GeneMapper ID-X Software Features
Features of the GeneMapper ID-X Software
GeneMapper ID-X implements functionality and features to support Expert System data analysis and increase the efficiency of traditional (manual) data analysis.
Included in the system are the following features:
- Analysis Requirement Check
- Allelic Ladder Quality Assessment
- Analysis Summary
- Comprehensive Quality Value System
- Quality Value Flags
- Manual Review Tools
- Color-Coded Marker Header Bars
- Labeling Scheme
- Label Edit Viewer
- Mixture Analysis Tool Features
- Quality Control
- Report Manager
- Multi-User Database Environment
- Chain-of-Custody Features
- Command Line Interface
Analysis Requirement Check
The analysis requirement check identifies unmet requirements before analysis starts and can be set up to stop analysis and display an alert if a specific sample type is not found.
Allelic Ladder Quality Assessment
The allelic ladder quality assessment evaluates allelic ladders before proceeding to sample analysis and automatically excludes low-quality ladders. There is an option to override the software assessment to use low-quality ladders to generate bin offsets.
For efficient data evaluation, the analysis summary provides easy-to-view summary of analysis results, an overview of allelic ladder, control and sample quality, and interactive links to specific categories of samples.
Comprehensive Quality Value System
GeneMapper ID-X incorporates a comprehensive quality value system which enables it to be used as an Expert System. The quality value system:
- Assesses the quality of allelic ladders before analysis and does not consider low-quality allelic ladders for genotyping.
- Assesses the quality of data at the sample and marker level using process quality values (PQVs). Some of these include:
- Sizing quality
- Off-scale peak detection
- Spike detection
- Evaluation of the number of alleles
- Minimum and maximum peak height
- Peak height ratio
- Broad peak detection
- Composite genotype quality (overall sample quality)
- Off-ladder allele detection
- Can be used to segregate samples that require manual review from those that do not
- Can be used by analysts to quickly identify quality issues and aid in data interpretation
- Incorporates automated concordance checks for positive and negative controls
- The ability to manually accept marker and sample genotypes
The PQV results of the quality assessment are displayed as color-coded flags:
The color of the flag depends on software-specified thresholds or user-defined thresholds.
Quality Value Flags
Quality value flags are the first review tool the analyst can use. This tool gives you an indication of the quality of the entire sample by identifying and interpreting anomalies within the data.
Manual Review Tools
For efficient data review in traditional manual review and expert systems workflows, the manual review tools provide:
- Process quality value (PQV) flags
- Automatic spike labeling based on intelligent rules
- User-defined "artifact" peak labels
- Marker-specific quality value details with thresholds and observed values displayed to show deviations from thresholds and identify sources of anomalies
- Mark Sample for Deletion and Delete All Labels from Sample functions in the Samples plot to allow easy elimination of low-quality samples directly from the plot window
- Override GQ and CGQ functions to "manually accept" genotypes at the marker and sample level
- Detailed label edit table display and visual indicators to indicate edits (gray PQVs) for electronic peer/technical review
Color-Coded Marker Header Bars
The marker header bars are now colored (green, yellow, or red) helping analysts quickly identify problem areas and determine the cause.
A new and more sophisticated labeling scheme has been introduced to improve the editing options available to the analyst. The software automatically labels spikes based on intelligent rules and provides the ability to assign "artifact" peak labels which do not get placed in the genotypes table. This feature saves time for analysts who normally manually change the labels.
Label Edit Viewer
The label edit viewer provides the analyst a detailed list of all allele edits and comments made within the project or for a selected group of samples.
Mixture Analysis Tool Features
GeneMapper ID-X Software v1.1 and v1.2 provides an integrated Mixture Analysis Tool to assist forensic analysts with mixture interpretation. The Mixture Analysis tool features:
- Segregate samples by minimum number of contributors
- Extract 2-person mixtures based on mixture proportion and peak height ratios
- Display a ranked set of possible genotype combinations to minimize the number of genotypes necessary to interpret
- Choose to designate a known contributor to aid in extraction if desired
- Calculate statistics including Random Match Probability (RMP), Combined Probability of Inclusion/Exclusion (CPI/CPE) and Likelihood Ratio (LR)
The Profile Comparison Tool allows the user to perform QC/QA checks on the data contained within a project and evaluate efficiently any potential contamination events. The profile Comparison tool allows the analyst to perform the following:
- Evaluate sample concordance and allele matching
- Include additional custom positive controls and allow automatic concordance checks of custom controls
- Compare samples in a project to one another to determine if they contain profiles similar to neighboring samples
- Compare samples in a project to laboratory reference and custom control profiles using a user-defined match percent threshold
For customized table-formatted reports, the Report Manager allows the analyst to change column names and column order and export a traditional horizontal allele table for a selected group of samples for use as a genotype summary or import into LIMS or other downstream applications.
Multi-User Database Environment
The multi-user database environment:
- Allows multiple users to share projects in a centralized database
- Facilitates efficient data sharing between analysts for second analysis and review
- Limits the need to import and export projects
- Allows central management of analysis settings
Electronic data chain-of-custody features allow controlled user access to software and data, auditing and reporting of some or all analyst actions, the option of a requirement for user-authentication before saving a change and custom configuration to meet the data management needs of each laboratory.
Command Line Interface
Enables streamlined integration with LIMS or other external software applications.