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BioNanomatrix, NHGRI, OpGen, Illumina, Broad Institute, Clinical Data, Applied Biosystems, EBI, Transgenomic, Agilent Technologies, Wellcome Trust Case Control Consortium, Biodiversity Institute of Ontario

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BioNanomatrix Gets $400K Grant to Continue Developing Single-Molecule Imaging Instrument
 
BioNanomatrix said last week that its has received a $399,020 grant from the National Human Genome Research Institute to continue development of its nanoscale imaging platform for haplotyping and gene mapping.
 
The Philadelphia-based firm said the grant would fund a two-year project led by Ming Xiao to develop a nanoscale platform for single-molecule haplotyping imaging and analysis of long strands of DNA at ultra-high resolution in a massively parallel format.
 
The latest grant is the fourth received by the firm from the National Institutes of Health to develop the single-molecule analysis technology. Last September, BioNanomatrix and partner Complete Genomics were awarded an $8.8 million grant from the US National Institute of Standards and Technology to develop a high-throughput sequencing technology that they said will be able to sequence a human genome in eight hours for less than $100.
 
Han Cao, CSO of BioNanomatrix, said in a statement that the newest grant is “explicitly intended to support the development of a platform to produce consistent linearization and imaging of individual DNA molecules, allowing for high-resolution mapping of labeled genomic sites. This added support will help us accelerate the development of the platform, which we believe could add significantly to the understanding of genetic diseases by increasing access to whole-genome analysis and by allowing researchers to view and analyze the critical haplotype information that is currently difficult to obtain.”
 
BioNanomatrix said that the goal of the project is to develop a fully integrated nanochannel chip and reader that can conduct single-molecule mapping of linearized genomic material extracted from a sample, thereby enabling direct visualization and analysis of the DNA at high resolution.
 

 
NHGRI to Fund Sequencing Technologies With Up to $12.6M Next Year
 
The National Human Genome Research Institute plans to provide up to $12.6 million in funding for the development of new sequencing next year that can help to bring the cost of sequencing a mammalian genome to around $1,000 by the year 2014.
 
The “Revolutionary Genome Sequencing Technologies” grant program, which started in 2004, will support high-risk, high-reward research that aims to develop full-scale sequencing systems or to investigate underlying system components or methods different than those currently being pursued.
 
Under one request for applications, which uses the R01 funding mechanism, NHGRI may grant as much as $5 million in fiscal 2009 to between two and seven awardees. Applicants for these funds may seek up to $1.5 million per year for a period of up to five years.
 
A parallel RFA, using the R21 funding mechanism, offers up to $2 million over three years to between two and seven grantees, for direct costs of up to $200,000 per year.
 
The Small Business Innovation Research part of the program will grant between four and six small businesses up to a total of $3.6 million in fiscal 2009. Phase I of this program will give up to $250,000 of total costs per year for up to two years, and Phase II applicants may seek up to $1.5 million total costs per year for up to three years.
 
A parallel Small Business Technology Transfer program part will award up to $2 million in fiscal 2009 to support between two and five awards to small businesses. This program will award up to $250,000 total costs per year for up to two years for Phase I programs, and it will support up to $1.5 million in total costs per year for up to three years for Phase II programs.
 

 
OpGen to Open New Facility in Maryland
 
OpGen said last week that it will open a new facility in Gaithersburg, Md., that will house its optical mapping services laboratory, R&D, manufacturing, and executive offices.
 
The company, which is based in Madison, Wis., said that the new facility will create more than 80 jobs over the next two years and will complement its current activities.
 
OpGen, which provides optical mapping technology and services, said it plans to operate its new facility in an ISO-certified environment.
 

 
Illumina Prices Public Offering
 
Illumina said last week that it has priced its public offering of 3.5 million shares of common stock at $87.50 per share.
 
The firm said that net proceeds from the offering were approximately $297.9 million. Illumina also has granted the underwriter an option to purchase an additional 525,000 shares of the stock within a period of 30 days after the date of the prospectus supplement related to the offering.
 
Illumina said in an SEC filing that it intends to use the proceeds from the offering to fund R&D efforts, expand its manufacturing capacity, and for working capital needs. It also said that it may use the money to acquire, license, or invest in other businesses, technologies, or products.
 
Goldman Sachs is acting as sole manager of the offering.
 

 
Broad Institute Makes Genomics Data Viewer Public
 
The Broad Institute of MIT and Harvard has created a genomics informatics tool that will allow researchers to visualize genomic information, and has made it publicly available for free, the institute said last week.
 
