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Max Planck Institute Leipzig, 454 Life Sciences, 23andMe, Decode Genetics, National Science Foundation, US Department of Agriculture, National Institutes of Health, Research Triangle Institute, Applera, Clinical Data, Cogenics

Svante Pääbo's Lab at MPI Leipzig Acquires Second 454 GS FLX to Sequence Bonobo Genome
Roche subsidiary 454 Life Sciences said this week that the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, has purchased a second Genome Sequencer FLX system.
The institute previously purchased a GS 20 in August 2006 and upgraded it to a GS FLX earlier this year. Both instruments will be based in the lab of Svante Pääbo, director of the department of evolutionary anthropology at the MPI, and will be used to sequence the genome of the Bonobo, a great ape that is closely related to humans. The Bonobo genome is expected to help researchers study the evolution of the chimpanzee genome. 
Pääbo’s group, in collaboration with 454 Life Sciences, has been using the 454 platform to sequence the genome of the Neanderthal, an ongoing project.

23andMe, Decode Genetics Launch Consumer Genomics Services
23andMe and Decode Genetics launched personalized DNA analysis services over the last week.
23andMe’s web-based service uses Illumina's genotyping arrays to analyze more than half a million SNPs in DNA from a saliva sample the customer provides. Customers then use 23andMe’s web tools to learn about their genomic profiles and gain information about their ancestry.
23andMe co-founder Anne Wojcicki said in a statement this week that the genomic information “provides intriguing insights into an individual's genetics, with the goal of expanding the collective knowledge base by enabling active participation in research."
The offering, priced at $999, will allow consumers to compare their genomes to family and friends that also participate.
Privately held 23andMe is backed in part by a nearly $4 million investment from Google. Besides Google, Series A investors included Genentech and New Enterprise Associates.
Decode’s DecodeMe service will analyze a cheek-swab sample and provide customers with an analysis of their genome, including knowledge about genetic variants associated with risks for common diseases, ancestry, and traits such as hair and eye color.
Decode will measure up to a million different DNA markers. While the company has not announced whose genotyping tools it is using in the DecodeMe service, the firm has an alliance with Illumina dating back to the spring of 2006 to co-develop and commercialize DNA-based diagnostics using Illumina’s genotyping platform.
The company is offering its services for an early promotional price of approximately $985.
Earlier this month, Navigenics, which has teamed with Affymetrix, launched its consumer genomics service. The company last week said that it has begun taking orders for its service, which will cost $2,500, but doesn't plan to begin testing until early next year (see In Sequence 11/13/2007).

NSF, USDA to Grant up to $10M for Microbial Sequencing Projects
The National Science Foundation said this week that it plans to provide up to $5 million in fiscal year 2008 for grants to support a joint microbial sequencing project with the US Department of Agriculture.
This funding will match the $5 million the USDA intends to grant for the program, which involves the high-throughput sequencing of the genomes of a number of microorganisms and developing ways to make that data more broadly available. Most of the grants will be for between $100,000 and $250,000 for periods of up to three years.
The program will be administered under the UDSA’s Cooperative State Research, Education and Extension Service, which will oversee the dispersal of between 15 and 20 awards.
Microbes of interest will include viruses, bacteria, archaea, fungi, oomycites, protists, and nematodes that possess agricultural importance.
The research will look into novel aspects of microbial biochemistry, physiology, metabolism, development and cellular biology; the diversity and the roles microorganisms play in complex ecosystems and in global geochemical cycles; the impact that microorganisms have on the productivity and sustainability of agriculture and natural resources, and on the safety and quality of the nation's food supply; the organization and evolution of microbial genomes, and the mechanisms of transmission, exchange, and reshuffling of genetic information.
The deadline for full proposals for the awards is Feb. 19. More information can be found here.

NIH Roadmap Issues Requests for Epigenomics Grants
The National Institutes of Health has launched its epigenomics program with a slew of new grants to be administered under its Roadmap plan.
The “Technology Development in Epigenetics” program will grant a total of $3.5 million to between four and eight investigators under the R21 funding mechanism over a two-year period. This grant aims to spur development of innovative new tools that will “significantly change the way that epigenetics research can be performed.”
A sibling “Technology Development in Epigenetics” initiative will grant another $3.5 million to fund between three and five programs for four years under the R01 funding mechanism to develop tools that are more mature. Both of these technology grants are intended to focus on the application of epigenetics to disease studies, diagnosis, and prevention.
Another grant will support the creation of “Reference Epigenome Mapping Centers” using a total of $50 million in funds over five years. The NIH expects to issue between three and five awards under this grant. These programs would aim to develop reference epigenomes from human embryonic stem cells, human differentiating and differentiated cells, cell lines, and tissues.
Another program will provide $7.5 million over five years to one grantee to develop and implement an “Epigenomic Data Analysis and Coordinating Center” that would support the Reference Epigenome Mapping Centers. This center also will be responsible for transferring standardized data to the National Center for Biotechnology Information for banking and public use.
The “Discovery of Novel Epigenetic Marks in Mammalian Cells” program will provide up to $3.5 million for each of three years under the R01 funding mechanism, and NIH expects to fund between four and six investigators or centers. The goal is to “establish and validate novel pathways of stable, differential silencing and activation of gene expression in mammalian cells.”
A companion program of the same title will provide a total of $3.5 million over each of two years under the R21 funding mechanism to between five and eight recipients. NIH said this program aims to discover “novel pathways of stable, differential silencing and activation of gene expression in eukaryotic organisms that may be applicable to human disease pathogenesis.”
Furthermore, the NIH is asking researchers to suggest targets for monoclonal antibodies “that would be useful for epigenetics research.”
More information can be found here.

