Applied Biosystems SeqStudio Genetic Analyzer Support—Getting Started

The SeqStudio Genetic Analyzer is a low-throughput, easy to use benchtop system that delivers gold-standard Sanger sequencing technology and fragment analysis with just a simple-to-use click-in cartridge. The cartridge contains the capillaries, polymer, and anode buffer, which minimizes the instrument setup and maintenance. More information about the SeqStudio Genetic Analyzer can be found here.

The specifications for the SeqStudio Genetic Analyzer are:

• Dimensions (W x D x H): 49.5 x 64.8 x 44.2 cm
• Weight: 53.6 kg
• Number of Capillaries: 4
• Number of Dyes: 6
• Sample Format: 96-well standard plates and standard 8-well strip tubes

More information on the specifications can be found in the SeqStudio Genetic Analyzer brochure.

The SeqStudio Genetic Analyzer can be used to perform both sequencing and fragment analysis applications. Specific applications tested include:

• De novo Sanger sequencing
• Targeted sequencing
• Plasmid sequencing
• Oncology research
• Species identification
• Next-generation sequencing (NGS) confirmation
• CRISPR-Cas9 genome editing analysis
• Human cell line authentication
• SNaPShot genotyping
• Multiplex ligation-dependent probe amplification (MLPA) analysis of human copy number variation

More information on applications that can be run on the SeqStudio Genetic Analyzer can be found in the SeqStudio Genetic Analyzer Application Guide.

The SeqStudio Genetic Analyzer cartridge contains POP-1 polymer, a universal polymer for performing sequencing and fragment analysis runs.

The 28 cm array that comes with the SeqStudio Genetic Analyzer cartridge is the only size available at this time.

The SeqStudio Genetic Analyzer cartridge only comes with 4 capillaries at this time. The Applied Biosystems 3500 series genetic analyzers and the Applied Biosystems 3730 series DNA analyzers are available for those labs requiring higher throughput.

The SeqStudio Genetic Analyzer cartridge can be kept on the instrument for up to 4 months or 125 runs.

The countdown on the 4 months begins when the cartridge is installed on the SeqStudio Genetic Analyzer so removing the cartridge will not prolong the life of the cartridge. The SeqStudio Genetic Analyzer also has an on-board refrigeration unit to preserve the life of the SeqStudio cartridge until the expiration date or until the 4 months is reached.

The SeqStudio Genetic Analyzer cartridge will be shipped with no less than 6 months before expiration and can be kept on the instrument for up to 4 months or 125 runs.

The SeqStudio software will give warnings once the expiration date or usage (125 runs) is reached but it will not hard stop until the polymer reaches a specific volume or if the cartridge or cathode buffer RFID tags are not found. Any usage past expiration or for longer than 4 months on the instrument is at your own risk as the results cannot be guaranteed at that point.

The SeqStudio Genetic Analyzer cartridge contains an RFID tag that is used to track usage and expiration. The information is updated and retained in the cartridge history, which can be accessed by going to Settings > Cartridge > Instrument-cartridge history.

On the SeqStudio Genetic Analyzer, when you run the installation check, the QC results indicators are:

• Green: all QC tests passed*
• Yellow: at least 1 warning quality alert was triggered
• Red: at least 1 failing quality alert was triggered

*QC tests check for offscale peaks, low/no data present for sequencing; size standard and sample peak quality, peak uniformity, peak morphology, and sizing quality values for fragment analysis runs.

The SeqStudio Cathode Buffer Container should be changed out every 2 weeks.

The Cathode Buffer Container Reservoir Septa for SeqStudio Genetic Analyzer are intended for single use only. We recommend replacing the Cathode Buffer Container Reservoir Septa after each run. If rinsed with water and reused, the septa can become sticky and gummy over time and may eventually start sticking to the array. This may potentially increase the risk of damaging the array.

Bleach, detergents, or solvents should not be used to clean the septa as this can cause the septa to dry out faster and risk contamination of the system.

The 96-well Septa for SeqStudio Genetic Analyzer are intended for single use only. We recommend replacing the plate septa after each run. If rinsed and reused, the septa can become sticky and gummy over time and may start sticking to the array. This may potentially increase the risk of damaging the array.

Bleach, detergents, or solvents should not be used to clean the septa as this can cause them to dry out faster and risk contaminating the system.

The 8-strip Septa for SeqStudio Genetic Analyzer are intended for single use only. We recommend replacing the strip septa after each run. If rinsed and reused, the septa can become sticky and gummy over time and may start sticking to the array. This may potentially increase the risk of damaging the array.

Bleach, detergents, or solvents should not be used to clean the septa as this can cause them to dry out faster and risk contaminating the system.

The SeqStudio Genetic Analyzer requires very little maintenance:

• Before starting a run, check the SeqStudio Cathode Buffer Container to make sure buffer levels are at the fill line prior to starting a run. If it is below the fill line, replace the SeqStudio Cathode Buffer Container prior to starting the run.
• If storing the array on the instrument, make sure the instrument is powered on and the SeqStudio Cathode Buffer Container buffer levels are at the fill line.
• Before starting a run, wipe down the autosampler with a damp (deionized water) lint-free cloth. Caution: do not pour water on to the autosampler as it can damage the system.
• Wipe down the exterior of the SeqStudio Genetic Analyzer with a damp lint-free cloth. Wipe down the LED screen using glass cleaner and a lint-free cloth.
• If storing the cartridge off unit, place the ICP cover over the capillaries and store upright.

