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Short Reads: Apr 7, 2009


New UK Sequencing Center to Open Doors in June

A new UK genome sequencing center is slated to open soon, the UK's Biotechnology and Biological Sciences Research Council said last week.

BBSRC said that the Genome Analysis Centre, located in the Norwich Research Park, will become operational over the next two months and open officially in June.

TGAC will be directed by Jane Rogers, the former human sequencing and mapping project manager at the Wellcome Trust Sanger Institute. The center is making "a significant investment in the latest range of genome sequencing and bioinformatics technology," and its work will be "complementary to the work of other genomics centres in the UK," according to the BBSRC.

TGAC, a BBSRC national center, plans to sequence and analyze the genomes of "scientifically and economically important" plants, animals, and microbes.

BBSRC said it will provide the "majority" of the center's £13.5 million ($19.9 million) in funding, and will underwrite its operating costs for several years. Other contributions come from EEDA, the Norfolk County Council, the Norwich City Council, the South Norfolk Council, and the Greater Norwich Development Partnership.

University of Barcelona Acquires 454 Sequencer

The University of Barcelona has recently purchased a Genome Sequencer FLX that will be installed at the genomics unit of its Scientific and Technical Services facility.

The researchers plan to use the platform for a variety of projects, including those aiming to improve aquaculture production, focusing on the vulnerability of benthonic populations, post-genomic analyses of the homeostasis and regeneration of complex multicellular organisms, and studies aiming to identify the molecular mechanisms that control embryogenic processes of bilateral organisms.

The platform will also be used in disease studies focusing on hepatic and digestive diseases, lymphoid neoplasia, osteoporosis, and other diseases, with the aim of contributing to the future development of diagnostic tools.

The Scientific and Technical Services facility offers its services to researchers of the University of Barcelona as well as researchers from other institutions and companies.

NIAID Grants $106M for Infectious Disease Sequencing

The National Institute of Allergy and Infectious Diseases recently awarded $106 million to three genome sequencing centers for research into infectious diseases.

Under the contracts, the Massachusetts Institute of Technology and the J. Craig Venter Institute have been awarded $43 million each, and the University of Maryland, Baltimore, has won $20 million.

The funds for the three Genome Sequencing Centers for Infectious Disease grants were awarded within the last week.

NIAID's Division of Microbiology and Infectious Disease supports genome sequencing activities, including high-throughput sequencing, comparative genomic sequencing, and genotyping.

The sequencing projects conducted at these centers will include microorganisms that are considered bioterror pathogens, clinical isolates, closely related strains, invertebrate disease carriers, and microorganisms that may be responsible for emerging and re-emerging infectious diseases.

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SeqWright Sequenced HPV Strains for Hologic Clinical Trial of HPV Diagnostics

Genomics service provider SeqWright said this week that it provided sequencing services as part of clinical trials of two human papillomavirus in vitro diagnostic tests developed by Hologic, formerly Third Wave Technologies, that recently received FDA premarket approval.

SeqWright said it provided DNA sequencing services under FDA-mandated quality standards, sequencing multiple HPV strains and providing bioinformatics to validate two Hologic HPV diagnostic tests, Cervista HPV High Risk and Cervista HPV 16/18.

SeqWright said it maintains a CLIA-certified lab and complies with Good Laboratory Practices as specified in the Code of Federal Regulations. Sequencing for Hologic's clinical trials was performed under GLP guidelines.

BioReference Laboratories' GeneDx Launches DCM Test on Illumina GA

BioReference Laboratories said this week that its GeneDx laboratory is now offering next-generation sequencing testing for dilated cardiomyopathy.

The test, which runs on the Illumina Genome Analyzer, is the company's second to use a next-generation sequencing platform. GeneDx launched its first test on the Illumina GA, for hypertrophic cardiomyopathy, last September (see In Sequence, 7/22/2008)

The company said it is preparing to offer additional tests based on second-generation sequencing to address other clinical conditions.

GeneDx currently provides testing for more than 250 rare disease conditions, based on more than 200 genes, using Sanger sequencing technology.

