FastFinder Analysis Results CSV
Interpreting and using the FastFinder Analysis Results CSV
FastFinder Analysis 4.12, 4.13, 4.14 - Lab management 1.12, 1.13, 1.14 – Workflow 2.2, 2.3, 2.4 - Lab Engine 1.0, 1.1, 1.2
Purpose of this document
This document describes the default FastFinder Analysis results CSV export that is available to integrate FastFinder interpreted results with external systems.
In this document, we will give a high level overview of Assay Plugins (AP) used in FastFinder, and cover the specification of the FastFinder Analysis CSV export.
Assay Plugins in FastFinder
An Assay Plugin contains all assay-specific information that is needed to allow conversion of the raw PCR data into test results with minimal manual intervention and is typically considered the analysis software component of a particular molecular assay. As such, an Assay Plugin contains the information as schematically shown below. Fields marked with * can be customized in FastFinder Lab management.
Export specification
After the analysis is authorized, a CSV export is automatically generated and stored in the FastFinder tenant storage Export container, or in the Outbox/<optional-subfolder> container depending on the configuration of the qPCR Analysis activity of the relevant workflow.
The export can also be downloaded from the FastFinder’s Analysis Results module, which is a part of the Archive. A single entry in the CSV is defined by a Sample - AssayResultTarget combination with the following information:
|
Header name |
Description |
|
Sample ID* |
Sample ID as specified in the PCR file. |
|
AssayResultTarget |
Name of the assay result as defined in the AP. Can be empty for controls (NegativeControl, PositiveControl) and standards used for standard curve computation (QuantificationStandard, QuantificationStandardWithEditableConcentration), or in case the sample was marked for retest depending on the configuration°. |
|
AssayResultTargetCode |
ShortCode of the assay result as defined in the AP. Can be empty for controls (NegativeControl, PositiveControl) and standards used for standard curve computation (QuantificationStandard, QuantificationStandardWithEditableConcentration)., or in case the sample was marked for retest depending on the configuration°. |
|
AssayResultTargetReference |
Reference for the assay result that can be configured in the LIMS tab of an Assay in Lab management. Can be empty for controls (NegativeControl, PositiveControl) and standards used for standard curve computation (QuantificationStandard, QuantificationStandardWithEditableConcentration), or in case the sample was marked for retest depending on the configuration°. |
|
Outcome* |
Final outcome of the AssayResultTarget. Possible values:Detected,Not detected,Void,Valid. Valid can only be used for controls or standards with no AssayResultTarget. |
|
IsInconclusive* |
Boolean:TRUE,FALSE. An optional result boolean that can be used to trigger external systems to interpret certain results differently. Inconclusive is a result classification that can be generated by the AP in cases where a certain result isdebatable. |
|
IsInvalid* |
Boolean:TRUE,FALSE. An optional result boolean that can be used to trigger external systems to interpret certain results differently. Invalid is a result classification that can be generated by the AP in cases where a certain result is deemed invalid. For instance when an internal control did not come up as expected. |
|
IsRetest* |
Boolean:TRUE,FALSE. An optional result boolean that can be used to trigger external systems to interpret certain results differently. Retest can only be triggered from the UI. No AssayResultTarget and other detailed information will be |
|
AssayResult* |
Final outcome of the AssayResultTarget, combining Outcome, IsInconclusive, IsInvalid and IsRetest information Possible values:Detected,Not detected,Invalid, Inconclusive,Valid, Retest. Valid can only be used for controls or standards with no AssayResultTarget. |
|
AssayResultNotifications |
Contains small texts that can be configured in the AP to be displayed in the UI if a certain result occurs. Concatenates multiple fields if multiple notifications. Example "Warning: Some text| Info: Other text". |
|
QualityControlResult |
Outcome of the Quality Control evaluation based on the configured QC trackings and Westgard rules of a control. Possible values:Valid, Invalid. |
|
ControlValidity |
Final validity of a control, taking both AssayResult and QualityControlResult into account. Possible values:Valid, Invalid. |
|
RetestReason |
Retest code when a sample is marked for retest. |
|
RetestAuditTrail |
Audit trails related to (un)marking the sample for retest. If there are multiple audit trails, they are separated using a pipe. |
|
SampleType* |
Possible values:PositiveControl, NegativeControl, Regular, QuantificationStandard, QuantificationStandardWithEditableConcentration. |
|
Filename(s)* |
Name of the PCR run file(s), comma-separated in case of multiple. |
|
Barcode(s) |
Plate barcode(s) referenced in the file(s), comma-separated in case of multiple. |
|
Instrument ID(s) |
Instrument ID(s) the PCR reading was conducted on, comma-separated in case of multiple. |
|
Analysis created at (UTC)* |
Analysis creation date in UTC time with format yyyy-mm-ddThh:mm:ss. |
|
Analysis created by* |
Analysis creation user. |
|
Analysis authorized at (UTC)* |
Analysis authorization date in UTC time with format yyyy-mm-ddThh:mm:ss. |
