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Appetite for Sequencing, Additional Instruments Remains High Among NGS Users, Survey Finds

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This article has been updated with additional data regarding instrument usage.

NEW YORK (GenomeWeb) – Most operators of next-generation sequencing instrumentation plan to increase the usage of their instruments over the next year, and about a third plan to purchase additional NGS platforms in the future, according to a recent survey conducted by GenomeWeb and investment bank William Blair.

In addition, interest in technologies that provide long-range genomic information remains high, though only among a subset of NGS users.

The survey, which was sent by email to a subset of GenomeWeb's subscribers, was conducted June 9 to June 18 and asked recipients about their current and future use of NGS instrumentation, purchase plans, and their opinion on long-range genomic analysis platforms and new genomic technologies in general.

About two thirds of respondents were based in North America, 20 percent in Europe, and 15 percent in Asia Pacific. They represented laboratories at academic and government institutions, pharmaceutical and biotech companies, hospitals and clinical facilities, and commercial service providers.

Of the 273 readers who answered at least part of the survey, 208 use next-generation sequencing. Of these, 113 operate sequencing instruments in their own laboratory and do not outsource sequencing, 68 outsource sequencing to a service provider, and 27 do both.

The 121 survey participants who told us about their in-house sequencing platforms operate at least 780 NGS instruments between them. We made the assumption that participants who said they have either 1 or 2 HiSeq X instruments in fact own 10 or 20 HiSeq X instruments, since these machines are sold by Illumina in increments of five (HiSeq X Five) or 10 (HiSeq X Ten). 

The vast majority of these instruments —75 percent — are manufactured by Illumina, demonstrating the company's continuing market dominance, followed by platforms from Thermo Fisher Scientific's Ion Torrent (17 percent, including 10 Vela Sentosa SQ301 machines mentioned under "other"), Oxford Nanopore (4 percent), Pacific Biosciences (2 percent), Qiagen, and Roche 454 (each under 1 percent).

Not all laboratories are running their NGS instruments at full capacity. Of note, more than half of MinION, Ion Torrent, MiniSeq, and PacBio customers who provided usage information said they run their machines at 50 percent or less capacity. HiSeq instruments seem to have the best usage — more than half of respondents said they operate their instruments at 50 percent or more of their capacity.

The majority of platform owners plans to increase the usage of their NGS instrumentation over the next 12 months: more than 50 percent of HiSeq 3000/4000, NextSeq, HiSeq X, MiniSeq, Ion PGM, and Oxford Nanopore MinIon users said they plan to ramp up usage of their respective instruments, and all Ion S5, Oxford Nanopore PromethIon, and Qiagen GeneReader users said the same.

We also asked participants whether they plan to purchase additional sequencing instrumentation, and what their motivation for doing so would be. Thirty-one percent of 226 respondents said they plan to buy additional NGS platforms, among them 19 percent who want to do so within the next 12 months and 12 percent who consider buying more than a year from now. Of the remainder, 43 percent said they are unsure and 24 percent said they do not plan to buy NGS platforms.

Among the reasons why respondents want to add more sequencing instrumentation, the need for additional capacity stood out as the most frequently cited one, followed by a desire to lower operating costs, decrease the time to result, and bringing NGS applications in house.

The most frequent reasons for not wanting to purchase NGS equipment were irrelevance of the technology to a participant's research, that it would be too expensive to purchase or maintain an instrument, and that a user's current capacity is adequate.

We also asked survey participants what they believe will be the biggest growth drivers for their lab's future use of NGS. Clinical applications were cited most frequently by 154 participants, followed by translational research and sequencing as a service.

Asked what types of NGS platforms participants plan to purchase, they mentioned the HiSeq 3000/4000 most often (15 percent of responses), followed by the Ion S5, the MiSeq, and the NextSeq.

 

To assess what type of sequencing technology is most frequently outsourced, we asked participants which sequencing platforms they utilize through a service provider. HiSeq family instruments were mentioned most often (46 percent), followed by MiSeq (22 percent), Ion Torrent instruments (9 percent) and PacBio platforms (9 percent).

We also asked respondents about their opinion and use of long-range genome analysis technologies, including single-molecule sequencing platforms, such as those from Pacific Biosciences and Oxford Nanopore Technologies, and non-sequencing platforms, such as 10X Genomics' platforms for generating synthetic long reads from short reads, and BioNano Genomics' platform for single-molecule DNA mapping.

Of 152 respondents, 36 percent said short-read data alone is not sufficient for their applications, whereas 53 percent said short-read data is good enough, with the remainder saying they are unsure.

10X Genomics and Illumina offer approaches that can stitch together long synthetic reads from short sequence reads, but it is unclear whether these can provide the same type of information as bona fide long reads. We asked participants for their opinion, and of 34 respondents, half said synthetic long reads are sufficient for their applications, and 32 percent said they are not, while 18 percent said they were unsure.

In terms of applications for long-range technologies, de novo assembly of genomes or genome finishing was cited most often by 57 respondents, followed by structural variant analysis, transcriptome sequencing, haplotyping/phasing, and hybrid assembly.

Long-range technologies are currently only used by about a third of 155 participants: 13 percent said they have them in house, 18 percent use a service provider, and 1 percent do both. Oxford Nanopore's MinIon sequencer is the long-range technology most often installed in house right now, possibly due to its comparatively low cost. However, among participants who outsource long-range genome analysis, most use PacBio's sequencing technology.

In terms of purchase plans for long-read/long-range technologies, only 16 percent of 201 respondents said they plan to buy such a platform, while 35 percent said they are not planning to do so, and 46 percent said they are unsure. Those who do plan to purchase cited Oxford Nanopore's system most frequently.

Asked about what other new genomic technologies they are excited about, 113 participants provided a variety of write-in answers, of which several stood out for multiple mentions: single-molecule analysis (including single-molecule sequencing) was referenced 23 times, with 15 mentions of nanopore sequencing in particular; single-cell analysis was mentioned 14 times; and CRISPR gene editing came up eight times.

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