Genetic Future

The big news from the JP Morgan investment conference today is the announcement of a brand new shiny sequencing machine from Illumina, the HiSeq 2000. The new machine boasts an impressive set of statistics, and looks likely to gradually replace Illumina’s GAIIx as the workhorse of most modern sequencing facilities.
So, how excited should we be?

Let’s be clear about this up front: this new machine, while impressive, represents an incremental advance rather than a dramatic technological leap forward. This is still second-generation sequencing, generating relatively small snippets of DNA sequence (around 100 bases, although that figure is sure to rise) that must then be stitched together to assemble a genome. The improvements in terms of sequence output are impressive, but represent only a five- to two-fold increase over the current throughput of the GAIIx.
There’s also some confusion about the decrease in the cost of sequencing, which has already been noted by Dan Vorhaus: while this Forbes article claims that sequencing with the new machine will be “five times cheaper than any other competing gadget on the market”, that may be based on a conflation of the reagent costs of generating a 30-fold coverage human genome sequence with the new machine ($10,000) with the retail price offered by Illumina using its old technology ($48,000). 
In fact it looks to me as though the cost per base of sequencing from the new machine is not hugely decreased relative to the GAIIx, although the HiSeq will be substantially more flexible in its applications – potentially decreasing wasted capacity. I’ll seek some clarity on this from Illumina.
[Added in edit 13/01/10: I gather that the cost per base is actually substantially reduced on the HiSeq relative to the GA, possibly by as much as 8 times. That's certainly a major improvement, and if these cost savings are in fact fully realised by end users this will definitely have an impact on the cost of genome sequencing. However, as noted above, this is still an incremental improvement, and it will also be important to factor in increasing informatics costs to users due to increased data volume.]
As Vorhaus also notes, the reagent cost per human genome from the HiSeq is actually substantially higher than that quoted by competitor Complete Genomics in its recent paper in Science. Complete doesn’t sell machines to genome facilities, but has instead devoted its attention to creating an efficient, factory-like infrastructure with the sole purpose of generating human genome sequences as quickly and cheaply as possible. That means it will be extremely difficult for Illumina to compete with Complete on the costs-per-human-genome front.
Illumina’s announcement will almost certainly help to cement its position as the technology provider of choice for genome facilities. As if to drive home the point, a second announcement today confirmed a long-rumoured major purchase by China’s BGI - 128 of the new Illumina instruments. That’s yet another blow for Illumina’s major competitor, Life Technologies’ SOLiD platform, and continues Illumina’s dominance of the second-generation sequencing market.
So, how excited are we by this announcement? A little. With every iteration the affordable human genome inches ever closer, and for that we should be grateful – but this is certainly not the announcement that rings in the era of true personal genomics.
Fortunately, the really exciting sequencing news of 2010 is yet to come. At the Advances in Genome Biology and Technology meeting next month, where I’ll be blogging along with my esteemed web denizens Luke Jostins, David Dooling, Dan Koboldt and Anthony Fejes, I’m expecting to hear announcements that will have a far greater impact on the future of sequencing: news on progress in third-generation sequencing by Oxford Nanopore, Pacific Biosciences, and Life Technologies’ new Visigen-based platform, among others. And if the buzz I’ve heard so far is anything to go by: then we should start getting excited.
Added in edit: David Dooling has plenty more technical details on the new technology for those inclined.

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Comments

  1. #1 ESLondon
    January 15, 2010

    One aspect which goes beyond mere throughput and cost per base is the annouced capacity to process 200 samples per day (for expression profiling,etc) for less 200USD$. That would blow microarrays away and would be a major step forward in expression profiling…

  2. #2 Comrade PhysioProf
    January 16, 2010

    It seems to me that even with a GAII, the cost of generating the sequence data is already a small fraction of the cost of analyzing it.