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what is known as copy number variation. As more and more researchers have identified major structural changes in the genomes of tumors, Complete Genomics has tailored its sequencing service to do much of the computational analysis to highlight the differences compared with the standard reference genomes that are publicly available, Reid says. Entire long stretches of DNA can get wiped out, or switched around in reverse order, he says.
Here’s how the order flow is basically supposed to work, as I gathered from Reid. A researcher may take a biopsy of, say, a prostate tumor along with an ordinary blood sample from the patient. That researcher sends the two samples in for complete genome sequencing, the company assembles the raw data, and highlights the variations it sees compared to public reference genomes, and identifies which variants are known to be associated with disease. The data gets uploaded to remote cloud computing servers operated by Amazon Web Services, which enables the researcher to download the data via the Internet. Often, the researcher asks Amazon to copy the data on a disk and send it to the lab through commercial shippers like FedEx. Then the researcher is supposed to be able to use his or her creative brain to look at the data and gain the kind of insights that get published in Science, Nature, or the New England Journal of Medicine.
The process—from the moment the sample gets shipped to Complete Genomics to the moment data gets sent back—is supposed to take 90 to 120 days, Reid says.
“We provide the data so that it’s research ready,” Reid says. “You shouldn’t have to take on an enormous amount of data analysis to get to the biologically important stuff.”
It’s still way too early in the game to really say how well Complete Genomics is doing with this approach. It started offering the commercial service in a serious way in the third quarter of this year, when it shipped 300 complete genomes to customers, Reid says. The company has now established the necessary technology and infrastructure in Mountain View so that it can sequence as many as 400 complete genomes per month, or roughly 5,000 through all of 2011.
So far, Complete Genomics has signed up 35 customers, including the National Cancer Institute, the Institute for Systems Biology, the Broad Institute of MIT and Harvard, Genentech, Eli Lilly, and Pfizer, according to a recent regulatory filing. Most of the orders start out small, Reid says, asking for a handful of genomes. Some customers have made repeat orders, and the company’s goal … Next Page »