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CLC Bio, Inqaba Biotec, Geospiza, Isilon Systems, Monosiga brevicollis, Electrophorus electricus, Agilent Technologies, Cold Spring Harbor Laboratory

CLC Bio Tests Next-Gen Sequencing Software In Collaboration with Inqaba
Bioinformatics company CLC Bio of Aarhus, Denmark, said last week that it will test its next-generation sequencing analysis software in a research collaboration on tuberculosis with Inqaba Biotechnical Industries of Pretoria, South Africa.
The goal of the study, the South African Mycobacterium tuberculosis genome sequencing project, is to find genetic differences between drug sensitive, extreme drug-resistant, and multi-drug-resistant strains that Inqaba is sequencing on its 454 GS FLX system.
To analyze the data, Inqaba Biotec will use CLC’s Genomics Workbench, software analysis tools the company plans to release this spring that will support several next generation sequencing platforms (see In Sequence 1/29/2008).
“The large amount of genomic data Inqaba Biotec produces offers us an exciting opportunity to test and fine-tune our algorithms on real and challenging data,” said CLC Bio Senior Scientific Officer Roald Forsberg in a company statement.
The project is funded by BioPAD, a biotechnology investment trust financed by the Department of Science and Technology of South Africa. The consortium includes the Chris Hani Baragwanath business unit of the National Health Laboratory Services, the Respiratory and Meningeal Pathogens Research Unit at the University of Witwatersrand, and Inqaba Biotec.

Geospiza Signs OEM Agreement to Include Isilon Storage System with FinchLab Next Gen Edition
Geospiza said last week that it has signed an original manufacturer equipment agreement with Isilon Systems to integrate Isilon’s clustered storage technology with Geospiza’s upcoming FinchLab laboratory information management system for managing data from next-generation sequencers.
The combined solution, which will include Isilon’s X-Series storage system as part of the FinchLab Next Gene Edition, will be available in April, Geospiza CEO Todd Smith told GenomeWeb Daily News, In Sequence’s sister publication, last week.
The combined system will come with an initial storage capacity of 7 terabytes, and is expected to scale to more than a petabyte.
Smith said that Geospiza is finding that most customers who are thinking about getting a next-generation sequencer plan on buying around 10 terabytes of storage. “After a year,” he said, “they’re thinking about 100 terabytes.”
Smith said that the first version of Finch Next Gen Edition will include data-management capabilities, as well as the ability to track samples and ordering. An upgrade for the system, called Phase 2, will be available in the fall and will include additional capabilities for data analysis, he said.
— Article from GenomeWeb Daily News by Bernadette Toner

Unicellular Genome Provides Clues to Multicellular Evolution
An international research team looking for the molecular mechanisms behind multicellular animal evolution has sequenced and analyzed the genome of a single-celled organism, Monosiga brevicollis, which has interesting similarities to animal genomes.
The scientists published their analysis online in Nature last week.
M. brevicollis, a unicellular organism living in marine environments, belongs to the choanoflagellates. Although these creatures live independently, they’re uncannily similar to the feeding cells, called choanocytes, that some sponges use to nab food. These cells line the inside wall of some sponges, beating their flagella to move water and food through the organism. Consequently, choanoflagellates have long been presumed to be animals’ closest living unicellular relative.
Previous nuclear and mitochondrial analyses and comparative genomics also have provided intriguing links between choanoflagellates and multicellular animals, suggesting the organisms preceded the metazoans.
Using approximately 8.5-fold, paired-end whole-genome shotgun sequencing, the scientists sequenced M. brevicollis and assembled the genome using the JAZZ assembler. They predicted and annotated M. brevicollis genes using the Joint Genome Annotation Pipeline and aligned 473 conserved M. brevicollis genes with similar eukaryotic genes, identifying nearly 2,000 intron splice sites.
The number of intron-containing genes was unexpectedly high, given the organism and the size of its genome, roughly 41.6 megabases coding for about 9,200 genes.
— Abridged version of an article from GenomeWeb Daily News by Andrea Anderson

Scientists Push for Electric Eel Genome Research
Six American researchers wrote a review, published this month in the Journal of Fish Biology, calling for seven- to 11-fold shotgun sequencing of the genome of the electric eel, Electrophorus electricus.
“[H]arnessing the full potential of bioelectrogenesis will require a complete understanding of mechanisms underlying the development, regulation, and modulation of electrogenic cells,” the authors wrote. “The availability of genomic sequences in electric fish will enable real progress on the development of new technologies to use electricity in medicine, agriculture, and other aspects of applied research.”
Another advantage, the authors noted, is the eel’s ability to regenerate some tissues and organs — including its spinal chord — after injury. Peeking into the eel’s genome may explain this, as well as its complex evolution and neurophysiology.
Although an electric eel genome project plan was developed several years ago but ultimately rejected by the Department of Energy’s Joint Genome Institute, the scientists are confident that the advent of more affordable and available high-throughput DNA sequencing will eventually help make the project a reality.

Agilent to Provide Oligo Libraries to CSHL for shRNA Library Generation
Agilent Technologies said last week that it has signed an agreement to provide oligonucleotide libraries to Greg Hannon’s lab at Cold Spring Harbor Laboratory for use in further developing small-hairpin RNA interference libraries.
Hannon, along with Stephen Elledge at Harvard Medical School, had previously developed shRNA libraries against all genes in the human and mouse genomes. Agilent is capable of synthesizing as many as 55,000 oligos per library, each oligo up to 200 base pairs in length.
Agilent is providing the same oligo libraries to early-access customers who are using them to capture portions of the genome prior to next-generation sequencing (see In Sequence 2/12/2008).

The Scan

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.

Circulating Tumor DNA Linked to Post-Treatment Relapse in Breast Cancer

Post-treatment detection of circulating tumor DNA may identify breast cancer patients who are more likely to relapse, a new JCO Precision Oncology study finds.

Genetics Influence Level of Depression Tied to Trauma Exposure, Study Finds

Researchers examine the interplay of trauma, genetics, and major depressive disorder in JAMA Psychiatry.

UCLA Team Reports Cost-Effective Liquid Biopsy Approach for Cancer Detection

The researchers report in Nature Communications that their liquid biopsy approach has high specificity in detecting all- and early-stage cancers.