First Papers on Solexa-Based ChIP-Seq Analysis Are Published in Science, Cell, and Nature Methods
Three studies based on sequence data from Illumina’s Genome Analyzer have been published over the last few weeks — the first peer-reviewed studies based on Solexa sequencing to appear in the literature.
This week, researchers from the British Columbia Cancer Agency’s Genome Sciences Center and Yale University published a paper in the June 11 issue of Nature Methods describing an approach called ChIP-Seq that combines chromatin immunoprecipitation with Solexa sequencing to identify mammalian DNA sequences bound by transcription factors (see In Sequence 5/15/2007).
The paper, “Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing,” compared ChIP-Seq with ChIP-PCR and ChIP-chip for four chromosomes and found that the approach performs as well as traditional ChIP analysis in terms of sensitivity and specificity, but offers several advantages over those platforms, including lower cost, need for less input material, and the capacity for whole-genome analysis.
That paper followed two other ChIP-Seq studies published in the June 8 issue of Science and the May 18 issue of Cell.
As previously reported by In Sequence, the papers, published by researchers at Stanford University and the National Heart, Lung, and Blood Institute, respectively, describe the use of the ChIP-Seq approach to scan the whole genome for DNA-binding sites of certain proteins (See In Sequence 05-01-07 and 05-29-07).
"Our ChIP-Seq study took advantage of the Genome Analyzer's ability to generate tens of millions of sequence reads per run," said Richard Myers, professor and chair of genetics at Stanford University School of Medicine and a co-author on the Science publication, in a statement last week. "This allowed us to turn ChIP into a simple counting assay, in which one sequence read per molecule of DNA was mapped from the sample back onto the reference genome across millions of molecules per sample.”
Myers added that “the amount and nature of these data meant we got exceptional positional resolution and statistical confidence."
According to the Cell paper, the NHLBI researchers "demonstrated that direct sequencing of ChIP DNA using the Illumina Genome Analyzer is an efficient method for mapping genome-wide distributions of histone modifications and chromatin protein targets."
Broad Expects to Receive ABI SOLiD Under Early-Access Program
The Broad Institute has confirmed that it expects to receive a SOLiD sequencing system under Applied Biosystems’ newly launched early-access program soon.
Chad Nusbaum, co-director of the genome sequencing and analysis program at the Broad Institute, told In Sequence via e-mail last week that the institute is planning to receive a SOLiD system, “hopefully this month.”
ABI kicked off its early-access program last week by shipping its first SOLiD system to Stanford University. Agencourt Bioscience also expects to receive an instrument shortly, along with the Joint Genome Institute, Washington University, Baylor College of Medicine, the Genome Institute of Singapore, and the University of Kiel in Germany (see In Sequence 06-05-07).
ABI said last week that it is developing applications for the SOLiD system with a number of research institutions, including the Broad Institute, but did not confirm that any of these groups would also receive an instrument.
Yale Receives $1M for Sequencing Equipment Under NCRR High-End Instrumentation Program
Yale University has received $1,054,868 to purchase “cutting-edge DNA sequencing/genotyping technologies” under the National Center for Research Resources’ High-End Instrumentation grants program, NCRR said this week.
The Yale grant is one of 14 awards totaling $20.65 million that NCRR announced under the program this week.
NCRR did not provide details of the specific sequencing technology that Yale will purchase with the funding, but noted that the university intends to use the system, which “can sequence DNA more quickly and economically than current instruments,” for research in epilepsy, psychiatric disorders, autism, cardiovascular disorders, and cancer.
The NCRR HEI awards are one-time grants to support the purchase of “sophisticated instruments costing more than $750,000,” NCRR said.
In order to qualify for a HEI award, institutions must identify three or more NIH-funded investigators whose research requires the requested instrument.
Further information on the program is available here.
JGI Adds Eucalyptus, Foxtail Millet, Red Algae, and Microbe Communities to 2008 Sequencing Agenda; 454 Sequencing to Help with Eukaryote Projects
The Department of Energy’s Joint Genome Institute last week announced the organisms that it plans to sequence in fiscal 2008 under its Community Sequencing Program.
Most of the plant and microbial targets in the program are geared toward reducing the nation's dependence on fossil fuel, JGI said.
The largest target is the eucalyptus tree, which has a genome of around 600 million nucleotides, and applications in biomass production and carbon sequestration. This sequencing project is led by Alexander Myburg of the University of Pretoria, South Africa, with Gerald Tuskan of the DOE’s Oak Ridge National Laboratory and Dario Grattapaglia of Brazil’s EMBRAPA Genetic Resources and Biotechnology.
The eucalyptus genome would be the second tree to be sequenced, which is expected to provide opportunities for comparative genomic analysis with the poplar, the first tree to be sequenced.
JGI has also selected foxtail millet (Setaria italica), a forage crop that is a relative of prospective biofuel crops such as switchgrass, napiergrass, and pearl millet. This project is led by researchers at the University of Georgia, the University of Florida, the University of Missouri, the US Department of Agriculture’s Agricultural Research Service, Cold Spring Harbor Laboratory, and the University of Tennessee.
The third largest genome project for 2008 is the marine red alga Porphyra purpurea, a photosynthetic organism that helps remove carbon dioxide from the atmosphere. Porphyra species are among the most common algae in the intertidal and subtidal zones of temperate rocky shores in both the northern and southern hemispheres.
