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Thermo Fisher's New Genetic Analyzer Provides Makeover for Sanger Sequencing, Fragment Analysis

Thermo Fisher Scientific: Applied Biosystems SeqStudio Genetic Analyzer

NEW YORK (GenomeWeb) – In an effort to update a decades-old technology without making changes to the underlying tried-and-tested chemistry, Thermo Fisher Scientific has launched the Applied Biosystems SeqStudio Genetic Analyzer, a low-throughput capillary electrophoresis platform for both Sanger sequencing and DNA fragment analysis.

The instrument, which has a list price of $57,000, uses a click-in cartridge with four capillaries that comes pre-loaded with polymer and buffer, making it easier and faster to operate than previous platforms. It uses the same fluorescence-based chemistry as Thermo's other CE instruments but has a new touch-screen user interface and connects to the internet. In the past, Thermo has partnered with Hitachi on CE platform development, but it developed the SeqStudio in house. According to the company, the system "gives you the same data quality, reliability, and support you have come to expect from the Applied Biosystems brand with a modernized experience."

Thermo showcased the SeqStudio for the first time at the European Society of Human Genetics annual meeting in Copenhagen this week. The platform will start shipping to early-access customers this month and be broadly available at the end of September. For several months, it has been in the hands of six beta testers across the world who have tested it for different applications. Among them is MRC Holland, a provider of MLPA (multiplex ligation-dependent probe amplification) kits for DNA copy number quantification.

"It's been 10 years or more since we've launched a new system for capillary electrophoresis," said Kim Caple, vice president and general manager for capillary electrophoresis in Thermo's Genetic Science division. "It's kind of like a car, at some point, you want to upgrade to a more current model."

Thermo is not alone in its thinking that capillary electrophoresis for genetics is ready for a facelift: earlier this year, Promega announced that it is developing two new CE systems — a small four-capillary instrument and a larger eight- or 24-capillary platform — that it plans to commercialize toward the end of the year. The smaller version, called Spectrum Compact, will cost less than $65,000 and will also use consumables that are prefilled with buffers and polymer.

Despite the interest of new players to enter the CE instrument market with user-friendly offers — so far, Promega has only been selling CE reagent kits but not a CE platform — Thermo is still the market leader, and wants to keep it that way. "We want to stay competitive and make sure our customers are well served," Caple said. "That was the purpose of this system."

"We're actually quite happy that there are more companies interested in playing in the capillary electrophoresis world," said Kim Kelderman, Thermo's vice president and general manager of genetic analysis. "That, for us, validates that there is a solid use case, so we're welcoming others to compete with us in this space."

Among Thermo's legacy low-throughput CE systems, which the company continues to support for now, are the single-capillary 310 Genetic Analyzer and the four-capillary 3130 Genetic Analyzer. Though still popular, the company expects that the new SeqStudio will replace some of these instruments, as it offers an easier workflow and remote data access.

In addition, the SeqStudio might make some high-throughput CE systems that are operated by specialists in core facilities redundant, like the 48-capillary 3730 or the 96-capillary 3730xl Genetic Analyzer, if labs decide to purchase and run their own SeqStudio instead.

The new instrument takes samples on a standard 96-well plate as well as on eight-tube strips. It can perform Sanger sequencing and fragment analysis analyses in the same run as it uses the same universal polymer for both applications.

The cartridge, which is designed for 125 injections or 500 samples, has a list price of $1,600, translating to $3.20 per sample. Once installed on the instrument, it has a shelf life of four month due to an internal cooling system, much longer than the two-week shelf life of capillaries for other systems. The platform comes with an on-board computer and requires a one-time-only starter package with a list price of about $3,000.

The system will also come with a number of software tools for secondary analysis, including Sequence Analysis, SeqScape, Variant Reporter, GeneMapper, and Minor Variant Finder software, as well as various cloud-based Applied Biosystems analysis modules for quality check, variant analysis, and next-generation sequencing confirmation. Caple said the system will launch with one software application for sequencing and one for fragment analysis, and additional applications will be added next year.

"The goal is, in the lower-throughput environment, to provide the easiest possible workflow for Sanger sequencing and fragment analysis," she said.

Thermo has only tested the SeqStudio with its own sequencing chemistry, but kits from other vendors that are compatible with Thermo's existing CE systems are likely to work on the new instrument as well.

In terms of forensics applications, Thermo has already validated the SeqStudio for paternity testing, showing that its performance is identical with that of its other systems, Caple said. It has also initiated validation for its other forensics kits and expects to have that completed within the next six months.

Jan Schouten, CEO of Netherlands-based MRC Holland, said his lab has had the SeqStudio in house since January. His company has been selling MLPA kits since 2002 for a variety of applications, including hereditary disease testing, cancer predisposition testing, and tumor analysis. The annual volume of MLPA reactions continues to grow, he said, despite competition from technologies such as next-generation sequencing.

MRC Holland has a keen interest in keeping capillary electrophoresis alive and well, since its business depends on the presence of CE instruments, so it was happy to be a beta tester for the SeqStudio. "For MRC Holland, it's important that Thermo sees a future for capillary electrophoresis," Schouten said, adding that Thermo currently dominates the CE instrumentation market. Beckman Coulter is the only other firm that currently offers a lower-throughput CE platform — the eight-capillary GenomeLab GeXP Genetic Analysis System — but that requires Beckman's own sequencing chemistry, he said.

Schouten said his lab was able to transfer its assays immediately to the SeqStudio, and the output files were suitable for its own data-analysis software. "It works fine," he said. "There is little to improve, at least in terms of results."

The most important differentiator he sees for the SeqStudio is its relatively low list price, about half that of Thermo's eight-capillary 3500 Genetic Analyzer. At the same time, he said, the instrument offers sufficient throughput for most laboratories, and while the cost per sample is slightly higher than that of other Thermo platforms, the SeqStudio is easier to use. "They did a nice job of making it easier to handle, smaller, and offering it at a low price," he said.