New OSIRIS Pull-up paper: Novel Method for Accurately Assessing Pull-up Artifacts in STR Analysis.
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Version 2.16 has been released with software to allow users to add new marker sets to OSIRIS.
Version 2.15 includes important new display features.
Recently improved features
- New software to help users add markers and marker sets to OSIRIS
- New display features: deleted allele labels, allele bins, locus bars, cursor coordinates, highlighted active table row, preview graph toolbar
- New Simplified Printing feature allows direct printing of single views or multiple samples with flexible formatting
- New Fragment Analysis function using internal marker for fragment sizing - no alleleic ladder required
- New Flexible Export formatting function allows user to design the data export format to suit downstream data uses
- Accurate, sensitive pull-up detection, including identification of partial pullup into alleles
- Alelle peak heights corrected for pull-up and used in threshold calculations
- Identify non-standard stutter - plus, minus, mutiple and fractional repeats
- Allele-specific stutter thresholds
- Display time or base pair on the X-axis
- Feature Highlights
- Version 2.16 Release notes
- Version 2.15.1 Release notes
- Version 2.15 Release notes
- Version 2.14 Release notes
- Version 2.13.1 Release notes
- Version 2.13 Release notes
- Version 2.12.2 Release notes
- Version 2.12.1 Release notes
- Version 2.12 Release notes
- Version 2.11.2 Release notes
- Version 2.11.1 Release notes
- Version 2.11 Release notes
Release notes are included with every download and are available on the Download page
Note the Version 2.15.1 bug fix release below
Note the Version 2.13.1 bug fix release below
Note the Version 2.12.2 bug fix release below
Note the Version 2.11.2 bug fix release below
Version 2.16 Release notes
Version 2.16 includes substantial improvements over previous versions.
New software to allow users to add novel kit and internal marker definitions to OSIRIS
Programs - three programs have been added to the OSIRIS distribution for:
• Adding a novel ILS internal marker – GenerateILSFamily.exe.
• Adding a novel kit definition – GenerateLadderFile.exe.
• Adding new loci and new Positive Control DNA profiles – BuildStandardControlFile.exe.
Additional directories - Added directories in the Osiris-Files “site” directory to support the user-added kits and ILSs, including:
• Configuration-Tools directory – for the resource and tutorial files for those programs.
• Config directory – for storing the user created kit definitions and Operating Procedures.
Instructions for using the kit and ILS generating programs can be found on the OSIRIS Help webpage.
Additional platforms and ILS's
- Added kit definitions for Promega Fusion, Fusion 6C, Y23, GenePrint 10 and GenePrint 24 analysis data collected on Promega Spectrum Compact capillary electrophoresis units.
- Fixed a bug that rarely caused the “OL” label to not be displayed on off-ladder peaks in the Graph view and the Table view, even though the peaks received an off-ladder designation which was marked as non-critical. This bug was present in previous versions as early as 2.10.3.
Version 2.15.1 Release notes
Version 2.15.1 fixes bugs in the pull-up identification algorithm.
Fixed bugs introduced in 2.15 where low to medium height peaks could be classified as pull-up and not be given an allele call.
Fixed a bug present in 2.15 and earlier versions that in situations where a large peak was close to a pull-up position, it might interfere with pull-up pattern identification. In very rare circumstances that could result in a pull-up peak being called as an allele.
Fixed a bug present in 2.15 and earlier versions that could infrequently result in a partial pull-up peak whose RFU value was either below (or corrected to be below) the allele calling threshold, however the peak would retain an allele call, requiring additional editing.
- Improved the robustness of the pull-up algorithm by taking into consideration additional pull-down and pull-up peak width information.
Version 2.15 Release notes
Version 2.15 includes major new features.
New Graph display options
- Version 2.15 includes frequently requested display options
• Allele locus bars – At the top of each plot the locus bar indicates the extent of the locus ladder alleles.
• Allele bins – Allows the user to display or hide allele bins. The bins indicate the ladder allele position and allele bin width. Bin width is set in the “Max. Residual For Allele” on the Sample Limits tab of the Lab Settings.
