FaSTR™ DNA
What can FaSTR™ DNA do for you?
FaSTR™ DNA is designed by scientists for scientists, combining a sophisticated and user-friendly graphical interface with easily understandable, transparent and laboratory customisable rules for DNA profile analysis. Now Able to Analyze 8-Color Files from the Promega Spectrum CE System.
Intuitive: FaSTR™ DNA’s interface helps streamline the otherwise time-consuming workflow of calling alleles.
Intelligent: FaSTR™ DNA incorporates optional artificial neural networks (ANN) for the independent classification of peaks detected[1].
Integrated: FaSTR™ DNA’s in-built Number of Contributors (NoC) estimator allows seamless integration with STRmix™ to make the analysis and interpretation process even easier.
With FaSTR™ DNA you will be able to:
Analyse raw DNA results more rapidly, particularly high throughput samples such as DNA databank samples.
Fully configure settings, including setting known kit artefacts.
Optionally estimate the Number of Contributors to a mixture.
Seamlessly integrate with STRmix™ (when in use) for even greater speed and efficiency from analysis to interpretation.
Easily generate informative electropherogram (epg) reports.
Customise export templates.
Carry out control concordance testing, including quality marker checks.
Perform sample to sample comparison checks.
Perform comparison checks against a database of reference profiles
Review two separately analysed projects side by side and resolve conflicts.
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Discover how FaSTR™ DNA simplifes the analysis of DNA profiles generated by capillary electrophoresis genetic analysers and standard profile testing kits.
About FaSTR™ DNA
Learn more about FaSTR™ DNA, including how it works, published data describing its validation and features, as well as product specifications and compatibilities.
FaSTR™ DNA is expert forensic DNA analysis software that allows DNA analysts to simplify the analysis of DNA profiles generated by capillary electrophoresis genetic analysers and standard STR profiling kits.
FaSTR™ DNA enables forensic laboratories to:
Expedite the otherwise time-consuming process of calling alleles.
Ensure consistency in DNA analysis and NoC estimation, which is critical to meeting quality assurance criteria.
FaSTR™ DNA applies a set of fully configurable rules to analyse most DNA profiles automatically. But DNA analysis is complex, and the rules alone cannot resolve all profiles. At times, the DNA analyst must intervene. FaSTR™ DNA signals when this human intervention (expert judgment) is required. These rules can also be configured to require fully manual data analysis.
As forensic provider to New Zealand Police and custodian of New Zealand’s National DNA Database, PHF Science (formerly ESR) understands the need for speed, accuracy, and simplicity. In developing FaSTR™ DNA, particular attention has been paid to simplifying the procedure. Reliable results can now be gained with minimal effort.
FaSTR™ DNA can analyse profiles generated using the most commonly used instruments and multiplex kits. The software is configurable, with easy addition of new kits, dye colours and internal size standards.
FaSTR™ DNA optionally proposes the number of contributors to a profile using an easily replicable decision tree process. Utilising all information within the profile, FaSTR™ DNA can be coupled with STRmix™ for seamless interpretation of complex mixed DNA profiles.
DNA analysis is a process of identifying alleles. The alleles appear as peaks in an electropherogram (EPG) and are identified from their locations within the EPG. The locations are determined using internal size standards and ‘ladders’.
FaSTR™ DNA
Contains the size-standard and ladder data for commonly-available testing kits. Additional kits and size standards can easily be added by importing panel, bin, and size standard information, or by manual entry.
Based on an adaptation of the methods implemented in OSIRIS[1], FaSTR™ DNA applies a set of fully configurable rules to identify and label alleles and reject artefacts within the EPGs of test samples.
The Analysis Process
EPGs are produced by genetic analysers in the form of .fsa, .hid or .promega data files. FaSTR™ DNA analyses EPG data in steps by:
Dynamic baselining of the EPG data.
Detection and assignment of size-standard peaks for the accurate sizing of peaks in the allelic ladder and test sample.
Size alignment of peaks detected in the allelic ladder with peaks detected in the test sample to apply allele calls.
Optionally applying a set of analysis rules to distinguish artefactual from allelic peaks.
Optionally carrying out NoC estimation.
Optionally carrying out sample to sample or sample to database comparison checks.
Carrying out full concordance testing on positive and negative controls, including quality marker checks.
Exporting the results as configurable outputs.
Carrying out a project review to compare two analysed projects and resolve conflicts to create a final reviewed project.
