NEW YORK (GenomeWeb) – Illumina continues to have a dominant presence in labs performing next-generation sequencing, and the majority of users planning to purchase a new NGS instrument are considering a platform from the company, according to a recent survey conducted by GenomeWeb in conjunction with investment bank William Blair.
But interest in technology that provides long-range genome information, which Illumina's short-read technology cannot provide on its own, is high, and Pacific Biosciences' PacBio RS II has been the instrument of choice for those operating a platform for long-range genomics.
Looking forward, most users consider purchasing an Oxford Nanopore sequencer for long-read applications. And when it comes to excitement about new technologies in general, users most often cited nanopore sequencing as well.
The online survey, which was emailed to a subset of GenomeWeb subscribers, was conducted from April 8 to April 15. One hundred and twenty respondents completed the survey in whole or in part, of which 64 percent said they currently operate NGS instrumentation in their laboratory, and 21 percent said they outsource NGS to a service provider.
Participants represented a wide range of laboratory types, including academic and government labs, hospital labs, commercial service providers and CROs, and pharmaceutical or biotech labs. Labs run by individual PIs, core facilities, and genome centers are all represented in the survey.
Almost 70 percent of the labs are located in the US or in Canada, about 15 percent in Europe, and the remainder in Asia-Pacific and elsewhere.
Sixty-six respondents operate a total of 338 next-gen sequencing instruments between them, according to the survey results. Of these, two-thirds are manufactured by Illumina, and 21 percent are Thermo Fisher Ion Torrent instruments. Pacific Biosciences and Oxford Nanopore each account for 5 percent of the machines, and Roche's legacy 454 for about 2 percent.
Almost half of the 223 Illumina instruments are HiSeqs 1000, 2000, or 2500, and about a third are MiSeqs/MiSeqs Dx. The remaining Illumina instruments are split between the ultra-high throughput HiSeq X Ten, the mid-throughput NextSeq, and the recently launched HiSeq 3000/4000.
Of the Ion Torrent platforms represented in the survey, about two-thirds are Ion PGM/PGM Dx and about a third are Ion Proton instruments.
Labs differ in how much they utilize their sequencers. Interestingly, the majority of HiSeq, MiSeq, and PacBio customers run their instruments at high capacity of more than 50 percent, whereas most Ion Torrent customers run their instruments at less than 50 percent capacity, and many at less than 10 percent. Maybe not surprisingly, utilization of Oxford Nanopore's MinIon, which is still in early-access testing, is also low at this point.
Forty-two percent of respondents said they plan to purchase a new NGS instrument, half of them within the next 12 months. Most often, labs are planning to purchase an Illumina HiSeq 3000/4000 or a MiSeq/MiSeq Dx, followed by a Next Seq 500/550, the Ion Torrent PGM/PGM Dx, Oxford Nanopore's MinIon, and the PacBio RS II.
Of note, among not-yet-available NGS platforms, interest in the Qiagen GeneReader appears high, whereas there is little to no interest yet in Roche's Genia, Oxford Nanopore's PromethIon, or new platforms to be launched by BGI and Complete Genomics.
Many companies have been developing sequencing-based and other technologies to obtain long-range genomic information, including Pacific Biosciences, Oxford Nanopore, BioNano Genomics, OpGen, NabSys, and, more recently, 10X Genomics. According to the survey, interest in these technologies is high, with about half of respondents stating they either operate such technology, outsource their needs for it, or are able to access instruments through a partner.
Of 11 participants operating their own long-range genome technology, eight have a PacBio RS II, underlining Pacific Biosciences' current dominance in this market, while two have nanopore sequencers, presumably Oxford Nanopore's MinIon, and one operates a BioNano Genomics Irys platform.
About 20 percent of respondents said they are planning to purchase a long-range genome analysis platform, either over the next year or longer term. Of 12 laboratories planning such a purchase, half mentioned they will consider the Oxford Nanopore MinIon, and four each said they are likely to purchase the not-yet-available Oxford Nanopore PromethIon or the PacBio RS II. Of note, only two respondents said they are considering the GemCode platform, launched by 10X Genomics earlier this year, which stitches short Illumina reads into long reads.
The survey also gauged participants' interest in new molecular technologies in general, asking them to write in what technologies they are most excited about. About half of 44 respondents mentioned new sequencing technologies, and of those, 70 percent pointed to nanopore sequencing, including Oxford Nanopore and others.
Non-sequencing technologies mentioned included those offered by RainDance Technologies and NanoString Technologies, as well as mass spectrometry, genome editing with CRISPR, DNA synthesis technologies, and DNA extraction methods.
In addition, a number of participants cited new or improved applications, such as RNA-seq, single-cell sequencing, and epigenetics, rather than technologies.