The Integrative Genomics Viewer was developed to help researchers find effective ways to visualize the “vast amounts of diverse genomic data” that scientists are accumulating with “ever increasing speed,” according to the institute. It can incorporate multiple types of genomic data and allows researchers to view them at various levels of resolution.
 
"This new tool offers a Google Maps-like view of integrative genomic data," said Jill Mesirov, chief informatics officer and director of computational biology and bioinformatics at the institute.
 
Broad said it allows researchers a “street view” of proteins that make up the genome, and they can visualize layers of information about gene expression, sequence alterations, mutations, and other genomic details such as copy number variation, chromatin immunoprecipitation data, and epigenetic modifications.
 
"Other tools offer detailed, localized views of genomic data, and a few tools are equipped to provide a whole genome view," Broad software engineer Jim Robinson said in a statement. But, Robinson added, “IGV was designed to integrate both and to provide smooth zooming and panning across all resolution scales."
 
The IGV allows these kinds of data to be overlaid or superimposed to help determine how changes at one level can affect another.
 
There are various display options, and users may view data as a heat map, histogram, scatter plot, and other formats.
 
The IGV is available at Broad’s website.
 

 
Growth in PGx, Services Units Boosts Q1 Revenues for Clinical Data
 
Clinical Data this week reported a 39-percent increase in revenues for its fiscal first quarter, driven by double-digit revenue growth in its PGxHealth and Cogenics divisions.
 
Clinical Data's total revenue for the quarter ended June 30 soared 39 percent to $9.2 million, from $6.6 million for the same period a year ago.
 
Revenue for Clinical Data's PGxHealth division grew 114 percent, to $2 million, from $950,000 in the prior-year period, including a 122-percent increase in sales of its Familion and PGxPredict tests.
 
Revenue for the company’s Cogenics genomics services group grew by 26 percent, to $7.2 million, from $5.7 million. The increase in Cogenics revenue is partly due to revenue of $1.1 million from Epidauros, which it acquired last year, as well as an “overall improvement” in the performance of Cogenics' core service lines, the company said.
 
R&D spending soared 344 percent, to $8.3 million, from $1.9 million for the three-month period ended June 30, 2007. The company attributed the increase to the ongoing safety and Phase III confirmatory trials for vilazodone, its drug candidate for the treatment of depression.
 
Sales and marketing expenses rose 82 percent, to $3.3 million, from $1.8 million in the prior-year period. The company said the increase was due to the development of a “new sales and marketing function” within PGxHealth, including the hiring of a new sales force and senior-level sales and marketing management, and the addition of Epidauros sales and marketing expenses. In addition, stock-based compensation expenses also increased, to $309,000, from $139,000 for the same period last year.
 
General and administrative expenses climbed 13 percent, to $6.1 million, from $5.4 million for the three months ended June 30, 2007. The company said that the increase was partly due to the addition of expenses of $620,000 for Epidauros and an increase in stock-based compensation expense.
 
Total operating expenses nearly doubled to $17.7 million from $9.1 million in the comparable period of 2007.
 
Clinical data’s net loss widened to $14.9 million, from $5.4 million in the prior-year period.
 
As of June 30, Clinical Data held $38.6 million in cash and cash equivalents.
 

 
ABI's Singapore Facility Gains ISO Clearance for IVD Devices
 
Applied Biosystems’ Singapore facility has received certification from the International Organization for Standards for in vitro diagnostic medical devices, the company said this week.
 
Specifically, the company received the ISO 13485:2003 certification from the British Standards Institution Americas, which enables CE marking to the In Vitro Diagnostics Directive 98/79/EC of products for sale within the European Community.
 
The company said that it obtained the certification to support its increased focus on commercial applications of molecular technologies, including quality and safety testing, human identification, food and environmental testing, forensics, pharmaceutical manufacturing, and clinical testing.
 
In addition to the ISO 124:2003 certification, BSI has awarded ABI’s environmental, health, and safety management system in Singapore certification to ISO 14001:2004 Environmental Management System, and OHSAS 18001:2007 Occupational Health & Safety Management System standards.
 

 
Standardization Groups Launch Initiative to Harmonize 'Minimum Information' Checklists
 
A collection of molecular biology standardization groups has launched a new initiative to coordinate a growing number of so-called “minimum information” checklists that have emerged to help researchers share data from genomics, proteomics, and other high-throughput biological experiments.
 
In a commentary published in the August issue of Nature Biotechnology, the researchers describe the harmonization effort, called “Minimum Information about a Biomedical or Biological Investigation,” or MIBBI, which aims to provide an overarching set of guidelines for standardization groups to ensure interoperability and prevent duplication of effort.
 
