Thermo Fisher's Life Technologies has begun shipping its Ion Chef system for sample prep on the Ion Torrent PGM. Several early access customers that have been using the system since last winter told In Sequence that compared to the One Touch 2 system, the Ion Chef is more automated, which saves time and makes the process less variable.
The Ion Chef is a $55,000 sample prep system that reduces hands-on time to about 15 minutes. Overall time is comparable to the One Touch 2, at about eight hours, but the Chef can process two chips at once, each of which can be loaded with different samples.
Life Tech originally planned to launch the system in the first half of 2013. In February, the company said at the Advances in Genome Biology and Technology meeting in Marco Island, Fla., that around seven early access customers were testing the system, including the National Cancer Institute's Joe Boland, who had completed about 36 runs at the time.
Last week, early access users from contract research organization AI Biotech and Sanford-Burnham Medical Research Institute discussed with IS their experiences thus far.
Brian James, who directs the Genomics DNA Analysis Facility at Sanford-Burnham, told IS that his lab has completed around 30 runs on the Chef since receiving the instrument in December.
One of the main advantages of the system over the One Touch 2, he said, is the amount of hands-on time it saves. While total time is about the same, he said, the Chef "removes a lot of the pipetting and saves a lot of hands-on work." Typically, he will set the system up to run overnight, and in the morning, two chips will be ready to be put on the PGM.
Loading efficiency between the Chef and OT2 is similar, between 70 percent and 80 percent, he said, but the Chef "takes out a lot of the art" of loading chips.
Performance-wise, the two systems are also comparable, he said. James said the lab is primarily running Ion's AmpliSeq Comprehensive Cancer panel using the 318 chip. With the Chef, the lab is generating around 5.2 million reads and a median raw accuracy of 99.5 percent from fresh-frozen cancer tissue samples.
Sanford-Burnham also has one Ion Proton, and James said he plans to start using the Chef for sample prep on that system once Life Tech begins selling the reagents. He anticipates that using the Chef with the Proton will yield even greater benefits, since the Proton is more labor-intensive than the PGM. Life Tech said it will ship kits for use on the Proton in the second quarter of this year.
Greg Meyers, vice president of DNA services at AI Biotech, agreed with James that the main benefit of the Ion Chef is its reduction of hands-on time compared to the One Touch systems.
AI Biotech operates 11 PGMs, Roche's 454 system, and an Illumina HiSeq 2500. Meyers said that in the lab's CLIA-certified and CAP-accredited laboratory it is running custom-designed AmpliSeq cytochrome P450 panels for physicians doing pharmacogenomics testing.
Meyers said that the lab began using the Ion Chef in the fall and has completed between 50 runs and 100 runs of two chips each. Data quality and performance has been roughly equal between the Chef and One Touch. One area that the Chef performs a bit better is that it produces between 10 percent and 30 percent more full-length amplicons than the One Touch systems, Meyers said. Amplicons are around 150 bases to 200 bases, and with the Chef, a "higher proportion are sequenced end to end, instead of being truncated."
Additionally, the lab had previously been using the 316 chip, but is planning to switch to the 318 chip, which will enable pooling of up to 64 samples or 96 samples per chip.
On average, Meyers said the lab generates around 7.5 million reads, about 99 percent of which map. Loading efficiency has been slightly lower, around 79 percent to 80 percent compared to 84 percent or 85 percent with the One Touch, but "it's a more even load," he said.
AI Biotech's CYP panel screens primarily for known SNPs and a few indels, and so far, Meyers said there has been no difference in accuracy.
The CRO also recently began moving into the oncology field and has validated Ion's AmpliSeq Hotspot panel in its CLIA laboratory. It will soon begin working with another firm that focuses on cancer proteomics to corroborate the firm's proteomics findings with the AmpliSeq Hotspot panel in order to guide cancer treatment.
Meyers said that the lab validated the panel with the One Touch system first because initially they will only be working with a handful of samples at a time, but once the lab scales up, the Chef "will be crucial to driving our production pipeline."