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Life Tech Launches Cancer Panel, Amplicon Sequencing Kit for Ion PGM; Plans 510(k) Filing in 2012


By Monica Heger

Life Technologies' Ion Torrent has launched a cancer gene panel for research purposes based on a new amplicon sequencing kit. The panel encompasses more than 700 mutations within 190 amplicons from 46 cancer genes.

The majority of the loci are covered at around 500-fold coverage when the AmpliSeq Cancer Panel is used with the company's Ion 314 chip, Maneesh Jain, vice president of marketing and business development at Ion Torrent, told Clinical Sequencing News. Variants can be detected at a frequency as low as 5 percent, according to the firm.

Separately, Jain said that the company plans to file in 2012 for 510(k) clearance of the PGM with the US Food and Drug Administration, though he declined to comment on what assay the company would submit for clearance alongside the instrument. He said that the company is currently in discussions with the FDA and did not have a timeline as to when it expects to gain approval.

However, he said, "we do have a precedent at Life," noting the company's 7500 Fast Dx Real-Time PCR instrument, which has 510(k) clearance, and its 3500 Dx capillary electrophoresis sequencer, which it submitted to the FDA for 510(k) clearance in August (CSN 8/3/2011).

The cancer panel is the first product based on Ion Torrent's AmpliSeq technology, which it is also launching this week. The new kit is able to multiplex-PCR 480 amplicons in one tube for sequencing.

According to Jain, the company identified a need for a "simple, up-front prep" for amplicon sequencing, particularly in the cancer space. PCR is typically not scalable, he said, and while target capture can enrich a large portion of the genome, it can take two to three days, he added.

Considering that sequencing on the PGM now takes only around 90 minutes, it is "inconsistent to have an upfront workflow that takes that long," he said.

In response, the team developed a 480-plex PCR that can be done in a single tube starting with 10 nanograms of DNA.

The initial cancer panel will target just 190 amplicons, so it can easily be scaled to include more genes. Additionally, the 480-plex protocol is also scalable. Researchers can use the 316 chip or the 318 chip for larger samples or to barcode, said Jain.

The 10 nanograms of starting DNA for the cancer panel can come from formalin-fixed paraffin-embedded, frozen, or fresh tissue. Sample prep takes three and a half hours, with under 10 minutes of hands-on time, so results can be obtained in a total of 10 hours, Jain said.

He said that the company collaborated with oncologists to develop the panel — including Christopher Corless, the medical director of the Knight Diagnostic Laboratories at Oregon Health and Science University — in order to choose the most relevant cancer genes.

Corless said in a statement that his team has so far achieved "perfect correlation, in that every mutation we knew about going into the study emerged on the other end."

Another collaborator, Marilyn Li at the Cancer Genetics Laboratory at Baylor College of Medicine, added that her team sees "great potential for diagnostic applications" for the panel.

Life Tech is also participating in a project funded by the UK's Technology Strategy Board to develop a 150-gene cancer panel for the PGM (CSN 6/21/2011).

For that program, which is funding six tumor-profiling projects with a total of £5.8 million ($9.4 million), the UK's Technology Strategy Board requires that each cancer panel must screen for at least 22 specified mutations in nine known cancer genes: KRAS, BRAF, TP53, PI3KCA, UGT1A1, PTEN, CYP2D6, EFGR, and CKIT.

The test Life Tech is developing for the UK program will sequence 150 genes, but clinicians will have the option of ordering either the basic report covering the mutations specified by the TSB, or the full report covering all 150 genes.

Have topics you'd like to see covered by Clinical Sequencing News? Contact the editor at mheger [at] genomeweb [.] com.