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Survey: Among New Platforms, MinIon Expected to Have Greatest Impact, NextSeq Most Likely Purchased

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This article was originally published May 5.

NEW YORK (GenomeWeb) − Several new sequencing platforms have hit the market or are scheduled to be released this year, including Illumina's HiSeq X Ten and NextSeq 500, Oxford Nanopore's MinIon, and Qiagen's GeneReader. According to a recent survey by Mizuho Securities USA in collaboration with GenomeWeb, users believe the MinIon will have the greatest impact, though they are most likely to purchase the NextSeq 500.

The survey was conducted at the end of the first quarter, targeting a subset of GenomeWeb's readership. Fifty-six individuals completed the survey in part or in whole, and about three-quarters of them said they actively produce or analyze sequence data.

Asked which of the new sequencing platforms they were most likely to purchase, about 30 percent chose the NextSeq 500, a desktop sequencer Illumina announced at the beginning of this year and started shipping during the first quarter.

Eighteen percent said they would purchase Oxford Nanopore's MinIon, which was recently sent to the first batch of early-access customers for testing, and about four percent chose Illumina's HiSeq X Ten, the high-throughput sequencing 10-pack that Illumina recently started installing at customer sites.

One respondent opted for Qiagen's GeneReader, which the company put in the hands of some early testers last year, and one wrote he will be receiving the GenapSys Genius, a desktop sequencer that startup GenapSys presented at a conference in February.

Almost half of respondents said they would not purchase any of the new platforms, a portion of them likely because they do not generate any sequence data.

One survey participant said that while he is "very interested" in the MinIon, he needs to see more data first to determine how it would fit his lab's sequencing needs. Another said he would be "more likely to get another MiSeq or HiSeq" from Illumina rather than one of the new platforms, and a third said the only instruments he is planning to purchase are multiple MiSeqDx machines from Illumina, not a new platform.

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Opinions about which new platform will have the greatest impact on the field differed somewhat from plans to purchase them. About 35 percent of respondents said they believe the MinIon will impact sequencing the most, followed by about 30 percent who opted for the X Ten and about quarter who chose the NextGen 500, while just one participant selected the GeneReader.

Several respondents commented on the impact of the X Ten, noting that it "will be interesting to see if the demand for human whole-genome sequencing exists," that "there will still be challenges associated with the analysis of large numbers" of human genomes, and that its impact will be limited by its focus on human genome sequencing.

Illumina restricts the use of the HiSeq X Ten, which consists of 10 individual instruments, to human genome sequencing and recently began shipping the first instruments to customers.

Regarding the MinIon, one participant said that it "fits a unique niche and therefore will likely change the field most," while another said "it could be a significant technological advancement," but will not replace targeted sequencing with short, high-fidelity reads.

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Asked to directly compare the Illumina MiSeq and the Ion Torrent PGM, survey participants placed the MiSeq first in most categories, namely usability, accuracy, ease of sample prep, read length, throughput, and promise. Both platforms fared about the same with regard to reagent price and price per base, and the PGM ranked first in terms of instrument price and run time.

Overall, these results do not differ much from last year's survey, with the exception of price per base, where the PGM scored better than the MiSeq this year.

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One respondent suggested that a direct comparison between the MiSeq and the PGM might no longer be appropriate, since "with the launch of v3 chemistry, the MiSeq competes with the [Ion] Proton more than the PGM."

According to specs posted on the manufacturers' websites, the MiSeq produces up to 15 gigbases per run with 2x300 base pair reads, using v3 reagent kits. The PGM currently produces up to 2 gigabases per run with 400 base pair reads, and the Ion Proton yields up to 10 gigabases per run with 200 base pair reads.

Asked to compare the Illumina HiSeq and the Ion Proton side by side, respondents ranked the HiSeq first in all but two metrics – run time and instrument price. This marks a shift compared to last year, when the Proton won out in two other categories, promise and reagent price.

One user commented that the Ion Proton is "nowhere near the HiSeq yet in terms of throughput and the data quality is also relatively poor," and another one noted that he is "still waiting for the PII chip for the Proton."

The HiSeq 2500 currently produces up to 1 terabase of data with 2x125 base pair reads, using the HiSeq SBS Kit v4 reagents.

The PII chip, scheduled to go out to early customers by midyear, will double the output per run to about 30 gigabases initially, and more later on. Its release, originally planned for mid-2013, has been delayed due to development challenges.

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Thermo Fisher's acquisition of Life Technologies, which owns Ion Torrent, was apparently a minor factor in ranking Illumina's platforms higher than Ion Proton's. Just a quarter of respondents said the merger caused disruptions in Ion Torrent's business, while three quarters either said it did not affect it or declined to comment.

Almost half of survey respondents work in academia or for the government, almost a quarter in the pharmaceutical or biotech industries, and the remainder in hospitals, at diagnostic product companies, medical device firms, or other areas.

Approximately two-thirds of participants are based in the US or Canada, 15 percent in Europe, 13 percent in Asia, 5 percent in the rest of the Americas, and 5 percent in Australia or New Zealand.

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