Q: How does the new 3500 system support the Human Identification (HID) laboratory?
A: Built on Applied Biosystems® proven capillary electrophoresis technology, the 3500 Genetic Analyzer is specifically designed to enhance productivity and confidence in the Human Identification Laboratory.

The integrated data collection software has an intuitive, workflow driven user interface that walks you step by step through instrument control, run setup, data collection and real-time data quality assessment. The software contains HID specific plate record templates with validated HID protocols to simplify implementation of the 3500 and run setup. Most runs can be setup by simply importing or entering sample names, and selecting a pre-defined assay. Real-time data analysis tools enable:

  • Preliminary data analysis with multiple plot options and size-calling
  • Rapid identification of samples that may need additional processing with data quality flags
  • Sample re-injection management

The 3500 system offers a number of QA/QC features that help enable compliance with ISO 17025 control of records and manage Quality Control requirements for forensic lab accreditation, including:

  • Innovative snap-in-and-go consumable design with Radio Frequency Identification (RFID) technology tracks and records key consumables data. This enables easy tracking of consumable lot, numbers, usage, and expiration dates, eliminating manual bookkeeping and improving troubleshooting.
  • Data Chain of Custody: user configurable security, auditing and e-signature functionality to maintain chain of custody of electronically generated data

Other key improvements:

8-capillary and 24-capillary options to enable increased throughput

  • New single-line 505 nm, solid-state long-life laser; utilizes a standard power supply; requires no heat-removal ducting, significantly reduces energy consumption, extends instrument lifetime
  • Reduced signal variation from instrument to instrument, run to run, and capillary to capillary
  • Advanced thermal system design improves temperature control for more consistent data migration and reduced run times
  • New, compact polymer pump design reduces instrument setup time and potential for bubble formation

Q: What HID PCR amplification kits have been validated on the 3500 Series instruments?
A: All currently supported 4-dye and 5-dye AmpFSTR® kit products have been validated on the 3500-series instruments.

Q: Has the 3500 series system been adopted by forensic laboratories?
Yes, over 100 forensic laboratories worldwide have purchased the 3500 instruments. To date, at least 25 forensic laboratories in North America, Latin America, Europe, and Asia have validated and currently utilize the 3500 instruments online for casework, databasing and paternity applications.

Q: Is the scaling on the 3500-series instruments different than that on the 31xx platforms?
Yes. The 3500-series systems data has approximately 4x RFU dynamic range increase over the 31xx platforms, so peak heights can approach 20,000 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. For more information on this topic, please attend the upcoming implementation webinar (see next FAQ).

Q: Where can I find more detailed information on the performance of these instruments in forensic laboratories?
A: In the spring of 2011, Life Technologies will host a “Considerations for Efficient Implementation of the 3500-series Genetic Analyzer for Human Identification” Webinar. This webinar is intended to help forensic laboratories take full advantage of the 3500 features as they approach validation and implementation. Presented by Life Technologies Forensic Application Scientists and an operational forensic laboratory with hands-on 3500 experience, this interactive online session will discuss the key factors to be considered when planning the implementation of the 3500-series instrument. For detailed information on this webinar, please contact your local sales or support representative.

Additional information on the 3500 system is available on the web at

Q: What is the sales and support status of the 3130 Series Genetic Analyzers?
The 3130 Series Genetic Analyzers were launched in 2004 and were validated for use with Human Identification applications in 2005. As communicated in our customer letter dated July 15, 2010, sales of the 3130 series instruments will be discontinued for HID customers on June 30th, 2011. (Sales of 3130 series instruments were discontinued for research customers on December 31, 2009, but this timetable was extended for HID customers.) Refurbished units, complete with a one year warranty, will still be available for sale after discontinuance (subject to availability).

As communicated in our customer letter dated July 15, 2010, Life Technologies remains committed to maintaining the highest level of service and support for 3130 and 3130xl Genetic Analyzers for a minimum of five years after sales discontinuance. This includes related software, reagents and consumables, as well as maintenance/repair service and technical/applications support.

Q: What is the sales and support status of the 3100 Series Genetic Analyzers?
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.

Q: Is there any change to the sales and support status of the 310 Genetic Analyzer?
No, the 310 Genetic Analyzer remains fully available and supported. This allows for multiple options to accommodate small (310), medium (3500), and high (3500xL) throughput laboratories.


Q: How has Radio Frequency Identification technology been implemented in the 3500 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.

Q: Are there security risks posed by the RFID tags used on 3500 instrument reagents?
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.

Q: What type of RFID tags are currently used on the 3500 Series instrument consumables?
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.

Q: Will an external RFID reader or RFID tags currently used in my laboratory interfere with the RFID reader or tags on the 3500 system?
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.

