By Julia Karow
Life Technology's Ion Torrent has been improving the Personal Genome Machine's throughput, read length, accuracy, and sample prep and believes it will achieve 400-base reads later this year and be able to sequence a human genome for $1,000 by early 2013, according to the company's founder, Jonathan Rothberg.
At the Consumer Genetics conference in Boston last week, Rothberg said that one of Ion Torrent's customers, the Broad Institute, recently beat the Life Technologies subsidiary's own throughput record for the Ion 316 chip by about 20 percent by generating almost 290 megabases of data in a single run. The 316 chip, which is currently in early-access testing and due to be released at the end of this month, has 6.1 million accessible sensors and is officially supposed to produce only about 100 megabases per run, or a million 100-base reads (IS 3/1/2011).
Recently, the company has also sequenced the Escherichia coli genome on the Ion 318 chip, which is currently in development and expected to increase the output per run to about a gigabase. This chip, which will have 11 million accessible sensors and is scheduled to be launched in the fourth quarter, reduces the number of transistors per sensor to two from three. Ion Torrent researchers were able to cover the 4.7-megabase E. coli genome 61-fold in one run on the chip, Rothberg said, translating to about 300 megabases of data, and achieved uniform genome coverage as well as good consensus accuracy. They detected 90 errors in the sequence data, most of them deletion errors.
Rothberg said that the company has achieved reads longer than 260 bases now internally, and low-quality reads of more than 300 bases. "We are very confident that this year, we will actually hit 400 bases," he said, but he did not mention when those reads would become available to customers.
In response to a question from the audience, Rothberg confirmed that the company is currently not working on paired-end reads but plans to introduce a kit for generating mate pairs. Given "limited resources," he explained, the company prefers to put its energy into longer reads than into paired ends, which he suggested may no longer be needed once read lengths reach 400 bases. He did not say when the mate pair kit will be commercially available.
The error rate at 100 bases is currently about 1.5 percent, which Rothberg said is "not that bad" compared to other technologies. In recent runs at the company, he added, the error rate has decreased to less than 1 percent.
The homopolymer accuracy has improved to 99 percent for 6-mers, he said, adding that homopolymer errors are "pretty much" due to software processing rather than the electronic sensors.
Sample prep for the PGM currently takes about five to six hours, he said, including two to three hours of library preparation and three hours of template amplification and preparation on the Ion OneTouch, a new system that the company plans to start shipping later this month (IS 4/26/2011).
Earlier this year, Rothberg reported that Ion Torrent had sequenced its first human genome on the PGM, that of Intel co-founder Gordon Moore. Last week, he added that the firm has sequenced Moore's genome to about 10.6-fold coverage. Despite this comparatively low coverage, the scientists were able to sequence 99.2 percent of his genome, which Rothberg attributed to the low bias of the technology. The researchers called about 2.6 million SNPs as well as more than 3,400 deletions and insertions in Moore's genome.
Based on the progress so far, Rothberg predicted that by January 2013, customers will be able to sequence a human genome at a cost of $1,000 using Ion Torrent's technology, and by July 2013, at a cost of $500. He did not mention whether that number includes only consumables or also labor and other cost factors.
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