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Complete Genomics, a Silicon Valley-based startup that promises supercheap sequencing, announced Monday that it had raised $45 million in its latest round of venture funding. The announcement follows a similar one from Pacific Biosciences, another Silicon Valley startup, which recently raised an additional $68 million.

Both companies have made big claims about their novel sequencing technologies, with Complete Genomics promising a $5,000 sequencing service this year. Pacific Biosciences predicted last year that its technology would be able to sequence a human genome in 15 minutes by 2013. In addition, Illumina, a genomics technology company headquartered in San Diego, announced the launch of a $48,000 genome-sequencing service in June. That doesn’t include analysis of the sequence, which will likely prove more expensive than the sequencing itself.

“This new capital will enable us to scale up our facilities in preparation for large customer projects. We now plan to launch our large-scale commercial sequencing center in January 2010 with the goal of sequencing 10,000 human genomes next year,” said Clifford Reid, chairman, president and CEO of Complete Genomics, in a statement. The company has adjusted its target sequencing capacity–when I spoke to Reid last fall, the company had a goal of sequencing 20,000 genomes in 2010.

According to the San Jose Mercury News,

[Complete Genomics] is already working with the Broad Institute of MIT and Harvard on two pilot studies of the cancers melanoma and glioblastoma, and another a project with the Institute for Systems Biology. Reid said the company anticipates several other projects to be announced in the coming months.

Two new investors, Essex Woodlands Health Ventures and OrbiMed Advisors, participated in the new funding. Previous investors Prospect Venture Partners, Enterprise Partners, OVP and Highland Capital Management reinvested in the Complete Genomics.

Complete Genomics has raised a little more than $90 million since it was founded in 2006. Pacific Biosciences, founded in 2004, has raised a total of $188 million since last summer. For more on the two companies technologies, check out Five Thousand Bucks for Your Genome and DNA in Real Time.

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Tagged: Biomedicine, sequencing, human genome, Complete Genomics, Pacific Biosciences

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