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Roche, 454 Life Sciences, University of Western Australia, 23andMe, NIH, Qiagen, Epigenomics, Eurofins Medigenomix, MWG Biotech, Genome Canada, EMBL, Sigma-Aldrich, Beckman Coulter

Roche Closes Acquisition of 454
Roche has closed its acquisition of CuraGen subsidiary 454 Life Sciences in a cash and stock deal valued at as much as $155 million, 454 and CuraGen said this week.
454's 167 employees will remain at the company's facilities in Branford, Conn., and will operate under the Roche Diagnostics division as part of the Roche Applied Sciences business unit.
"Now that 454 Life Science is part of Roche, we are prepared to further strengthen our sequencing business and to provide cutting edge sequencing technology to the worldwide research community," said Manfred Baier, head of Roche Applied Sciences, in a statement.
454 President Christopher McLeod said the deal brings his company "added resources to the research and development and manufacturing activities ... both of which are expected to expand as we see increasing demand for our sequencing products and services."
Roche Diagnostics has been the sole worldwide distributor for 454's Genome Sequencer systems and reagents since 2005. 
Roche announced its plans to buy 454 for $140 million in cash and as much as $14.9 million in outstanding stock options in late March [In Sequence 04-03-07]. 

Cane Toad Sequencing Grant Represents First Aussie Genome Project
The Australian Research Council has awarded the University of Western Australia a three-year grant worth AUS$274,000 ($224,000) to sequence the genome of the Australian cane toad, an environmental pest in Australia that is considered among the world’s worst invader species.
According to a report in The Australian, the project represents the first genome sequencing project carried out in Australia.
"Even the wallaby and platypus genome programs are made in the US," Grant Morahan, principal investigator on the grant, told The Australian.
According to the award abstract, more than a billion cane toads currently infest Northern Australia, and they will soon invade Western Australia and are expected to move into New South Wales.
“Their poisons and voracious appetite could make many native mammals, birds and reptiles extinct,” the abstract states. “The only possibility to eradicate the toad is by biological control, but there is no known control agent.”
The researchers expect that the genome sequence will provide the toads “Achilles' heel, against which control agents can be developed.”
The Australian reported that Morahan and colleagues requested a AUS$1.2 million grant for the project, but received only AUS$274,000.
"We will try to cover the gap in funding somehow," Professor Morahan said.

23andMe Completes Series A Financing; Google Holds Minority Stake
23andMe, a startup that describes itself as a “personal genetics” company, has closed a Series A round of financing with investments from Google, Genentech, MDV-Mohr Davidow Ventures, and New Enterprise Associates. Genentech CEO Arthur Levinson is a Google director.
Terms of the financing were not disclosed.
23andMe said in a statement that it is focused on enabling individuals to “access, explore, and better understand their genetic information, making use of recent advances in DNA analysis technologies and proprietary web-based software tools.”
The company currently plans to launch at the end of the year and will provide more information at that time.
In an SEC document filed May 22, Google disclosed that it invested around $3.9 million in the firm and that it now holds a minority interest in the company as a result of this investment.
23andMe’s investors include Anne Wojcicki, who is married to Google founder Sergey Brin. Google noted in its SEC filing that its audit committee reviewed and approved the transaction “as part of Google’s procedures for entering into transactions with related parties.”
Mohr Davidow Ventures has also invested in Pacific Biosciences, a Menlo Park, Calif.-based company that is commercializing a new DNA sequencing platform based on zero-mode waveguide technology developed at Cornell University [see In Sequence 4/24/2007].
23andMe states on its website that its goal “is to connect you to the 23 paired volumes of your own genetic blueprint (plus your mitochondrial DNA), bringing you personal insight into ancestry, genealogy, and inherited traits.”
The company claims on its website that it is “building on recent advances in DNA analysis technologies to enable broad, secure, and private access to trustworthy and accurate individual genetic information.”

Researchers Sequence Genome of Bacteria Responsible for Botulinum Neurotoxin
A team of researchers from the UK and Canada has sequenced the genome of Clostridium botulinum, the bacteria that produces botulinum neurotoxin and the causative agent of botulism.
The researchers published the results of their analysis last week in Genome Research. The genome contains a chromosome with 3.9 million base pairs and 3,650 predicted genes and a plasmid with 16,344 base pairs and 19 predicted genes.
The C. botulinum genome includes many genes that encode proteases and enzymes involved in uptake and metabolism of amino acids — a not unexpected finding, given the fact that the organism obtains its nourishment from the decaying tissue of its host. “This pathogen relies on its toxin to rapidly kill a wide range of prey species, and to gain access to nutrient sources, it releases a large number of extracellular enzymes to soften and destroy rotting or decayed tissues,” the authors note in the paper.
The authors also note that they identified “a hitherto unknown ability of C. botulinum to degrade chitin,” as well as a lack of recently acquired DNA, which indicates stable genomic content.
Researchers from the Wellcome Trust Sanger Institute; the UK’s Institute of Food Research; the Institute of Infection, Immunity and Inflammation at the School of Molecular Medical Sciences at the University of Nottingham, the School of Life Sciences at Heriot-Watt University, and the Bureau of Microbial Hazards at Health Canada contributed to the project.

