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Roche, Invitrogen, Applied Biosystems, BGI Shenzhen, International Human Microbiome Consortium, Joint Genome Institute, Myriad Genetics, Decode Genetics, NHLBI, NIDDK, Zygem, Advalytix, ImaGenes

Roche’s Applied Science Business Posts 10-Percent Growth in Nine-Month Sales
Roche this week reported a 10-percent increase in sales for its Applied Science business, which includes 454 Life Sciences, for the nine-month period ended Sept. 30.
Roche Applied Science posted nine-month sales of 546 million Swiss francs ($473 million), a 10-percent increase over 498 million Swiss francs in the first nine months of 2007.
Roche said that sales of its Genome Sequencer FLX “nearly doubled despite increased pressure from competitors” during the period. The company also saw double-digit growth for its qPCR analysis products, particularly its LightCycler 480 instruments, and said that its Roche NimbleGen microarrays “also contributed to sales.”
Overall sales for the Diagnostics division, which includes Applied Science and four other business areas, increased 4 percent to 7.1 billion Swiss francs for the period, from 6.8 billion Swiss francs a year ago. The biggest contribution to growth came from the Professional Diagnostics and Applied Science units.
Total nine-month sales for the Roche Group, which includes the Pharmaceuticals and Diagnostics Divisions, declined 2 percent to 33.3 billion Swiss francs, from 33.9 billion Swiss francs a year ago.

Invitrogen, ABI Delay Shareholder Vote on Merger
Invitrogen and Applied Biosystems have delayed their respective special meetings of stockholders to vote on their proposed $6.7 billion merger in order to give shareholders more time to consider an amendment to the deal.
The firms said last week that they have amended the agreement to eliminate a condition to closing requiring that each company receive certain opinions of their respective counsel regarding tax treatment of the transaction.
The special stockholder meetings, which were initially scheduled to convene last week, have been rescheduled for Oct. 28.
“Given the unprecedented market conditions of the past few weeks, and the current trading price of Invitrogen’s common stock, the parties determined that they currently might not be able to obtain the necessary opinions because of the relative value of the cash consideration to be received by Applied Biosystems stockholders as compared to the value of the stock consideration they will receive,” the firms said in a joint statement.
Tax regulations related to mergers limit the percentage of the consideration that can be paid in cash if a transaction is to qualify as a tax-free reorganization.
Under terms of the deal, ABI shareholders are to receive $38 for each share they own in the form of Invitrogen stock and cash — if the 20 day volume-weighted average price of Invitrogen common stock is in the range of $43.69 to $46.00 three business days prior to the close of the transaction. The firms expect cash to account for an estimated 45 percent of the split. However, ABI shareholders have the option to request all cash or all stock, subject to possible proration.
Invitrogen’s shares closed at $38.73 on June 12, the day that the acquisition was announced. Its shares were down 2.2 percent at $29.74 in Wednesday morning trade on the Nasdaq.
The firms still expect the transaction to close next month.

BGI Shenzhen Completes Panda Genome Sequence 
Researchers at the Beijing Genomics Institute’s Shenzhen branch have completed the genome sequence of the giant panda, the institute said earlier this month.
BGI Shenzhen’s deputy director Jun Wang announced the project’s completion during the 10th High-Tech Fair in Shenzhen.
The institute launched the International Giant Panda Genome Project in March. At the time, BGI-Shenzhen said it was planning to sequence a panda using high-throughput sequencing technology and to complete a draft genome within six months.
According to the Xinhua News Agency, the researchers sequenced the genome of a three-year-old female panda, named Jing Jing, from the Chengdu Research Base of Giant Panda breeding in southwest China’s Sichuan Province. Jing Jing was also the model for one of the five mascots of the Beijing Olympics.
The Xinhua report said the institute plans to generate a “more detailed” genome sequence of the panda by the end of the year.
BGI-Shenzhen did not respond to a request for more information about the project.