University of Michigan Installs Genomatix Genome Analyzer

Genomatix Software said last week that the CCDU bioinformatics core of the Center for Computational Medicine and Biology at the University of Michigan has installed a Genomatix Genome Analyzer at its laboratories in Ann Arbor.

The GGA is a high-performance computer with terabytes of database and software technology for the analysis of NGS data, and the University of Michigan plans to make the GGA tools available campus-wide.

Genomatix Software is a computational biology company headquartered in Munich, Germany, with a seat of business in Ann Arbor.

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NHGRI to Award $120M in Stimulus Funding Over FY '09, '10

The National Human Genome Research Institute plans to award a total of approximately $120 million in fiscal years 2009 and 2010 under the American Recovery and Reinvestment Act.

The institute plans to distribute approximately $60 million in each fiscal year but has not yet allocated specific amounts to the programs under which the awards will be made, according to Jeff Schloss, NHGRI's program director for technology development coordination.

NHGRI will award Recovery Act grants under a variety of programs, listed on its website here. A few additional funding opportunities will be added over the next few weeks, according to Schloss.

Under the Research and Research Infrastructure "Grand Opportunities," or "GO," grants program, NHGRI intends to commit $20 million in each of fiscal year 2009 and 2010 to fund up to 25 awards, according to the website.

Though applications under this program may address any aspect of the institute's mission, requests in a number of scientific areas that NHGRI deems of "particularly high interest" will receive priority.

These areas are enhancements to the ENCODE and modENCODE projects; the development and application of statistical and computational data analysis methods for DNA sequence, variation, GWAS, genomic function, chemical biology, and related genomic data sets; the development of a software pipeline for sequence data for quality checking, alignment, and variant calling; the development of a data analysis and coordination center for cancer genomics; sequencing technology development; and cellular responses to perturbations.

Letters of intent for the GO program are due April 27, and applications are due May 27.

Overall, the GO Grants will provide $200 million through a variety of NIH institutes.

NHGRI has also selected specific topics related to its mission for awards it plans to make under the NIH Challenge Grants in Health and Science Research program. NHGRI's "challenge topics" that list funding opportunities on its website include bioethics, enabling technologies, genomics, and health disparities.

The deadline for applying for NHGRI challenge grants is April 27.

In addition, NHGRI plans to provide supplementary funds to current grantees that "accelerate the tempo of scientific research on active grants and, at the same time, can promote job creation and retention."

Under the Administrative Supplements to NHGRI Grants and Cooperative Agreements program, the institute will give priority to requests that will help retain existing and create new jobs, and that will aid in "accelerating science" in a number of research areas, including data analysis methods, sequencing technology development; ENCODE/modENCODE; model organism database enhancement; population genomics collaborative programs; and ethical, legal, and social implications. The next round of applications for these supplements is due April 30.

Researchers may also submit "revision applications" — previously called "competitive supplements" — to support "a significant expansion of the scope or research protocol of approved and funded projects" under the Competitive Revision Applications for NHGRI Grants and Cooperative Agreements program. The application deadline for these grants is April 21.

Finally, NHGRI-funded researchers may apply for funding to support summer students and research by science educators under the Administrative Supplements for Providing Summer Research Experiences for Students and Science Educators. The next round of applications under that program is due April 30.

The Scan

Study Links Evolution of Longevity, Social Organization in Mammals

With the help of comparative phylogenetics and transcriptomics, researchers in Nature Communications see ties between lifespan and social organization in mammals.

Tumor Microenvironment Immune Score Provides Immunotherapy Response, Prognostic Insights

Using multiple in situ analyses and RNA sequence data, researchers in eBioMedicine have developed a score associated with immunotherapy response or survival.

CRISPR-Based Method for Finding Cancer-Associated Exosomal MicroRNAs in Blood

A team from China presents in ACS Sensors a liposome-mediated membrane fusion strategy for detecting miRNAs carried in exosomes in the blood with a CRISPR-mediated reporter system.

Drug Response Variants May Be Distinct in Somatic, Germline Samples

Based on variants from across 21 drug response genes, researchers in The Pharmacogenomics Journal suspect that tumor-only DNA sequences may miss drug response clues found in the germline.