Expanding Laboratory Access to Gene Sequencing

Expanding Laboratory Access to Gene Sequencing

December 09, 2020PAP-Q4-20-CL-022

Genetic sequencing has traditionally required complex and expensive instruments, limiting the number of laboratories able to purchase them. With the introduction of an affordable benchtop instrument for Sanger sequencing and fragment analysis, Promega Corporation is enabling a wider range of researchers to take control of testing.

Gold Standard

Genetic sequencing generally involves DNA extraction, PCR purification, and detection. Sanger sequencing is an established, widely used technique providing single-base resolution. Even with advances in next-generation sequencing (NGS), Sanger sequencing remains the gold standard; if a sequence determined using NGS requires confirmation, Sanger sequencing is performed. Similarly, Sanger sequencing proves that the desired insertion or deletion was achieved in applications of CRISPR or other gene-editing tools.

Limited Access

Unfortunately, access to instrumentation to perform Sanger sequencing is limited, owing to the high costs and complexity of the capillary electrophoresis instruments required for this analysis. Buffers have to be prepared, the capillary must be flushed of the old polymer and the new polymer must be introduced. Instead of investing in an expensive machine and the time needed for training, most smaller labs send samples out to centralized labs. 

Twenty years ago, it could take a week after a sample was sent to a central lab with Sanger sequencing capabilities to receive results; today, that time frame has been reduced to several days. However, granting researchers the ability to perform Sanger sequencing in-house presents a range of benefits. Researchers can set the run conditions of their assays and have direct control over quality during an analysis in case anything needs to be adjusted. Sometimes, the results are needed immediately, particularly with clinical case work or forensic analyses for high-profile cases. In such cases, there is also elevated concern about the chain of custody for samples, which makes sending samples out to external labs undesirable.

From Chemistry Kits to Benchtop Instrument

Promega Corporation has been offering reagent tool kits for laboratory tests in the fields of cell biology; DNA, RNA and protein analysis; drug development; human identification; and molecular diagnostics for nearly 50 years. We provide the chemistry solutions that enable gene sequencing for a host of different applications.

Examples include our PowerPlex® STR Systems used by forensic labs worldwide; GenePrint® Systems used for cell line authentication, mixed sample analysis; and other applications; and a microsatellite instability kit (MSI). We make robust amplification enzymes and understand master mixes. We offer a complex 24-multiplex system comprising more than 50 different primer combinations.

Customers who rely on this specialized chemistry expertise — and appreciate the service and support that we provide — frequently asked Promega to develop a single-base–resolution instrument that could be used with our chemistry solutions. However, this was not an easy instrument to develop — if it was, options would be on the market already. 

In response, Promega had the vision of complementing our chemistry product line and offering a more complete workflow solution to our customers. To do that, we partnered with Hitachi High-Tech, which has been developing and manufacturing the larger-scale, expensive capillary electrophoresis instruments for genetic sequencing for many years. We talked with customers to better understand their needs, and then Hitachi contributed their instrument expertise and Promega brought its chemistry to the table. The end result was the Spectrum Compact CE system, a complete solution for our customers.

Introducing the Spectrum Compact CE System

Our new compact gene sequencing system is very easy to install and use, requires only a small footprint, and provides results rapidly, making it a true personal benchtop sequencing machine. It is designed for use with existing sequencing chemistries using fluorescently labeled dideoxynucleotide triphosphate (ddATP) and 4-, 5- and 6-dye short tandem repeat (STR) kits from Promega, as well as other commercially available kits.

The consumables are pre-dispensed and designed to snap into place. There is no need to flush polymers or wash the capillary cartridge between runs. The software wizard provides a step-by-step guide to touch-screen operations including run set-up, consumables and an array usage of information, including system maintenance reminders. It is also possible to monitor run progress and view results during a run. 

Many assays (at least 20 different dye set combinations) are preloaded and compatible with Sanger sequencing and fragment analysis (single-base resolution). It is also easy to make modifications to create customized run conditions. Export files (.ab1 for Sanger sequencing and .fsa for fragment analysis) are compatible with commercially available data analysis software. Promega is also developing a data analysis package called Gene MarkerHID® For Spectrum Systems. The instrument can also be connected to a separate computer on the same network so that setup can be completed in the office before going into the lab. 

With on-site installation and operational training and in-depth training on the chemistry side for all assays and applications, the integrated and efficient instrument brings independence to the laboratory, placing Sanger sequencing and fragment analysis directly under the control of scientists and researchers, regardless of expertise.

Built-In Flexibility

The Spectrum Compact CE system includes a barcode scanner, and all consumables used with the system have barcodes, the wizard-like workflow guides users through scanning and use of the consumables and keeps track of the number of injections performed and how many remain, the on-instrument expiration date, and warnings as the limit of uses and the expiration date approaches. Users have flexibility in how to use their consumables, which was an often-repeated request during development discussions with potential customers.

The benchtop CE system has just been launched, and Promega is focused on educating potential users about the benefits it offers and providing consumables for all application areas, including CRISPR confirmation. We are also planning features for a second version of the software based on input from customers who participated in early product evaluations. We will continue to listen to our customers with respect to their needs for different software, chemistry, or other capabilities.  

Democratizing Genetic Sequencing

We are excited about the launch of the Spectrum Compact CE system after years of dedicated development efforts. Finally placing the instrument in the hands of customers so they can take full ownership of their sequencing needs gives them control and flexibility. It is easy to use and affords the opportunity to ensure chain of custody and the quality of the experiment for each sample. Promega is happy to help make capillary electrophoresis accessible to a broader customer base, thus democratizing the use of gene sequencing in a laboratory setting. 

Adaptability Continues to be Key

Looking forward, adaptability will be essential in the testing arena. In 2020, when the COVID-19 pandemic emerged, we dropped our strategic plan and completely changed gears to support the development and implementation of diagnostics for the SARS-CoV-2 virus worldwide. 

That type of agility will be required going forward. We expect a continued focus on viral research over the next several years to better prepare for the next epidemic/pandemic. With our expertise across the key fields of cell biology; DNA, RNA, and protein analysis; drug development; and molecular diagnostics in both chemistry and instrumentation, Promega is positioned to support and facilitate these critical efforts. 

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