Since the publication in 2001 of the first minimum information checklist, “Minimum Information About a Microarray Experiment,” or MIAME, a number of projects have formed to create similar guidelines for reporting “metadata” about different biological experiments.
 
However, this proliferation of projects presented a challenge because “different communities were at risk of developing mutually incompatible standards,” Chris Taylor, a researcher at the European Bioinformatics Institute and co-author of the Nature Biotech paper, said in a statement.
 
In addition, the authors note in the paper, “overlaps in scope and arbitrary decisions on wording and substructuring [for different checklists] inhibit their use in combination” — an issue of particular concern for researchers who “routinely combine information from several disciplines.”
 
As a result, several existing checklist projects formed MIBBI in an effort to “facilitate the development of an integrated checklist resource site for the wider bioscience community,” the authors write.
 
To date, 21 checklist development projects have registered with MIBBI, including MIAME, MIAPE (Minimum Information about a Proteomics experiment), MIARE (Minimum Information about an RNA interference Experiment), MIGS (Minimum Information about a Genome Sequence), MIACA (Minimum Information about a Cellular Assay), and MIRIAM (Minimum Information Requested In the Annotation of biochemical Models).
 
“Communities working together through MIBBI will produce non-overlapping minimal information modules,” said Dawn Field, a researcher at the UK’s Natural Environment Research Council Environmental Bioinformatics Center and a co-author of the paper. “The idea is that each checklist will fit neatly into a jigsaw, with each community being able to take the pieces that are relevant to them.”
 
MIBBI has two parts. The first is the MIBBI Portal, which provides summary information for each of the registered projects and exists “simply to raise awareness of, and afford more straightforward access to, a wide range of checklists by providing researchers, journal editors, reviewers, funders, and the wider community of checklist developers with a quick and simple way to discover (whether there is) a checklist addressing a particular area and to establish the scope and progress of the underlying project,” according to the paper.
 
The second component of the project is the MIBBI Foundry, which plans to closely examine the available checklists and eventually develop a suite of “self-consistent,
clearly bounded, orthogonal, integrable checklist modules.”
 
These modules will be released through MICheckout, a tool that is currently under development by the EBI and the NERC’s Environmental Bioinformatics Center. MICheckout will assist users in compiling the correct list of modules and downloading them in a form that they can use, the paper said.
 

 
Transgenomic Posts Flat Sales in Q2
 
Transgenomic last week reported nearly flat revenues in the second-quarter of 2008. The company’s profit dropped 55 percent in the quarter, compared with the year-ago period.
 
The Omaha, Neb.-based genetic test provider said that it brought in revenues of $6.2 million for the three-month period ended June 30, roughly the same number it recorded in the second quarter of 2007.
 
The company said its third consecutive quarter of profitability came from stable instrument and consumables sales and growth in its Molecular Clinical Reference Library and from its Pharmacogenomics Services Laboratory business.
 
Specifically, Transgenomic said it saw a 52-percent increase in net sales from its lab services business, and a decrease of 7 percent in its instrument-related sales.
 
Transgenomic President and CEO Craig Tuttle said the company continues to build customer validation of its discovery and detection services, and is working to increase sales from its reference lab and its pharmacogenomics business with drug makers. Tuttle also said that the company is seeking new collaborations in Phase III clinical trials that could bring in more revenue.
 
Transgenomic posted a profit of $101,000, compared to a net profit of $226,000 million in the second quarter of 2007. Last year’s second quarter included a $937,500 gain on the sale of an investment in equity securities, which was partially offset by restructuring charges of $624,000 related to the closing of a production facility in England and an administrative office in France, the firm said
 
The firm’s R&D spending rose to $560,000, from $492,000, while its SG&A costs were flat at $3.1 million.
 
Transgenomic finished the quarter with $5.7 million in cash and cash equivalents.
 

 
Wellcome Trust Genotyping Study Using Agilent Arrays
 
Agilent Technologies said last week that the Wellcome Trust Case Control Consortium will use the firm’s custom-made, whole-genome copy number variation microarrays in the next phase of the genetic variation study.
 
Agilent is the third company to announce that the WTCCC is using its arrays for the second phase of the project. Previously, Illumina and Affymetrix both announced their technologies are being employed by researchers in the study.
 
The WTCCC is a group of UK researchers who began in 2005 studying thousands of genotyped human samples for genes associated with coronary heart disease, hypertension, types 1 and 2 diabetes, bipolar disorder, Crohn's disease, rheumatoid arthritis, tuberculosis, autoimmune thyroid disease, ankylosing spondylitis, multiple sclerosis, and breast cancer.
 
