By Kevin Davies
April 1, 2008 | Amelia, Barb, Clara, Florence, Joan, and Liz.
No, they're not the girls in the final top twelve on American Idol. They are the affectionate nicknames of various next-generation sequencing instruments at Applied Biosystems' Beverly, Mass., research facility, corresponding to famous female scientists. In case you're wondering, that would include Amelia Earhart; Nobel laureate Barbara McClintock; Clara Barton, founder of the Red Cross; Junko "Joan" Tabei, first woman to climb Everest; and the first American female doctor, Elizabeth Blackwell. (Ten years ago, scientists at Applied Biosystems' sister company Celera Genomics named its fleet of sequencing machines after famous science fiction characters.)
It's unwise to read too much into "science by press release," but an announcement from ABI last month is, on the face of it, impressive: Amelia et al., under the direction of Kevin McKernan's group, has sequenced a complete human genome sample for about $60,000*! Until a peer-review publication, the figure warrants an asterisk: ABI says the estimate refers to the cost of the reagents for the SOLiD platform's sample prep and ligation chemistry. It does not include staff, overhead, or instrument depreciation costs. (Embossing might be additional, too.)
We visited McKernan, senior director of product operations, twelve months ago as his team put Amelia et al. through their paces (See "The Drive for the $1000 Genome," Bio•IT World, May 2007). At that time, his goal was primarily to get the SOLiD platform ready for commercial release. But as McKernan and Gina Costa noted at Marco Island earlier this year, the group has made remarkable progress in increasing the per run output from the SOLiD system.
The DNA came from an anonymous Nigerian donor to the International HapMap Project. McKernan's group produced a total of 36 Gigabases of sequence data, for 12-fold coverage, in seven runs of the SOLiD system using a paired-end strategy, reaching a maximum output of 9 Gigabases in a single instrument run. ABI also touted the inherent accuracy of SOLiD's two-base color encoding system, which resulted in almost 99.95% accuracy in distinguishing millions of naturally occurring polymorphisms from artifacts and sequencing errors.
McKernan's group has transferred the sequence data to the National Center for Biotechnology Information (NCBI), where the files are publicly available via FTP: ftp://ftp.ncbi.nih.gov/pub/TraceDB/ShortRead/SRA000272
For now, ABI appears to have edged ahead in the pursuit of the $1,000 genome. It was only in February that Illumina said it had fully sequenced another HapMap sample for about $100,000 (See, "PacBio Sparks Florida Fireworks," Bio•IT World, March 2008).
The plummeting cost of sequencing is truly impressive. J. Craig Venter estimated that his genome sequence, published last fall, cost $70 million. (It began in 1999, and did not involve next-generation sequencing.) James Watson's genome, in press in Nature, cost 454 Life Sciences between $1-2 million. (See "Project Jim: Watson's Genome Goes Public," Bio•IT World, June 2007) But Watson isn't advising the rich and famous to splash out just yet. "Would I rather have my genome sequenced or have a Bentley?" he said recently. "Uh, toss up."
Earlier this year, George Church's new company, Knome, sold Dan Stoicescu, a Romanian biotech entrepreneur living in Switzerland, and a Chinese businessman their personal genomes for the retail price of $350,000. That sequencing work is being done at the Beijing Genome Institute in Shenzen, China.
The sequencing field has seen plenty of hype over the years. When one hears Helicos predicting a clear path to the $1,000 genome within two years, or Pacific Biosciences proclaiming a $100 genome by 2013, it's easy to scoff. But asterisks notwithstanding, ABI and Illumina have already surpassed the original NIH timetable, which didn't envision the $100,000 human genome before 2009 .
Do the math: output goes up, price goes down. In the words of Victoria, Geri, and that other band of girls, the sequencing revolution is going to spice up your life!
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This article appeared in Bio-IT World Magazine.
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