Analysis of DNA fragments with the Spectrum Compact CE system

In this interview, News Med talks to Gabriela Saldanha about DNA fragmentation and Sanger sequencing.

What is Sanger sequencing and DNA fragment analysis? Where are these analyzes used?

Sanger sequencing by capillary electrophoresis is the gold standard for DNA sequencing, even with the advent of next-generation sequencing (NGS). The test and its interpretation are simple and targeted and best suited for DNA fragments 75 to 1000 bases in length. Current best practice in many laboratories is to confirm NGS results with Sanger sequencing, and Sanger sequencing is the most cost-effective method for sequencing single samples.

Fragment analysis separates and analyzes PCR-amplified DNA fragments. Short tandem repeat (STR) analysis is a subset of fragment analysis and has historically been most often used in forensic and paternity analysis. However, STR analysis can also support non-forensic applications such as cell line authentication, MLPA, microsatellite analysis, and mixed sample deconvolution.

Image credit: Promega

What instrumentation is needed for Sanger sequencing and fragment analysis? Will most researchers have these instruments in their labs or will they outsource the work?

A single-base resolution capillary electrophoresis system is standard equipment for performing these analyses. In the past, many labs sent samples to the main labs for analysis, as the equipment was often too big or too expensive for labs that only needed to process a handful of samples.

To solve this problem, we developed the Spectrum Compact CE system, an automated benchtop 4-capillary electrophoresis instrument that can process as few as four samples or as many as 32 samples in a single run without wasting consumables. With the Spectrum Compact, labs can perform their own Sanger sequencing or fragment analysis on demand.

What value does the Spectrum Compact CE system bring to a laboratory?

One of the huge advantages of this instrument is that it is personal. A person can walk into the lab and, with minimal training, change all the consumables, select the chemicals they want to use, and perform the experiment. It is an incredibly flexible and affordable system that is accessible to everyone in the lab – it democratizes the use of the instrument in the lab. By eliminating the need to send samples to main facilities, the Spectrum Compact also helps laboratories reduce costs per sample and control their own lead times.


Image credit: Promega

How is the Spectrum Compact CE system different from other genetic sequencers?

The Spectrum Compact CE system is of low flow design. We have heard from many scientists who do not process enough samples to justify purchasing a high throughput instrument. This instrument has therefore been designed to meet these specific needs.

Which application areas use the Spectrum Compact CE system?

The Spectrum Compact is the solution for academic, clinical research and forensic labs looking to take DNA testing to the next level. The instrument supports applications as diverse as microsatellite instability research, mixed sample analysis, STR forensic analysis, and cell line authentication.

What is cell line authentication and how does the Spectrum Compact CE system support this application?

Misidentification of cell lines is a major problem in biological research. When scientists work with cell lines, it is important that cell identities are regularly authenticated to ensure that research results are valid. Many funding agencies and journals now require scientists to perform cell line authentication to submit grants or manuscripts. STR profiling is considered the best practice for authenticating cell lines. The Spectrum Compact CE system can perform cell line authentication using standard STR profiling chemistries, such as GenePrint® 24 system. This STR instrument and kit combination complies with ANSI/ATCC ASN-0002-2021 guidelines for authentication of human cell lines.

Image credit: Promega

What consumables are needed to use the Spectrum Compact CE system?

The instrument is compatible with existing Sanger sequencing chemicals and 4-, 5- and 6-dye STR kits from Promega and other companies.

Plug-and-play consumables make the instrument extremely easy to set up and use. Installation is simple and the format prevents contamination and spillage. Every person who touched the instrument during in-house training commented on the ease of installing the consumables.

The consumables are also separated, providing more efficiency, flexibility and durability compared to other instruments that require you to change each consumable at the same time.

Are the interface and software easy to use? Is this also something anyone in the lab can work with?

Spectrum Compact Control software provides a simple user interface with a clear display of useful features, including runtime configuration, consumables status and array usage information, plus system maintenance reminders . Users can monitor run progress and view parsed results while a run is in progress. You can also export files in formats compatible with commercially available data analysis software such as GeneMarker® HID for spectrum systems, GeneMarker®mutation expert® and GeneMapper®.

Image credit: Promega

What kind of support can Spectrum Compact CE system users expect from Promega?

There’s an extendable one-year warranty with preventative maintenance included with purchase, plus on-site installation and training. Users also have access to Promega’s team of scientists who can support chemical validation of new workflows, application training and additional preventative maintenance.

What’s next for the Spectrum Compact CE system?

An upcoming control software update in Q4 2022 will provide customers with even greater flexibility with consumables and chemicals. For more information on the Spectrum Compact CE system, visit the product page.

About the Author:

Gabriela Saldanha is responsible for strategic commercialization within the Genomics Solutions portfolio at Promega. Gabriela’s career spans over 25 years in the laboratory and in the development, strategy and implementation of products related to nucleic acid amplification, expression analysis and genotyping, most recently leading the launch and commercialization of the ProDye Terminator Sequencing System and the Spectrum Compact CE System. One of his passions is to share the need for cell line authentication to preserve cell line integrity.

About Promega

With a portfolio of over 3,000 products spanning the areas of genomics, protein analysis and expression, cell analysis, drug discovery and genetic identity, Promega is a leader worldwide in providing innovative solutions and technical support to life scientists in academia, industry and government. .

Promega products are used by life scientists who ask fundamental questions about biological processes as well as by scientists who apply scientific knowledge to diagnose and treat disease, discover new therapies and use genetics and DNA testing to human identification.