Agilent said that genetic samples will be processed by Oxford Gene Technology, which is a UK-based Agilent microarray certified service provider.
 
“This is an important new study of human genetic variation in common disease for which we require high-resolution microarrays with extremely reproducible performance,” said Matthew Hurles of the Wellcome Trust Sanger Institute in a statement.
 

 
DNA Barcoding Helps Expose Wasp Diversity
 
A new study that weds traditional taxonomy, morphology, and ecology with DNA barcoding has uncovered more than a hundred previously unrecognized parasitic wasp species — and provided insights into their host specificity.
 
In a paper appearing online this week in the Proceedings of the National Academy of Sciences, a team of North American researchers applied DNA barcoding to thousands of parasitoid wasps from a decades-old collection in northwestern Costa Rica. Their results illustrate the potential benefits of combining different types of biological data to document and understand biodiversity. And, researchers say, this approach could ultimately yield clues about the patterns that drive biological systems.
 
“Ultimately, we’re interested in understanding the rules that promote the rise and fall of species,” senior author Paul Hebert, director of the Biodiversity Institute of Ontario at the University of Guelph in Canada, told In Sequence’s sister publication GenomeWeb Daily News.
 
A DNA barcoding pioneer, Hebert was among the first to propose using a standard, predetermined stretch of DNA to catalogue and identify as many eukaryotic organisms as possible. The goals of such efforts, he said, are to create a digital identification system for life that is based on DNA sequences and to find rules that scientists can apply when going into new regions and trying to understand species diversity.
 
For the latest paper, Hebert and his team focused on six genera from a subfamily of parasitoid wasps called the Microgastrinae, which parasitize caterpillars. About 1,500 Microgastrinae species have been described to date, but biologists estimate it may actually consist of more than five to ten thousand species. There is also relatively little known about just how specialized the parasites are — partly due to an incomplete understanding of their species diversity.
 
“Efforts to estimate parasitoid host specificity that do not include DNA-based discrimination of the parasitoid species are likely to underestimate host specificity because of the inadvertent labeling of morphologically similar but genetically isolated lineages as being a single species,” the authors wrote.
 
For the study, the researchers turned to a unique resource — Costa Rica’s Area de Conservacion Guanacaste — which includes caterpillars and associated parasitoid wasps collected over 30 years. The collection, which houses approximately 400,000 wild-caught and reared caterpillars, proved invaluable for the study, Hebert explained, because a wealth of morphological and taxonomic information and ecological correlates had been collected for the specimens.
 
Biologists were able to integrate this information with new genetic technology, Hebert explained, barcoding 2,597 parasitoid wasp specimens. Usually, he said, the goal is to get about 650 base pairs of sequence information. But since some specimens had degraded DNA from sitting on pins for decades, the researchers generally settled for sequences longer than 500 base pairs.
 
Based on morphological and taxonomic assessments, the parasitoid wasps fell into 171 provisional species groups. DNA barcoding increased the detected species richness in this group by some 70 percent, uncovering nearly 150 new provisional species. In the most striking example of hidden, cryptic species found by barcoding, the researchers identified 36 provisional species that had originally been classified as one.
 
In another case, they identified wasps that shared a nearly identical DNA barcode but had distinct hosts, parasitizing caterpillars in different families.
 
Together, the combination of morphology, DNA barcodes, and host/ecological records revealed 313 provisional wasp species in the collection, each parasitizing just one, two, or a few closely related caterpillar species. “This kind of host specificity is so strongly correlated with the host’s ecology that the wasps cannot be labeled as generalists in any useful sense of the word,” the authors argued.
 
This specialization may eventually change the way in which community ecologists look at food webs, Hebert noted. “[B]arcoding can provide a rapid and relatively inexpensive first screen of a large, diverse, and understudied biota in a way that dramatically improves understanding of species richness and trophic webs,” he and his colleagues wrote.
 
Eventually, Hebert and others involved in the International Barcode of Life project (see In Sequence 8/5/2008) would like to see barcoding applied to millions of specimens in order to characterize 500,000 species. That undertaking is expected to provide information that can be used to understand species diversity and increase the rate of new species discovery. And, Hebert noted, DNA barcoding is being applied to other fields as well. For instance, DNA barcodes are being used for tracking food products and in efforts to curb poaching.
 
— By Andrea Anderson, originally published on GenomeWeb Daily News

The Scan

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Trying in the Eye

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PLOS Papers on Cerebellum Epigenetics, Copy Number Signature Tool, Acute Lung Injury Networks

In PLOS this week: epigenetics analysis of brain tissue, bioinformatics tool to find copy number signatures in cancer, and more.