GENEMAPPER® ID-X v1.4: SOFTWARE UPDATES – FEATURES & SPECIFICATIONS

 

Q: What new features are available in the GeneMapper® ID-X Software v1.4?
A: As the newest version of automated genotyping software for forensic casework and databasing data analysis, GeneMapper® ID-X v1.4 Software includes fragment analysis and Expert System functionality designed specifically to streamline the review of data generated by the GlobalFiler™ Kits and has been validated for use with the newest Data Collection Software as well as data from all previously released AmpFLSTR® PCR Amplification Kits run on the Applied Biosystems 3130 Series and 3500 Series Genetic Analyzers and the 3730 DNA Analyzer.

More detailed information on this software is available on the GeneMapper® ID-X Software v1.4 Product Bulletin and User Bulletin.


 

Q: What are the computer specifications for GeneMapper® ID-X Software v1.4?
A: The supported computer hardware and system requirements for GeneMapper® ID-X Software v1.4 (standalone configuration with Full and Client versions) are as follows:

– Recommended configuration

  • Core 2 Duo 3 GHz or newer
  • 4 GB RAM
  • 200 MB available on boot drive
  • 10GB available on install drive for full install; 450MB available on install drive available for client install
  • DVD-ROM drive
  • 10/100 NIC with RWU (internal) or above installed
  • TCP/IP installed

– Minimum system configuration

  • Core 2 Duo 2.2 GHz or compatible processor
  • 2 GB RAM
  • 200 MB available on boot drive
  • 10GB available on install drive for full install; 450MB available on install drive available for client install
  • DVD-ROM drive
  • 10/100 NIC with RWU (internal) or above installed
  • TCP/IP installed

The following OS options are supported for the GeneMapper® ID-X Software v1.4 standalone configuration:

– Windows® 7 Professional OS (Service Pack 1), 32 bit
– Windows® XP OS (Service Pack 3), 32 bit


 

Q: I am using an earlier version of GeneMapper® ID-X Software – how do I upgrade to GeneMapper® ID-X Software v1.4?
A: You will need to install an upgrade license for each instance of GeneMapper® ID-X you wish to upgrade. For example, if you have 1 Full GeneMapper® ID-X v1.1 Software and 3 Client GeneMapper® ID-X v1.1 Software , you will need to install 1 License GeneMapper® ID-X v1.4 Full Upgrade Software and 3 Licenses of GeneMapper® ID-X v1.4 Client Upgrade Software to upgrade all existing installations. Laboratories should run their own internal studies to confirm the performance of the software and if necessary, validate the optimal analysis parameters for their laboratory’s protocols.


 

Q: If I were to upgrade to GeneMapper® ID-X Software v1.4, can I still view and analyze my old data?
A: Yes, GeneMapper® ID-X Software v1.4 can analyze .fsa and .hid files generated from all Applied Biosystems Genetic Analyzers , all AmpFLSTR® and GlobalFiler™ PCR Amplification Kits as well as projects created using GeneMapper® ID-X Software and previous versions of GeneMapper® ID-X Software.


 

Q: Can I upgrade from GeneMapper® ID to GeneMapper® ID-X v1.4?
A: There is no upgrade pathway from GeneMapper® ID-X to GeneMapper® ID-X v1.4. To start running GeneMapper® ID-X Software v1.4 you will require at least 1 Full Install version. To minimize the implementation and validation burden GeneMapper® ID-X software utilizes the same trusted and validated features and functionality of GeneMapper® ID-X with the addition of a set of features that specifically support the human identification (HID) data analysis workflow and the latest computer requirements of many laboratories. These features include:

– An advanced set of data analysis and sample review tools:

  • Comprehensive quality value system that can be optimized and validated for use in both Expert System and traditional data analysis workflows to identify anomalies, flag samples and controls for review, and greatly reduce the amount of analysis time required.
  • Integrated profile comparison, mixture analysis and statistical calculation functionality that enables streamlined, consistent data analysis and interpretation of single source and mixed DNA samples.

– Configurable electronic data chain-of-custody and auditing functionality that includes tracking changes to data, user-authentication, controlled user access and audit history reports that support the peer/technical review process.

– Supports data generated from HID genotyping applications on all currently available Applied Biosystems capillary electrophoresis instruments including the 3500 series Genetic Analyzers.

