HPC in the Cloud: Thus Begins the Era of the $1,000 Genome

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January 11, 2012

Thus Begins the Era of the $1,000 Genome

Michael Feldman

On Tuesday, Life Technologies Corporation unveiled its newest DNA sequencer, which they claim can map a human genome in a day for a $1,000. That's just a fraction of the cost ($4,000 - $10,000) and time (two weeks or more) incurred by current platforms. Meanwhile rival Illumina Inc. has launched its latest DNA sequencing platform, which also purports to map a genome in a day. If the companies' claims hold up, such a performance increase will usher in a new era of genome sequencing.

But, as we've reported here before, interpreting those genes will limit how widely the technology can be applied. The analysis is the important step that turns the raw data into something useful, such as pointing the way to personalized drug treatment or assessing future risk of developing specific diseases.

Since such analysis requires sophisticated bioinformatics software and lots of computing muscle (that is, HPC-type hardware), this tends to be the most expensive and drawn-out step in the process. In general, interpreting the data can cost between 10 and 100 times as much as the sequencing. As was summed up rather well last year in a Genomics Law Report article:

[T]he goal is not inexpensive genomics, but personal genomics. What matters is not how much it costs to generate a genome sequence (i.e., raw data), but what you can do with that genome once you have it. Thus, genomics is only personal once both the data and the interpretation are individually tailored.

Because the analysis is costly, most analysts are skeptical that clinical genomics will be a reality anytime soon. The article quotes William Blair analyst Amanda Murphy, who believes that "the wide-scale incorporation of whole genome sequencing into the clinical realm is 10 or more years away."

Nevertheless, a glut of genomes will certainly spur demand for more "creative" solutions to the problem. The same Genomics Law Report piece points to a year-old Wired article that suggest DIY genomics will be an option for people who want to side-step the traditional health care system:

None of this is simple, but it will become easier with time. As the retail costs of sequencing drops, a substantial niche will develop for innovators providing affordable, intuitive, accurate interpretation tools (embryonic versions already exist: see, for instance, Promethease or Enlis Genomics). Open-source academic software built for large-scale sequencing projects will be adapted for use by non-specialists. The increasing availability of large-scale computing power (for instance, via Amazon EC2), coupled with this intuitive software, will make even compute-intensive analyses available to the educated, motivated lay-person.

Given the wariness traditional doctors have shown toward alternative healthcare, the medical establishment is not likely to embrace this approach. And as the article notes, such solutions are not suitable for everyone. But for those willing to educate themselves about the technology, "there's no reason why a DIY genome couldn't be every bit as useful (or indeed as useless, in many cases) as one obtained through the doctor-as-gatekeeper route."

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