• Deleted allele labels – Display or hide the labels of deleted alleles. The labels of deleted alleles display with a strikethrough.
• Cursor coordinate display – The cursor coordinates (BP/Time and RFU) are displayed in the lower left corner of the Graph and Preview Graph.
• Sample rows in Table view – The selected row in the table is highlighted with black top and bottom borders to help visually identify cells in wide rows.
• Default Graph window display - The Graph window has been improved to default zoomed in to the peaks in the plot, showing less blank data to the right and showing less of the primer peaks to the left. Print settings allow this as well.
New Preview Graph toolbar
- Added a toolbar like that found in the Graph view window to the Table view Preview Graph allowing simple access to display changes that otherwise required stepping through menus, which makes the Preview graph significantly more usable. This includes the ability to change or display multiple channels, change the raw vs. analyzed data, change the artifact label display, display deleted alleles, and more.
Improved Pull-Up identification algorithm
- Implemented an improved pull-up algorithm that better handles cases in which negative and positive pull-up are both present (due to linear and non-linear pull-up). In some of those cases the previous algorithm could result in an allele peak being called as a pull-up. An option allows users to choose to apply the improved algorithm either to all pull-up cases, or only to mixed positive and negative pull-up, with the previous algorithm (versions 2.8-2.14) applied to positive-only pull-up. The new algorithm handles both and provides better results with mixed positive and negative pull-up.
Added “Errors” and Details” tabs to the New Analysis window
- Added a new pane to the New Analysis window with “Errors” and “Details” tabs. The Errors tab opens automatically and lists any errors identified that could have caused an analysis to fail, such as selecting a kit with the wrong number of channels or missing ILS or ladder peaks. The Details tab displays the analysis run information formerly displayed by clicking the “Details button”. Details information regarding run failures will be found at the bottom of the details associated with the analysis.
Added a search box to the Lab Settings window Sample Limits tab
- Added a search box to the Sample Limits tab that will highlight the settings rows that have matching text to allow users to quickly locate the desired row.
Folder Icon to find Operating Procedures
- A folder icon at the top right of the Lab Settings window will open the folder where user-created custom Operating Procedures are stored, making it simple to find their location. This is helpful when needing to share an Operating Procedure.
Updated OSIRIS 2.15 User Guide
• The STR analysis tutorial is updated to demonstrate some of the new display features in OSIRIS 2.15.
• The Fragment analysis tutorial is updated to include both a section on determining the number of data channels in an .fsa/.hid file for fragment analysis and a list of the predefined internal standard markers (ILS) in OSIRIS 2.15.
- Fixed a bug that prevented the Mac version from displaying bold and italic font in the Table view to indicate an edited cell that still needed review.
- Fixed a bug where if the number of users to “Review editing” was set to zero, the first column of the Table window that shows checks (✓) and “X” would not show “X”, only checks.
- Fixed a bug which caused the “Primary Pull-Up Threshold: Computed” setting to not be used, rather the minimum height specified was used. If the specified threshold was very high or very low, it could have impacted identification of pull-up. Currently, unless specified by the user, the default minimum height for a primary pull-up is the channel analysis RFU.
- Fixed several bugs in the pull-up algorithm that in rare cases could lead to pull-up peaks not being identified or an allele being identified as a pull-up.
Version 2.14 Release notes
Version 2.14 includes major new features.
- Version 2.14 introduces Simplified printing of both individual views and entire analysis batches. Single samples may be printed and is customizable via the onscreen view so that labels, thresholds, channels and views will print as displayed on the screen. Entire analysis batches can be printed and customized to display as the user desires, including labels, thresholds, Y-axis ranges, X-axis range in base pairs or time, and the number of channels per page. The number of channels per page can be customized individually for ladders, negative controls and samples to optimize the display of peaks and peak labels for ladders and samples with many peaks. Print color intensity can be optimized for different printers.
Peak and label colors
- Peak and label colors have been adjusted to make both more easily distinguishable if a label overlays a peak.