There is a no-charge recycling program for used SeqStudio cartridges available in many countries. To see if your country has a recycling program and to learn more about the program itself, please go here.

If your country does not have a recycling program or if you do not wish to participate in the recycling program, please dispose of the cartridges in accordance with the Material Safety Data Sheet (MSDS) and local regulations.

The SeqStudio Genetic Analyzer is not 21CFR compliant. There are plans for a future release that will have features to aid in meeting 21CFR compliance.

The SeqStudio Genetic Analyzer does not require a computer in order to run. The sample files are saved to a local hard drive and can be exported to a connected computer, network computer, or Thermo Fisher Connect account. Once the data has been extracted from the SeqStudio Genetic Analyzer, we recommend deleting old runs on a regular basis to free up space on the hard drive.

The SeqStudio Genetic Analyzer can store approximately 3500 injections or 14,000 sample files.

The SeqStudio Genetic Analyzer does not require anti-virus software but if you connect a computer to it that has the secondary analysis software packages installed, we recommend using Symantec (Norton) Anti-Virus Software. Some other anti-virus software have been known to sequester files used by the secondary analysis software which prevents the secondary analysis software from launching.

The SeqStudio Genetic Analyzer supports the following dye sets:

• E
• Z
• D (DS-30, DS-31)
• F (DS-32)
• G5 (DS-33)
• J6 (DS-36)
• Any dye (up to 6 dyes)

Custom dye sets can be set up using the Any Dye template; please see manufacturer recommendations for use on the SeqStudio Genetic Analyzer.

Yes, any dye set that is currently being used on the 3500 Genetic Analyzer or the 3730 DNA Analyzer can be used on the SeqStudio Genetic Analyzer.

Many of the calibrations that are required on other platforms have been automated for the SeqStudio Genetic Analyzer. A spectral is performed on install for BigDye Terminator v.3.1 and for the DS-33 (G5) Dye Set. We recommend that a spectral be run for any other fragment analysis dye sets that will be run on the system. A spectral only needs to be made once on the instrument and does not change when you change the cartridge. If you see spectral issues on the SeqStudio, verify that you have selected an instrument protocol with the correct dye set.

The Thermo Fisher Connect applications have been tested with the following browsers:

• Mozilla Firefox v.32.03+
• Google Chrome v. 38.02+
• Apple Safari v. 7 +
• Internet Explorer v. 10+

The updates to the SeqStudio Genetic Analyzer software can be found here.

The patches to the Sequencing Analysis Software that enable analysis on the SeqStudio Genetic Analyzer can be found here.

The patches to the SeqScape Software that enable analysis on the SeqStudio Genetic Analyzer can be found here.

The patches to the Variant Reporter Software that enable analysis on the SeqStudio Genetic Analyzer can be found here.

The patches to the GeneMapper Software that enable analysis on the SeqStudio Genetic Analyzer can be found here.

The SAE Administrator Console is the tool that is used to configure the Security, Audit, and Electronic Signature (SAE) module. The SAE module can be configured to meet specific requirements for security, audit, and e-signature. In the SAE Administrator Console, a software or instrument that is configured for the SAE module is called an "application". Example applications include the SeqStudio Data Collection Software or the QuantStudio Design and Analysis Software v2.

The SAE module is a client-server software configuration that includes three components:
- SAE Administrator Console: Tool that is used by an SAE administrator to configure the SAE module.
- SAE server (server): Service that runs in the background and stores SAE settings, user accounts, audit records, and e-signature records. By default, the SAE server is installed on the same computer as the SAE Administrator Console.
- SAE screens (client): Screens that are displayed in an application (sign in, audit, and e-signature) and that require user input. The SeqStudio Data Collection Software runs on the client.

The SAE Administrator Console can be installed on a Windows 7 or Windows 10 operating system.

When the SAE module is enabled:
- The SAE module controls the access to and the available functions for the SeqStudio Data Collection Software.
- The SAE module does not affect SeqStudio Plate Manager desktop or cloud.
- The Connect cloud-based platform and remote monitoring functions are disabled in the SeqStudio Data Collection Software.

When SAE is enabled in the SeqStudio Data Collection Software, the SAE functions are set to the following:
- Audit: Enabled by default, but can be disabled
- E‑signature: Enabled by default, but can be disabled. By default, no actions are set to require e‑signature.

The following user actions are audited silently (no audit reason dialog box is displayed), and you cannot change the Audit mode:
- Enable or disable SAE functions in the SeqStudio Data Collection Software
- Sign in to or sign out of the SeqStudio Data Collection Software
- Start, pause, resume, or cancel an instrument injection or plate run
- Perform a dye calibration or an install run
- Perform cartridge maintenance: Refresh PDS or Fill Array

There is no way to recover a forgotten password. If the SAE administrator forgets their password, the software must be reinstalled. Export all data before reinstalling the software.

The system security function cannot be disabled in the SAE Administrator Console. To disable user sign in to an application, you must disable SAE in the application.

Auditable actions in the SAE Administrator Console are:
- Enable or disable security, audit, or e-signature
- Sign in to or out of the SAE Administrator Console
- Import or export an SAE configuration
- Install an application profile
- Archive, purge, or restore audit records
- Manual sync with LDAP (Lightweight Directory Access Protocol) Directory

Archiving audit records removes the records from the SAE Administrator Console and saves them in an internally specified location on the same computer on which the SAE Administrator Console is installed. Note: Archived audit records are accessible for viewing in the SAE Administrator Console.

You may use the export and import functions to transfer settings from one installation of the SAE Administrator Console to another.