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EdgeBio Assessment Finds Illumina, Ion Cancer Panels Perform Equally Well, with a Few Differences


Less than a year after gaining CLIA certification and launching a clinical exome sequencing test, service provider EdgeBio has been testing targeted cancer panels from Life Technologies' Ion Torrent and Illumina and exploring targeted sequencing of formalin-fixed, paraffin-embedded samples in its research lab.

EdgeBio maintains a variety of sequencing platforms, including several Ion Torrent PGMs, which it has had for almost three years, several Illumina HiSeqs, and a MiSeq, which it added about six months ago. The company is also considering purchasing an Ion Proton.

Exome sequencing is the company's "bread and butter," according to Justin Johnson, EdgeBio's director of bioinformatics, but lately, the firm has also investigated panels from both Illumina and Ion Torrent.

In a recent post on its blog, the company compared the Illumina TruSeq Amplicon Cancer Panel to the Ion Torrent AmpliSeq Cancer Hotspot Panel v2. EdgeBio currently offers both panels as a research service but not as a clinical sequencing service.

The TruSeq panel covers 28.6 megabases of sequence, including about 3,150 mutations from the COSMIC Catalogue of Somatic Mutations in Cancer, while the AmpliSeq panel covers about 22 megabases of sequence, or about 3,000 COSMIC mutations.

According to EdgeBio's analysis, both panels share about 13.4 megabases of sequence and about 2,600 COSMIC mutations.

Using three well-characterized cancer cell lines from the Cancer Cell Line Encyclopedia, the researchers sequenced the TruSeq panel on the MiSeq with 2x150 bp reads. Previously, they had sequenced the AmpliSeq Cancer Hotspot panel – along with other AmpliSeq panels — in one of these cancer cell lines, HCT-15, using a PGM 314 chip, results of which they published on their blog late last year.

Both panels identified all the known COSMIC mutations in the cancer cell lines. "Both of them performed equally well in our hands," said Johnson.

The company has been conducting these types of comparisons to give its customers some guideline for choosing the most suitable technology for their projects, he said.

The assessments also serve as a community resource, providing researchers with free datasets on which to test their software, for example. "Typically, when you get datasets released by the vendors themselves, they are the best of 50 runs that they tried," Johnson told CSN. "We like to show kind of real, everyday datasets that may not be the best, but it's what you can probably expect on a day-to-day basis."

Since both panels performed well in the comparison, Johnson recommended that customers focus on content, and how many of their mutations of interest are covered by the panels.

Prices for both panels are "pretty similar," he said, though coverage is higher from a MiSeq run, which generates about 8 gigabases of data, compared to a PGM run, which yields about one gigabase with the 318 chip, making for a lower cost per base for MiSeq than PGM.

Regarding the informatics, EdgeBio is "well equipped" to handle both data types, he said, though most open-source data analysis software is currently geared towards Illumina data.

Another difference between the panels – which is also the case for custom panels – is that Ion Torrent allows customers to order smaller quantities than Illumina, so customers can try them on smaller pilot projects first. "With Illumina, you really need 96 [samples] minimum to do this, which is a challenge because a lot of people either don't have that many samples, or when they do have that many, they want to start out with a lower amount and see some modicum of success before they open it up on their entire sample collection," Johnson said.

For EdgeBio, offering targeted panels in its CLIA lab "would probably be more straightforward to do with the MiSeq," Johnson said, because many of the processes and the informatics overlap with the HiSeq that already runs in the CLIA lab.

After validating targeted panels in the research lab, "[we] hope to eventually roll these out under our clinical offering," he said, probably within six to nine months. On the customer side, the greatest interest in clinical panels has been for cancer, he said.

Customers are also very interested in FFPE sequencing, and EdgeBio has conducted a lot of internal research in this area, but the company is still a "ways away" from offering this clinically.

Its research arm is currently offering FFPE sequencing for both AmpliSeq and TruSeq panels, and has seen good results with those, "but we haven't really gone full-scale production on accepting FFPE samples through our research arm," Johnson said. "FFPE is a tricky beast."

For whole-genome and exome sequencing of FFPE samples, the firm is "still in the piloting phase of doing some internal R&D," he added.

EdgeBio plans to conduct additional panel comparisons in the future, Johnson said, including one between Illumina's TruSight Cancer set, which the company announced last September, and Ion's AmpliSeq Comprehensive Cancer Panel; as well as one between the Illumina TruSight Exome set, which covers the "actionable" exome, and the Ion AmpliSeq Inherited Disease Panel.

The firm already tested the Ion AmpliSeq Comprehensive Cancer Panel and the Ion AmpliSeq Inherited Disease Panel last year and found that they each missed a few known variants, mostly located near homopolymer regions and regions of low coverage. However, Johnson said that these problems will be addressed with future software releases from Ion Torrent, according to feedback he received from the company.