Improved analysis robustness
- Analysis has been improved to prevent poor quality samples from occasionally causing an entire analysis to fail. Additional error messages have been added to explain why samples or analyses failed.
Analysis correction function for artifact peaks
- Occasionally, poor data quality in the ladder controls or sample internal marker ILS makes it impossible for OSIRIS to analyze. A function has been added to accept a list of peaks in the ladder or in the sample ILS that should be ignored to allow the software to recognize the correct known peaks and complete the analysis. This allows users to rescue ladders and samples.
Running OSIRIS from the command line
- An explanation of how to run OSIRIS from the command line has been added to the User’s Guide, so that OSIRIS can be called by other software without the need to start the user interface first. This allows OSIRIS to be incorporated into a computing workflow or into other software.
Added homozygote threshold settings
- Added a setting that prevents a “Homozygote too low” artifact in positive control samples.
- Added a homozygote threshold above which a peak is considered to be a valid homozygote even if peaks are found between the Min RFU Analysis threshold and the Detection threshold.
Removed off ladder allele setting
- The setting “Do not call OL allele if pull-up” was removed to prevent the possibility of a valid allele not being called if it also contained signal from a pull-up, given that the current pull-up analysis algorithm deals appropriately with that situation.
Changed uncertain pull-up artifact priority
- Changed the artifact priority of “Partial Pull-up Uncertain” peaks, where the pull-up algorithm is unable to determine a pull-up pattern, from non-critical to conditional. If the peak is pure pull-up or partial pull-up corrected below minRFU from another channel, pull-up uncertain is non-critical. Otherwise, it is a critical artifact to ensure analyst review.
- Fixed a bug that in certain circumstances could have prevented the maximum threshold artifact from being triggered when a peak’s height exceeded the maximum RFU threshold.
- Fixed a bug in the baseline offset calculation that would prevent analysis in rare circumstances where dynamic normalization was not selected.
- Fixed a bug that caused off-ladder alleles to trigger a non-critical artifact at the peak level, but a critical artifact at the locus and sample level. Off ladder peaks now give a critical artifact at all levels.
- Fixed a bug introduced in v. 2.12.2 which caused sigmoidal pull-up to be called as partial pull-up rather than pure pull-up and to receive an allele call in addition to the artifact, if above the analytical threshold.
Version 2.13.1 Release notes
Version 2.13.1 corrects version data in three kit Operating Procedures that prevents settings from being changed.
- Corrected the version data in kit Operating Procedures that prevented them from being saved as a custom Operating Procedure with changes to the lab settings in OSIRIS version 2.13. The following Operating Procedures that could not be modified in version2.13 will function normally in version 2.13.1. This change has no impact on the accuracy or results of analysis in OSIRIS beyond the ability to use these Operating Procedures.
• [IdentifilerPlus w/o ILS @250]
Version 2.13 Release notes
Version 2.13 includes major new features.
- Version 2.13 introduces size-based fragment analysis using an internal size marker, without the need of an allelic ladder. This allows users to analyze home-made multiplexes without needing to construct their own fragment size ladder. Included are Lab Settings that allow analysis of 2, 3, 4, and 5 channel analyses, and settings to allow users to designate the channel in which the marker data resides.
Flexible export formats
- Added an export that allows users to format their data export without any programming, so they can easily export in multiple different formats for downstream use or processing. Users can choose the type and order of the data they are exporting and whether they want a row to be a sample, a locus, or a peak.
Simultaneous Mixed/Single Source Analysis
- OSIRIS can apply the stutter-, adenylation-, fractional-, and pull-up fractional-filters differentially to single source samples (knowns and references) and possibly mixed samples (casework or chimerism study samples) that are in the same analysis run. Sample type can be detected by matching character strings within the file or sample name. This can be particularly helpful when running reference and mixed samples, either to reduce the amount of editing of the reference samples or where the exported data will be used in mixture analysis software that requires stutter peaks to be called. Added settings to allow either sample type to be the default and to allow character strings to specify the other sample type, simplifying use of this function.
