Another Stop on the Road to the $1,000 Genome

hiseq_2000_The latest stop on the road to the $1,000 genome? San Francisco, CA, where J.P. Morgan’s 28th Annual Healthcare Conference is in full swing. There is an abundance of real-time Twitter coverage from the conference, but certain announcements warrant a more detailed discussion.

The announcement generating the biggest buzz today came from Illumina, Inc., whose CEO Jay Flatley unveiled a new genome sequencing machine, the HiSeq 2000. According to Matthew Herper of, Illumina’s new machine “will decode a person’s DNA in one week using $10,000 worth of materials – five times cheaper than any other competing gadget on the market.” Herper adds that the machines will begin shipping in February with a cost of $690,000 (compared to $500,000 for Illumina’s current model). Illumina’s own product page for the HiSeq 2000 provides more technical details, including coverage (~30x) and read length (2×100 bp). There have also been unconfirmed rumors that the machine will come equipped with an iPhone user interface, a concept that Flatley first pitched at last summer’s Consumer Genetics Show.

If it performs as advertised, the HiSeq 2000 is likely to be a huge hit with large genome sequencing centers, as evidenced by the announcement that the BGI (formerly the Beijing Genomics Institute) has agreed to purchase a whopping 128 of the new sequencing systems. But what, if anything, does the Illumina announcement mean for individuals consumers interested in receiving a complete genomic sequence?

Although Herper declares that Illumina’s machine is “five times cheaper than any other competing gadget on the market,” I’m not entirely sure that is true. According to Illumina, the $10,000 price tag is for “reagent costs at list price” and does not include other significant costs, including purchasing the machine itself or analyzing the raw genomic data. In fact, it’s not even clear to me that the announcement represents a five-fold drop from the commercial whole-genome sequencing Illumina announced last June. That service offered consumers the opportunity to purchase a whole-genome sequence at the same 30x coverage for $48,000 and, although interpretation was similarly not included, consumers weren’t required to purchase their own sequencing machine and did receive a free iMac as part of the bargain.

Also in the middle of the whole-genome sequencing competition is sequencing-as-a-service provider Complete Genomics, which is presenting at the J.P. Morgan conference tomorrow morning and may well have at least a partial answer for Illumina’s announcement. Even if there’s no big news forthcoming from Complete, the company’s November announcement that it had sequenced three whole-genomes for an average materials cost of $4,400 and reports that it is selling whole-genome sequences at $20,000 apiece in minimum orders of five, with the price dropping as the order size increases positions Complete as a clear competitor to Illumina, at least from a pure price standpoint.

All told, Illumina’s announcement strikes me less as a sequencing milestone and more as a tightening of an already extremely fierce race toward the $1,000 genome. Nonetheless, if there are consumers out there who are awaiting a whole-genome sequence and look at $10,000 (and not $1,000) as the magic number, Illumina’s announcement could bode well. It seems likely that Illumina will drop the price of its own commercial whole-genome sequencing service from its current $48,000 and direct-to-consumer (DTC) whole-genome sequencer Knome, which uses the BGI to perform its sequencing, is also a likely candidate to announce a price reduction in the coming weeks (the current cost is believed to be $68,000).

Finally, the substantial buzz surrounding Illumina’s announcement and the continued tightening of the race to the $1,000 genome encourages me to reiterate what I wrote just last week in Five Questions for Personal Genomics in 2010:

The success of personal genomics, which is what really matters to consumers, patients and healthcare providers, requires more than inexpensive genomic data. The real breakthrough in personal genomics will come when we can offer individuals affordable access to their whole-genome sequence as well as to the genomic tools and knowledgebase necessary for those individuals to put that data to use.


Update 1/12: Ed Winnick of GenomeWeb has additional details on Illumina’s launch of the HiSeq 2000 and its partnership with BGI, including Jay Flatley’s statement that BGI’s order will ultimately allow it to sequence 11,000 human genomes per year.

Update 1/13: Daniel MacArthur of Genetic Future, Luke Jostins of Genetic Interference and David Dooling of PolITiGenomics all offer their analysis of what Illumina’s announcement means for the present and future of genomic sequencing. Also, in breaking news, Linda Avey is covering Complete Genomics’ presentation this afternoon and reports that the company has delivered 50 genomes to date and expects to deliver another 5,000 in 2010.

Update 1/14: GenomeWeb Daily News has more coverage of Complete Genomics’ announcements, including that the company plans to sequence up to one million human genomes worldwide over the next five years and is interested in exploring the IPO market. Also worth noting is the fact that the Complete Genomics sequencing-as-a-service model includes analysis and reporting, not just raw data, which makes comparing the current price tags for Complete ($20K) and Illumina ($10K for reagents only, no analysis) a bit like comparing apples to oranges.