– Utilizes a multi-user centralized database configuration for better data sharing and storage. The most recent version incorporates, Oracle® 11g Release 2, which represents the latest technology to maximize compatibility with current operating systems and offer superior performance compared to the database found in GeneMapper® ID-X.

– Compatible with Microsoft® Windows® 7 Professional and XP Operating Systems (OS) on 32 bit systems.

Some laboratories use a step-wise approach to implementing GeneMapper® ID-X software in their laboratory by first implementing the use of the fragment analysis functionality followed by the optimization and validation of the Expert System (for single source samples) or Expert Assistant (for casework samples) functionality into their workflow. Laboratories should run their own internal studies to confirm the performance of the software and if necessary, validate the optimal analysis parameters for their laboratory's protocols.


 

Q: Expert system software seems like it is more for Database Laboratories. How can this type of software be useful for traditional manual analysis of forensic samples?
A: By utilizing the automated, rule-based, subject-specific knowledge on which an Expert System is based, much of the analysis process can be simplified empowering you to make key interpretation decisions more quickly, confidently and consistently. By leveraging the expert system functionality in GeneMapper® ID-X as well as the integrated mixture analysis tool, you can quickly assess controls and QC data, easily review and edit single source, routine samples and process mixed samples more efficiently, with maximum consistency and reproducibility.


 

Q: How do I access the Mixture Analysis tool and what are the main functions it performs?
A: The Mixture Analysis tool is fully integrated within the GeneMapper® ID-X software and is accessible via the Tools menu. The Mixture Analysis tool performs the following functions:

1. Identifies samples within the GeneMapper® ID-X project that are eligible for Mixture Analysis. Samples are assessed according to sample type, analysis status and allele label status.
2. Categorizes and segregates eligible samples by the minimum number of contributors contained in each sample (1, 2, or 3 or more contributors).
3. Extracts and separates contributor profiles into individual major and minor genotype combinations for all markers present. (2 contributors only).
4. Filters known profiles from selected sample profiles (2 contributors only).
5. Calculates statistics using population databases stored within the software.


 

Q: What analysis parameters are utilized by the Mixture Analysis tool in performing extraction of contributor profiles from 2-person mixtures?
A: The Mixture Analysis tool extracts all possible genotype combinations from detected peaks at each locus and utilizes heterozygote peak height ratio and a measure of mixture proportion to evaluate each genotype combination.


 

Q: Will I have control over the parameters used by the Mixture Analysis tool?
A: You will be able to define the Mixture Interpretation Threshold (MIT) used to filter peaks which meet your criteria for mixture interpretation and the peak height ratio thresholds applied to peaks falling within specific peak height ranges. The residual value used to evaluate the fit to expected mixture proportion is set within the software and cannot be changed by the user. Mixture analysis methods may be defined that correspond to the interpretation criteria developed by your laboratory based on your internal validation studies.


 

Q: Does the Mixture Analysis tool extract individual contributors from mixtures containing more than 2 people?
A: The GeneMapper® ID-X Software v1.1 Mixture Analysis tool only extracts individual contributors from mixtures containing 2 contributors which represent a high proportion of the mixtures encountered by forensic laboratories. Statistical calculations can however be performed on mixtures containing 3 or more contributors.


 

Q: Which statistical calculations will the Mixture Analysis tool perform?
A: The statistical calculations available depend upon the number of contributors contained within the sample. The software will calculate the following:

  • Likelihood Ratio (LR): For samples categorized as containing 1 or 2 contributors
  • Random Match Probability (RMP): for samples categorized as single source and for each contributor extracted from a 2 person mixture.
  • Combined Probability of Inclusion/Exclusion (CPI/CPE): for samples categorized as containing 2 and 3 or more contributors

 

Q: Can extracted genotype combinations and statistical results be exported?
A: Yes, all results are exportable in .csv format.


 

Q: Can I import my own population databases to use in statistical calculations?
A: Yes. Three population databases are provided with the GeneMapper® ID-X v1.1 software for use with the Mixture Analysis tool but full instructions on how to create and import custom databases are provided in the GeneMapper® ID-X Software Help.


