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ASM Report Calls for Large-Scale Microbial Sequencing Effort to Help Define Concept of ‘Species’ in the Genomic Age
A new report from the American Society for Microbiology recommends that the international microbial research community “coordinate an initiative to construct draft genome sequences of each of the roughly 6,500 type strains catalogued by the International Committee on the Systematics of Prokaryotes,” as part of a broader effort to reconsider the way microbial species are categorized.  
The report, Reconciling Microbial Systematics and Genomics, is available here. It was compiled by the ASM’s American Academy of Microbiology and is the result of a colloquium on the subject that was held in September 2006. 
"It is clear that the current system for designating microbial species is somewhat functional, but inadequate in many ways,” said Richard Roberts of New England Biolabs, one of the authors of the report, in a statement. “It is unclear whether this system should be replaced or renovated.”
Microbial taxonomists have traditionally categorized microorganisms by their physical characteristics, but the rise of genomic sequencing has “fundamentally changed” scientists’ understanding of the relationships between different microorganisms, according to the ASM.
Other recommendations include the establishment of a subcommittee within the ICSP to consider “a paradigm shift in the species definition,” as well as a more thorough study of the mechanisms of speciation “before a meaningful and practical species theory can be developed.”

NRC Recommends Global Metagenomics Initiative, Proposes Steps to Help Discipline Grow
The National Research Council wants a global effort, similar to but larger than the Human Genome Project, to push the metagenomics field into the international scientific spotlight.
Metagenomics will contribute to the fields of medicine, agriculture, energy, and environmental management, the NRC’s Committee on Metagenomics said in a report released last week.
But the fledgling science needs nurturing in the form of big-picture thinking and large-scale support, the committee recommended in its report, entitled “The New Science of Metagenomics: Revealing the Secrets of our Microbial Planet.”  
The committee, which comprises senior researchers and directors from major US universities and institutes, made a number of recommendations to the field at large, including the need for a “Global Metagenomics Initiative.”
This initiative would include small-, mid- and large-scale projects. An interagency group should ensure free and open communications concerning metagenomics portfolios and bring researchers together through meetings and workshops, the committee suggests.
Metagenomics training programs should be patterned on the Cold Spring Harbor or Marine Biological Laboratories, which offer postdoctoral programs and summer courses that train researchers in metagenomics tools and principles, the committee said.
The group also advised funding agencies to develop mechanisms to identify widely used analytical tools and develop them to “robust standards.”
The report can be purchased or reviewed here.

NIH Neuroscience Array Consortium Installs Affy and Illumina Genotyping Tools
A National Institutes of Health-led group of research facilities has installed Illumina and Affymetrix genotyping technologies to support collaborative neuroscience whole-genome association studies.
The group, the Neuroscience Microarray Consortium, has centers at the Translational Genomics Research Institute; the University of California, Los Angeles; Duke University; and Yale University.
NMC chairman and TGen Neurogenomics Director Dietrich Stephan told In Sequence’s sister publication GenomeWeb Daily News that the NMC is working with roughly $25 million in NIH funding. He said the group bought an Illumina BeadLab 1000 in late 2006, which is “up and running” at Yale, and that TGen’s lab in Phoenix is running an Affy Human Mapping 500K Array Set.
As many as 10,000 researchers will have access to the hardware for whole-genome studies, particularly researchers studying genes linked to neurological disorders.
The consortium member institutions each offer different services, the NMC said: TGen offers expression profiling and SNP-genotyping using Affy’s Gene Chips; Yale offers genotyping using both Affy and Illumina services; UCLA uses the Affy platform; and Duke contributes laser capture microdissection services.

UK Biotech Agency Contributes $74M to EU Systems Bio Initiatives
A group of European countries is launching a new initiative to fund projects that apply systems biology principles to the study of single-cell animals, a UK research group said last week.
The UK’s Biotechnology and Biological Sciences Research Council contributed ₤37.4 million ($74 million) to the projects, collectively called the Systems Biology of Microorganisms Program.
BBSRC said it will work with German and Dutch scientists to study the Clostridium acetobutylicum bacterium, which is used in the production of butanol, a potential biofuel.
The group said this bacterium also causes hospital infections, and suggested the research may offer knowledge that could be useful in combating those as well.
Another study looks into extremophiles to try to learn more about how temperature affects the biological pathways inside these organisms.
Another project would study why small genetic differences cause “stark and important differences in species,” and would look in particular at Lactococcus lactis, Enterococcus faecalis, and Streptococcus pyogenes.
Other countries involved in the project besides the UK include Spain, Norway, Germany, Austria, the Netherlands, France, the Czech Republic, and Switzerland.

NHGRI to Grant $8.5M for Phenotype, Exposure Measures for Genome-Wide Association Studies
The National Human Genome Research Institute said last week that it will grant $8.5 million for a public health study to identify, develop, and disseminate “readily standardized and implemented phenotypic and environmental exposure measures” to be used with ongoing genome-wide association studies.
The NHGRI said the study should define 15 to 20 high-priority phenotypic and exposure domains such as cancer, pulmonary disease, and others. Investigators should identify standardized measures that are available or are in development; recommend 10 to 15 high priorities for inclusion in genome-wide association studies; and disseminate recommendations to related research communities.
The investigator would develop a “basic tool set” to assess phenotypic and environmental exposure that could be applied to ongoing or future genome-wide association studies and other large-scale genomic research.
Measurement tools could include assays based on stored biospecimens. The study also could identify measures to be drawn from large-scale prospective gene cohorts or from ongoing biorepositories.
Applications for funding must be received by May 17. Additional information can be found here.

University of Washington Hires OpenHelix to Run Informatics Training Courses
The University of Washington said last week that it has hired OpenHelix to provide training programs for its SeattleSNPs tool and Genome Variation Server.
SeattleSNPs is used to identify and genotype the associations between SNPs and genes and pathways linked to human inflammatory responses.
The GVS is a repository of dbSNP and HapMap databases that allows users to upload their own data for analysis and visualization.
The program will offer online training, tutorials, exercises, and presentation materials, the university said.
Financial terms of the agreement were not disclosed.

The Scan

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.

Analysis of Endogenous Parvoviral Elements Found Within Animal Genomes

Researchers at PLOS Biology have examined the coevolution of endogenous parvoviral elements and animal genomes to gain insight into using the viruses as gene therapy vectors.

Saliva Testing Can Reveal Mosaic CNVs Important in Intellectual Disability

An Australian team has compared the yield of chromosomal microarray testing of both blood and saliva samples for syndromic intellectual disability in the European Journal of Human Genetics.

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.