Life Technologies provided updates for several upcoming product launches, including the PII chip for its Ion Proton system, a new AmpliSeq Exome kit, the Ion Chef system for automated sample prep, and its Hi-Q sequencing chemistry, at last week's Advances in Genome Biology and Technology meeting in Marco Island, Fla.
Additionally, a couple of customers presented early data from the Ion Chef, Hi-Q chemistry, and the AmpliSeq Exome RDY kit.
Ion Chef and the PII chip were originally scheduled to launch commercially in the first half of 2013 and mid-2013, respectively. The company said last week that the Ion Chef is currently in the hands of seven early access users with full commercial launch slated for the end of the month or early March. The PII chip, meantime, will be sent to early access users late in the second quarter. The company has not yet decided how long the early access program for the PII chip will run, but commercial launch will occur after that concludes, likely the second half of the year.
Joe Boland, director of the National Cancer Institute's Cancer Genomics Research Laboratory, has been testing the Ion Chef system since mid-November. During a Life Tech-sponsored workshop at AGBT, he said that his lab has completed 37 runs on the Ion Chef, 36 of which were successful. Mechanical issues due to not having cleaned the centrifuge caused the one failed run.
The laboratory runs six Ion Torrent PGMs, four Ion Proton systems, two Illumina HiSeqs, and one MiSeq. The PGMs are the "primary workhorse for amplicon sequencing," Boland said, while the Protons are used for exome sequencing, as well as larger panels or to obtain deeper coverage on panels.
The Ion Chef processes two chips at a time and at the NCI's CGR lab, it uses the 200-bp chemistry and is hooked up to two different PGM machines so that the chips go immediately from the Chef to sequencing. However, Boland said that he has also run two chips through the Chef for sample prep, and then through the PGM one at a time.
Boland said the lab ran a comparison of the Ion Chef to the One Touch 2 on a custom-designed AmpliSeq panel for cervical cancer. The lab ran 56 barcoded samples and "all metrics improved with the Chef," including the number of mapped reads and loading efficiency. Additionally, using the Chef for sample prep yielded about 1 million more reads compared to the One Touch 2. Concordance between the two systems was greater than 97 percent, with overall accuracy slightly better with the Chef, he said. Out of 3,280 calls, 82 were discordant, mostly due to a lack of reads at those positions, Boland said.
"We are approaching the point where we will have a complete pipeline of automation," Boland said.
Boland's lab has also been testing the company's new Hi-Q chemistry, which was designed to reduce systematic errors on Ion sequencing systems, particularly the indel error rate.
Life Tech has made the sequencing kit available through its Technology Access Program, where it makes products available prior to their full commercial launch.
Boland said his lab received the Hi-Q sequencing kit in January. On its first run, he tested the kit on 89 barcoded breast cancer samples and ran the BRCA1/2 AmpliSeq panel using the 318 chip.
Compared to the standard sequencing kit, Hi-Q improved accuracy and uniformity of coverage, Boland said. Looking at indel calls specifically, sequencing with the Hi-Q chemistry yielded 20 total calls, 13 of which were errors; while the old chemistry resulted in 40 calls, 33 of which were errors, he said.
Boland did not specify the overall error rate of the Hi-Q system, but Alan Williams, vice president of R&D at Ion Torrent, said that the overall error rate is between .2 percent and .4 percent.
One customer that has used the kit through the Technology Access Program has achieved a 70 percent reduction in deletion error rate and 30 percent reduction in insertion error rate, while another customer has reported a 64 percent reduction in deletion error rate, Williams said.
Also during the Life Tech workshop, Milan Radovich an assistant professor at Indiana University School of Medicine, presented on work he has been doing using the Ion Proton for transcriptome sequencing of breast cancer patients. He is using the Proton to do RNA-seq of patient-derived xenografts, as well as within the context of clinical trials to see how treatment impacts changes in gene expression.
Additionally, he is an early access user of the AmpliSeq Exome RDY product, in which primers are pre-spotted in 96-well plates. The product can be configured to run either two exomes per plate or eight exomes per plate.
Radovich ran a matched tumor/normal sample and said that his lab "got robust product of sequence data," generating around 14 gigabases with 200-bp reads. From the normal blood sample, 95 percent of reads were on target and 91 percent of the target was covered at 20x or greater. While the product is not designed specifically for formalin-fixed paraffin-embedded tumor DNA, he said that the group found that the FFPE sample also produced "robust metrics." Around 92 percent of the bases were on target and 83 percent were covered at 20x or greater.
The company did not give a timeline for when the AmpliSeq Exome RDY product would be commercially launched. According to Williams, the kit will have a six-hour workflow, including 50 minutes of hands-on time. Compared to the standard AmpliSeq Exome, the Exome RDY kit improves amplicon representation, Williams said.
Williams also gave an update on the company's Proton PII chip. Life Tech received the first chips in-house three weeks ago. He described the PII chip as akin to a 660-megapixel proton video camera and said it contains four times as many wells and transistors.
Thus far, the company has run two human genomes, in one case designing a 91-bp fragment library and in another a 125-bp fragment library. Additionally, in collaboration with Leonid Moroz, a professor of neuroscience, biology, and chemistry at the University of Florida, the company did transcriptome sequencing from a 75-bp library.
Data was only extracted from one quadrant of the chip in each case, Williams said. He added that initial applications will be transcriptome sequencing and other counting applications. The PII chip will enter early access in May or June, with commercial launch sometime in the second half of the year.