International Human Microbiome Consortium Launched
Scientists meeting in Heidelberg, Germany, last week announced the formation of the International Human Microbiome Consortium.
So far, participants in the consortium include representatives from Australia, Canada, China, the European Union, France, Ireland, Japan, Korea, and the United States.
Several projects are already underway, including the US National Institutes of Health’s Human Microbiome Project; the European Union’s Metagenomics of the Human Intestinal Tract, or MetaHIT, project; China’s Meta-GUT project; and Ireland’s DAFF/HRB Elderly Gut Metagenomics project. Others have just formed and are in the process of securing funding. Projects will coordinate their efforts to avoid duplicating their genome sequencing efforts.
Last month, the NIH and the European Commission agreed to combine data from the Human Microbiome Project and the MetaHIT project.
Data generated by IHMC projects will be made available through the National Institute of Health’s Human Microbiome Project Data Analysis and Coordination Center and an equivalent center at the European Molecular Biology Laboratory. The data will also be distributed to other public databases, including those supported by the National Center for Biotechnology Information and the European Bioinformatics Institute.
The IHMC will set up a steering committee that will include representatives from each country's research funding agency and from each scientific project. That steering committee will develop standards related to data quality and coordinate microbial strains for complete genome sequencing projects, data access, and release and informed consent. 
IHMC chairmanship will rotate annually. Co-chairs for 2009 are Christian Desaintes from the European Commission and Dusko Ehrlich, coordinator of the MetaHIT project.
The consortium is also inviting other countries to participate in the effort to collect the genomes of microbes in and on the human body. In a conference call with last week, IHMC representatives noted that other countries, including Mexico and India, have already expressed interest in the project.

JGI, Collaborators Sequence Pennate Diatom Genome
An international team of researchers led by investigators at the US Department of Energy’s Joint Genome Institute sequenced the genome of Phaeodactylum tricornutum, a diatom, and compared it to the genome of another sequenced diatom called Thalassiosira pseudonana. Their findings, appearing online last week in Nature, reveal just how distinct the two diatoms are and provide new clues about diatom evolution and the nature of diatom diversity.
In 2004, researchers from JGI and elsewhere sequenced the genome of a centric marine diatom called T. pseudonana. For the latest paper, the researchers sequenced the genome of P. tricornutum, using whole genome shotgun sequencing. They also used information gleaned from more than 130,000 expressed sequence tags to help characterize the genes and gene functions in this pennate diatom.
Their results suggest that the roughly 27.4 megabase P. tricornutum genome contains an estimated 10,402 genes — fewer than the 11,776 found in the centric diatom T. pseudonana. And while about 57 percent of the P. tricornutum genes resemble those in T. pseudonana, about 40 percent of its genes are distinct.
In addition, P. tricornutum contains more species-specific gene families than T. pseudonana, a finding that the researchers suspect may reflect specialized pennate diatom functions.
Both P. tricornutum and T. pseudonana contain an abundance of genes involved in polyamine metabolism — an expansion that may be related to the organisms’ ability to produce silica. By identifying these and other cell wall silicification genes, the researchers may eventually understand how diatoms create glass at ambient temperature and pressure.

Myriad to Split Drug-Development, Molecular-Dx Businesses
Myriad Genetics said this week that it plans to spin off its drug development business from its molecular diagnostics business, creating two separate publicly traded firms.
The company’s core molecular diagnostics business will operate under the name Myriad Genetics, will employ around 800 staffers, and will focus on the company’s stable of molecular diagnostic tests, which include BRACAnalysis, COLARIS, COLARIS AP, MELARIS, and TheraGuide 5-FU.
The research and drug development business will operate under the name Myriad Pharmaceuticals, and will employ around 200 people who will focus on developing therapeutic candidates for cancer and infectious diseases. The company currently has four drug candidates in human clinical trials: Axiza, Vivecon, MPC-2130, and MPC-0920.
Myriad said it expects that Myriad Genetics’ stock will trade on the New York Stock Exchange under the ticker symbol MGX, and Myriad Pharmaceuticals will be listed on the NASDAQ Global Market under the company's current ticker symbol, MYGN.
The company has been considering such a split since at least August, when it announced that it had retained JP Morgan to conduct a strategic review of its options, including the possibility of separating its molecular diagnostic business and pharmaceutical business as independent entities.
Myriad said it will provide further details on the spin-off in a Form 10 registration statement for Myriad Pharmaceuticals, which it expects to file with the Securities and Exchange Commission in the second quarter of 2009.
The company did not provide a timeline for when it expects the spin-off to be complete, noting that it is subject to “numerous conditions,” including the filing of the Form 10, obtaining solvency and adequate capital surplus opinions, and receiving an independent opinion that the stock distribution will be tax-free.

