Illumina, ABI Sequencers Record Double-Digit GB Runs; Illumina Sequences Three HapMap Samples
Illumina said this week that as part of an internal sequencing project, it has obtained 10 gigabases of high-quality sequence data with 50-base paired-end reads from a single run on its Genome Analyzer, which contains a single flow cell.
The company added that internally it is generating runs of nearly 15 gigabases of data per run.
The news comes less than two weeks after Applied Biosystems said during a conference presentation in San Diego that it has internally generated 15 gigabases of data from a single paired-end run on its SOLiD system, which runs two flow cells.
Illumina said it has been sequencing the genomes of three related anonymous African Yoruban HapMap samples in-house. In February, it reported data from the first project, that of an adult man, at a conference, along with ABI, which sequenced the same sample with its SOLiD technology (see In Sequence 2/26/2008).
Last month, Illumina started sequencing the other two samples, a mother and her child, and has generated an average of 14 fold coverage, or 45 gigabases of data, for each of them. Systems improvements of the Genome Analyzer enabled company scientists to obtain 7.5 gigabases of high-quality data from a single run, but software improvements, which Illumina said will become commercially available this summer, increased the data output from the same runs to 10 gigabases per run.
Company researchers used short-insert and long-insert paired-end reads with each read at least 50 base pairs in length. Some runs generated reads of up to 75 base pairs from each end of a fragment, Illumina noted.
“We are now internally generating runs of nearly 15GB of data. Furthermore, we have active programs, which will further increase the read length, the throughput per day, and the quality of the data generated by the Genome Analyzer,” Christian Henry, acting general manager of Illumina’s sequencing business, said in a statement.
“We expect that the combination of these improvements will enable our customers to achieve this level of high-quality data on a single flowcell later this year,” he said. “These improvements, which rely solely on chemistry and software developments, can be readily implemented on the existing Genome Analyzer platform.”
Illumina has submitted the sequence data for the first HapMap sample to the National Center for Biotechnology Information database and plans to submit the data for the other two samples in the future.
Illumina, Genpathway to Offer ChIP-Sequencing and -Analysis Service
Illumina and Genpathway are planning to offer whole-genome chromatin immunoprecipitation-sequencing and -analysis services, Illumina said last week.
Under the partnership, Genpathway will prepare samples using its FactorPath ChIP assays and will provide the data analysis using its software. Illumina will sequence the samples on its Genome Analyzer.
The combined services include cell or tissue processing, antibody selection and qualification, ChIP DNA amplification, ChIP sequencing, and data analysis, Illumina said.
Because ChIP sequencing is “a notoriously time-consuming and difficult procedure,” the partnership will offer scientists “a faster path to discovery,”Genpathway CSO Mary Harper said in a statement.
Genome Canada Awards $9.24M; Several Projects Involve Sequencing
Genome Canada said this week that it will provide CDN$9.37 million (US$9.24 million) to 13 projects in the Genome Canada Technology Development Competition.
The competition received 51 proposals for genomics and proteomics projects from across Canada. Genome Canada, which receives funding from the Canadian government and international partners, said the winners received an additional CDN$9.63 million in co-funding from Canadian and international partners.
At least three Genome Canada-funded projects appear to be sequencing-related: Marco Marra, Steven Jones, and Rob Holt from the BC Cancer Agency in Vancouver, received CDN$956,260 for production-scale deployment of next-generation sequencing instruments; Marra and colleague Carl Hansen received CDN$912,139 for working towards single-cell genomics; and Paul Hebert at the Biodiversity Institute of Ontario in Guelph received CDN$800,000 for environmental barcoding through massively-parallelized sequencing.
The projects will begin this spring and run for two years, Genome Canada said. A full list of the grant winners can be found here.
ABI Declares $.0425 Per-Share Dividend in Q3
Applera this week declared a quarterly dividend of $.0425 per share for Applied Biosystems common stock.
The company said the dividend is payable on July 1 to stockholders of record as of the close of business on June 2.
Late last month, ABI reported a four-percent rise in revenues and an increase in net income of almost ten percent for its fiscal third quarter of 2008.
Applera Corporation Declares Dividend
State Street Takes 5.1-Percent Stake in Applied Biosystems
Boston-based State Street Bank and Trust has acquired a 5.1-percent stake in Applied Biosystems, the bank disclosed in a filing with the US Securities and Exchange Commission this week.
According to the filing, State Street owns 8,590,589 shares of ABI stock and these shares “were acquired in the ordinary course of business and were not acquired for the purpose of and do not have the effect of changing or influencing the control of the issuer.”
Last week, investment firm SAC Capital Advisors disclosed in an SEC filing that it had increased its stake in ABI to 5.1 percent and encouraged ABI’s board of directors to explore strategic alternatives for the firm, including a possible sale (see In Sequence 4/29/2008).