[1] R.M. Goor, L. Forman Neall, D. Hoffman, S.T. Sherry, Mathematical approach to analysis of multiplex DNA profiles, Bull Math Biol 73(8) (2011) 1909-1931
Outputs
FaSTR™ DNA displays the results of its analysis (the ‘DNA profile’), as a labelled EPG and as a table of loci and peak designations. With FaSTR™ DNA you can:
Easily print EPGs and include snapshots of areas of interest.
Easily print a report of changes made to peaks during analysis.
Export analysed data to STRmix™, the supplied CODIS tool or a data table.
Save the analysis as a ‘project’ for future reference.
Configuration parameters
The analysis settings can be general or specific to each STR kit type and locus. FaSTR™ DNA contains easily customisable default kits and methods. You can also create (and save) customised sets of parameters appropriate to different types of DNA samples (e.g. single-source samples and crime-scene samples).
Papers describing the validation, features and models of FaSTR™ DNA:
[1] D. Taylor, A. Harrison, D. Powers, An artificial neural network system to identify alleles in reference electropherograms. Forensic science international. 2017; Genetics 30 114-126.
[2] R.M. Goor, L. Forman Neall, D. Hoffman, S.T. Sherry, A mathematical approach to the analysis of multiplex DNA profiles. Bulletin of mathematical biology. 2011; 73(8) 1909-1931.
[3] M.-H. Lin, S.-I. Lee, X. Zhang, L. Russell, H. Kelly, K. Cheng, S. Cooper, R. Wivell, Z. Kerr, J. Morawitz, J.-A. Bright, Developmental validation of FaSTR™ DNA: Software for the analysis of forensic DNA profiles. Forensic Science International: Reports. 2021; Volume 3, 100217.
[4] D. Taylor, D. Powers, Teaching artificial intelligence to read electropherograms, Forensic Science International: Genetics 25 (2016) 10-18.
[5] D. Taylor, M. Kitselaar, D. Powers, The generalisability of artificial neural networks used to classify electrophoretic data produced under different conditions, Forensic Science International: Genetics 38 (2019) 181-184.
[6] M. Kruijver, H. Kelly, K. Cheng, M.H. Lin, J. Morawitz, L. Russell, J. Buckleton, J.A. Bright, Estimating the number of contributors to a DNA profile using decision trees, Forensic science international. Genetics 50 (2021) 102407.
[7] L. Volgin, D. Taylor, J.-A. Bright, M.-H. Lin, Validation of a neural network approach for STR typing to replace human reading, Forensic Science International: Genetics (2021) 102591.
[8] T. Kalafut, C. Schuerman, J. Sutton, T. Faris, L. Armogida, J.-A. Bright, J. Buckleton, D. Taylor, Implementation and validation of an improved allele specific stutter filtering method for electropherogram interpretation, Forensic Science International: Genetics 35 (2018) 50-56.
FaSTR™ DNA is designed to run either standalone or in a networked environment.
1 Will allow analysis of a batch of 96 single source samples and/or complex mixtures, but may require additional memory for larger batch sizes.
2 Will allow analysis of a batch of 96 single source samples and/or complex mixtures and analysis interactions on groups of multi-selected peaks and/or samples simultaneously. May require additional memory for larger batch sizes.
3 Will comfortably allow analysis of a batch of 96 or more single source samples and/or complex mixtures and analysis interactions on groups of multi-selected peaks and/or samples simultaneously. May require additional memory for very large batch sizes (eg 250 plus samples).
4 This is the space required for the application itself and does not include the space required for results of FaSTR™ DNA runs.
5 Provisions should be made to anticipate that storage space requirements will continue to increase over time as more analyses are stored.
Software
Operating System: Windows 10 64-bit or Windows 11 64-bit recommended.
FaSTR™ DNA is not supported by a MacOS environment.
FaSTR™ DNA developmental validation is available by clicking here(external link)[1]
Find out more about:
· Compatibility
· STRmix™ Integration
· Review Module
· Stutter Models and Filters
· Artificial Neural Network
· A More Efficient Workflow
· NoC Estimation
· Comparison Module
· Artefact Detection
Compatibility
FaSTR™ DNA 1.1.1 (and above) can read .fsa, .hid, and .promega files from the following instruments:
CE Instrument
File Format
Thermo Fisher Scientific 3100, 3130, 3500, and SeqStudio™ Flex
.fsa and .hid
Promega Spectrum and Spectrum Compact
.fsa and .promega
FaSTR™ DNA is compatible with Windows 10 and 11 operating systems.
