(UPDATED: See below.)

Knome logoKnome, the Cambridge, Mass., startup that will sequence the entire genomes of 20 customers for $350,000 apiece, launched its business back in November without ever explaining exactly how it planned to carry out the heavy lifting of whole-genome sequencing. At the time, CEO and co-founder Jorge Conde said only that unspecified “partners” would be helping out Knome with the actual work of reading out and analyzing six billion “letters” of DNA for each customer.

Yesterday, however, Knome announced a “strategic alliance” with the Beijing Genome Institute that strongly suggests the startup will be relying on the Chinese research institute for much, if not all, of its early sequencing efforts. (The release is here.) BGI, founded in 2002 — a precursor organization apparently dates back to 1997 — has played a major role in several major sequencing projects over that time. BGI’s Web site states that the institute was responsible for sequencing roughly one percent of the human genome in the Human Genome Project, and later independently mapped the genome of a hybrid strain of Chinese rice. BGI has also participated in international projects to sequence the genomes of pigs, chickens and silkworms.

Although BGI’s Web site isn’t fully translated into English, one page does boast that the institute can sequence 50 billion million “base pairs” (that is, “letters”) a day, with computing power — required to assemble and analyze sequenced DNA fragments — to match. Of course, it seems unlikely that Knome will have access to more than a fraction of that capability, as BGI presumably has multiple other projects underway as well.

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Knome, which claims to take an almost paranoid approach to protecting the privacy of its “clients,” has said in the past that it will only send its partners anonymous, coded blood samples for genome sequencing. That, presumably, will be enough to allay any customer concerns about the new arrangement, although it’s impossible not to wonder whether Knome’s well-heeled clients had previously realized that their DNA might travel as far as Beijing for decoding.

Meanwhile, it’s also intriguing that BGI has struck what amounts to a commercial relationship with the U.S. startup. The institute is an arm of the Chinese Academy of Sciences, and according to its published material is devoted purely to scientific and technical advancement (see last paragraph, but be warned — it’s pretty dense).

Given that Knome aims to give its customers “full control” over how their genomic information is used, it’s not immediately clear that BGI stands to gain much in the way of raw knowledge from its work with Knome. As a result, I can’t help wondering how the institute’s stated goals are compatible with taking on work-for-hire for a U.S. startup, although I suppose it’s possible that BGI could look at the project as a sort of test bed for shaking out new sequencing technologies.

UPDATE: As Deepak notes in comments, BGI announced last month that it will begin offering sequencing services to the global market. See, for instance, this GenomeWeb Daily News story from Dec. 24 (registration possibly required), which updates the institute’s capacity to 250 million base pairs a day with standard equipment, and up to four billion a day using next-generation sequencers.

Also, Knome CEO Jorge Conde tells me by email that the company’s arrangement with BGI is exclusive, so it looks like all blood samples taken by Knome will be making the long trip to Beijing.

LATER UPDATE: As noted in comments, I originally wrote “billion” forĀ  “million” in describing BGI’s base-sequencing capacity.