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Illumina Remains NGS Leader But Competitors Expected to Gain, Survey Finds


NEW YORK (GenomeWeb) – More than a third of next-generation sequencing users plan to purchase a new NGS system within the next year, according to a recent survey conducted by GenomeWeb in collaboration with investment bank William Blair, demand that appears to be driven by increased assay sizes, new applications such as liquid biopsy testing, and large-scale cohort sequencing projects.

In addition, three quarters of survey participants expect their investment in sequencing instrumentation will increase over the next two to three years, and more than 80 percent anticipate their sequencing consumables purchases will go up over the same time period.

The results indicate that demand for next-gen sequencing platforms remains strong and a significant set of users is willing to upgrade their existing platforms with improved technology that promises better performance, lower cost per base, and increased capacity.

Illumina short-read NGS platforms, in particular the NovaSeq and the NextSeq, remain most popular among customers planning to buy a new sequencer, but their stated purchase plans also indicate that Qiagen, Oxford Nanopore, and Pacific Biosciences may gain market share, at the expense of Illumina and Thermo Fisher Scientific.

The survey was conducted in the first half of December 2017. A link to questions was emailed to a subset of GenomeWeb subscribers, targeting a variety of organizations and excluding instrument manufacturers/vendors, management consultants/venture capital/law firms, and public relations/advertising firms. Overall, 303 readers provided answers to at least a subset of the questions.

About two thirds of responses came from North America, 18 percent from Europe, 11 percent from Asia-Pacific, and 5 percent from other countries.

Forty-two percent of the responses came from academic government labs, genome centers, or core facilities; 29 percent from biopharmaceutical companies or commercial service providers/contract research organizations; 16 percent from independent clinical labs or hospital labs; and 13 percent from other organizations, many of which indicated they do not operate laboratories.



Almost 60 percent of respondents said they currently operate NGS instrumentation, and of these, 34 percent stated they expect to buy a new sequencer within a year, and another 19 percent at some point in the future beyond a year.

In total, these laboratories operate more than 910 sequencers (some labs stated having more than 10 instruments of the same type, which we counted as 10). Of those instruments, 74 percent are manufactured by Illumina, 12 percent by Thermo Fisher Scientific, 5 percent by Oxford Nanopore Technologies, 4 percent each by Pacific Biosciences and Qiagen, and 1 percent by other vendors.

These numbers underpin Illumina's continuing dominance in the market and roughly mirror numbers from a similar survey conducted by GenomeWeb and William Blair in 2016, with Thermo Fisher having slightly lost market share and PacBio and Qiagen having gained some.

When it comes to planned instrument purchases, the picture shifts a little in favor of non-Illumina providers. Of the more than 306 instruments labs said they intend to purchase over the next year and beyond, 60 percent are Illumina platforms (the majority NextSeq and NovaSeq instruments), 10 percent Qiagen GeneReader platforms, 10 percent Oxford Nanopore sequencers, 9 percent Thermo Fisher instruments, 8 percent PacBio sequencers, and 2 percent other platforms.

Reasons mentioned most often by labs for wanting to purchase a new sequencer were improved performance, a need for increased capacity, and lower cost per base.

Asked what will drive growth in their use of NGS in coming years, research labs most often cited sequencing large cohorts, new applications such as liquid biopsy sequencing, and increased assay sizes. Twenty-eight percent also said they expect an increase in government research funding over the next year or two, and 21 percent said they expect a decrease.

Clinical labs cited liquid biopsy testing as the top growth driver for their NGS use, followed by increased assay sizes and tissue-based cancer testing. Their outlook for reimbursement from payors for NGS tests over the next year or two was rather optimistic, with 51 percent stating they expect better reimbursement and just 10 percent saying they anticipate decreased reimbursement or more coverage denials.

Asked about remaining limitations for the adoption of NGS, about a third of respondents mentioned the technology's cost. An additional 30 percent or so cited data- or analysis-related challenges, including variant classification, bioinformatics capacity, computational power, lack of bioinformatics standardization, data processing, data storage, and interpretation of results, for example in non-coding regions. As one participant put it, "we are good at generating heaps of sequencing data, but translating that into therapeutic decisions is difficult."

Another 12 percent of respondents mentioned a lack of reimbursement from payors for NGS as a barrier, which one said is "hopefully getting better." Other limitations cited were challenges with sample or library preparation, including multiplexing samples; the general complexity of NGS technology; the error rates of NGS; a lack of guidelines for clinical assays; regulatory hurdles; and a lack of physician education about NGS.

Survey participants were also asked to state which genomic technologies they are most excited about and why. About 30 percent of responses were about long-read sequencing or long-range analysis technologies, stating, for example, that long reads can "lead to more complete and contiguous genomes", enable "better variant calling and phasing", and can "detect all structural variants." Most of these specifically named nanopore sequencing, and Oxford Nanopore in particular, and pointed out that platform's low price, high portability, and capability to do methylation sequencing and direct RNA sequencing.

More than 10 percent of participants named liquid biopsy or circulating free DNA analysis, though none mentioned specific applications.

Single-cell genomics was mentioned by almost 10 percent of respondents. They included single-cell epigenetics to study gene regulation and single-cell RNA-seq "to know what individual cells are expressing instead of tissue-level expression."

Other technologies and methods mentioned by readers were whole-genome sequencing, CRISPR, microRNA-seq, RNA-seq, CITE-seq, REAP-seq, BS-seq, ChIP-seq, ATAC-seq, Hi-C, DNA barcoding, chromosome conformation capture sequencing, NIPT, and immunotherapy.