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Complete Genomics Books Orders for More than 500 Human Genomes; Eli Lilly Among New Customers

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By Julia Karow

This story was originally published on February 22, 2010.

Six months after disclosing some of its first early-access customers for its human whole-genome sequencing service, Complete Genomics said this week that it has booked orders for a total of more than 500 human genomes from more than 30 customers, including three projects that comprise at least 100 genomes each. New customers include academic research groups as well as pharma giant Eli Lilly.

Later this week at the Advances in Genome Biology and Technology conference, the company plans to talk about several customer projects, and to give an update on future improvements of its proprietary sequencing platform and its analysis service. Two customers — Genentech and the Institute for Systems Biology — are scheduled to present results at a company workshop.

Last year, Complete Genomics delivered 50 human genomes to more than 10 customers. Among the new customers that have signed up for its service are Eli Lilly, the University of North Carolina, the Institute of Molecular Medicine at the University of Texas Health Science Center, Children's Hospital of Philadelphia, the Institute of Cancer Research UK, the Academic Medical Center of the University of Amsterdam, and the department of bioinformatics at the Erasmus Medical Centre in Rotterdam, the Netherlands.

Company officials declined to say how many of the firm's more than 30 customers are conducting pilot projects, and how many have moved on to larger projects. But according to Aaron Solomon, Complete's vice president for business development, current projects range in size, including small studies of 8 to 10 genomes, mid-sized studies of up to100 genomes, and large studies of more than 100 genomes. While the firm anticipates finishing the smaller projects "pretty quickly," the larger ones could take several months to complete, partly because customers often do not have all their samples ready for sequencing at once.

Some new customers are now starting with "much bigger" projects than the 5- to 10-genome projects that first-time customers signed up for last year, Solomon said. Three existing customers are planning studies involving "north of 100" genomes — Pfizer; the Flanders Institute of Biotechnology, VIB; and ISB.

Customers receive volume-based discounts from the $20,000-per-genome price for smaller projects, with prices starting to drop by an undisclosed amount at 100 genomes, and hitting $5,000 per genome for 1,000 genomes or more. While the firm has not yet received an order of that magnitude, it is in talks with potential customers about such projects, Solomon said.

Project types and disease areas vary among customers: among them are family disease studies that include affected and unaffected members, as well as cancer studies with normal, primary tumor, and metastatic samples from the same patient.

Complete Genomics said it is still on target for a full commercial launch of its service in April, and it still plans to sequence 5,000 human genomes this year, a number it recently revised down from an earlier target of 10,000 (see In Sequence 1/19/2010). At launch, it plans to have 16 sequencing instruments in place. While that number might sound small compared to genome centers that have installed on the order of 100 sequencers from Illumina or Life Technologies, each Complete Genomics instrument will have an output of up to a terabase per run, greater than that of any commercially available sequencing platform, chief scientific officer Rade Drmanac explained. This will be achieved by packing more DNA nanoballs on each chip, and by running more chips on each instrument. "We are scaling up by scaling down," Drmanac said.

VIB decided to enlist Complete Genomics for a second, larger sequencing project after analyzing results from a five-genome pilot project that the institute received last October. After assessing the quality of the data for about a month — mostly through bioinformatics analyses, for example of how much of each genome and its exome was covered, and at what depth — "we were really convinced the data they delivered was exactly like they said it would be," Mark Veugelers, VIB's integration manager, told In Sequence.

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For the second project, Complete Genomics will sequence "several more genomes" for a number of research groups at VIB, spanning neurodegenerative brain diseases, congenital diseases, and rare tumor types, Veugelers said. He declined to specify the total number of genomes to be sequenced for these studies.

VIB will continue to check incoming data for quality using the same set of bioinformatics scripts that it developed for the pilot project, he said. At the moment, VIB scientists are still analyzing the pilot data in order to answer biological questions. For those analyses, they have been using both the variant calls provided by Complete Genomics and the sequence reads, for example to study structural variations. They have also initiated collaborations with bioinformatics groups for some analyses.

Since last year, the company has made the format in which it delivers the sequence reads "much easier to work with," Veugelers said, and has provided help with viewing the data and suggesting tools and algorithms for downstream analyses.

According to the company, several customers are only using the SNP and indel calls it provides for their analyses, looking at the sequence reads only to verify the data quality. "The fact that we are delivering a variant file, which is nicely curated with variants that are both SNPs and indels and other features as well, allows researchers to start on the work of understanding the biology of the disease much more quickly," Solomon said. Several customers have already submitted studies for publication, he added. The company is also "constantly improving our output and our variant list in terms of covering other types of variation," according to Drmanac.

Asked whether VIB is considering even larger whole-genome sequencing projects in the future, Veugelers said that the more costs come down, "the more interesting larger studies become." Other parameters, however, would also come into play, such as turnaround time and data quality.

At the moment, he said, Complete Genomics' service model is an attractive choice. "From an economic perspective, they are currently the cheapest one to deliver the data, plus also the fastest," he said, compared to installing and running a large number of instruments in house.

However, he said VIB will keep its options open as some genome centers — such as BGI in China and the Ignite Institute of Individualized Health — have said they are also offering, or planning to offer, sequencing capacity to outside groups. "Of course we are aware that they are also looking to position themselves as a service provider," Veugelers said. "We are keeping an eye open for all the possibilities that are out there."

In the meantime, Complete Genomics is pursuing its plans to build genome centers in other locations. Last week, government officials from the Flanders region of Belgium, where VIB is located, visited the company as part of a tour of various California firms. According to Solomon, the officials are "interested in us putting a center there," though discussions are still at an early stage.

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