3500 Series Genetic Analyzer FAQs

New 96-sample polymer pouch, extended 14-day on instrument storage of POP-4 polymer and buffers, and a new 36-cm seq module for mitochondrial analysis.

Data collection (DC) 1, 2, and 3 software will not fully recognize the 96-sample pouch. The gauges on the dashboard will incorrectly display the type of polymer size used, and the limits, max samples offered, or shelf life limits will be incorrect. 

See the example below of what DCS 2 and DCS 3 will display if customers use the 96 sample pouch. 

The red box shows the incorrect information on the gauges (for the polymer ABC and CBC). Polymer gauge should show 96 samples and the ABC and CBC should show 14 days remaining, while the injection number should show 100 injections. However, the green box will display the correct information.

Yes. Since the on-deck time of consumables is programmed on the consumable RFID tag itself, basic recognition happens in DC1, 2, or 3. However, dashboard gauges will be inaccurate. Only DCS 3.1 will recognize and fully support the extended shelf life of 14 days.

All currently supported Applied Biosystems STR amplification kit products have been validated on the 3500 Series instruments.

Yes. The 3500 Series systems data has approximately 3-4x RFU dynamic range increase over the 31xx platforms, so peak heights can approach 20,000–30,000 RFUs. With this scale, pull-up peaks could appear higher than what is seen normally on previous instruments; however, the ratio of parent peak and pull-up peak is comparable to the 31xx instruments. 

As with any new instrument platform, accurate determination of analytical thresholds requires appropriate validation studies on the specific instruments within the laboratory. 

As stated in our letter dated November 2009, we discontinued the sale of new 3130 series Genetic Analyzers effective December 2011. We also announced our intention to support the 3130 instruments five years from the date of our final discontinuance in December 2011. We are very pleased that we are able to extend our support of the 3130 instruments. Thermo Fisher Scientific intends to use commercially reasonable efforts to support 3130 and 3130xl Genetic Analyzer users with related software, reagents, and consumables, as well as maintenance and repair service and technical and applications support at least up to December 2018. However, please note that our ability to provide support may be limited by circumstances beyond our reasonable control, such as availability of parts in our inventory.

 The 3100 instruments were launched in 2000 and sales were discontinued in 2005 for the Human Identification market. Due to age of the 3100 Systems, the sourcing and support of essential components, software and parts has become increasingly difficult. (For example, Microsoft has retired the support for both Windows NT and 2000.) As communicated in our customer letter dated November 18, 2010, we can no longer provide full support for the 3100 series instruments after December 31, 2011. Limited instrument maintenance and repair service may be available beyond December 31, 2011 subject to the availability of spare parts in our inventory.

No, the 3500-series Genetic Analyzers remains fully available and supported. We continue to provide innovative updates to the 3500-series instruments such as the smaller polymer pouch size and extended on instrument consumable life and welcome feedback on other improvements to the system.

RFID technology simplifies run setup, and helps to ensure optimal instrument performance by tracking the type of consumable installed, lot number, part number, install date, expiration date, and sample usage information for polymer, buffers, and capillary arrays. This also helps enable compliance with ISO 17025 control of records requirements for forensic lab accreditation.

During and after development of the 3500 system, we have consulted with personnel from several forensic laboratories with extremely stringent security protocols.  Based on their feedback we are not aware of, nor do we anticipate, security barriers/issues related to the 3500 RFID tags.  This is due to the specific nature of the RFID tags used on the 3500 system.  Please refer to the FAQs below for more information. 

The RFID tags used on 3500 instrument consumables are fixed passive RFID tags.  For fixed types of RFID tags, the reader reads tags in a stationary position and the tag must be very close to the reader (within a few centimeters) to even be read.  This is not like active RFID tags and battery assisted passive (BAP) RFID tags that can potentially transmit signals once an external source has been successfully identified. Fixed passive RFID tags have no power source and require an external electromagnetic field to initiate a signal transmission.

No, the read distance between the reader in the instrument and the tag on the consumables is only a few centimeters so there is no risk of interaction with other RFID devices.

It would be extremely difficult to reprogram an RFID tag after manufacturing.  We add a checksum, which is a mash-up of the tag's unique information to the tag.  So if any changes are made to the information on the tag we would detect a checksum failure and the 3500 software will not accept the tag.