NIH Plans to Issue Funding Requests for Human Microbiome Project this Month
The National Institutes of Health said last week that it plans to issue a funding request for demonstration projects under the NIH Roadmap 1.5 Human Microbiome Project later this month.
Applicants will be asked to identify “an important biological system that holds the potential to demonstrate the relationship between the human microbiome and health or disease” and to use “high-throughput, cost-effective technologies to produce a data set that can be used to study the human microbiome in the selected body region(s) under specified conditions.”
The expected deadline for applying is May. NIH recommends that investigators interested in applying attend an international meeting Dec. 9-10, during which there will be discussion of forming an International Human Microbiome Consortium.
More information is available here.

NIH Offers $3M for ELSI Studies of Human Microbiome Research
The National Institutes of Health said last week that it plans to fund studies that address the ethical, legal, and social implications of human microbiome research.
NIH will make approximately four awards totaling $1 million per year for three years. 
The application deadline is Feb. 15, and the earliest anticipated start date is Sept. 30.
More information can be found here.

RTI Lands up to $6.8M NHGRI Grant to Create Population Genomics Standards
Research Triangle Institute International has received a grant for up to $6.8 million from the National Human Genome Research Institute to develop standards for large genome-wide association and epidemiological studies, RTI said last week.
RTI said the three-year project, called PhenX, will use population-based genomics studies initially to focus on cardiovascular, neurologic, endocrinologic, and renal disorders.
"In recent years, there have been many good studies looking at the relationship between genetics and various health conditions and diseases," Carol Hamilton, RTI’s director of bioinformatics, said in a statement. "Unfortunately, the lack of standard measures in these studies often does not allow researchers to combine or compare their findings.”
Hamilton said the goal of the project is to develop standards that will help integrate population-based studies with smaller, complementary studies in ways that enable researchers to better understand genetics and environmental factors.

Applera Declares Dividend for Applied Biosystems Stockholders
Applera’s board of directors last week declared a quarterly dividend of $.0425 per share for holders of Applied Biosystems’ stock.
The dividend is payable on Jan. 2 to shareholders of record as of the close of business on Dec. 3.

Canadian Consortium Wins $473K Gov't Grant to Develop DNA Barcoding Tool to ID Species
Genesis Genomics, Genoma, and two Canadian Universities have formed a three-year venture to develop a tool and database to rapidly identify species based on their DNA sequences, Genesis Genomics said last week.
Using a CA$465,000 ($473,000) Natural Science and Engineering Strategic grant from the Canadian government, the group aims to develop and sell a handheld device that will analyze a tissue sample and compare the results against a database of life forms.
Genesis Genomics, which has facilities both in Thunder Bay, Ontario, and in the UK, will work with Genoma, the University of Guelph, and the University of Western Ontario to develop the technology for a government-sponsored project called the Canadian Barcode of Life Network.
The technology will be designed to analyze 648 nucleotides of mitochondrial DNA used to classify eukaryotic organisms at the species level. Genesis Genomics will coordinate and manage the project and will get the option to commercialize the technology.
The Barcode of Life Network has currently collected more than 300,000 DNA barcodes from 30,000 species and plans to eventually make the database global, with barcodes available for all of the world’s life forms.
Much of the technology for the device and for the database is being developed by Heinz-Bernhard Kraatz of the University of Western Ontario, Robert Hanner of the Canadian Barcode of Life Network and the University of Guelph, and Kenneth Crandall of Brigham Young University and Genoma, a consulting company specializing in phylogenetic and population genetic analysis and genomic data and bioinformatics.

Clinical Data's Fiscal Q2 Revenue Up 25 Percent on Strong Cogenics, PGxHealth Sales
Clinical Data said last week that fiscal second-quarter 2008 revenues swelled 25 percent as R&D spending fell 10 percent and net loss rose 34 percent.
Total receipts for the three months ended Sept. 30 increased to $9.1 million from $7.3 million in the second fiscal quarter of 2007.
Revenue for the company's Cogenics genomic division, which offers sequencing and other genomic services, rose 22 percent to $7.7 million and included $1.8 million of grant revenue from Icoria product lines that are expected to wind down by December.
Revenue for the company's PGxHealth business, which is developing pharmacogenetic tests and targeted therapeutics, rose 17 percent during the period to $1.1 million, within which sales of the FAMILION cardiac channelopathy tests rose 23 percent.
Net loss widened to $10.9 million from $8.1 million in the year-ago period.
As of Sept. 30, Clinical Data had around $61.1 million in cash and equivalents. Evan Ballantyne, senior vice president and CFO said that number excludes $22 million in proceeds from the sale of its Electa and Vital Scientific businesses, which the company realized in the current quarter. 
The company said it has roughly $80 million in cash and equivalents.

The Scan

Self-Reported Hearing Loss in Older Adults Begins Very Early in Life, Study Says

A JAMA Otolaryngology — Head & Neck Surgery study says polygenic risk scores associated with hearing loss in older adults is also associated with hearing decline in younger groups.

Genome-Wide Analysis Sheds Light on Genetics of ADHD

A genome-wide association study meta-analysis of attention-deficit hyperactivity disorder appearing in Nature Genetics links 76 genes to risk of having the disorder.

MicroRNA Cotargeting Linked to Lupus

A mouse-based study appearing in BMC Biology implicates two microRNAs with overlapping target sites in lupus.

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.