Ambry Genetics Buys Illumina Genome Analzyer
Ambry Genetics said last week that it has purchased a Genome Analyzer from Illumina, which it will use to perform pharmacogenomics services for customers.
The Aliso Viejo, Calif.-based genetic-testing firm said that it has already begun running research samples on the GA with its new probe-capture technology.
“To date we’ve run assays with hundreds of genes on the probe-capture technology; with new bioinformatics software, SNP annotation and exon identification, we’ve been able to find many novel mutations,” Ambry CEO Charles Dunlop said in a statement. “We are now expanding the types of candidate gene lists we’re assaying to suit various research interests.”
JGI-Led Team Sequences Biomass-Degrading Fungus
A team of researchers led by the US Department of Energy’s Joint Genome Institute has sequenced Trichoderma reesei, a biomass-degrading fungus.
The researchers sequenced the 34-megabase genome of T. reesei and compared it with 13 previously characterized fungi. They published their results online in Nature Biotechnology this week.
In World War II, the fungus was responsible for deteriorating military fatigues and tents in the South Pacific. Variants of the fungus are used in industry today as an enzyme source, particularly of cellulases and hemicellulases. It is also being explored for breaking down plant cell walls as a first step towards biofuel production from lignocellulose.
One of their findings was that T. reesei has fewer enzyme types than other fungi. “We were aware of T. reesei’s reputation as a producer of massive quantities of degrading enzymes, however we were surprised by how few enzyme types it produces, which suggested to us that its protein secretion system is exceptionally efficient,” lead author Diego Martinez said in a statement.
The research “is a major step towards using renewable feedstocks for the production of fuels and chemicals,” said study collaborator Joel Cherry, director of research activities in second-generation biofuels for Novozymes.
US House Passes Genetic Anti-Discrimination Bill
The US House of Representatives last week passed the Genetic Information Nondiscrimination Act by a vote of 414 to 1. The Senate approved the measure one week earlier.
The bill is the closest it has ever come to being signed into law after being considered in various iterations by both chambers of Congress over the past decade. GINA, which would protect Americans from discrimination based on information from genetic tests, had previously passed in the House twice before — most recently last year, when the vote was 420 to 3 in favor of its passage.
"With the long-awaited federal passage of GINA, researchers and clinicians can now actively encourage Americans to participate in clinical trials without the fear of genetic discrimination," Joann Boughman, executive vice president of the American Society of Human Genetics, said in a statement. "Furthermore, under the federal protection provided by GINA, health care practitioners will be able to recommend appropriate genetic testing and screening procedures unencumbered by the fear of discrimination based upon the results."
The lone congressman voting against the bill was Representative and Republican Party candidate for president Ron Paul (R – Tex.). Congressman Paul’s office was not available at deadline for comment.
As reported last month by In Sequence sister publication, GenomeWeb Daily News, the US Senate unanimously passed the bill after senators agreed to compromises that had held up the bill since last summer.
The legislation prohibits insurance companies from using an individual’s genetic profile from assigning adverse coverage or making unfair pricing decisions. It also bars employers from making adverse employment decisions based on genetic data. In addition, the bill prohibits insurers and employers from requesting or demanding a genetic test.
"By prohibiting the improper use of genetic information, Americans will be encouraged to take advantage of the tremendous life altering potential of genetic research," Representative Louise Slaughter (D – NY) said in a statement last week.
Slaughter wrote the House version of the bill and championed it for over a decade. She has a bachelor’s degree in microbiology and a master’s degree in public health.
Senator Edward Kennedy (D – Mass.), who co-sponsored the Senate bill and who helped to work out the compromises that gave the bill new life last week, said the legislation "paves the way for every American to benefit from the vast potential of this new age of genetic information."
Kennedy also said he hopes President George W. Bush "will sign it immediately and open the door to a new era of medical progress."
The White house has said in several policy statements in recent years that it supports a bill barring discrimination based on genetic information, and an aide for Senator Tom Coburn (R – Okla.) told GenomeWeb Daily News that the president’s earlier concerns about the bill have been addressed in this draft and that GINA is now a done deal.
Oklahoma Medical Research Foundation Licenses Software from DNAStar
The Oklahoma Medical Research Foundation has licensed Lasergene sequence-analysis software from DNAStar.
Under the four-year site license agreement, Lasergene will be available to an unlimited number of users at the foundation, which is located in Oklahoma City.
Lasergene is a desktop software that allows researchers to analyze sequence data generated by conventional Sanger sequencing as well as by new high-throughput sequencing systems from samples ranging from small plasmids up to large bacterial genomes.