 

Q: What resources are available to me if I want to learn more about the Mixture Analysis tool?
A: Comprehensive information regarding the functions performed in the Mixture Analysis tool are available in the GeneMapper® ID-X Software Help installed with the software. Two additional documents, the GeneMapper® ID-X Software v1.1 Getting Started Guide and the GeneMapper® ID-X Software v1.1 Quick Reference Guide will also be provided with the software. If you are interested in a demo version of the software, contact your account manager.


 

Q: How many clients connected simultaneously GeneMapper® ID-X software support?
A: The number of clients connected per database could impact the speed of the system and is dependent on variables such as individual laboratory network performance and laboratory workflow. Initial evaluations performed by Applied Biosystems indicated no dramatic degradation in speed of operation when 96 samples were analyzed simultaneously by 10 clients connected to a single database. Each laboratory can use this as general guidance and determine the appropriate number of clients to ensure flexibility of operation whilst maintaining an acceptable speed of operation for their particular laboratory environment.


 

GLOBALFILER™ KIT INFRASTRUCTURE REQUIREMENTS

 

Q: What do I need to collect and analyze 6 dye data on the 3130 and 3730 Genetic Analyzers?
A: Functionality was specifically developed and protocols were optimized to collect and analyze 6-dye data from the GlobalFiler™ Kits on the 3130 and 3730 Genetic Analyzers. To enable 6-dye data collection on the 3130, 3130xl and 3730 you will need to upgrade your systems to Data Collection v4 and install the DCSv4 6 Dye Module License. To perform efficient fragment and mixture analysis of GlobalFiler™ Kit data you will also need GeneMapper® ID-X v1.4. GeneMapper® ID-X was developed specifically to handle the expanded loci and dye set and the additional Y Marker information present in the GlobalFiler™ Kits.


 

Q: What do I need to collect and analyze 6 dye data on the 3500 Genetic Analyzers?
A: To collect and analyze GlobalFiler Data on the 3500 Genetic Analyzers you can use either Data Collection v1 or v2. We have also developed and optimized instrument protocols for the data collection of GlobalFiler samples. To run GlobalFiler with the optimized protocols, ensure that the HID Updater 3500 Data Collection Software v2.0 has been applied to the Data Collection Software v1 or v2. Version 2 of the 3500 Data Collection Updater installs HID-specific Run Modules, Assays, and plate templates and adds new objects to support the GlobalFiler™ Kits to the 3500 Library (Datastore). This installer also incorporates all of the updates that were included in the v1.0 3500 HID Updater and is a replacement for that version.
If the 3500 Updater v2 has not been installed on your system go to
http://www.lifetechnologies.com/br/en/home/technical-resources/software-downloads.html
to download a copy and install it on your 3500 Data Collection v1 or v2.


 

Q: What are the computer specifications for the new Data Collection Software?
A: The upgrades have been tested on the Dell Optiplex XE system. The software will be Windows 7, 32-bit compatible only.


 

Q: What are the computer specifications for GeneMapper® ID-X Software v1.4?
A: The supported computer hardware and system requirements for GeneMapper® ID-X Software v1.4 (standalone configuration with Full and Client versions) are as follows:

– Recommended configuration

  • Core 2 Duo 3 GHz or newer
  • 4 GB RAM
  • 200 MB available on boot drive,
  • 10GB available on install drive for full install; 450MB available on install drive available for client install
  • DVD-ROM drive
  • 10/100 NIC with RWU (internal) or above installed
  • TCP/IP installed

– Minimum system configuration

  • Core 2 Duo 2.2 GHz or compatible processor
  • 2 GB RAM
  • 200 MB available on boot drive
  • 10GB available on install drive for full install; 450MB available on install drive available for client install
  • DVD-ROM drive
  • 10/100 NIC with RWU (internal) or above installed
  • TCP/IP installed

The following OS options are supported for the GeneMapper® ID-X Software v1.4 standalone configuration:

– Windows® 7 Professional OS (Service Pack 1), 32 bit
– Windows® XP OS (Service Pack 3), 32 bit


 

Q: What is meant by Windows 7, 32-bit vs. 64-bit. What's the difference?
A: Microsoft defines the difference as: The terms 32-bit and 64-bit refer to the way a computer's processor (also called a CPU), handles information. The 64-bit version of Windows handles large amounts of random access memory (RAM) more effectively than a 32-bit system. There are more details available at:
http://windows.microsoft.com/en-us/windows-vista/32-bit-and-64-bit-windows-frequently-asked-questions
Life Technologies Data Collection computers will be running 32-bit. We are currently evaluating 64-bit systems for 3500, 3130 and 3730 Data Collection Software. Once this testing is completed we will have information on the compatibility of 64-bit systems. Currently there are no plans for 64-bit compatibility for GeneMapper® ID-X.