No, the tags are never directly read by the computer, they are only read by the 3500 firmware.  The 3500 Data Collection Software sends a command to the 3500 firmware that instructs the firmware to read the tag and return the tag contents to the PC.  In addition, the tag data is Base64 encoded and any potential virus code would likely fail the encode/decode operation.

No, the tag is just memory and cannot execute code.

The RFID tags contain information only about the consumable part number/lot number/expiration date/installation date and the usage allowances (amount originally available and amount remaining).  While a third party could potentially extract this information (subject to the limitations of fixed passive RFID tags as described in these FAQs), much of this information is already printed on the label (part num/lot num/expiration) and the usage information is encoded in a manner which is not easily understandable.

Yes. However please note the 3500 system was developed with a goal to provide stringent quality control in order to help maximize instrument performance and first pass success. A significant amount of R&D work went into testing and determining on instrument life for each consumable.  This testing demonstrated that the shelf- life of the POP polymer could be extended from 6 months to 9 months for polymer in pouches, and the prepared anode and cathode buffer can remain on the instrument up to 14 days with no drop in performance 

(current recommendation is to prepare and replace the buffer every other day). Using expired consumables and/ or reagents prepared with poor quality water may negatively impact performance of the system. Expired reagents and/or reagents prepared with poor quality water can lead to loss of resolution, and/or system contamination resulting in extensive efforts on the part of service to recover proper performance on the system. The cost per sample for the 3500 consumables is comparable to the 31xx system with the added benefits of pre-filled containers and RFID tracking.

The 3500-series system has been validated by Thermo Fisher Scientific using POP-4 polymer and 36cm array protocols for all validated Applied Biosystems PCR Amplification  Kits.

The 3500-series system has been validated for forensic applications using both 96-well and 384-well reaction plates.

No, they have not been shortened and in most cases they have been extended.  For example, the prepared anode and cathode buffer can remain on the instrument for up to 14 days (as opposed to recommendation to replace the buffer daily for previous instruments).   

A key development goal of the 3500 series instruments was to provide stringent quality control to help maximize instrument performance and first pass success rate.  Expired reagents, or reagents prepared with poor quality water, have led to loss of resolution or system contamination resulting in instrument downtime and extensive efforts to recover proper performance on the system.  The consumables recommendations for expiration dates and on-instrument residence have been specified to ensure system performance and the generation of high quality data.  The Data Collection Software provides a warning or “hard stop” (via information collected from the RFID tag) when a specified limit is reached. A “hard stop” cannot be overridden however for the warning messages the customer may choose to override the message and continue running.  For example customers may choose to continue using the array even beyond the guarantee of 160 injections or the polymer beyond the on-instrument residence recommendation of 14 days. Any departure from the recommended values should be evaluated in each individual laboratory.

The table below describes the RFID parameters that are tracked:

*For DC 1.0 and 2.0: The days on instrument will be properly stated/ recorded in the Consumable field listed below the gauges. The actual gauges on the dashboard will be incorrect.

Yes, the running cost per sample for the 3500-series instruments is comparable and in some instances lower than that for the 31xx platforms, with the added benefits of the pre-filled quality controlled consumable packages and RFID technology.  The 3500 system also consumes significantly less power than previous instrument platforms, enabling substantial energy cost savings.  For some low throughput laboratories, consumable costs may increase slightly; however, the 310 Genetic Analyzer remains available and fully supported as an option for these laboratories.

The Conditioning Pouch is designed to provide washing reagent that is protected from contamination.  Reuse of the Conditioning Pouch may introduce undesired contaminants to the system.   Also, the conditioning pouch and polymer pouch cannot be emptied entirely.  The system requires a certain minimum volume to remain in the pouch to enable proper uptake of the reagent.

No, the spatial and spectral calibrations are stored via the RFID tag of the array.  However, developmental testing has shown that the data quality is improved by running a new spectral each time an array is changed or if the array has been adjusted or shifted in the detection cell window.  While the software does not force the user to do so, it is recommended in the User Manuals.

Only sample injections increase the total sample count.  There is sufficient overfill in the polymer pouch to accommodate a limited number of installation and wizard operations. However, if the number of wizard operations exceeds a certain limit, the number of remaining samples or injections will be reduced. For example, if you run the total bubble remove option in the bubble remove wizard more than four times, or run other wizard operations excessively, the number of remaining samples or injections will be reduced. Refer to the polymer gauge on the dashboard for the up-to-date number of remaining samples or injections at any given point.

