To call the next-generation DNA-sequencing market “mature” would be an understatement. But that doesn’t mean developers are content to rest on their laurels. Last week, exciting innovations in genomic research took center stage at the Advances in Genome Biology and Technology (AGBT) conference in Orlando, Fla., and Biocompare was there to cover the event. 

Sequencing firms as well as manufacturers of ancillary equipment and reagents continue to innovate, releasing tools that will both extend the ongoing democratization of technology access and streamline the sample-preparation workflows that drive that equipment on the front end.

Illumina

Illumina has expanded its sequencer portfolio with the MiniSeq, announced in mid-January.

Intended for customers who have not typically embraced next-gen sequencing (NGS), such as molecular pathologists and clinical researchers, the MiniSeq has a maximum output of 25 million reads at 2 x 150 bp, for 7.5 Gb total, says Diane Lince, associate director of product marketing.

“These new types of customers to NGS would likely not have a lot of samples to run through [the instrument] at any particular time, and the output of this box is really amenable to smaller sample volumes, allowing a lot of flexibility from day to day,” she explains.

The MiniSeq represents Illumina’s new entry-level instrument, Lince says, and it is intended mostly for targeted sequencing applications. With a price tag of $49,500, the instrument is half the price of the MiSeq and produces half the output. Users can select from three “high-output” kits of 25 million reads at 300, 150 or 75 cycles, as well as a 300-cycle, 8-million read kit. That latter kit should prove especially attractive, Lince says, as it reduces the per-run cost, thereby enabling users to use fewer samples per instrument run.

At AGBT, Illumina CEO Jay Flatley announced progress on a “semiconductor-based sequencing system” dubbed Project Firefly. Slated for the second half of 2017, the system will produce about a gigabase of output per run, with four million reads per run and a cost of approximately $100 per sample. Consisting of two small boxes, one for library preparation and the other for running the sequencing preparation, the unit will sit neatly stacked on a benchtop and use an iPad as the user interface. The entire system should cost less than $30,000.

Pacific Biosciences

Pacific Biosciences launched its new sequencer, the Sequel system, at the end of September 2015.

Though based on the same long-read chemistry as the company’s previous PacBio RS II system, the Sequel system is about a third as big and half as expensive ($350,000 list price)—and it outputs about seven times as much data per run, says chief scientific officer Jonas Korlach. “In comparison to the RS II, which has 150,000 zero-mode waveguides, the Sequel system has one million.”

As a result, researchers can use the Sequel system to run the same experiments they ran on the RS II, only more rapidly and less expensively, Korlach says. But they also can pursue studies that “would have been slow or expensive to do on the PacBio RS II,” he says, such as de novo reference genome assembly of plant and animal genomes, as well as population genetics. In fact, he notes that at the annual Plant and Animal Genome conference in San Diego in January, there were “over 80 presentations and posters” highlighting PacBio sequencing.

According to a January press release, the company had received orders for 49 Sequel systems by the end of 2015—nearly a third as many as total RS II installations to date, Korlach says.

Thermo Fisher Scientific

Thermo Fisher Scientific has expanded its Ion Torrent product line with the new Ion S5 and Ion S5 XL systems, launched in September 2015.

According to Andrew Felton, vice president of product management for next-gen sequencing and oncology, the two systems differ mainly in speed of data analysis. Each uses cartridges for easy reagent loading and offers a choice of three semiconductor chips for experimental scalability. The ‘520’ chip generates five million reads of up to 400 bases for 2 Gb output; the ‘530’ chip generates 15-20 million reads and 6-8 Gb output; and the ‘540’ chip generates 60-80 million reads and 10-15 Gb output. That range places the S5 above the Ion PGM and equivalent to the Ion Proton in terms of data yield.

The system requires about 15 minutes to set up, Felton says, though users typically can get the system up and running in less than five minutes. When coupled with the company’s Ion Chef library preparation and clonal amplification system, total hands-on time is less than 45 minutes, with just two pipetting steps. “That is, we believe, the best workflow in terms of hands-on time and number of manual steps for any sequencing platform in the industry,” he says. (The S5 costs $65,000; with the Ion Chef, it costs $120,000.)

Felton says Thermo is targeting the S5 and S5 XL at the clinical and translation medicine market, particularly in oncology (which the company supports with its Ion AmpliSeq™ oncology panels), though there also are applications in forensics, metagenomics and food testing.

Ancillary products

Sequencer developers aren’t the only ones to have been busy during the past year.

Advanced Analytical Technologies Inc. (AATI) in January launched the Fragment Analyzer INFINITY, an automated version of its earlier Fragment Analyzer, which launched in 2012.

In a presentation at AGBT, Steve Siembieda, vice president of commercialization at AATI, detailed the features of the company’s Fragment Analyzer ($45,000 to $55,000), a capillary electrophoresis-based system for assessing the quality and quantity from 12 to 96 NGS libraries. It can also analyze genomic and large-fragment DNA, as well as small and microRNA samples, all at once, repeatedly loading samples from up to three 96-well plates. The INFINITY system enables users to further automate the process by integrating robotics that feed the system from a microtiter plate tower.

Although not at AGBT, BioChain (which has traditionally supplied tissue samples and other biospecimens to the research community) in late 2015 launched a control product called CancerSeq. According to general manager Bingfang Huan, CancerSeq is a set of clinical formalin-fixed paraffin-embedded (FFPE) tumor samples that have been NGS-characterized for mutations in up to 67 cancer-related genes. These can serve as positive controls for clinical laboratories that wish to validate their extraction and sequencing procedures.

According to Huan, the company has sequenced more than 500 FFPE samples to arrive at its current collection of 60, as some samples simply don’t sequence well (because of the variable quality of DNA from FFPE samples), and some lack the mutations of interest. Now the company is preparing to expand its portfolio with samples containing rare gene fusions and translocations, which can be particularly hard to come by. “For the average customer, it is just impossible for them to develop their own internal controls,” she says.

Roche NimbleGen expanded its SeqCap targeted sequencing product line with the SeqCap EZ MedExome Enrichment kit. According to Mike Leous, group marketing manager for life science and sequencing, the SeqCap MedExome, which is based on the latest human genome build (hg38, rather than hg19), captures about 38 Mb, including the entire exome, but it was particularly designed to ensure capture of regions that consortia have identified as medically relevant.

“Some regions capture well [with any enrichment methods], and some do not. So we went a step further and made sure we captured those particularly medically relevant ones to a 98% threshold of 20X coverage,” Leous says.

The company also offers SeqCap kits for epigenetic analysis of DNA methylation, as well as targeted capture of specific RNAs, an approach that enables researchers to focus on lower-abundance transcripts. “When you do conventional RNA-seq, the majority of reads are consumed by high expressors that are likely irrelevant to your research,” Leous explains.

Finally, 10X Genomics last week launched its new Chromium™ system. This represents the “next-gen” evolution of the company’s GemCode™ technology, which uses a barcoding system that enables researchers to identify which short reads are physically connected to each other. Examples discussed during the company’s workshop at AGBT described how the new platform supports single-cell sequencing, full-genome, de novo assembly and targeted sequencing and variant detection. The system enables scientists to perform a diverse array of applications, including RNA-seq, an expanding area of opportunity for researchers seeking greater understanding of the genome in various disease states.

The year 2016 promises to be an exciting one for advances in NGS instrumentation, reagents and software analysis. With numerous tools emerging in these areas, many opportunities to further characterize and understand the genome will become available to scientists.