By Monica Heger
This story was originally published Oct. 14.
MONTREAL ― Life Technologies has launched a number of improvements for its Ion Torrent PGM and is planning several more products that will improve the speed and throughput of its benchtop sequencer, company officials said last week at the combined International Congress of Human Genetics/American Society of Human Genetics meeting here.
The company is also developing new sample-prep technology for its SOLiD 5500 machine that will eliminate the use of emulsion PCR. The new protocol, dubbed Wildfire, is slated for launch in the first half of 2012.
Among the new launches for the PGM are a new library prep kit that reduces the time required from four hours to two hours with a few minutes of hands-on time. The company has also released a new version of its Torrent Suite analysis software; a new barcode adapter kit that is scalable up to 384 barcodes; and the TargetSeq custom enrichment kit, which it launched for SOLiD this summer but has now made available for the PGM (IS 5/31/2011).
Additionally, Ion plans to release in the coming weeks a kit for sequencing 200-base pair reads ― twice the length of the system's current read length. It has posted data from the new kit on its website, as well as datasets from its 318 chip, which it plans to launch by the end of the year.
Further down the road, the company plans to start offering exome sequencing for the PGM, company founder and CEO Jonathan Rothberg said at an Ion Torrent user meeting at the conference. It is also developing paired-end protocols for the platform, Maneesh Jain, Ion Torrent's vice president of marketing and business development, told In Sequence.
200-Base Reads
Jain said that the company was able to achieve longer read lengths for the system by improving both its enzymology and the algorithms it uses for data analysis. On the enzymology side, he said that the researchers were able to improve the "fidelity of the polymerase" so that it essentially maintained its signal for longer.
The 200-base read kit will start shipping in a "few weeks," he said. He said the company is already achieving even longer reads internally, in some cases obtaining perfect reads of over 500 bases.
At the PGM user group meeting in Montreal, Donna Muzny, the director of operations at the Human Genome Sequencing Center at Baylor College of Medicine and an early-access user of the long-read technology, said that her team has done around 20 runs on the 316 chip with the long-read technology, obtaining an average of 250 megabases of aligned Q17 data per run and an average read length of 158 base pairs.
Most recently, she has used the platform to do amplicon sequencing of four cancer genes, including KRAS and TP53, pooling 1,400 amplicons around 150 kilobases long. For that experiment the team generated reads of 200 base pairs with 98 percent of the bases covered at 20-fold. Comparing the results to data from the Roche 454 platform, 830 out of 931 validation sites were validated on both platforms. There were 21 PGM unique calls, six 454-specific calls, and five discordant calls.
Also at the user group meeting, Rothberg said that the company has internally started sequencing exomes. He said the team has compared its internally generated data to recently published exome sequencing data by Mike Snyder's group at Stanford, and that the Ion team was able to "cover more of the genome." He did not provide a timeline for when customers would be able to do exome sequencing on the PGM.
Aside from longer reads and faster sample prep, Ion also launched this week a kit for amplicon sequencing, along with a 46-gene cancer panel (CSN 10/12/2011).
SOLiD 5500
While Life Tech said recently that it would primarily focus its efforts on the PGM going forward, it has not completely abandoned its SOLiD instrument (IS 9/20/2011).
At ICHG/ASHG, Mark Gardner, Life Tech's vice president and general manager of advanced genomic systems, said that the company is working on a new sample-prep technology, dubbed Wildfire, that will be based on isothermal amplification, eliminating emulsion PCR. Additionally, the entire protocol will take place on the instrument, reducing hands-on time.
Using Wildfire, the amplification step will take 30 minutes and the total sample-prep from library construction until sequencing starts will take two hours. Sample prep for the 5500 using LifeTech's EZ Bead system currently takes around eight hours with one hour of hands on time.
Essentially, Gardner said, "you coat the flow cell with primers, which is like the wood for the fire, and then add template and isothermally amplify." As the templates grow and abut against each other, that causes them to "put each other out," so that each fragment remains isolated.
The Wildfire technology will also make the 5500 more flexible, Gardner added. Researchers can run one lane or 12 lanes, and use only the necessary reagents, which will "significantly reduce cost," bringing the price of an exome down to just a few hundred dollars.
The technology also has the ability to increase throughput five-fold, when the machine is fully loaded, by increasing the density of DNA fragments on the flow cell. Currently, the flow cells have a density of about 400,000 "features" ― independent DNA colonies ― per square millimeter. With the new technology, that density will increase to one million features per square millimeter and both sides of the flow cell can be used.
Gardner said that the company plans to start rolling out the technology to customers in the first half of next year.
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