Use of Non-Roman and Other Unicode Characters
- OSIRIS now allows use of non-ASCII characters in file paths and filenames, so international users can use non-Roman and other Unicode characters in directory/folder and file names.
Identify Lab Settings Folders
- OSIRIS now allows users to easily identify and find the location of Lab Settings folders. Clicking the folder icon button in the Lab Settings window will open the parent folder with the Lab Settings folder selected. This allows users to zip or compress the Lab Settings folder for easy exchange.
- Fixed the Mac version of OSIRIS so that windows open correctly with the latest version of the Mac OS Software. (Fixed in both 2.13 and 2.12.2.)
- Fixed a bug that could prevent analysis in RAPID-DNA samples that had high levels of noise.
- Fixed a bug in the pull-up algorithm that incorrectly applied the spike artifact to some peaks that were not spikes.
- Fixed pull-up identification bugs that existed in previous versions that in rare circumstances might have prevented calling pullup but would not have prevented alleles from being called.
• Fixed a bug that in rare circumstances prevented suspected pull-up crater side-peaks and sigmoidal peaks from being called as pull-up.
• Fixed a bug in the pull-up algorithm that did not identify some pull-up peaks because the peaks were wider than expected.
• Fixed a bug in the pull-up algorithm that failed to identify some spikes.
Version 2.12.2 Release notes
Version 2.12.2 fixes bugs in the pull-up identification algorithm and in opening windows on the Macintosh version.
Fixed a bug in the pull-up algorithm that prevented flagging sigmoidal peak artifacts. A positive sigmoidal side peak could be flagged as a possible off-ladder allele, requiring additional editing.
Fixed a window display issue on the Macintosh caused by changes in a Mac OS update. In certain cases, Mac users would need to click the OSIRIS icon in the Dock at the bottom of the screen to display a newly opened OSIRIS window. The fix causes windows to open correctly with the latest version of the Mac OS Software.
Version 2.12.1 Release notes
Version 2.12.1 fixes a bug that prevents the COrDIS kit from working.
Version 2.12 Release notes
Improved Artifact Analysis
- Improved pull-up reporting so that pull-up is not reported when the pull-up peaks have no impact, such as when the pull-up is below detection threshold or is negative in the raw data.
- It is no longer necessary for the user to specify a minimum height below which a peak will not cause pull-up. Added a pull-up analysis setting to allow the OSIRIS pull-up algorithm to calculate the parameter from the sample data. This makes the algorithm accurate over a broader range of data, and relieves the laboratory of having to empirically determine a value. We strongly encourage users to take advantage of the new “Primary Pull-up Threshold: Computed” setting.
- Improved pull-up analysis use of peak saturation data.
- Improved pull-up analysis where primary peaks have significant noise
- Improved analysis of split peak “craters” by taking peak widths into account.
New Kit /Lab Settings
- Added the COrDIS kit
OSIRIS version 2.12 collects non-identified usage statistics to help us improve the software. It does not collect information on samples, profiles, batches or information that would reveal the context of the analysis. Users can opt out or disable the statistics reporting. Details are in the Privacy Information section in the appendices of the User’s Guide or see Privacy Information on the Help page.
- Fixed minor bugs that did not impact accuracy.
- Fixed a bug in normalization algorithm that in rare cases could cause a spike in normalized data. This would not have caused incorrect allele calls.
- Fixed a bug that prevented the peak residual from displaying in the allele hover box when the residual was zero.
- Fixed a bug that could cause OSIRIS to crash on the Mac under rare circumstances.
Version 2.11.2 Release notes
Version 2.11.2 fixes a bug that could occur under rare conditions, causing a sample to fail if the bug is triggered.
Fixed a bug that under rare circumstances, with a particular lab setting combination, could cause intermittent analysis failures of certain samples. When the bug manifested, certain array values were not initialized. The result was an off-scale raw data baseline in one or more channels causing the channel to not analyze. The bug had absolutely no impact on the accuracy of any successful analysis.
