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Mar 1, 2011 (Vol. 31, No. 5)

Range of NGS Applications Rises Quickly

Advanced Technological Approach Generates Genomic Data Better, Faster, and Cheaper

  • Going Public

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    Complete Genomics reports that its commercial genome sequencing center provides high-quality and low-cost DNA sequencing. The technology consists of three components: DNA nanoarrays, assembled into flow sides; a liquid-handling robot; and a high-speed imager.

    Complete Genomics, which leverages its human genome sequencing capabilities through a service delivery platform, employs a sequencing method based on DNA nanoball (DNB™) arrays and combinatorial probe-anchor ligation read technology. The company optimized its sequencing technology specifically for the human genome and delivers to its customers annotated sequence data, identifying key sites of sequence variation.

    It recently expanded its suite of analytical tools and announced the addition of copy number variation and structural variation results as part of its standard service. This enhancement has particular relevance for sequencing cancer genomes.

    Complete Genomics became a public company in November 2010 and is moving forward with a number of large genome sequencing projects and partnerships. It recently received an order from the Institute for Systems Biology (ISB) to sequence 615 human genome samples for a study on neurodegenerative disease.

    The company is also collaborating on a project with the NCI to sequence 100 genomes (50 tumor-normal pairs) as part of a pediatric cancer study to identify and validate somatic mutations associated with tumorigenesis. On successful completion of this initial phase, a follow-on NCI project will commence involving more than 514 tumor-normal pairs representing five different pediatric cancers.

    The company recently made genome sequences generated for three members of a Yoruba family accessible to the global research community—they are part of the 1000 Genomes Project. At the AGBT meeting Complete Genomics announced plans to release 60 complete, high-coverage human genomes (including the Yoruba trio)—representing >12.2 terabases of mapped reads—to its newly established public genome repository.

    Complete Genomics has the capacity to sequence as many as 400 complete human genomes per month, according to president and CEO Clifford Reid, Ph.D. It delivers the sequence data to customers on a hard drive or through the Cloud. Dr. Reid describes the company’s method as the “only unchained read technology in the industry. We can read bases in any order,” which contributes to higher accuracy and lower chemistry costs.

    Confident that the size of the clinical sequencing market will one day surpass the research market, Dr. Reid described work under way at Complete Genomics to produce clinical quality sequencing data. Optimization of Complete Genomics’ long fragment read technology, which is now in development, will reportedly allow the company to reduce the error rate for its sequencing technology from 1 in 100,000 bases to 1 in 10 million bases, the latter equivalent to about 300 errors across an entire human genome.

    The error detection/correction technology in development combines a DNA-engineering step upstream and an error correction step during data collection and analysis.

    Intelligent Bio-Systems president and CEO Steven Gordon, Ph.D., will give a presentation at the upcoming “XGEN” conference. Dr. Gordon will describe a sequencing system that can produce diagnostic-quality test results on multiple samples without the need for batching or bar-coding.

    Intelligent Bio-Systems’ three-step sequencing-by-synthesis technology involves amplifying DNA fragments, attaching them to a DNA sequence primer, and then immobilizing them in a high-density array on a glass chip. Fluorescently labeled bases (a different color for A, C, G, and T) are then introduced and attach to the growing DNA strand. The array is scanned and the fluorescent signal emitted by each replicating strand indicates with base was incorporated at the completion of each base addition step.

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