The days of spending only $1,000 to sequence an entire human genome may be five years or more away, but Synamatix of Kuala Lumpur, Malaysia, is taking steps to establish itself as the data analysis company of choice for next-generation sequencing technologies.
The company recently launched FragBase, a new module in a line of products built upon its “pattern-aware” data storage and management technology. The core of this technology platform, SynaBase, uses pattern-recognition technology to assign significance to certain sequence patterns and then stores the relationships between these patterns. Because the database stores each of these patterns only once, in a hierarchical structure, entire genomes can be stored in a much smaller amount of space than in relational databases or flat files, and can therefore be searched much more quickly, according to the company.
Right now, the core application areas for the company’s technology have been in comparative genomics and high-throughput genomic searching, but Synamatix hopes to lay the groundwork for widespread adoption of its methods in future years.
One area that Synamatix has identified as a good fit for its approach is next-generation sequencing methods currently under development at companies like 454, US Genomics, Solexa, and others. These methods promise to greatly speed the sequencing process, but one potential bottleneck is in the assembly of large amounts of sequence data. Truly personalized medicine won’t be practical if physicians require server farms to process their patients’ genome sequence data — regardless of the platform that generated it.
FragBase was developed in collaboration with an undisclosed US company developing a next-generation sequencing platform, according to Arif Anwar, vice president of Synamatix. It’s been adapted to assemble “very large numbers of very small bits of DNA” — less than 100 base pairs.
— Bernadette Toner
US Patent 6,871,147. Automated method of identifying and archiving nucleic acid sequences. Inventors: John Schlager, Richard Sweeney, Douglas Avery. Assignee: The United States of America as represented by the Secretary of the Army. Issued: March 22, 2005.
This patent covers “a method of identifying and archiving a nucleic acid sequence,” according to the abstract. It includes means for entering raw nucleic acid sequence into a computer, creating a file directory for storing information, trimming the raw sequence, and facilitating search capabilities.
US Patent 6,872,816. Nucleic acid detection kits. Inventors: Jeff Hall, Victor Lyamichev, Andrea Mast, Mary Ann Brow, Robert Kwiatkowski, Stephanie Vavra. Assignee: Third Wave Technologies. Issued: March 29, 2005.
According to the abstract, this invention “relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. … The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.”
Scientists completed the genome sequence of Wolbachia pipientis, a symbiotic bacterium required for fertility and survival of the human filarial parasitic nematode Brugia malayi. The team included researchers from New England Biolabs, the National Center for Biotechnology Information, Integrated Genomics, and the Institute for Genomic Research.
454 Life Sciences announced the installation of its first commercial genome sequencing system at the Broad Institute. The CuraGen subsidiary’s technology relies on microfluidics and other miniaturized technology to accelerate the sequencing process.
The US Department of Agriculture and researchers in the Netherlands have teamed up to sequence the genome of Mycosphaerella gramninicola, a wheat pathogen.
The National Institute of Neurological Disorders and Stroke will fund a number of core resources at research institutions offering genomic technologies that support neuroscience research. Eligible cores — those that provide services in DNA sequencing, assay development, mass spectrometry, microarrays, proteomics, and protein crystallography — can receive as much as $500,000 per year for up to five years.
Agencourt Bioscience and Amplicon Express say they will join forces to offer their customers BAC library construction and sequencing services.
Approximate number of base pairs in the genome of Rhodococcus sp. RHA1, the largest bacterial genome sequenced to date. The work on this organism, a soil bacterium of interest for bioremediation purposes, was led by researchers at the University of British Columbia.