Default analysis methods are available for the following DNA typing kits:
Thermo Fisher Scientific
Promega
Qiagen
GlobalFiler™
PowerPlex® 35GY
Investigator® 24 Plex
Identifiler™ Plus
PowerPlex® Fusion 6C
Identifiler™
PowerPlex® Fusion
Profiler Plus®
PowerPlex® 21
SGM Plus™
PowerPlex® 16
Yfiler™ Plus
PowerPlex® Y23
Note: Additional kits can be added manually or using manufacturer supplied bin and panel files.
Stutter Models and Filters
· FaSTR™ DNA can detect and filter stutter peaks during analysis and results can be exported with or without the stutter peaks included.
· The FaSTR™ DNA stutter filters have the option of utilising any combination of the following stutter models:
ü Locus average
ü Allele average
ü Generalised stutter filters
ü Allele-specific regression
ü LUS regression
The stutter regression and exception files used in FaSTR™ DNA to filter stutter peaks can also be used in STRmix™.
· FaSTR™ DNA can detect and automatically adjust the thresholds for composite stutters (peaks positioned in multiple stutter types). All modelled stutter types (unrestricted) are included in the composite stutter detection.
Number of Contributors Estimation
FaSTR™ DNA can automatically estimate the number of contributors (NoC) using either the MAC/2 or the Decision Tree methods. Currently, decision trees are available for GlobalFiler™ and PowerPlex® Fusion 6C DNA typing kits. Additional decision trees can be trained, pending availability of sufficient exemplar data.
Users may also manually assign the NoC, which will supersede the FaSTR™ DNA assigned NoC.
The NoC estimation decision path and covariate information are fully auditable via output files.
STRmix™ Integration
· Projects of samples analysed in FaSTR™ DNA can be exported directly into STRmix™ versions 2.5 and above as pre-populated Batch interpretations. FaSTR™ DNA can optionally export samples into Batch Maker (STRmix™ v2.10 and above) for interpretation customisation (e.g. to assign references).
· The NoC assigned in FaSTR™ DNA will automatically be imported into STRmix™. For STRmix™ versions 2.6 and above, NoC values assigned as a range in FaSTR™ DNA will be interpreted in STRmix™ with a variable number of contributors (varNOC).
FaSTR™ DNA integration validation plans are available for laboratories already using STRmix™. Support assistance is available upon request.
Artificial Neural Network
· Full analysis functionality in FaSTR™ DNA does not require an artificial neural network (ANN). However, when available, the ANN is a helpful tool that can assist users in the determination of peak type assignment as it is able to provide independent peak type classifications of detected peaks.
· Pre-trained neural networks for the classification of GlobalFiler™ and PowerPlex® Fusion 6C DNA typing kits are available.
Comparison Module
· Negative controls and/or samples can be compared against other samples within a project or to a database for quality checks.
Review Module
The Review module provides a seamless integration of the technical review workflow into the analysis software.
Designed to assist with the comparison of two FaSTR™ DNA projects containing the same set of samples and analysed using the same method.
The Review module is flexible and can be utilised for laboratories with various reader workflows, such as two independent analysts or one analyst with a reviewer.
Any differences in analysis (e.g. peak label, peak removal/retention, peak nature (allele or stutter), or peak size) will be flagged. Differences at the sample level (e.g. NoC assignment and sample status) are also detected.
Reviewers can evaluate the conflicts between the two projects while viewing the samples side-by-side. All sample and peak information is provided, just as it appears in the analysis review screen.
A report of the review can be generated for audit purposes, documenting edits with analyst ID and time of change.
A final project can be created from the Review module including electropherogram PDF reports, NoC assignment, and genotypes tables. Samples can also be sent directly from the review module to STRmix™ for deconvolution.
Artefact Detection
· FaSTR™ DNA can detect various artefacts (e.g. pull-ups) based on customisable analysis rule settings. Peaks identified as potential artefacts requiring further investigation are marked for review.
Users also have the option to automatically filter peaks that fall within a specified artefact range.
A More Efficient Workflow
Shortcut keys allow for quick action commands or access to various functions, such as the pull-up investigation screen and visualising raw data.
Snips (or snapshots) of the graph can be captured and the images added to the end of the sample electropherogram PDF report.
Informative displays, such as total peak height per locus, total allele count per locus, and maximum allele count for the sample, are available in analysis review screen to optimise efficiency.
Control concordance is automatically performed, including evaluation of quality markers (for applicable kits) and any number of known control profiles can be added to FaSTR™ DNA.
Better resolution of in 1bp minor peaks allows for more accurate interpretation of results.
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