NIH Releases GAIN Study Data, Details Data-Access Procedure
The National Institutes of Health announced last week that it has released the first data from the Genetic Association Information Network, or GAIN, project, via the dbGAP database at the National Center for Biotechnology Information.
In a notice released on Friday, the NIH announced the availability of the data and outlined the process under which researchers can apply for access to GAIN project datasets.
GAIN is a public-private genome-wide association study project coordinated by the NIH and the Foundation for the NIH. FNIH awarded the first grants under the effort last October.
Last week, NIH released the data through GAIN dbGaP, the database of Genotype and Phenotype, which offers two levels of access: summary-level data that is available to anyone with no restrictions; and individual-level data that requires preauthorization.
Researchers can request access to the individual-level data from GAIN studies through the dbGaP data access request system. Further information about the process is available here.
Summary-level data is already available, and NIH said it expects to begin releasing individual-level data by June 9.

Qiagen, Epigenomics Expand DNA Sample-Prep Alliance to Include Molecular Dx
Qiagen said this week that it has licensed exclusive worldwide rights to Epigenomics' sample-handling technologies for applied testing and in vitro diagnostics as part of an expansion of an earlier alliance.
The companies inked an OEM agreement two years ago that gave Qiagen exclusive rights to Epigenomics' bisulfite DNA treatment technology and Methylight assay technology for research uses.
Under the new agreement, Qiagen will pay Epigenomics an up-front fee, milestone payments, and royalties, Qiagen said. Financial terms of the deal were not disclosed.
Epigenomics will retain the rights to its sample technologies in its own or partnered development projects and for commercializing diagnostics through a non-exclusive back-license from Qiagen.
Qiagen said the expansion follows the launch of the EpiTect Bisulfite kit, which uses Epigenomics' DNA-methylation technology and is for research use only. Based on the results of that program, Qiagen said the companies now plan to use DNA methylation to develop and sell a complete and validated IVD pre-analytical sample technology portfolio.
Qiagen CEO Peer Schatz said the companies expect DNA methylation technology to play an important role in the molecular diagnostics market, particularly in areas such as cancer screening.
Schatz said Qiagen's epigentic testing portfolio now includes "sample technologies such as DNA sample collection, stabilization, purification, and bisulfite conversion to assay technologies such as PCR- and sequencing-based methods for DNA methylation analysis."

Eurofins Medigenomix and MWG Biotech Use 454 GS 20 to Sequence E. coli Strain for Wacker Chemie
Eurofins Medigenomix and MWG Biotech said this week that they have sequenced the genome of a proprietary strain of Escherichia coli for industrial biotech firm Wacker Chemie.
The goal of the project was to enable Wacker Chemie to compare the genome of the proprietary K12 strain, used for protein synthesis, to that of its corresponding parental strain.
Eurofins Medigenomix and MWG Biotech used 454 Life Sciences’ GS 20 sequencer for the project. The data was analyzed with MWG’s genome-comparison tool and displayed with MWG’s Annotation Viewer software.

Canadian Government Pledges $32M for Population Genomics Consortium
The Canadian government and the government of Québec plan to pump CA$34.5 million ($31.9 million) into a human genomics consortium, government officials said last week.
The Public Population Project in Genomics, or P3G, could receive as much as CA$64.5 million when funds from other partners are counted, government ministers and the head of Genome Canada said at the Human Genome Organization’s annual meeting in Montreal last week.
The primary aim of the Montreal-based P3G consortium is to foster “collaboration between researchers and projects in the field of population genomics." The group also includes the ongoing CARTaGENE project, Genome Canada said.
One of the major projects will be the creation of a large biobank that will hold data from 20,000 residents of Québec between the ages of 40 and 69.
Claude Laberge, a population genomics expert at the Laval University in Québec City who is involved in CARTaGENE, said the infrastructure “will function as a precursor for the development and testing of standards for large biobanks.”

EMBL-Bank Turns 25
The world’s first public database for DNA and RNA sequencing has celebrated its 25th anniversary. On May 22, the European Molecular Biology Laboratory culminated over two decades of work as Europe’s primary nucleotide sequence resource.
EMBL-Bank is maintained by the European Bioinformatics Institute, in collaboration with its US and Japanese counterparts GenBank and the DNA Databank of Japan.
“The databases are now the primary record for high-throughput science,” EBI’s associate director, Graham Cameron, said in a statement. “We and our partners in Japan and the US are custodians of that record.”
EMBL-Bank currently hlods more than 97 million entries corresponding to 170 gigabases of sequence from more than 280,000 organisms.

Sigma-Aldrich Unit Licenses Beckman Coulter's Fast Deprotection Chemistry
SAFC, a Sigma-Aldrich unit, last week said that one of its businesses has licensed Beckman Coulter’s fast deprotection chemistry.
The license covers Beckman’s acetyl-protected cytidine DNA- and 2'-O-methyl phosphoramidites for the synthesis of oligonucleotides, according to SAFC, whose Supply Solutions business attained the IP.
Through the deal, SAFC becomes the first company to license the “full range” of these phosphoramidites, which the company will produce at its Proligo Reagents ISO 9001-certified manufacturing facility in Hamburg, Germany.

It also expands SAFC's oligo synthesis reagents product offerings in the sector. 

The Scan

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

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.