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November 05, 2009

Complete Genomics Sequences Human Genome for $1726 Cost of Materials and a New Project to Sequence 10 thousand Vertebrate Genomes

1. Complete Genomics has a report in the journal Science describing its proprietary DNA sequencing platform, including analysis of sequence data from three complete human genomes. The consumables cost for these three genomes sequenced on the proof-of-principle genomic DNA nanoarrays ranged from $8,005 for 87x coverage to $1,726 for 45x coverage for the samples described in this report.

Complete Genomics' sequencing process includes four distinct steps:
1) Sample preparation and library construction
2) Self-assembling DNA nanoarrays
3) Imaging, assembly and analysis
4) Combinatorial probe -- anchor ligation (cPAL).

Complete Genomics’ scientists generated high-quality diploid base calls in as much as 95 percent of the genomes sequenced, identifying 3.2 million to 4.5 million sequence variants per genome processed.

Detailed validation of one genome dataset demonstrates a sequence accuracy of just
one false variant per 100 kilobases, a remarkably low error rate, particularly for such an affordable technology.

Patterned genomic DNA nanoarrays and 70-base, unchained sequence reads are unique technical achievements. The company’s new patterned genomic DNA nanoarrays, which achieve a record high density of 2.85 billion spots per slide at 0.7 micron pitch, will enable Complete Genomics to sequence 10,000 human genomes in 2010.


Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays

Genome sequencing of large numbers of individuals promises to advance the understanding, treatment, and prevention of human diseases, among other applications. We describe a genome sequencing platform that achieves efficient imaging and low reagent consumption with combinatorial probe anchor ligation (cPAL) chemistry to independently assay each base from patterned nanoarrays of self-assembling DNA nanoballs (DNBs). We sequenced three human genomes with this platform, generating an average of 45- to 87-fold coverage per genome and identifying 3.2 to 4.5 million sequence variants per genome. Validation of one genome data set demonstrates a sequence accuracy of about 1 false variant per 100 kilobases. The high-accuracy, affordable cost of $4,400 for sequencing consumables and scalability of this platform enable complete human genome sequencing for the detection of rare variants in large-scale genetic studies.


51 page pdf with supplemental material



2. A group of genome and museum experts today launched an ambitious plan to decipher 10,000 vertebrate genomes. The Genome 10K plan, formally announced today and described online in the 5 November issue of the Journal of Heredity, is short on details: where funding will come from; what sequencing strategy to use; how to process and make use of data generated.

O’Brien, Haussler, and Ryder want to see sequencing genomes cost $2500 each—a hundred-fold decrease in the current cost or more. By waiting a few years for better sequencing technology, they expect to spend $50 million for the whole project


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