic support resource for non-geneticists.
 
Public interest in genetic and genomic testing may actually spur increased knowledge about such tests within the primary care community, McInerney speculated.
 
There were also hints that the personalized genomics companies may ultimately share information and strategies — at least in the early days of genomic test marketing and application.
 
In particular, Avey expressed interest in collaborating with Navigenics and Decode on reporting information, predictions, and associations revealed by genomic tests, adding, “if we’re not standardized and we don’t have a consistent message, it’s going to confuse the [primary care] community.”
 
By Andrea Anderson; originally published on GenomeWeb Daily News

The Scan

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