Decode Genetics Seeks to Sell Non-Core Assets; Signs Up Middle East Distributor
Decode Genetics said last week that it is conducting a review of its long-term business strategy, with a goal of sharpening its business focus and selling non-core assets.
The Reykjavik, Iceland-based firm said it has hired the Stanford Group Company to assist it in evaluating strategic alternatives and executing quickly on the results of the review by identifying buyers or partners for its non-core business units, programs, and intellectual property.
Decode did not say what parts of its business or technologies it considers non-core. The firm has early-stage drug development programs and a portfolio of DNA-based tests for diabetes, cardiovascular, and oncology applications, which it offers through its own CLIA-registered laboratory.
“We are in the process of creating a smaller, leaner Decode that will devote its efforts and resources to one line of business,” Decode CEO Kari Stefansson said in a statement. “We have created a unique and growing portfolio of intellectual property, as well as a range of products and programs in both our drug development and diagnostics work, and we are engaged in discussions with potential partners and purchasers for various programs and business units.”
Decode intends to provide an update on the review during its third-quarter conference call on Nov. 6.
In addition, the firm said that it has elected to utilize a 30-day grace period for the scheduled Oct. 15 interest payment on its outstanding 3.5 percent senior convertible notes due 2011, as it completes the review and considers the sale of assets.
Earlier this month, Decode received a letter from Nasdaq informing the firm that it currently does not comply with regulations regarding the market value of its stock. If Decode does not regain compliance by Oct. 30, Nasdaq said that its shares would be delisted.
Separately last week, Dubai, UAE-based Eastern Biotech said that it has signed an agreement to promote Decode Genetics’ DNA-based tests for diabetes and other diseases in the Middle East.
The firm, which also runs a clinical reference lab, said that it would offer Decode’s tests for assessing risk of type 2 diabetes, myocardial infarction, atrial fibrillation, prostate cancer, glaucoma, breast cancer, and other tests under development.

NHLBI Plans $25M in Funding for Pediatric Genomics of Congenital Heart Disease
The National Heart, Lung and Blood Institute plans to provide $25 million for a six-year program to fund up to six centers that will focus on using collaborative genomics studies to learn more about the genetic causes of congenital heart disease.
The NHLBI Pediatric Cardiac Genomics Consortium, through a collaboration with the Canadian Institutes of Health Research, seeks investigators to conduct clinical and translational research that can lead “to a comprehensive understanding of congenital heart disease,” NHLBI said in a request for applications.
The research centers will investigate the genetics and genomics of one or more human cardiac malformations with the aim of identifying genetic influences on patient outcomes and genes that may cause congenital heart disease.
NHLBI plans to award up to $160,000 in direct costs to each of the selected centers in the first year, which will increase to $535,000 in each of the second through sixth years of the program. The total funding for the program in fiscal year 2009 is $1.44 million. Future funding will be commensurate with the beginning of recruitment into clinical protocols.
The PCGC centers may focus their resources on a number of different aspects of congenital heart disease genomics studies, including identifying genetic causes and modifiers of common human congenital cardiac malformations, myopathies, and rhythm disturbances; identifying genetic causes and modifiers of anatomically related malformations; association of genetic variants of components of specific regulatory or signal transduction pathways with cardiovascular malformations or syndromes; identifying genetic variations that influence clinical outcomes; pharmacogenomics in congenital heart disease; epigenetic regulation of candidate genes; and the influence of gene-environment interactions on congenital heart disease.
The centers will work with the NHLBI’s Cardiac Development Consortium and with the NHLBI Pediatric Heart Network. More information about the PCGC program is available here.

