Complete Genomics Analysis Platform

Complete Genomics has developed and commercialized an innovative DNA sequencing platform for whole human genome sequencing and analysis. Our platform combines our proprietary human genome sequencing technology with our advanced informatics and data management software and our innovative, end-to-end, outsourced service model to provide customers data that is immediately ready to be used for genome-based research.

Our technology provides academic and biopharmaceutical researchers with whole human genomic data and analysis at an unprecedented quality, cost and scale without requiring them to invest in in-house sequencing instruments, high-performance computing resources, and specialized personnel. By removing these constraints and broadly enabling researchers to conduct large-scale whole human genome studies, Complete Genomics provides a solution to drive medical research and expand understanding of the basis, treatment and prevention of complex diseases.

Proprietary Sequencing Technology

We believe that our human genome sequencing technology, which is based on our proprietary DNA arrays and ligation-based read technology, is superior to existing commercially available whole human genome sequencing methods in terms of quality, cost and scale. Because we have optimized our technology platform and our operations for the unique requirements of high-throughput whole human genome sequencing, we are able to achieve accuracy levels of 99.999% at a total cost that is significantly less than the total cost of purchasing and using commercially available DNA sequencing instruments.

Our Novel Array and Read Technology

There are two primary components of our proprietary human genome sequencing technology: DNA nanoball, or DNB™ arrays and combinatorial probe-anchor ligation, or cPAL™, reads.

Our patterned DNB arrays, due to their small size and biochemical characteristics, enable us to pack DNA very efficiently on a silicon chip. We have developed a proprietary process that causes the DNA to adhere to desired spots on the chip, while conversely preventing the DNA from adhering to the area between these spots. This enables us to affix individual particles of DNA to over 90% of these spots, leading to increased efficiency in nanoarray assembly.

In addition, we have developed a highly accurate cPAL read technology, which enables us to read the DNA fragments more efficiently using small concentrations of low-cost reagents, while retaining extremely high single read accuracy. We believe this unique combination of our proprietary DNB and cPAL technologies is superior in both quality and cost to other commercially available approaches and provides us with significant competitive advantages.

The publication in Science in January 2010 demonstrates the cost and quality advantages of our technology, as we sequenced a whole human genome at a consumables cost of approximately $1,800 and with a consensus error rate of approximately 1 error in 100,000 nucleotides. Our read accuracy was further independently validated by one of our customers as described in Science Express published in March 2010.

Advanced Informatics and Data Management Software

Sequencing whole human genomes generates substantial amounts of data that must be managed, stored and analyzed. While many users of instrument-based sequencing systems have historically conducted their own in-house data analysis on a limited number of genomes, many of these users lack the computing, storage and network bandwidth necessary to manage the massive data sets generated by larger scale whole human genome studies. As the reagent cost of sequencing declines, we believe that the cost and complexity of data analysis and management will emerge as the primary limiting factor for researchers conducting whole human genome analysis. In response to this need by our customers, we have built a genomics data processing facility with computing infrastructure for managing both small and large-scale genomic sequencing projects.

There are two major components of our complete data management solution: assembly software and analysis software.

• Assembly. Assembly is the process of using computers to organize all of the overlapping 70-base nucleotide sequences to reconstruct the whole human genome. Our proprietary assembly software uses advanced data analysis algorithms and statistical modeling techniques to accurately reconstruct over 90% of the whole human genome from approximately two billion 70-base reads.
• Analysis. After assembling the genomic data, we use our analysis software to identify key differences, or variants, in each genome. Detected variants include SNPs, indels, substitutions, Copy Number Variants (CNVs), Structural Variants (SVs), and Mobile Element Insertions (MEIs). For the Cancer Sequencing Service, we identify somatic variants based on tumor-normal comparison, in addition to the variants detected by comparing each genome to the human genome reference. We then access publicly available databases of variants and genomic information to annotate each variant in the genome that is described in these databases. By using our analytical tools and data management software, our customers can significantly reduce their investments in computing and data storage infrastructure.

Our customers are provided with reliable access to assembled and annotated sequence data in multiple formats to ease data sharing and comparative analyses.