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. In addition, several examples will be provided.
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
Export specification
Upon authorization of an analysis, a CSV export is generated automatically and stored in the FastFinder tenant storage Export container. The export can also be downloaded in FastFinder’s Exports module, which is part of the Archive. One 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). |
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). |
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 is debatable. |
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". |
SampleType* |
Possible values: PositiveControl, NegativeControl, Regular, QuantificationStandard |
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. |
For every target linked to the AssayResultTarget - x = variable target name |
|
Target_x |
Target name as defined in the AP. |
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 Target x. |
Target_x_Cq |
Cq value of Target x. Empty if result was Not detected. Only applicable for amplification targets. |
Target_x_endpoint |
Normalized end point fluorescence of Target x. Only applicable for end-point measured targets |
Target_x_notifications |
Concatenation of Target x notifications, e.g. "Warning: Some text| Info: Other text". |
Analysis external reference* |
Analysis reference to FastFinder |
Target_x_concentration |
Concentration of target x. Only applicable for amplification targets that are quantified. |
* required fields
Other configurable options:
- We can configure an AP not to return all AssayResultTarget in case a certain result occurs.
- We can configure an AP not to return any AssayResultTarget for controls (see example below).
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.
Changes compared to previous versions
- 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
- Name of the Export itself is updated to contain the file name as well Export-<file name>-<analysis external reference>-AssayTargets.csv
Examples
Qualitative amplification
One multiplex Assay for multiple samples
Example of a qualitative amplification analysis for Assay COVID that has 1 AssayResultTarget 2019-nCoV and 3 linked Targets ORF1ab, S Protein and N Protein for Sample IDs Sample-283 and Sample-284.
Download the entire CSV here.
Multiple Assays and AssayResultTargets for a sample
Example of a qualitative amplification analysis for Sample ID CS-609; 2 assays were tested: Measles with 1 AssayResultTarget Measles and Bordetella with 2 AssayResultTargets B. pertussis and B. parapertussis.
Download the entire CSV here.
Quantitative amplification
Example of an absolute quantitative analysis for Assay QuantitativeAssay that has 1 AssayResultTarget ART1 and 3 linked Targets QuantTargetA, QuantTargetB and TargetC. Targets QuantTargetA and QuantTargetB can be quantified
Download the entire CSV here.
End point
Example of an end point analysis for Assay SARS-CoV-2 that has 1 AssayResultTarget SARS-CoV-2 and 1 linked Target N for Sample IDs Sample00123 and Sample00124.
Download the entire CSV here.
Specific examples
Mark for retest
Example of a sample that was marked for retest.
Control with no AssayResultTargets
Example of a control that outputs no AssayResultTargets.
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