The New Spectrum CE System in a UK Forensic Genomics Laboratory
Dr. Caroline Parker, Forensic Genomics Innovation Hub (FGIH)
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Introduction
The use of massively parallel sequencing in specialised casework has unique benefits over the traditional CE STR methods by providing a solution to challenges associated distinguishing true allele variation from PCR artifacts, interpreting mixtures and obtaining better profiles from degraded DNA. But it is not without its own challenges and hence why the analysis of STRs using traditional fragment analysis remains the method of choice in many forensic laboratories. Our laboratory recently purchased the new Spectrum CE System to support our Forensic Genomics service. With 8-capillaries, 8-dye multiplex capabilities and continuous plate accessibility, it is a perfect fit into the FGIH laboratory.
Any laboratory looking to invest in a new instrument spends many hours ensuring that they have thoroughly investigated all the platforms available. From price, to cost effectiveness in implementation, validation, and day-to-day running, capability, ease of use and reliability, there are many factors to consider when making a large investment. Neither CE nor DNA sequencing platforms are inexpensive and are often associated with substantial service, maintenance, and software costs.
The Forensic Genomics Innovation Hub is all about Innovation in DNA and after careful deliberation decided to invest in the new-to-market Spectrum CE System from Promega Corporation, due to the additional benefits this new CE system offers over previous CE systems.
Implementation and Validation
The instrument installation was a simple process and the Promega UK team provided the staff with thorough training on the new Spectrum Control Software, as well as the analysis software GeneMarker®HID for Spectrum CE Systems. Multiple injections of PowerPlex® ESI17 Fast System allelic ladder were run to assess the reproducibility and resolution of the capillary array and the new polymer pouch delivery system. The large D2S441 marker in the PowerPlex® ESI17 Fast System ladder has only a single base pair difference between alleles and is ideal for testing resolution capability of the polymer and capillary array.
In order to validate the instrument’s performance for use in paternity and relationship DNA testing, DNA extracts run previously on an Applied Biosystems™ 3500 Genetic Analyser were run on the Spectrum CE System. All profiles were concordant between the two instruments. Detailed reproducibility and sensitivity studies were then performed using DNA extracts and direct amplification reactions from blood spots and swabs, all with the Promega Corporation 6-dye PowerPlex® Fusion 6C System.
Figure 1: Spectrum Control Software electropherogram (PowerPlex® ESI17 Fast System Allelic Ladder)
Capability
The new Spectrum CE System really does appear to be the next-generation in CE that provides unmatched flexibility in processing samples for short tandem repeat (STR) analysis, making it well suited for forensic labs now and into the future. The instrument has capacity for up to 4 plates of samples, which can be continuously loaded. This feature enables our lab to offer a same day result service for paternity and relationship DNA testing as samples can be loaded as soon as they are ready for CE analysis. These plates can be partial plates and there is no wastage of reagents, optimising consumable usage better. Partial plates don’t delay other samples. It is easy to change injection and plate order during a run, allowing prioritisation of urgent samples with minimal disruption to routine sample workflow.
The system is 8-dye ready, and our lab has recently begun validating the new Promega PowerPlex® 35GY System. This is where the instrument really excels. The 8-dye matrix standard and associated kit allelic ladder is well resolved, with excellent balance between colours. The balance across the profile is outstanding with no evidence of loss of resolution or peak height in all the larger markers. This kit has the potential to assist enormously with complex kinships and forensic casework samples, such as sexual assault mixtures, which previously required more than one STR kit, or a sequencing run.
Figure 2: PowerPlex® 35GY Ladder
Figure 3: PowerPlex® 35GY. 40pg DNA, 25µl reaction
Figure 4: PowerPlex® 35GY. 8pg DNA, 25µl reaction
Ease of Use
When embarking on the decision-making process for a new platform how it performs in situ is paramount. In busy DNA labs the user must be able to operate it, maintain it, and run it with relative ease. Getting used to the new Spectrum Control Software, after so many years’ experience with other CE platforms, was easier than anticipated. Navigating around the software is easy, changing buffers and polymer pouches quick, and plate record generation flexible and straightforward, with the ability to automate plate handling and linking with an integrated plate barcode reader. Except for the polymer, the consumables do not have any hard stops built in and come in a ready to use format so there is minimal down time whilst changing them. The integrated data collection and analysis software provides automatic data quality assessment, reducing the time needed to screen for re-injections. The software also comes with free of charge upgrades, as and when necessary. Another feature that is unique to the Spectrum CE System is spatial and spectral calibrations occur together, saving time and effort.
Reliability
The Spectrum CE System is the newest addition to the Forensic Genomics Innovation Hub instrumentation base, and since installation in December 2022 it has been running routinely, performing in house validations and verifications, and our familial DNA testing service. The system has only crashed once. This was overnight halfway through a full plate where an external anti-virus software overpowered the memory of the PC whilst the camera was busy capturing fluorescence. This had to be removed to prevent that from happening again. The instrument is not on the lab network. Our Spectrum CE System runs daily with around 1% of runs requiring re-injections.
Service and Support
Laboratories offering testing services to the Police and the public rely on their suppliers to help them maintain business continuity. Instrument down time can impact significantly on lab turnaround times and their service to their clients. The Promega UK team and Promega Corporation are a trusted supplier in the field of molecular diagnostics and forensics and the support our lab receives is second to none. The team are extremely knowledgeable on the new Spectrum CE System and clearly well placed to support labs making the leap into the next generation of Capillary Electrophoresis. Finally, the instrument is well priced with no hidden costs. It also includes a single GeneMarker®HID Software for Spectrum CE Systems license as well as an excellent service and maintenance contract, at a fraction of the price of a DNA sequencer.
The Spectrum CE System is a perfect fit to our current instrument complement. Established in 2020, the FGIH have a uniquely positioned team of DNA experts dedicated to applying next generation DNA sequencing to crime fighting, family DNA testing and molecular diagnostics. With solutions and support to forensics and the public the FGIH is also an open-door training facility supporting academia, giving future medical/forensic scientists access to the latest technologies.
Dr. Caroline Parker Chief Scientific Officer and Founder Forensic Genomics Innovation Hub Ltd
Caroline founded the Forensic Genomics Innovation Hub in 2020. After spending over 20 years in private forensics and family DNA testing, clinical genetics and infectious diseases in Europe and South Africa she merged her passion for both forensic biology and clinical genetics in her hometown of Southampton, England. She began her career as a Wellcome Prize PhD student under the supervision of Prof. Pat Jacobs Wessex Regional Genetics Lab. Caroline then joined Promega’s Genetic Identity team before moving to South Africa. She joined the largest private pathology group in Sub-Saharan Africa as a Senior Medical Scientist in DNA analysis in forensic casework, familial testing, and clinical molecular genetics. Never short on energy Caroline enjoys running and hoping on a cruise ship whenever possible.
White Paper: Developmental Validation of the Spectrum CE System for Fragment Analysis
The ability to detect 8 colors with the new Spectrum CE System allows for the development of 8-color STR systems with more loci as smaller amplicons for better performance with degraded and inhibited samples. The 8-color PowerPlex® 35GY System combines the CODIS 20 core loci along with Penta D, Penta E, SE33 and ten Y STR markers for familial searching and analysis of sexual assault evidence.