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Complete Genomics Teams with DNAnexus to Offer Clients Cloud-based Informatics for Sequence Data


This article has been updated to correct an error in the previously reported price per genome for pharmaceutical companies.

By Uduak Grace Thomas

Complete Genomics' customers will be able to store and visualize their human genome sequencing data in DNAnexus’ cloud-based platform as a result of an agreement between the two firms announced this week.

Under the terms of the deal, customers of Complete Genomics' sequencing services will have access to DNAnexus’ suite of informatics tools, via Amazon web services, that will, among other features, enable them to visualize structural and copy number variations and small variants using the DNAnexus Genome Browser as well as query multiple human genome datasets.

The partnership with DNAnexus marks Complete Genomics’ first partnership with an informatics vendor, Jennifer Turcotte, the company's vice president of marketing, told BioInform.

She added that Complete selected DNAnexus because both companies “had similar goals and strategies regarding cloud computing and storage for genomic data analysis.”

Meantime, DNAnexus CEO Andreas Sundquist told BioInform that in addition to a shared “business philosophy,” both companies already have several customers in common, some of which participated in beta tests of the combined offering.

The testers included research groups at Stanford University and the University of California, San Francisco, as well as major pharmaceutical companies, although Sundquist declined to mention specific names.

Although Complete already offers some bioinformatics analysis, Turcotte noted that there isn’t any overlap with the DNAnexus technology. Rather, the two companies' services “complement each other,” she said.

Sundquist explained that while Complete Genomics will continue to provide tools for “primary [and] secondary analysis” of client data, such as data assembly and mapping, DNAnexus will provide tools to manage data inside the web browser and visualize datasets.

The management tools will enable users to, for example, filter genomic datasets based on parameters such as ethinicity or gender, and by project identification number.

“We also allow [users] to query all the types of results that Complete Genomics produces — for example, copy number variants [and] structural variants,” he said.

Furthermore, the partners plan to integrate into DNAnexus Complete Genomics Analysis Tools, which is open-source software developed by the sequencing company for further downstream analysis of its sequence data.

CGA Tools provides applications for genome comparison, format conversion, annotation, and building copies of reference genomes.

DNAnexus will also provide customers with access to 40 publicly available genomes published by Complete Genomics earlier this year (BI 02/04/2011).

Sundquist said that the partners plan to make CGA Tools available in the cloud in the second quarter of 2011.

Turcotte also said that Complete Genomics has other informatics partnerships in the offing, but declined to mention specific vendors.

Etching Its Mark

Although Complete Genomics faces competition on two fronts — from instrument vendors such as Illumina, Life Technologies, and Pacific Biosciences, as well as sequencing service providers like SeqWright and BGI — Complete Genomics seems to be trying to etch its mark on the sequencing market.

Recently, the firm said that so far this year it has signed orders for more than 1,400 human genomes, including a previously announced 615-genome order from the Institute of Systems Biology, excluding an existing multi-year contract with the National Cancer Institute that may add another 1,128 genomes (IS 03/15/2011).

Last year, the NCI tapped the sequencing firm to identify SNPs, insertions and deletions, copy-number variations, and somatic variations in 50 pediatric cancer cases culled from several research centers as part of a nationwide study on pediatric cancer (BI 09/10/2010).

The company’s focus on human whole-genome sequencing has given it a “unique foothold,” Sutherland told BioInform.

He added that in 2011 Complete Genomics will focus on improving the quality of its sequencing and analysis technology, increasing the number of genomes it sequences per month, and “adding value for our customers.”

Currently, the Mountain View, Calif.-based firm accepts a minimum eight genomes per order priced at $9,500 per genome — although the price drops as the number of genomes increases. The service includes quality control of the customer’s incoming material, library construction, sequencing, assembly, full annotation of the genome, and delivery to the customer, Sutherland said. Users receive their results in 72 to 74 days.

On DNAnexus’ side, patrons of the combined companies’ offering will benefit from an introductory price — available until June — of $450 per genome for academics while the cost for pharma companies will be in the vicinity of $1,600 per genome.

Sundquist said that the service will likely cost more after June to cover the cost of additional functionality that will be included in the next several months.

This is DNAnexus’ second partnership with an instrument vendor this year. Last month, the company was listed among several bioinformatics companies that will provide data analysis and cloud computing services to users of PacBio’s Single Molecule Real-Time Sequencer.

Simultaneously, the firm rolled out a cloud-based workflow to help researchers analyze and manage genomic variation datasets (BI 02/04/2011).

Have topics you'd like to see covered in BioInform? Contact the editor at uthomas [at] genomeweb [.] com.