|
Analysis authorized by* |
FastFinder user that authorized the analysis. |
|
FF analysis software version* |
FastFinder Analysis module version used to generate the AP results. |
|
Assay* |
Name of the Assay Plugin. |
|
AssayCode* |
ShortCode of the Assay Plugin. |
|
AP version* |
Assay Plugin version |
|
SampleTypeName* |
Name of the sample type as defined in the AP. |
|
CorrectionFactor |
Dilution or other correction factor, if defined for the given sample, that is used to compute corrected concentrations for amplification targets that are quantified. |
|
For every target linked to the AssayResultTarget - x = variable target name. In case the sample was marked for retest depending on the configuration, the following information will be outputted°. |
|
|
Target_x |
Target name as defined in the AP. |
|
Target_x_reference |
Reference for the target name that can be configured in the PCR tab of an Assay in Lab management. |
|
Target_x_plates |
PCR filename(s), comma-separated in case of multiple. |
|
Target_x_wells |
Well positions. Multiple in case of replicate samples. |
|
Target_x_dye |
Dye name. |
|
Target_x_result |
Result of Targetx. |
|
Target_x_cq |
Cq value of Targetx. Empty if result wasNot detected. Only applicable for amplification targets. |
|
Target_x_endpoint |
Normalized end point fluorescence of Targetx. Only applicable for end-point measured targets |
|
Target_x_notifications |
Concatenation of Targetxnotifications on the combined replicate result, e.g. "Warning: Some text| Info: Other text". |
|
Target_x_QCnotifications |
QC notifications releated to Targetx, e.g. “Warning: Violation of Westgard rule(s) 1:2s |
|
Target_x_concentration |
Concentration of Targetx. Only applicable for amplification targets that are quantified. |
| Target_x_RQ
|
RQ (relative quantification) value of Target x. |
|
Target_x_correctedconcentration |
Corrected concentration of Targetxin case a correction factor was defined. Only applicable for amplification targets that are quantified. |
| Target_x_RQ_perwell
|
RQ (relative quantification) value of Target x per well. RQ values are
|
|
Target_x_tm |
Tm value of Targetx. Empty if result wasNot detected. Only applicable for melt targets. |
|
Target_x_endfluorescences |
Baseline-corrected or normalized end fluorescence. Multiple in case of replicate samples. Only applicable for amplification and end-point targets. |
|
Target_x_rawendfluorescences |
Raw end fluorescence. Multiple in case of replicate samples. Only applicable for amplification and end-point targets. |
|
Target_x_audittrail |
Audit trails of Targetx. |
|
Target_x_result_perwell |
Result of Targetxper well. Results are comma-separated in the same order as Target_x_wells. |
|
Target_x_cq_perwell |
Cq value of Targetxper well. Cq values are comma-separated in the same order as Target_x_wells. Only applicable for amplification targets. |
|
Target_x_notifications_perwell |
Notifications of Targetxper well. Notifications are comma-separated in the same order as Target_x_wells. |
|
Target_x_concentration_perwell |
Concentration value of Targetxper well. Concentration values are comma-separated in the same order as Target_x_wells. Only applicable for amplification targets. |
|
Target_x_correctedconcentration_perwell |
Corrected concentration value of Targetxper well in case a correction factor was defined. Values are comma-separated in the same order as Target_x_wells. Only applicable for amplification targets. |
|
Target_x_tm_perwell |
Tm value of Targetxper well. Tm values are comma-separated in the same order as Target_x_wells. Only applicable for melt targets. |
|
Target_x_extractionplates |
Extraction plate barcodes of Targetxper well. Barcodes are comma-separated in the same order as Target_x_wells. |
|
Target_x_extractionwells |
Extraction plate well position of Targetxper well. Wells are comma-separated in the same order as Target_x_wells. |
|
Target_x_acquisitiontype |
Acquisition type of Targetx. |
|
Analysis external reference* |
Analysis reference to FastFinder |
| Target_x_lotnumber | Lot number of Target x. |
| AssayResultCustomOutputs
|
Custom output results, they are separated using a pipe. If no |
|
AuthorizationState* |
Possible values:NewAuthorizedResult,ChangedAuthorizedResult,AlreadyAuthorizedResult - NewAuthorizedResult: for this analysis, this is the first time the result of this Sample-AssayResultTarget combination is authorized and thus available in an Analysis export - AlreadyAuthorizedResult: this value can occur when the analysis was first partially authorized and now fully authorized. It means that for this analysis, the result of this Sample-AssayResultTarget combination was already authorized and available in a previous Analysis export; there is no difference in result between both Analysis exports - ChangedAuthorizedResult: this value can occur when the analysis was first partially authorized and now fully authorized. It means that for this analysis, the result of this Sample-AssayResultTarget combination was already authorized and available in a previous Analysis export; however, there may be adifferencein result between both Analysis exports |
*required fields
° In case the setting "Output results for samples marked for retest" is enabled, AssayResultTarget(Code/Reference) and linked Target_x_yy information are also outputted in the CSV. The Outcome and AssayResult however remain respectively Void and Retest.
