This article lists the most important changes made in Coffalyser.Net v.220513.1739 as compared to the previous version, v.210604.1451.

Read more about updating. We recommend updating capillary electrophoresis devices in Coffalyser.Net after installing the new version to benefit from the updates in this version.

Improvements

Most prominent improvements

• Adjusted the way that results for mutation-specific probes are shown. These results are now always displayed as intra ratio percentages. More details.
• Added support for the ABI SeqStudio Flex, ABI 3500XL and Hitachi DS3000 capillary electrophoresis devices. More details about using the Hitachi DS3000 device.
• Added additional colors for probe ratios to PDF reports to enhance the visibility of aberrant results. More details.
• Modified colors for certain situations in sample report and experiment report grids. More details.
• Improved default zoom of ratio charts in dialogs and PDF reports to reduce overlap between chart titles and probe name labels, and reintroduced the option to manually set the y-axis scale of ratio charts.
• Improved robustness of size marker recognition in the presence of extra small peaks in the size marker channel, e.g. due to noise or due to signal bleed-through from the MLPA channel due to suboptimal spectral calibration of the capillary electrophoresis device. The previous versions, v.210226.1433 and v.210604.1451, were more sensitive to this issue than v.140721.1958, but the new version is even more robust.
• Increased minimum peak amplitude for detectable size marker peaks for ABI devices from 70 to 200 (ABI 310, ABI 3100, ABI 3130, ABI 3130xl) or 300 (ABI 3500, ABI 3700, ABI 3730, ABI 3730xl, ABI SeqStudio) to help further reduce the effect of small peaks in the size marker channel. To benefit from these changes, please update CE devices.

Dependencies

• .NET Framework v4.8 is now required (instead of v4.6.1). View all system requirements.

Other improvements

• Improved consistency of results display for probes with low signals ≤ 10% of the median signal of the reference probes, which are now more consistently displayed as intra ratio percentages to increase visibility of unexpectedly low signals (also in e.g. ratio charts). More details.
• Improved consistency of results display for digestion probes in digested reactions, which are now consistently displayed as final ratios (if they are >10% of the median signal of the reference probes).
• Added method to export final ratios for probes with low signals ≤ 10% of the median signal of the reference probes for certain applications. More details.
• Added support for the GeneTek-500 (GT500) size marker.
• Added issues with the PSLP and FSLP scores to the identified problem(s) box in the sample overview in all conditions.
• Adjusted FMRS score and probe counter based on the results from slope correction in the comparative analysis.
• Removed FMRS score for no-DNA reactions as it provided no useful information.
• Excluded mutation-specific probes from RSQ/RPQ calculations as they are no longer compared to reference samples.
• Improved clarity of the wording used in a tooltip shown for RPQ warnings.
• Replaced HHA1 with HhaI.
• Replaced references to mlpa.com with references to mrcholland.com on PDF reports.
• Improved information on, and layout of, the About dialog
• Removed an asterisk without explanation from PDF reports.
• Renamed the Show Probe Ratio Type > Final Normalized Ratio option in the context menu of the experiment results to Default Ratio to better reflect that both final and intra ratios may be shown.

(Bug) fixes

• Fixed sex determination in the absence of the 92 nt benchmark fragment throughout the software.
• Fixed incorrect warning text in the identified problem(s) box for an orange median probe signal warning caused by low signals.
• Fixed rounding inconsistency that could lead to different warning levels for the max probe length deviation score in different dialogs in borderline data.
• Fixed crash that could occur if the automatic binning algorithm created overlapping bins on very poor or incorrectly configured data.
• Fixed rare crash when a digested sample with a very low quality was included in the comparative analysis.
• Fixed rare incorrect display of the digestion part of the FMRS score in a regular MLPA experiment when there were size calling issues.