Introducing the SeqStudio Genetic Analyser

The SeqStudio Genetic Analyser is the newest member of the Applied Biosystems™ line of capillary electrophoresis (CE) instruments. It combines the same workflow and same trusted technology of Sanger sequencing with convenient cloud based data analysis and remote monitoring.

Just Click-and-Go    -     Sanger Sequencing in any science lab

With its small footprint benchtop design and easy to use all-in-one cartridge system the SeqStudio Genetic Analyser is the ideal choice for research laboratories. The cartridge contains the capillary array (4 capillaries), polymer reservoir, and anode buffer. With the all-in-one cartridge design, there is no need for calibration before each run and no technical experts are needed for the installation of capillaries, polymer and anode buffer. Each cartridge contains a new, unique to the SeqStudio Genetic Analyser polymer that allows Sanger sequencing and Fragment analysis to be performed with no reconfiguration. After installation the cartridge is stable on the instrument for 4 month. The cartridge and cathode buffer uses RFID (radio-frequency-identification) tags to track the number of injections and the length of time on the instrument. This feature allows multiple users using the SeqStudio Genetic Analyser in a core-facility to maintain custody of their own cartridges.

Samples can be analysed from 8-well strip tubes or 96 well plates and the instrument is utilising the known BigDye chemistries.

Set up-Run-Monitor-Analyse – Cloud based remote control from anywhere, anytime

                Runs can be set up using either the on-board instrument interface, the SeqStudio Plate Manger software on a separate computer or via the Thermo Fisher Cloud. By using the web-browser-based software runs can be accessed and monitored on-line. The Thermo Fisher Scientific Instrument Connect mobile App provides real-time monitoring using any Android or iOS mobile device. Injection conditions, reinjections, reordering of injections can all be modified during the run. This allows for maximising quality data collection by correcting injection parameters when poor traces or poor QC values are observed after initial injection. These features are also available through a web browser providing flexibility and convenience for users.

After Run Completion DNA sequence variants, alignments and fragment analysis are available and further Cloud based applications such as Sanger Variant Analysis, Sanger Quality Check and Next Generation Confirmation (NGC) can be used. Collaborating scientists can also benefit from easy and rapid data sharing through the cloud.

Applications

• Plasmid Sequencing

One of the most common application's of Sanger sequencing is the analysis of inserts subcloned into plasmid vectors. This application is utilising the Applied Biosystems™ BigDye™ chemistries with new features. There are three pre-loaded sequencing read length modules available (<300bp, 500bp and 600bp<), but this feature can be further customised. Analysis of the sequencing quality is available via Sanger Quality Check cloud application.

• Oncology Research and Next Generation Confirmation (NGC)

The SeqStudio Genetic Analyser in a clinical setting can be used to confirm (NGS) Next Generation Sequencing Data. The cloud-based NGC module allows for verification of NGS .vcf file variants using Sanger sequencing traces. The Applied Biosystems™ Minor Variant Finder (MVF) allows for the detection of down to 5% allelic variants. Additionally the instrument is pre-loaded with a running module optimised for fragmented DNA isolated from FFPE tissue. The Applied Biosystems™ BigDye Direct™ and Big Dye XTerminator™ chemistries simplify the workflow by performing the sequencing and clean-up in the same tube.

• Species Identification

Sanger sequencing is a useful tool in identifying species of unknown samples coupled with readily available genomic data of DNA fingerprint loci. Sanger sequencing of ribosomal DNA (rDNA) of prokaryotes and fungi can be utilised for identification of microbial organisms. For the identification of eukaryotic organisms known mitochondrial loci are used (cytochrome oxidase C1) For further reference see http://www.barcodeoflife.org/

• CRISPR-Cas9-mediated Genome Editing

Sanger sequencing data generated using SeqStudio Genetic Analyser is compatible with Tracking of Indels by Decomposition (TIDE) software, a widely available tool for analysisng genome editing events. Sequence traces can also be analysed using the Sanger Variant Analysis module. Using this module the position of the genome editing can be visualised by abundant mixed based peaks downstream from the break point.

• Human Cell Line Authentication

Highly variable short tandem repeats (STR) can be used as a ‘fingerprint’ to identify cell lines. It is an increasingly acknowledged problem that in vitro cell cultures can be misindentified or contaminated with unrelated cell-lines. The Applied Biosystems™ Gene Mapper Software can be used for analysing alleles, identified by Applied Biosystems™ Identifiler™ Plus and Identifiler™ Direct kits and is compatible with the data produced by SeqStudio instrument. The results can be used to verify authenticity through ATCC or other STR database.

• Applied Biosystems SNaPshot genotyping

Applied Biosystems™ developed the SNaPshot Multiplex System to analyse SNP (single nucleotide polymorphism) variants. The color-coded and differing size fragments, corresponding to specified alleles are analysed by fragment analysis. The SeqStudio SNapShot system is customizable and includes built-in reporting of size and peak area analysis results. The new SeqStudio Genetic analyser enables users to perform Sanger sequencing and SNP analysis in a single run from one plate. The SeqStudio Genetic Analyser’s SNaPhot analysis performance was successfully demonstrated from 1ng FFPE-extracted DNA samples. 

• Multiplex ligation-dependent probe amplification (MPLA) analysis of human copy number variation (CNV)

The SeqStudio instrument results are also compatible with the MRC Holland’s Coffalyzer.Net software for analysing multiplex ligation-dependent probe amplification (MLPA) data. This method is developed and commercialised by MRC Holland and widely used for studying inherited human diseases related to CNVs (copy number variations) of a locus. The sizing precision, high dynamic range and peak-height fidelity makes the SeqStudio an ideal platform performing MPLA studies, where up to 50 multiplexed pair of adjacently located probes are hybridised to the loci of interest.

Service, Support and Warranty

Applied Biosystems provides high level Support and Service with Seq Studio Genetic Analyser. The SmartStart In-Lab-Application training will get you up and running quickly. The Secondary Analysis Software package and one year warranty is included with the purchase.

The New SeqStudio Genetic Analyser makes Sanger sequencing and its related applications easily available to everybody. It is reliable and flexible without pre-existing expertise in its setup and operation. It is the ideal choice for core laboratories with multiple users with up to 2000 sample per year throughput.

Gyongyi Lukacs, PhD

Field Application Specialist

Bio-Sciences Limited