 

SOFTWARE UPDATES – FEATURES & SPECIFICATIONS: DATA COLLECTION

 :

Q: What is the latest version of Data Collection software for the 3500 series instruments and what new features does it offer?
A: 3500 Data Collection Software v2 is the latest version of software for the 3500 and offers the following features/benefits:

– RFID limit updates (expiration date hard stop →warning changes)
– Windows® 7 Professional SP1 compatibility, 32 bit
– New PC (Dell Optiplex XE - 4 GB RAM, 500 GB RAID Disk)
– Data migration from Data Collection v1 -> v2
– Modern Licensing Technology with a new license scheme that utilizes on-line registration
– Minor software updates


 

Q: Do I need to upgrade to 3500 DC v2.0 to run data from the GlobalFiler Kits?
A: No, GlobalFiler™/GlobalFiler™ Express Kit data can be run using Data Collection v1 but Data Collection v2 offers multiple benefits to forensic laboratories including Windows® 7 compatibility.


 

Q: If I upgrade to 3500 Data Collection v2 do I also need to upgrade my GeneMapper® ID-X Software?
A: No, .hid sample files generated by the 3500 Data Collection software v2 can be viewed and analyzed with GeneMapper® ID-X Software v1.2 and later.


 

Q: What is the latest version of Data Collection Software for the 3130/3730 series instruments and what new features does it offer?
A: 3130/3130xl/3730 Data Collection Software v4 is the latest version of software for the 3130/3730 series instruments and offers the following features/benefits:

– Ability to upgrade to 6-dye module to run GlobalFiler™ Kit data
– Windows® 7 Professional SP1 compatibility, 32 bit
– New PC (Dell Optiplex XE - 4 GB RAM, 500 GB RAID Disk)
– Modern Licensing Technology that utilizes on-line software registration*
– Oracle 180 day password expiration fix
– MAC address Hotfix integrated
– Updated Sapphire pump wizard settings (CCB)
– BigDye® Direct mobility files
– Data migration from UDC3.0, 3.1 -> UDC4.0


 

Q: If I upgrade my 3130 series instrument to run 6-dye data, can it still analyze 4 and 5 dye data?
A: Yes. The upgrade does not affect compatibility with current STR systems.


 

Q: If I upgrade to 3130/3130xl/3730 Data Collection v4 do I also need to upgrade my GeneMapper™ ID/ID-X Software?
A: If you upgrade to Data Collection v4 but do not activate the 6-dye module, you can analyze data using your current software version. If you have enabled the 6-dye module and are running GlobalFiler™ data, you will require GeneMapper® ID-X Software v1.4.


 

Q: How are previous versions of Data Collection upgraded?
A: The Data Collection Software upgrade is performed by a Field Service Engineer and involves the following steps:

– Set up new, Dell Optiplex XE Computer and Install OS Image
– Run a script to copy data from original computer
– Install the new Data Collection software, import data from original computer
– Run functional tests using Negative Controls to verify Data Collection is communicating properly with the instrument


 

Q: What is the new licensing scheme for the new versions of Data Collection Software?
A: To help us provide better communication on software updates or fixes we will use FlexNet licensing to register your Data Collection Software license. This model utilizes the computer’s ID and a license key to generate a unique installation ID to register the computer and activate the software at regular intervals.
A Service Engineer will install the initial license and walk you through the registration process for future license renewals. A wizard within the Data Collection software will record the Computer ID and License Key, this information is used to register the license key at the Life Technologies License Registartation website. (The instrument computer DOES NOT need access to the internet). The license registration process can be completed by transferring information via a thumb/flash drive. After the on-line registration is complete, a license file is sent from Life Technologies to the PC (internet connection) and to an email address of your choice. If the instrument does not have internet access, the user saves the license and returns to the License Activation Dialog within the Data Collection software to complete the installation and registration process. The data collection software license will need to be renewed every year. To renew the license, you will be prompted by the Data Collection software via the renewal process which essentially requires you to resubmit the computer MAC ID and a license key to the Life Technologies registration site.