Q: Can the 3500 RFID tags be reprogrammed during transportation or storage?
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.

Q: Can RFID tags introduce a virus to the instrument computer?
No, because 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.

Q: Can the RFID tag extract information from the computer connected to the 3500 and then transmit the information elsewhere?
No, the tag is just memory and cannot execute code.

Q: What information remains with the RFID tags when the 3500 consumables are discarded? Would it be possible for a third party to extract information from the tag?
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.

Instrument Consumables

Q: What polymer and array length will be supported for HID use?
The 3500-series system has been validated by Life Technologies using POP-4™ polymer and 36cm array protocols for all validated AmpFSTR® Kits.

Q: What sample plate configurations are supported on the 3500 Series system?
The 3500-series system has been validated for forensic applications using 96-well reaction plates; however, both the 3500 and 3500xL are configured to support 8-strip tubes and 96-well plates, and 384-well plates are also supported on the 3500xL.

Q: Have shelf-life and on-instrument lifetime of the consumables been shortened on the 3500?
No, they have not been shortened and in some cases they have been extended. For example, the prepared anode and cathode buffer can remain on the instrument for up to 7 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 specified limit of 160 injections or the polymer beyond the on-instrument residence recommendation of 7 days. Any departure from the recommended values should be evaluated in each individual laboratory.

Q: What consumable RFID parameters are tracked by the 3500 software?
The table below describes the RFID parameters that are tracked:

Consumable On Instrument Life RFID Tracked
Hard Stop Warning
POP™ Polymers
  • 960 sample size
  • 384 sample size
7 days
  • Expiration Date
  • Exceeding the sample limit (depending on the pouch size)
  • Exceeding the number of allowed injections
    • 960 pouch: 120 for 8 cap, 50 for 24 cap
    • 384 pouch: 60 for 8 cap, 20 for 24 cap
7 day
Arrays160 injectionsNo Hard Stop
  • Expiration Date
  • 160 injections
7 days
  • Expiration Date
  • Exceeding seven days on the instrument
  • Exceeding the number of allowed injections
    • 120 for 8 cap
    • 50 for 24 cap

Q: Is the cost per sample for the 3500-series instruments comparable to the 31xx platforms?
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.

Q: The conditioning reagent is a single use pouch. For some operations, there appears to be ample liquid remaining for additional functions. Why does the software not allow the user to reuse a Conditioning Pouch?
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.

Q. When I install a new capillary or re-install a capillary that was previously removed for storage, will the software require a new spectral to be performed?
No. 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.

Q: Do spatial fills or bubble remove wizards count against the allowed sample count in a polymer pouch?
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.

Q: When is the information on the consumables updated on the dashboard screen?
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

Q. If a reagent expires while running a plate overnight as the date changes, will the run stop in the middle of the injection list?
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.

Data Collection and Analysis Software

Q: Is the information in the 3500 data collection files different from the information in the 31xx files?
Yes. The 3500 Data Collection software generates data files with significantly more information for all applications. The software was designed with numerous key features requested by the HID community, including simplified plate set-up, real-time data review and streamlined re-injection, as well as consumable tracking and data chain of custody to address ISO 17025 requirements.

Q: Can the data from 3500 Series systems be read or analyzed by previous versions of GeneMapper® ID or GeneMapper® ID-X Software?
No. The 3500 Data Collection software generates data files with information that cannot be read by previous versions of GeneMapper® ID or GeneMapper® ID-X Software. Current GeneMapper® ID-X Software customers will be given a free upgrade to the GeneMapper® ID-X v1.2 Software with the purchase of a 3500 series instrument. GeneMapper® ID customers will pay a standard conversion fee for GeneMapper® ID-X v1.2 Software with the purchase of a 3500-series instrument.

Q: If the 3500 can still generate .fsa files, can HID laboratories analyze this file with older versions of GeneMapper® ID and GeneMapper® ID-X Software?
No. As stated above the new 3500 data collection software generates data files with significantly more information for all applications, regardless of whether it is a .fsa file or any other file type. Therefore, even the .fsa files generated by the 3500 for general fragment analysis applications cannot be read by older versions of GeneMapper® ID and GeneMapper® ID-X Software. In order to facilitate analysis with the 3500 Data Collection software, a new version of GeneMapper® ID-X Software had to be developed.

