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Complete Aims for Clinical Market as it Readies its WG Haplotyping Tech for Launch

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This article was originally published July 12.

Complete Genomics is planning to introduce technology next year that will enable whole genome sequencing and haplotyping with an error rate as low as one in 10 million.

The company published a paper in Nature last week detailing its long-fragment read technology, which Complete Genomics CEO Cliff Reid said would truly enable clinical grade genomes.

Reid told Clinical Sequencing News that the company is now "in the process of folding this into our factory," including doing collaborations with different customers, and said it plans to launch it commercially in 2013.

Reid said the company already has sequenced around 50 genomes with collaborators using the technology. The company collaborated with George Church's lab for the Nature publication but would not disclose other collaborators.

Reid said the initial projects have been in both the research and clinical realms.

Additionally, Complete Genomics expects to be CLIA certified in the third quarter of this year, so when the long fragment read technology launches, it will be out of the CLIA lab, enabling the technique to be used for clinical purposes.

The technology is "much less targeted at the research community and much more targeted at the clinical community," Reid said, adding that he anticipates the "primary buyer" will be clinicians.

Reid said he expects that the company eventually would sequence all genomes using the long fragment read technology.

"For the short term, we'll have two different production paths, the long fragment read and the regular," he said. "In the long run, I would expect us to shift over 100 percent to the long fragment read genomes, but the specific timing of that I don't know."

Implementing the technology will also not have a big impact on turnaround time or the amount of sequencing capacity required, said Reid. The technology requires additional preprocessing biochemical steps, which would add around 24 hours to the workflow, and the difference in the time it takes to do the informatics is "insignificant," he said.

The technology also uses just about the same sequencing capacity, with the exception of an additional four to 10 bases of barcoding that are attached to each fragment before sequencing.

Jill Hagenkord, Complete's chief medical officer, told CSN that the technology would likely initially be used in the hereditary disease area, particularly to sequence children with apparent genetic disorders.

Currently, if two pathogenic variants are found in the same gene, there's no way to know if those mutations are both in the same copy of the gene, or if there is one variant in each parental copy.

"That has a dramatic impact on choices that the patient will make and the prognosis of that patient," because it can be the "difference between being a carrier for a certain genetic disease, or being affected," she said.

Now, ancillary testing has to be done to determine whether the mutations are both from one parent, or whether the patient inherited one mutation from each parent. Having a fully phased, highly accurate genome would reduce the amount of ancillary testing and the amount of confirmatory testing, "saving time to diagnosis and cost," she said.

Complete Genomics also has its sights set on using the technology for cancer testing. Again, having phase information about cancer mutations can be important because it can be the difference between having a functional copy of a tumor suppressor, such as TP53, or having no functional copies of that tumor suppressor, which is associated with very aggressive forms of cancer.

Additionally, Hagenkord said, the technique is well-suited for any application for which little DNA is available. In the Nature study, the researchers demonstrated that only between 10-20 cells, or around 120 picograms of DNA, were needed.

"This means we can start getting into the scant sample market … things where clinically, you're only getting a few cells to make a diagnosis," such as embryos being used for in vitro fertilization, circulating tumor cells, or cancer cells taken from fine needle aspiration or bronchial biopsies, Hagenkord said.

Ultimately, said Reid, the technology will enable sequencing to be done once, stored in a database and then queried. "Once nearly perfect whole human genomes are available, if you get your genome sequenced and put in a secure database, every genetic test becomes a query," he said. "It will be a game changer in the genetics diagnostic industry."

Following the news of the publication, analyst Jeffrey Elliot from investment bank Robert W. Baird, wrote in a memo that while the paper is a "positive step for the company to eventually move its sequencing offering into more clinical applications,the bank remains "cautious … given recent disappointing results led by rapid price declines in the whole genome sequencing market."

Additionally, he noted that Complete Genomics is continuing to evaluate its strategic options, and "a number of alternatives (merger, business combination, equity investment or sale) are up for consideration."

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