Transgenomic, NCI to Characterize Mitochondrial Genomes in Cancer Cell Lines
The National Cancer Institute has approved a proposal by the genetic-analysis and -services company Transgenomic to sequence and analyze mutations in mitochondrial genes found in the NCI 60 panel of cancer cell lines, the company said last week.
The collaboration is expected to be the first comprehensive evaluation of the mitochondrial genome in this cell panel, which has been used to test compounds in NCI’s pharmacological database.
Omaha, Neb.-based Transgenomic said the work may provide clues about early disease states and insights into some cancer treatments and diagnostics, since mitochondrial damage can be an early warning sign for some types of cancer.
“This collaboration makes it possible to test whether in vitro responses to anti-cancer agents are linked to alterations in the mitochondrial genome and can be detected with our sensitive mutation detection technology,” Transgenomic Chief Scientific Officer Eric Kaldjian said in a statement.
Qiagen Licenses BioHelix's Amplification Technology
Qiagen said last week it has obtained a non-exclusive, worldwide license to use BioHelix’s Helicase Dependent Amplification technology, which can detect and analyze target molecules such as DNA and RNA.
Unlike PCR amplification, HDA is isothermal, which Qiagen said eliminates the need for some expensive hardware. It also is compatible with qualitative and quantitative fluorescent detection technologies and with instrumentation that is designed for use with real-time PCR.
In addition, Qiagen said the HDA technology is compatible with its Hybrid Capture detection platforms, which includes an instrument used in the company’s tests for human papillomavirus, Chlamydia trachomatis, and Neisseria gonorrhoeae.
The HAD technology also could be used to develop simple and portable DNA point-of-care diagnostic devices, Qiagen said.
“The ability to amplify DNA or RNA using an isothermal amplification system opens up a wide field of new assays in many areas, in particular in human molecular diagnostics and applied testing,” Jim Godsey, senior VP of R&D in North America for Qiagen, said in a statement.
Metagenomic Study Shows Great Diversity Among Acquatic Methane-Oxidizing Microorganisms
A metagenomic study that used 454’s sequencing technology has uncovered new physical associations between species of deep-sea microorganisms in methane vents, information that could help scientists unravel the functional interactions between these bugs.
Researchers from the California Institute of Technology used a so-called “magneto-FISH” strategy, which combines fluorescence in situ hybridization with immunomagnetic cell capture, to pull out groups of bacteria associated with anaerobic methane-oxidizing archaea — single-celled prokaryotes that oxidize methane in the absence of oxygen.
The results, appearing this week in the Proceedings of the National Academy of Sciences, suggest that the relationships between these sediment archaea and bacteria are much more diverse than previously recognized. They also provide insights into nutrient cycling in these deep-sea sediment communities.
“There were groups we didn’t expect,” Caltech geobiologist Victoria Orphan, senior author on the paper, told In Sequence sister publication GenomeWeb Daily News. “It suggests that there’s a bit more versatility in this syntrophy than previously realized.”
Orphan said anaerobic metabolism, decaying organic matter, and geothermal sources can produce ocean methane, which could potentially end up as greenhouse gas in the atmosphere. Roughly 80 percent of this methane is sequestered deep in the ocean by methane-oxidizing microorganisms.
Orphan and her colleagues are studying a group of these microorganisms, called anaerobic methane-oxidizing archaea, or ANME, which do “the lion’s share of methane oxidation in marine environments.” So far, all of the members of this group remain uncultured and are recognized only genetically — in particular, by 16S rRNA sequences.
After collecting the organisms, the researchers analyzed them by metagenomic sequencing using 454’s sequencing technology, and by PCR and microscopy approaches. Through these analyses, Orphan and her colleagues found a surprisingly diverse group of bacteria interacting with the ANME-2c methane-oxidizing archaea.
For instance, sequencing revealed many reads associated with the sulfate-reducing bacteria Deltaproteobacteria, including one new sulfate-reducing Deltoproteobacterium species, and Methanomicrobiales. The researchers also detected a Betaproteobacterium species that wasn’t previously known to reduce sulfate.
— By Andrea Anderson; originally published on GenomeWeb Daily News
CLC Bio to Integrate Software with Microsoft Platform
CLC bio will integrate its bioinformatics software with Microsoft technologies under the auspices of the Bio-IT Alliance, CLC said last week.
So far, CLC bio has added support for a Microsoft SQL Server to its database solution, CLC Bioinformatics Database. In addition, its high-performance computing solution, CLC Bioinformatics Cell, supports Microsoft’s high-performance computing solutions, Windows Compute Cluster Server 2003, and Windows HPC Server 2008.
Jan Lomholdt, a CLC bio vice president, told In Sequence sister publication BioInform that the company’s software is also integrated with Microsoft’s Office tools, such as PowerPoint and Excel, and that integration with SharePoint is “in the works.”