Q: Why was the .hid file developed for HID laboratories?
Recognizing that HID laboratories would require a new GeneMapper® ID-X software version for use with the 3500, the .hid file was developed to add substantial value for forensic laboratories. The .hid file enables:

  • Simple management of file archives to distinguish HID data generated on the 3500 Genetic Analyzers as opposed to other systems or applications
  • Streamlined, HID specific workflows. Most runs can be setup by simply importing, or entering, sample names and selecting a pre-defined assay
  • Easy tracking of consumable lot, numbers, usage, and expiration dates, as well as instrument status and electrophoresis and analysis parameters, within GeneMapper® ID-X v1.2 software. This helps eliminate manual bookkeeping and improves troubleshooting
  • Data Chain of Custody: user configurable security, auditing and e-signature functionality to maintain chain of custody over electronically generated data
  • Signal Normalization option for use within GeneMapper® ID-X v1.2 software.

Q: How is the new GeneMapper ID-X v1.2 Software different from previous versions of GeneMapper®ID and GeneMapper®ID-X Software?
GeneMapper® ID-X v1.2 Software was developed to support the new 3500 Data Collection Software, normalization options and RFID capability, as well as improved printing speed, CODIS export options, and other features requested by the community. Previous versions of GeneMapper® ID and GeneMapper® ID-X do not support these features. The new GeneMapper® ID-X v1.2 Software is also compatible with .fsa file data generated with previous capillary electrophoresis platforms.

Q: What Windows operating system can be used for the 3500 Series data collection software?
The data collection software for the 3500 Series is currently supported on Windows Vista only. GeneMapper® ID-X v1.2 Software is currently supported on both Windows Vista and XP. Support for GeneMapper® ID-X v1.2 Software on the Windows 7 platform is currently in development. We will provide more information regarding a time-line for release as it becomes available.

Q: How does the 3500 Data Collection software help the laboratory keep track of maintenance tasks and monitor the state of the consumables?
Maintenance notifications and warning messages regarding the consumable and instrument status are recorded and displayed throughout the software. Warning messages alert the user that the validated usage has been exceeded and will describe the appropriate action.

Q. Previous Capillary Electrophoresis platforms contained raw data information from sample runs stored in the Oracle database. If the data extraction process to convert the raw data to a .fsa file failed, a mechanism to re-extract run information from the database was present. How is this accomplished in the 3500 data collection software?
The 3500 Data Collection Software does not utilize a database, such as Oracle. Therefore, the re-extract feature employed in other versions of Data Collection software is not appropriate for this version. The raw data is contained in a flat file on the hard drive rather than in an encrypted database.

Q. Are there any restrictions to utilizing the defragmentation component of Windows on the hard drive containing the 3500 Data Collection Software?
There are no specific restrictions regarding hard drive defragmentation on the instrument computer since there is no Oracle database associated with the 3500 Data Collection Software. However, if other programs, such as GeneMapper ID-X are installed on the same computer as the instrument, follow recommendations for those programs regarding defragmentation.

Q: What is the best method to close the 3500 Daemon window?
Activate the Daemon window by clicking on the window. Press and hold the Control button on your keyboard followed by the letter “c”. The window will ask you to confirm your action. Press “y” and hit Enter.

Q. When you change the order of injections in the injection list, can the injections alternate between plates A & B or does it have to perform all injections from an individual plate first?
An injection list can be created where the order of injections alternate between plates A and B.


Q: What is Internal Standard Normalization, and how does it work?
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, a new version of GeneScan™ 600 LIZ® 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.

Q: What standard is used for the optional Internal Standard Normalization?
A new version of the GeneScan™ 600 LIZ® size standard, 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. The previous version of the GeneScan™ 600 LIZ® Size Standard cannot be used for optional normalization.

Q: Can the GeneScan™ 500 LIZ® Size Standard be used for internal lane normalization?
No. The GeneScan™ 600 LIZ® Size Standard v2 was specifically designed and optimized to support normalization.

Q: I have seen graphs that compare data with a percent CV. What does this mean, and how is it calculated?
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.


Q: Many audit records are set to collect silently by default in the system. Is there a limit to the amount of collected audit records and when users should be purging these audit records?
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.

Q: How often should users purge the library?
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.

Q: Can I delete only plates when purging objects from the library, and keep the assays, protocols, and results groups that I have created?
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.

Q: How do I retain Library objects but make them invisible in Data Collection?
To permanently save non-HID objects, navigate to the Datastore folder (C:Applied Biosystems3500datastore) 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.

File Locations

Q: Where are the audit records saved?
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.

Q: What type of information should I provide to HID Tech Support for troubleshooting purposes?
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>DataSampleDataRun <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.

Q: How do I view reagents and consumable RFID information in addition to the screens in the 3500 Data Collections Software?
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 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 Biosystems3500LogFiles and "3500UsageStatistics.txt" in C:Applied Biosystems3500UsageData.


Q: How should the instrument be cleaned?
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.