The bug fix in version 2.11.2 has been tested with 33 samples and settings that intermittently triggered the bug to demonstrate that the results of analysis with version 2.11.2 is identical to successful analysis with version 2.11.1, including allele calls, peak RFU, peak bp size, artifact calls, etc.
This bug does not affect versions prior to version 2.11 or version 2.12 and higher.
Version 2.11.1 Release notes
Version 2.11.1 fixes two bugs that could occur under rare conditions.
Pull-up analysis bug Fixed an uncommon bug that in extremely rare circumstances could result in an allele that comigrates with a peak in another channel being called a pull-up in circumstances where the “Min RFU for a peak to be considered as a peak that causes pull-up” in the Sample Limits tab of the Lab Settings is set too high.
ILS peaks with no label Fixed a bug in which ILS peaks that were also called as pull-up were not given a base pair label. While this produced no analysis errors, it could result in display issues.
Version 2.11 Release notes
- OSIRIS now allows users to display either Time or Bases on the x-axis of the Graph view.
Improved Artifact Analysis
- Allele-specific stutter analysis has been added as an option. Allowing the stutter threshold to increase with increasing allele size gives more accurate discrimination between alleles and stutter. Users can set their own threshold levels.
- Allele peak heights corrected for coincident pull-up signal can be used in stutter and adenylation analysis when determining whether a peak falls under a threshold, to make discrimination between alleles and artifacts more accurate.
- Improved pull-up analysis by including low-level raw data peaks below analytical threshold in the overall pull-up pattern analysis, resulting in better identification of very low level pull-up peaks.
- Added settings to reduce the possibility of extraneous “excessive residual displacement” artifact calls.
Improved Baseline and Peak Analysis
- Added options for improved peak curve fitting at the base of large peaks, which can also improve the analysis of low level shoulder peaks.
- Improved baseline estimation at the edges of peaks.
Process Quality Control Metrics
- Multiple metrics have been added that can be exported for quality control of the DNA analysis process. This includes data regarding the performance of the genetic analyzer and sample extraction/amplification to allow predictive monitoring for issues like poor spectral color separation matrix, capillary failure, and extraction/amplification problems.
- Reduced editing due to artifacts in ILS and ladders. Many minor artifacts do not impact the spacing, accuracy and validity of ILS and ladder profiles, but previously required editing. Options have been added allowing users to specify that artifacts that do not impact ILS or ladder validity be non-critical and not require editing. These artifacts are still called and displayed for review.
- Added options to allow editing of “restricted priority” peaks and peaks that are below analytical threshold (and above detection threshold).
Improved Network Administration
- Implemented shared Lab Settings and Export settings in a network environment where both Windows and Macintosh versions of OSIRIS are in use.
- Improved the management of user permissions for Lab Settings and Exports.
Improved CODIS CMF file exports: Can include comments in the Sample Comments field of the Plate Template in the ABI Genetic Analyzer Data Collection Software that OSIRIS can export to the CODIS CMF Comment field.
Improved ladder analysis: Improved robustness of bi-allelic loci, such as Amelogenin. Reduces artifacts.
New Kit / Lab Settings
Added example Lab Settings for Sole Source and Mixed samples
PowerPlex Fusion HID Sole Source and GlobalFiler HIG Mixture lab default settings include all of OSIRIS novel features and updates and can serve as a starting point for laboratories to optimize their settings for sole source and potential mixed samples. Both can be modified for use with .fsa files, and the settings can be copied to other kits. Both will need to be modified for lab’s own analytical thresholds and desired peak sensitivity.
Pull-up analysis bug
Fixed an uncommon bug that in extremely rare circumstances could result in an allele that comigrates with a peak in another channel being called a pull-up. This bug was fixed by making better use of peaks that did not comigrate with a peak in the pull-up channel, or that comigrate with raw data above the noise level for the channel.
ILS peaks with no label
Fixed a bug in which ILS peaks that were also called as pull-up were not given a base pair label. While this produced no analysis errors, it could result in display issues.
Fixed minor bugs that did not impact accuracy