JGI will also conduct eight smaller eukaryotic projects in 2008 “using both traditional Sanger sequencing and next-generation pyrosequencing technology.” These projects include the fungus Paxillus involutus, two species of Phaeocystis phytoplankton, the leaf-degrading fungus Agaricus bisporus, the ciliated protozoan Tetrahymena thermophila, the soybean pathogen Heterodera glycines, and the liverwort Marchantia polymorpha. They also include a pine and conifer EST resource.
JGI will also collaborate on four metagenomic projects during 2008: Anammox, or anaerobic ammonium oxidation bacteria, which live in the ocean and are able to synthesize the rocket fuel hydrazine from ammonia and hydroxylamine; a biogas-degrading community; a population of Accumulibacter, and the Yellowstone geothermal environment.
Further details on the JGI’s CSP 2008 sequencing projects are available here.
NIH Aims to Pump $30M Into Roadmap Update; Human Microbiome Project Approved
The National Institutes of Health plans to pump $30 million into its Roadmap initiative in fiscal 2008 as part of an effort to advance and assess several new ‘omics areas, the institute said last week.
While the NIH has not asked for more money to fund the new programs, it said the Roadmap update was outlined in its 2008 budget, although it was not ready to list specific programs when the budget was drafted.
The NIH also has not determined how it plans to break down the $30 million for these projects, according to NIH public affairs specialist Joseph Balintfy.
New initiatives that will or could be conducted under the updated Roadmap include metagenomics, epigenetics, protein capture, proteome tools, and phenotypic tools. Coordination groups will also consider drafting new efforts in pharmacogenomics, bioinformatics, and regenerative medicine, Balintfy said in an e-mail to GenomeWeb Daily News, In Sequence’s sister publication.
The upcoming initiatives are the product of a call the NIH put out in 2006 for new ideas from intramural and extramural researchers, patient advocates, and the general public.
According to the Office of Portfolio Analysis and Strategic Initiatives, which oversees the Roadmap, the update will include four Major Roadmap Initiatives, one pilot study, and three coordination groups.
Major new roadmap initiatives that have been approved for funding include a Human Microbiome Project to characterize microbial content in the human body; an epigenetics and epigenomics study that measures changes in gene expression and gene function; and a pilot study for a genetic connectivity map that could help demonstrate linkages between diseases, drug candidates, and genetic manipulation, according to the NIH.
This summer the NIH will consider funding studies of protein capture and proteomics tools that would try to make high-quality probes that are specific to those in humans and in some animal models.
The NIH will also review a proposal for a human phenotype initiative to develop tools and services that could be used to catalogue human phenotypes in relation to various complex diseases and disorders.
Balintfy also said that the NIH recently highlighted three areas “needing greater coordination across the NIH” that could see funds under the update, including pharmacogenomics, bioinformatics, and regenerative medicine.
— Matt Jones, a GenomeWeb News reporter
Bielefeld University to Host Next-Gen Sequencing Conference
The Center for Biotechnology of Bielefeld University in Germany will host a symposium, "The Future of Genome Research in the Light of Ultrafast Sequencing Technologies," July 4-6 at Bielefeld University’s Center for Interdisciplinary Research.
The German Genome Research Network "Functional Genome Research on Bacteria Relevant for Agriculture, Environment and Biotechnology" is co-organizing the conference, which aims to “present a survey of next generation sequencing technologies as well as the application of these novel technologies in the various fields of genome research.”
Topics to be addressed include next-generation technologies, bioinformatics, bacterial genomics, metagenomics, plant genomics, and animal and human genomics.
Further information is available here.
Sigma-Aldrich Gains Rights to Epigenetic Technologies from Epigentek Group
Sigma-Aldrich said this week that it has signed a licensing agreement with Epigentek Group for DNA modification, methylation quantitation, and protein/DNA interaction technologies that it will commercialize for the epigenetics research market.
Under the agreement, Sigma-Aldrich gained exclusive rights in the US and co-exclusive rights globally to market Epigentek’s technologies.
Sigma-Aldrich said it plans to launch several products for epigenetic research, beginning with the Imprint DNA Modification Kit, which will hit the market this month. Other products launching under the Imprint brand include kits for global methylation quantitation and chromatin immunoprecipitation based on Epigentek's technologies.
Sorenson Genomics Buys DNA-Testing Company Identigene
DNA-testing company Sorenson Genomics said this week that it has acquired Identigene, a forensic and paternity DNA-services shop, for an undisclosed amount.
Sorenson COO Douglas Fogg said the deal will benefit both the forensics and relatedness DNA-testing industries. Sorenson serves the same markets as Identigene through its Relative Genetics and Sorenson Forensics division.
Salt Lake City-based Sorenson said Identigene will retain its name and will remain based at its current facilities in Houston.
Acacia Acquires Rights to IP for Purifying Nucleic Acids
Acacia Research said last week that its wholly owned subsidiary Acacia Patent Acquisition Corporation has acquired rights to patents relating to purifying nucleic acids.
The patents “relate to methods and equipment used to purify plasmid DNA products,” Acacia said, noting that the technology is applicable to manufacturing pharmaceutical-quality nucleic acids for DNA-vaccines and gene therapies.
The company did not disclose the licensor of the IP or other details of the transaction.