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AGBT: Ion Torrent to Launch 400-Base Reads for PGM this Year; User Reports Exome Sequencing


By Julia Karow

Life Technologies' Ion Torrent
plans to launch 2x200-base paired-end reads and 400-base fragment reads for the PGM later this year, along with new sets of custom and fixed-content AmpliSeq panels for targeted resequencing.

As some of its customers are beginning to use the instrument for clinical applications, the company also said that it plans to submit the PGM for clearance by the US Food and Drug Administration and CE-IVD certification this year.

Life Tech presented a roadmap for the PGM during a workshop at the Advances in Genome Biology and Technology meeting in Marco Island, Fla., last week. To showcase the instrument and its small footprint, company employees also sequenced a variety of samples in a mobile lab on an "Ion bus" parked on the beach in front of the conference hotel.

In addition, the company provided an update on the Proton, a new instrument based on the Ion semiconductor technology that will have increased throughput and is expected to ship to early-access customers by the middle of this year (IS 1/10/2011).

At the beginning of the year, Ion Torrent launched the 318 chip for the PGM, which has a nominal output of about a gigabase of sequence data. Internally, Ion researchers have already pushed the chip's performance further, generating more than 1.4 gigabases of data from a single run on the 318, and 2.2 gigabases from a 2x200-base paired-end run where 60 percent of the reads had a quality of Q47.

They have also generated an 877-megabase run on the 316 chip, which has a stated output of 100 megabases, and a 173-megabase run on the 314, which is officially supposed to generate only 10 megabases of data.

During the second half of this year, the company plans to launch a 400-base kit for the PGM. Internally, it is already generating reads exceeding 500 base pairs, Ion Torrent CEO and co-founder Jonathan Rothberg said during the workshop.

Ion also plans to launch additional custom and fixed AmpliSeq panels for targeted resequencing on the PGM. Last year, it launched the AmpliSeq Cancer Panel, which includes mutations in 604 loci from 46 oncogenes and tumor suppressor genes.

In the second quarter of this year, it plans to add an AmpliSeq panel for inherited diseases as well as a "comprehensive" cancer panel. It will launch the custom panel by the end of the first quarter.

Several PGM users provided examples at the workshop and meeting of how they have been using the platform so far.

Joe Boland, director of R&D development at the core genotyping facility of National Cancer Institute contractor SAIC-Frederick, reported at the meeting that his lab, which received its first PGM a year ago, recently purchased another five instruments and has been using them for exome sequencing.

His lab was already sequencing exomes routinely on the Illumina HiSeq 2000, where each run of up to 36 exomes takes six to eight days, but was looking for a second platform for this application in order to be faster and more flexible. For example, he said, fast exome data might be needed for a reviewer of a paper, if a single exome from a family study has failed, or if the HiSeq machine has downtime.

Boland and his team have been using the TargetSeq Exome Enrichment Kit in combination with Ion 316 and 318 chips to sequence exomes on the PGM, starting with a well-characterized HapMap trio. Their initial workflow took on the order of five days, including library preparation, capture, template prep, sequencing, and data analysis.

Since then, they have implemented a rapid exome pipeline, which they have applied to sequence families — for example, a five-member family afflicted by inherited melanoma. Library prep, sample capture, and template prep now take four days, followed by four-hour PGM runs, four to six hours of data processing time, and about half a day for variant calling. This allows for an "exome in a day," or about 24 hours from starting a sequence run to receiving results, Boland said.

To improve exome sequencing on the PGM further, he and his colleagues are working on better loading of the 318 chips to increase yield, using the OneTouch template prep device with 200-base kits, and adapting NimbleGen capture for the PGM. His lab will also be looking at the Ion Proton for exome sequencing.

Another customer, Sean Grimmond from the University of Queensland in Australia, said during the workshop that his lab has used the PGM, which it received January of last year, to look for mutations in pancreatic cancer for a project under the International Cancer Genome Consortium. Specifically, he and his colleagues have used the PGM to estimate tumor cellularity and to validate mutations.

Marilyn Li, director of the Cancer Genetics Laboratory at Baylor College of Medicine, reported using the PGM to detect clinically actionable mutations in cancer using the AmpliSeq Cancer Panel, a test the lab launched in December (CSN 11/30/2012).

Her lab has also been successful in identifying cancer mutations in archived FFPE samples using the technology, she said.

Timothy Triche from the Children's Hospital Los Angeles has performed RNA-seq on the PGM, generating RNA profiles on both primary and metastatic cancer samples. During the workshop, he noted that RNA appears to be more important in cancer than previously thought.

Ion Proton

The Ion Proton, which will be available to early-access customers by the middle of this year, has a list price of $149,000, but Rothberg said it is offering it for $99,000 to current users of the PGM, SOLiD, or rival Illumina’s HiSeq.

The Proton I chip, to be launched mid-year, will enable users to sequence two human exomes within a few hours, at a total cost of $500 per exome. The Proton II chip, to be released about six months later, will allow them to sequence a human genome at about 20x to 30x coverage for $1,000 in total, including sample prep, chip, and reagent costs.

Rothberg said that Ion has already sequenced exomes in a single day on the Proton using reagent kits developed for the PGM.

It has also sequenced the genomes of a family trio on the machine for a group at Yale University, work that the researchers plan to publish.

This story has been updated from a previous version to clarify the launch date and expected specifications of some upcoming Ion Torrent products.

Have topics you'd like to see covered in In Sequence? Contact the editor at jkarow [at] genomeweb [.] com.

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