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Complete Genomics Sees Future in Cancer Genome Sequencing; Plans New Cancer-Specific Product


By Julia Karow

Complete Genomics said last week that it plans to launch a new "cancer product" this year and that it sees cancer pathology as a major future market opportunity, in addition to genome sequencing for clinical trials and consumer genomics.

More than half the genomes ordered by customers so far are cancer genomes, according to a company official.

At the Cowen Healthcare Conference in Boston last week, Complete Genomics CEO Cliff Reid said that the company is currently serving the research market, "but in the long run, we plan to be the tumor sequencing company."

In 2010, the firm won a multi-year contract from the National Cancer Institute to sequence at least 100 genomes, and potentially another 1,128, to study five types of pediatric cancer (IS 9/7/2010). During the company's fourth-quarter earnings call last week, Reid said that company scientists have completed sequencing the first 100 genomes and are currently working with the NCI to validate mutations of interest, after which Complete can recognize revenue for this part of the project.

The company is working on improving its assembly of cancer genomes, which Reid said are "the hardest genomes to sequence" because they have so many structural variations and copy number variants. "We have not licked the cancer problem — nobody has — but we stay ahead with our continued investment in software technology," he said.

Sometime this year, Complete plans to launch a new "cancer product" to identify differences between tumor and normal cells. "We believe our new cancer product will benefit our existing customer base but will also attract new customers to our service," he said.

Complete also plans to add a whole-genome methylome sequencing service "as part of our enhancements for doing cancer projects," though Reid did not provide a timeline for that service.

Including the NCI contract, more than half the orders the company has booked so far are for cancer genomes. "A significant portion of cancer researchers are completely convinced by the published scientific evidence from us and others that complete human genome sequencing is critical for understanding the genetic basis of cancer," Reid said. "So we are doing particularly well in the cancer segment."

Citing a UBS report, Reid said that there is currently no clinical market for human whole-genome sequencing, but that this market is expected to grow to $550 million per year by 2015.

When the price of whole-genome sequencing falls to around $2,000, Reid said, the estimated 5 million annual new cancer cases in developed countries will all be "candidates for complete human genome sequencing." These 10 million genomes — tumor and normal for each patient — would translate to a $20 billion market.

Reid did not say when the $2,000 genome will arrive, but by the end of the year, Complete Genomics plans to offer basic genomes at less than $5,000 (see related story, In Sequence).

"We think breaking through the $5,000 price barrier is important, and then breaking through the $3,000 price barrier or beyond that is every bit as important," he said. "That takes us into the price of clinical sequencing."

However, he also said that the company may charge a premium for "high-value, high-accuracy cancer datasets" over the basic $5,000 genome.

Clinical whole-genome sequencing will likely not be restricted to cancer. "For the first time, we are seeing a body of evidence accumulate that other disease indications are likely to miss a lot by doing exome sequencing rather than complete human genome sequencing," Reid said. "So the combination of the experiences of the community with exome sequencing and the continued price decline of complete human genome sequencing, we think, will continue to shift the mix toward complete human genome sequencing for many of these large projects."

Regarding whole-genome sequencing for clinical trials in particular, low prices remain "the key issue," according to Reid. While Complete's services are already suited for clinical trial sequencing "from a feature and function point of view," he said, "the price will have to go significantly below $5,000 in order to be attractive to the pharmaceutical companies and for the [contract research organizations] who are running large clinical trials."

Clinical genome sequencing will also not be performed at the bedside, he said. "Hospitals are not going to be doing complete human genome sequencing inside, they are going to be outsourcing it, and we are going to be the preferred partner for that."

A new haplotyping technology Complete is developing and plans to introduce in 2012 will be particularly important for clinical sequencing. Not only will this "long fragment read technology" provide separate sequences for the two parental chromosomes, but it will also improve the error rate from 10-5 to 10-7, or from 30,000 errors per genome to 300 errors per genome.

"This new long-fragment read technology is elevating our genomes from research quality up to clinical quality starting in 2012," he said.

In addition, improvements to the company's sequencing instruments that will decrease the fully loaded cost per genome will "open the door for pricing that is really going to meet the need of the clinical marketplace," he said.

Reid said that over the next three years, he expects human whole-genome sequencing to become "as routine as a blood test."

Have topics you'd like to see covered in Clinical Sequencing News? E-mail the editor at jkarow [at] genomeweb [.] com.

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