Other configurable options:
- We can configure an AP not to return allAssayResultTarget in case a certain result occurs.
- We can configure an AP not to return anyAssayResultTargetfor controls.
Future export updates
This CSV file will inevitably grow over time to include more data. In order to ensure your integrations work smoothly across FastFinder updates, please use column headers to distinguish between different pieces of data, these will never change over time.
Furthermore, to prevent issues when updating FastFinder, a new functionality to configure CSV exports is added. In the Settings module, users with the Admin role can now configure which fields to export and in which order. New fields are disabled by default so that the Analysis results CSV remains unaltered when updating FastFinder.
Changes compared to previous versions
- FastFinder Analysis 4.14 Lab management 1.14:
- Target_x_lotnumber is added. The ‘mark for retest’ functionality has been renamed to ‘mark as failed’. This will not impact the existing CSV connections as the output in these columns (e.g. IsRetest) and values is unchanged.
- FastFinder Analysis 4.12 – Lab Management 1.12:
- Target_x_RQ, Target_x_RQ_perwell and AssayResultCustomOutputs are
added
- Target_x_RQ, Target_x_RQ_perwell and AssayResultCustomOutputs are
- FastFinder Analysis 4.9 – Lab Management 1.9:
- Export folder can now be configured differently for different workflows, in an ‘Outbox’ folder with optional subfolders
- FastFinder Analysis 4.8 – Lab management 1.8:
- CorrectionFactor, Target_x_correctedconcentration and Target_x_correctedconcentration_perwell are added
- FastFinder Analysis 4.7 – Lab management 1.7:
- Target_x_result_perwell, Target_x_cq_perwell, Target_x_notifications_perwell, Target_x_concentration_perwell, Target_x_tm_perwell, Target_x_audittrail, Target_x_extractionplates, Target_x_extractionwells, RetestReason and RetestAuditTrail are added
- An option “Output results for samples marked for retest” is added
- FastFinder Analysis 4.6 – Lab management 1.6:
- AssayResultTargetReference and Target_x_reference columns are added
- FastFinder Analysis 4.5 - Lab management 1.5:
- Target_x_tm, Target_x_acquisitiontype, Target_x_endfluorescences and Target_x_rawendfluorescences columns are added
- FastFinder Analysis 4.4 - Lab management 1.4:
- QualityControlResult, ControlValidity and Target_x_QCnotifications columns are added
- CSV export configuration is added as a new feature in FastFinder (see Future export updates).
- FastFinder Analysis 4.3 - Lab management 1.3:
- AuthorizationState column is added at the end
- When partially authorized, the Export name is: Export-<file name>-<analysis external reference>-AssayTargets-preliminary.csv
- FastFinder Analysis 4.1 - Lab management 1.1:
- SampleType column can contain a new sample type “QuantificationStandard”
- Target_x_concentration column(s) is/are added at the end (after Analysis external reference)
- FastFinder Analysis 4.0 - Lab management 1.0:
- AssayResult column is added
- Order of target details (Target_x) is updated according to the mix, dye and target order that is defined in the AP. An example:
- AP has 2 mixes, with 2 dyes (FAM, VIC). In total, there are 4 targets
- Mix 1: FAM - target A, VIC - target C
- Mix 2: FAM - target B, VIC - target D
- with an AssayResultTarget that is linked to targets A, B and C. The details in the CSV will be ordered according to:
- Column Target_1: target A
- Column Target_2: target C
- Column Target_3: target B
- AP has 2 mixes, with 2 dyes (FAM, VIC). In total, there are 4 targets
- Name of the Export itself is updated to contain the file name as well Export-<file name>-<analysis external reference>-AssayTargets.csv