A Googol of Genomes?

[Editor’s Note: this was originally posted over at the Genomics Law Report but we’d like to survey Genomes Unzipped readers as well. How many complete genomes do you think will be sequenced in 2011? Poll is at bottom.]

Earlier this week we took a look back at 2010 and offered our projections for the coming year in personal genomics. Topic #1, just as it was last year: the $1,000 genome.

In hindsight, it might have been ill-advised to offer predictions about the near-term future of genome sequencing during the same week in which one of the year’s major industry conferences (the JP Morgan annual Healthcare Conference) is taking place.

There have been a number of high-profile announcements from genome providers over the past two days. Life Technologies disclosed it had booked 60 orders for the recently unveiled Personal Genome Machine (PGM) and, more importantly, announced that the PGM’s output would be increased by an order of magnitude (10 megabases to 100 megabases) in Q1. Not to be outdone, Illumina, the current market leader in genome sequencing technology, responded later the same day by unveiling its new MiSeq machine. As both Matthew Herper and Keith Robison explain in detail, the MiSeq is a direct and formidable challenger to the Personal Gene Machine as a result of its price, speed and utilization of Illumina’s established sequencing platform.

But the biggest stories, at least by one metric, belong to sequencing newcomer Complete Genomics and Illumina (again). Complete Genomics announced this week that the Institute for Systems Biology (ISB) has ordered a whopping 615 whole-genomes as part of the ISB’s ongoing research into the genetics of neurodegenerative diseases, including Huntington’s. Meanwhile Illumina, at the same time it was launching the MiSeq machine, disclosed that it “currently has a 1,000-genomes backlog” for its own whole-genome sequencing service.

Let’s forget, for a moment, about how much these whole-genome sequences cost and reflect on simply how many of them there are. Just over a decade ago, Bill Clinton and Tony Blair were lauding the first draft human genome sequence; and the Human Genome Project would not declare the first genome “complete” until the spring of 2003.

Again, seven and a half years ago, there was only one single genome sequence to be had anywhere in the world. And it took 13 years and $3 billion dollars to get just the one. Today? We casually discuss hundreds and even thousands of genomes to be sequenced in a matter of months and for thousands of dollars apiece (not $1,000, but likely less than $10,000).

Even if the $1,000 genome does not arrive this year, 2011 will almost certainly see 1,000 genomes sequenced. And in many ways, that may be the worthier milestone to celebrate. Every significant increase in the number of sequenced genomes means a corresponding increase in the amount of genomic data available to elucidate the genetic bases of human traits and disease. There is still a tremendous amount of work to be done to make sense of all that data (and a tremendous amount of environmental, trait and other data that must also be correlated), but sequencing thousands of genomes is a significant step in that process.


GNZ Reader Poll: How many complete genomes do you think will be sequenced in 2011?

View Results

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5 Responses to “A Googol of Genomes?”

  • I feel a bit over-cautious voting for only 2-5K. In some of my talks I quote the slightly fudged figures of a genome costing $2billion in 2000 and $20K in 2010, so you knock a zero off the end every 2 years. Better than Moore’s Law in that respect, but if you plot it out, not quite so consistent, and certainly not quite clear how things will progress now that there are fewer zeroes left…

  • Daniel MacArthur

    Of course, much of this depends on what is meant by the term “complete genomes”. I answered 5,000-10,000 assuming the definition was “high-quality genome, say >30X coverage of >90% of the reference”; but if the definition is “genome-wide coverage of 1X or greater”, the number will be far larger.

  • Yeah, plus the poll is not 100% clear that we are talking about human genomes. As the BGI mentioned on twitter, they plan to sequence 10K vertebrates…

  • Complete Genomics can now sequence ~400/month.
    I assume llumina (just counting the IGN) can do the same. Add quite a few :-) from Beijing. We are @ > than 1k / month. Plus there are a bunch of Illuminas out there (and Solids) and many more (especially HiSeqs) are on gonna be installed in 2011 –> I suggest we will get @ least 20k HQ genomes this year hopefully reaching 50k if things keep rolling as fast as today.

  • All good points. This is what happens when you send non-scientists out to gather data. The post referred to human genomes, and I was assuming reasonably high quality/coverage.

    Also, Ewen Callaway, in his recent post where he reminds us that, soon, only our mothers will care about our genomes, links to a Nature feature from last fall that projects more than 30,000 genomes in 2011.

    That includes high- and low-coverage, but doesn’t include any private biotech/pharma sequencing, which is significant but also difficult to measure.

    I answered 5-10K as well, but in retrospect wish I’d gone higher.

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