NIDDK Marks $20M for Type 1 Diabetes Gene Studies
The National Institute of Diabetes and Digestive and Kidney Diseases will spend $20 million over five years to fund fine mapping and other studies of genes that may be involved in type 1 diabetes.
NIDDK seeks to support scientists who are studying replication and fine mapping of genetic regions that are putatively associated with type 1 diabetes. The institute also intends to fund studies that apply new technologies to studying the genetics of type 1 diabetes.
Genome-wide association studies of this disease have shown promise, according to NIDDK, but in order to provide follow-up support the institute aims to support studies of genetic regions.
NIDDK expects to fund between four and ten awards ranging between $1.5 million and $5 million, with total direct costs of up to $5 million over the five years.
NIDDK will consider various types of studies that address its needs. Researchers could seek to identify specific genetic variants that influence type 1 diabetes risk, which could be prioritized, and gene-to-gene interactions could be studied as well.
This research could also include association analysis mapping, including sequencing and resequencing regions, or constructing high-density SNP maps. Scientists also may study methylation patterns in dinucleotides in regulatory regions of genes that appear to affect gene expression in type 1 diabetes. In addition, investigators could propose conducting analyses in families of paternally/maternally expressed genes that are likely candidates for diabetes susceptibility.
More information about the NIDDK’s program, “Fine Mapping and Function of Genes for Type 1 Diabetes,” is available here.

Zygem, Advalytix Partner on DNA Extraction Products
Zygem said last week that it has signed an agreement with Advalytix, a unit of Olympus Life Science Research Europe, to develop and sell a private-label line of DNA extraction products.
The partnership will combine Zygem’s enzymatic nucleic acid extraction technology with Advalytix’s expertise in single-cell molecular tests for life science research and diagnostic applications. Advalytix will market the DNA extraction products, which are designed to work with Advalytix’s single-cell molecular diagnostics and miniaturized diagnostic and biological tests for research and development.
Zygem’s technology uses a thermophilic enzyme to extract DNA from samples using a single closed-tube system. The Solana Beach, Calif.-based firm said that the technology has been validated for use in research, forensic, diagnostic, agriculture, and animal health applications.

ImaGenes Joins ORFeome Collaboration
Berlin, Germany-based ImaGenes has joined the international ORFeome Collaboration, an effort spearheaded by the NIH’s National Human Genome Research Institute.
The goal of the ORFeome collaboration is to provide the research community with an unrestricted source of fully validated human and mouse cDNA clones covering the entire protein-coding sequence of the respective genes. The clones allow for the production of native or modified human proteins for functional analyses or for therapeutic applications.

ImaGenes said that it will contribute proprietary clones and will provide high-quality sequencing of 2,000 single clones out of poorly characterized clone pools.

The Scan

Quality Improvement Study Compares Molecular Tumor Boards, Central Consensus Recommendations

With 50 simulated cancer cases, researchers in JAMA Network Open compared molecular tumor board recommendations with central consensus plans at a dozen centers in Japan.

Lupus Heterogeneity Highlighted With Single-Cell Transcriptomes

Using single-cell RNA sequencing, researchers in Nature Communications tracked down immune and non-immune cell differences between discoid lupus erythematosus and systemic lupus erythematosus.

Rare Disease Clues Gleaned From Mobile Element Insertions in Exome Sequences

With an approach called MELT, researchers in the European Journal of Human Genetics uncovered mobile element insertions in exomes from 3,232 individuals with or without developmental or neurological abnormalities.

Team Tracks Down Potential Blood Plasma Markers Linked to Heart Failure in Atrial Fibrillation Patients

Researchers in BMC Genomics found 10 differentially expressed proteins or metabolites that marked atrial fibrillation with heart failure cases.