The Data Collection software will read the RFID tag at the beginning of each operation such as an instrument run or maintenance or calibration function.  If the user replaces a consumable and would like to instantly capture the RFID information, click the Refresh button on the Dashboard to update consumable information.

IMPORTANT! The Days Remaining for buffers updates only when you click Refresh or start a run. As part of daily startup, click Refresh to update consumable status

No.  The RFID information is checked upon initiation of an injection list and all injections in the list will be completed regardless of the RFID status when the run is completed.  Prior to the start of the run, the instrument is designed such that enough reagent, such as polymer, is available for completion of all samples in the injection list.

To maximize peak height consistency from instrument to instrument, capillary to capillary and injection to injection, an optional chemistry and software based method of normalization has been introduced in the 3500.  If you choose to normalize data, GeneScan 600 LIZ v2.0 size standard is used and the normalization size standard is specified in the quality control analysis method of the data collection software.  During data collection, the software calculates a Normalization Factor for each sample by dividing the Normalization Target (experimentally defined expected peak height) by the observed average peak height of the size standard fragments in the sample.  This Normalization Factor is a multiplier and the peak heights of the sample are adjusted accordingly.  

GeneScan 600 LIZ v2 (PN: 4408399), has been validated for both general fragment sizing and the optional Internal Standard Normalization method.  This product has also been validated for use on existing CE instruments.  Previous versions of the GeneScan 600 LIZ Size Standard cannot be used for optional normalization.

No. The GeneScan 600 LIZ Size Standard v2 was specifically designed and optimized to support normalization.

The %CV is a way of describing the amount of variation from the mean of a sample set.  It tells you how closely the data is centered around the mean.  Since the result is unit-less, it can be used to compare different data sets more easily.  It is calculated by dividing the standard deviation by the mean: SD/mean*100.

No, there is no software imposed limit.  However, the system may slow down as the number of records increases.  See Chapter 1 of the 3500 Series Genetic Analyzers User Guide for more information regarding managing audit records.

It is recommended that user-created items stored in the library are purged or archived every 3 months (See the 3500 Series Genetic Analyzers User Guide for more information Computer Maintenance).  Factory-provided items are not purged. You have an option to archive the items.  Allowing library objects to build indefinitely may result in slower performance, especially in navigating the library.

The Tools/Purge function purges all user created objects from the library.  To just delete plates you would have to manually delete them in the library.  Alternatively, users may export desired library objects, perform a purge, then re-import the user defined objects.  NOTE: purge does not remove factory provided objects.

To permanently save non-HID objects, navigate to the Datastore folder (C:\Applied Biosystems\3500\datastore) and create a new folder (e.g. "Unused Assays"). Go into the "Assays" folder and move all non-relevant objects to the previously created new folder. Perform a similar operation for other objects. Restart the PC and log back into the 3500 Data Collection folder. The objects you have moved are no longer visible in the Library.

The records are saved in an .aud file with the same name as the audited object.  For example, PlateA.xml audit info is in PlateA.aud.

A .cid file is created for each run on the instrument including spectral calibration runs and HID Install Standard runs.  The customer can send the .cid files associated with a run for analysis by AB HID Technical Support staff.  By default, these files (.cid) are located at:

X:\Users\<logon name>\Data\SampleData\Run <timestamp>

The default drive is generally the D: drive on most systems.  The .cid files are not automatically deleted by the instrument.  Users may back them up or delete them as needed.  

The lot number information is included with each sample file and can be viewed in the sample info tab within GeneMapper ID-X v1.2 or higher for each sample. This information is therefore permanently stored with the .hid file. Additionally, the Data Collection software generates the following logs that you can access: "3500ConsumableUpdates.txt" in
C:\Applied Biosystems\3500\LogFiles and "3500UsageStatistics.txt"
in
C:\Applied Biosystems\3500\UsageData.

Use only the cleaning methods described in Chapter 8 of the 3500 Series Genetic Analyzers User Guide.  As with all capillary electrophoresis instruments, some commercial detergents may contain dyes and other components that can interfere with data quality or contaminate the pump components of the instrument.