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Elizabeth Huth Coates Foundation, Illumina, NHGRI, U of Louisville, UC Davis, Applera, ABI, Celera, TIGM, Genbank

Elizabeth Huth Coates Foundation Awards SFBR $300K for Illumina Sequencer
The Southwest Foundation for Biomedical Research, based in San Antonio, said this week that it has received $1.3 million in philanthropic gifts to support genomic research, including a $300,000 gift from the Elizabeth Huth Coates Charitable Foundation to fund the purchase of an Illumina Genome Analyzer. 
SFBR also received a $1 million gift from the AT&T Foundation to double the size of the computational cluster at the AT&T Genomics Computing Center from 1,500 processors to 3,000 processors.
“This leap in computing power makes our facility more than 2.5 times the size of that of any of our competitors around the globe and guarantees the primacy of SFBR as the world’s leading center for the genetic analysis of common complex diseases,” said John Blangero, a scientist in the SFBR Department of Genetics and director of its AT&T Genomics Computing Center, in a statement.
Sarah Williams-Blangero, chair of the SFBR Genetics Department, said in a statement that the Illumina sequencer will allow SFBR scientists “to undertake much larger investigations and examine much broader stretches of DNA than previously thought possible.”
SFBR will use the new resources to support 16 human genetic research projects involving more than 20,000 study volunteers. These projects are studying a range of diseases, including heart disease, diabetes, obesity, osteoporosis, malaria, and worm infections. Williams-Blangero said the foundation also plans to use the new technology to move into cancer genetics.

NHGRI Sets Aside $27.5M for Population-Based GWA Studies for Complex Diseases
The National Human Genome Research Institute plans to award $27.5 million in grants for large-scale genome-wide association studies aimed at identifying genetic variants that relate to unspecified common complex diseases.
The allocation will support between three and five studies over four years that aim to create population-based data to speed the process of understanding how certain genes are related to certain complex diseases.
According to an NHGRI RFA, the research will use information from population-based cohort studies or clinical trials with “detailed existing information on demographics, health characteristics, environmental exposures, and disease risk factors and traits.”  
The NHGRI said it expects the studies to attempt to “determine the population-based profile, or ‘epidemiologic architecture,’” of variants such as those in racial and ethnic subgroups in the US.
The studies also would identify modifiers of gene-trait associations, such as lifestyle or medicinal factors, and would identify clues that link causal variants to phenotypes.
The program will support assaying selected SNPs and other genetic variants with “strong evidence” for a possible causal association with a disease or trait; statistical analysis of the prevalence and associations of these variants on a population basis; provision of calculated descriptive and association data in readily interpretable form to a central database; cataloguing and disseminating the characteristics of participating population studies to be used for such investigations; and inviting collaborations with outside investigators for further functional or translational research. 
It would also provide “limited funding” for whole-genome amplification of “scarce, high priority” DNA samples, such as those from rare or severe disease cases or persons with extreme phenotypes; for researchers to isolate DNA from “uniquely valuable” stored samples; and for those who transform cryopreserved cells in “highest priority participants.”
The RFA points out that “although future plans may describe sequencing and functional studies, only genotyping is currently anticipated for inclusion in this program,” noting that support for future sequencing or functional studies may be available through other funding mechanisms.
Letters of intent for the grants are due on Oct. 19, and applications must be received by Nov. 19.

U of Louisville, UC Davis Land $12M in NIEHS Grants for Environmental Genomics and Disease
The University of Louisville and the University of California at Davis have been awarded $4.4 million and $7.5 million, respectively, from the National Institute of Environmental Health Sciences to conduct environmental genomics studies, the universities said separately last week.
The funding was awarded under an NIEHS program aimed at studying how gene-environment interactions may lead to diseases. NIEHS announced the $74 million Genes and the Environment Initiative program last October.
The University of Louisville will use its $4.4 million award to establish the Center for Environmental Genomics and Integrative Biology.
"By bringing together disciplines such as bioinformatics, biostatistics, and computational biology, we hope to pinpoint the genetic effects of environmental exposures," added the center's director Kenneth Ramos.
The $7.5 million NIEHS granted to UC Davis is renewed funding that will go to the school's Center for Children's Environmental Health
This center will study the role of genes and exposure to environmental chemicals during fetal development in autism.

Applera Mulls Spinning Out ABI and Celera into Two Independent Firms
Applera said last week that it has hired investment bank Morgan Stanley to advise the company as it considers restructuring its Applied Biosystems and Celera groups, which are currently traded as tracking stocks under the parent firm.
Applera said it will explore alternatives to its current structure, and will look into “creating two independent publicly traded companies in place of the two tracking stocks.”
ABI markets instruments, consumables, software, and services for the research and applied markets. Celera, originally formed to sequence the human genome, has evolved into a molecular diagnostics firm.
"We regularly review Applera's corporate structure, and in view of Celera's continued strong financial progress, we believe the time is now right to explore alternatives to our tracking stock structure, including the possibility of creating two independent publicly traded companies in place of the two tracking stocks," said Applera CEO, president, and chairman Tony White.
"While the tracking stock structure has facilitated the interests of both Celera and Applied Biosystems,” White added, “the evolution of our businesses makes it timely to explore the potential benefits of these businesses going their separate ways."
Applera’s board of directors also has nearly doubled its share repurchase authorization for ABI’s stock to $1.2 billion, which represents around 20 percent of the company’s outstanding common stock.
Through that repurchase, Applera expects to buy $600 million shares either through a tender offer or an accelerated share repurchase, the company said.
The balance of that deal will come “from open market purchases or privately negotiated transactions” over the next year to year and a half, the company said.
"The substantial increase and acceleration of the Applied Biosystems share repurchase program reflects our confidence in its business outlook and our belief that its shares continue to be undervalued in the market,” added White.
White also said ABI’s “strong cash position” makes the share repurchase program “an effective way to return value to shareholders.”

TIGM Deposits Knockout Mouse Sequence Data in Genbank
The Texas Institute for Genomic Medicine has deposited more than 275,000 nucleotide sequence tags from its knockout mouse library into the National Institutes of Health's Genbank, TIGM said last week.
Houston-based TIGM, which joined the International Knockout Mouse Consortium in May, said it offered the genetic sequence information to NIH after the institute called for mouse data to be widely shared throughout the international scientific community.
TIGM said the samples were pulled from its library of C57BL/6 mouse embryonic stem cells and deposited into Genbank’s Genome Survey Sequences division.
The institute said that the deposit is “one of the largest single submissions” to Genbank since it was created in 1982.

Illumina Files Resale Registration Statement for Previously Issued Convertible Senior Notes
Illumina said this week that it has filed a resale registration statement with the US Securities and Exchange Commission.
The filing relates to the company’s prior sale of $400 million aggregate principal amount of its 0.625 percent convertible senior notes due 2014.
The registration statement registers the offer and sale of the notes, and the shares of common stock underlying the notes. Illumina sold the notes initially to qualified institutional buyers in an offering that closed in February.

The Scan

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.

Study Reveals Potential Sex-Specific Role for Noncoding RNA in Depression

A long, noncoding RNA called FEDORA appears to be a sex-specific regulator of major depressive disorder, affecting more women, researchers report in Science Advances.

New mRNA Vaccines Offer Hope for Fighting Malaria

A George Washington University-led team has developed mRNA vaccines for malaria that appear to provide protection in mice, as they report in NPJ Vaccines.

Unique Germline Variants Found Among Black Prostate Cancer Patients

Through an exome sequencing study appearing in JCO Precision Oncology, researchers have found unique pathogenic or likely pathogenic variants within a cohort of Black prostate cancer patients.