QIAGEN, QIAcuity Configuration Guide

Purpose

To provide details about the necessary steps to implement the QIAGEN, QIAcuity Connector for use with the Benchling Connect platform.

Introduction

The QIAGEN, QIAcuity Connector is a component used in the context of the Benchling Connect platform to parse data from QIAcuity software to an Allotrope Simple Model (ASM) and make those data available within the Benchling UI in the context of a Run. The QIAcuity software is used in conjunction with the QIAcuity Digital PCR System.

The Benchling Connect - QIAcuity Connector is a ‘file-based’ based connector, meaning that it processes comma-separated values file (.csv) exports generated by the QIAcuity software. The data within the file export (.csv) is then accessed by Benchling Connect through the use of a ‘watched’ file directory on the local computer hosting a Benchling Gateway, which has been configured via a Connection from within Benchling.

In order to successfully implement the QIAcuity Connector for use with the Benchling platform, there are specific steps that need to be followed across the QIAcuity software.

This guide details the steps to be taken in the QIAcuity software for manual export of the results file in order to configure the integration. 

Steps within QIAcuity software

The following steps should be performed by the user within QIAcuity software.

1. Select wells that you want to get results for.
2. Choose if you want to analyze per Target and select targets you are interested in.
3. Select Vertical wells results presentation.
4. Click on the Show results button.
5. In the List tab, above the table, on the right-hand side you can see the Export to CSV... option.
6. Click on the Export to CSV option and select the Current results option.
7. Remember that data in CSV reflects data from List View are structured as follows:

• Plate name – name of the plate
• Plate ID – unique identifier of the plate
• Plate type – type of the plate
• Well – identifier of well
• Hyperwell – identifier of hyperwell
• Sample/NTC/Control – name of Sample/NTC/Control
• Type – Type (Sample/Control/Non Template Control)
• Reaction Mix – name of reaction mix
• Target – target name
• IC – internal control if selected
• Conc. [cp/μL] (dPCR reaction) – calculated concentration in dPCR reaction
• Conc. [unit] (dPCR reaction) – converted concentration in dPCR reaction, in user-defined unit
• CI (95%) (dPCR reaction) – confidence interval parameter in dPCR reaction

The user should set the file destination to be the target directory (watched directory) specified during Connection configuration.

Sample files can be found here.

Steps within Benchling

From within Benchling, a user must:

1. Enable the QIAcuity Connector on the tenant [internal admin console]
2. Configure a QIAcuity Connection
3. Create a Result schema to structure the data to be recorded
4. Configure a Run schema to accept data from QIAcuity and records Results

For steps 1 - 4, please reference the Benchling Connect Installation Guide for details related to creating and installing a Gateway and configuring a Connection.

Create Result Schema for QIAcuity data

The Benchling Connect - QIAcuity Connector uses the Allotrope Simple Model (ASM) to structure the information parsed from the QIAGEN QIAcuity file export (.csv). The data is processed in a two step process; step one from QIAcuity export to the .json based ASM, and step two from the ASM .json to .csv files available for ingest to Benchling - the well file in which each each row corresponds to a well in the dPCR plate, the measurement file in which each row corresponds to a measurement, and the group file in which each row corresponds to a ‘group’ with results aggregated across sample identifier , sample role type, and target DNA. 

Details about the dPCR ASM schema can be found here:

https://github.com/Benchling-Open-Source/allotropy/tree/main/src/allotropy/allotrope/schemas/adm 

The well file can contain the following columns (if available within the data):

• device identifier
• model number
• device serial number
• data system instance identifier
• asset management identifier - this represents the computer from which the data was retrieved
• file name
• UNC path - this corresponds to the complete file path of data file 
• software name
• software version
• product manufacturer
• ASM converter
• ASM converter version
• analyst
• submitter
• analytical method identifier
• experimental data identifier
• experiment type
• container type
• plate well count
• well volume
• measurement identifier <reporter dye>
• measurement time
• target DNA description <reporter dye>
• sample identifier
• batch identifier
• sample role type <reporter dye>
• well location identifier
• well plate identifier
• device type
• detection type
• measurement method identifier
• total cycle number setting
• pcr detection chemistry 
• denaturing temperature setting
• denaturing time setting
• annealing temperature setting
• annealing time setting
• extension temperature setting
• extension time setting
• reporter dye setting <reporter dye>
• quencher dye setting <reporter dye>
• passive reference dye setting 
• total partition count
• fluorescence intensity threshold setting
• number concentration <reporter dye>
• positive partition count <reporter dye>
• negative partition count <reporter dye>

Those parameters whose values may differ between channels in a multiplexed assay are appended with the <reporter dye> (e.g. VIC, FAM).

The measurement file can contain the following columns (if available within the data):

• device identifier
• model number
• device serial number
• brand name
• product manufacturer
• data system instance identifier
• file name
• UNC path 
• software name
• software version
• ASM converter
• ASM converter version
• experimental data identifier
• measurement identifier
• experiment type
• container type
• plate well count
• measurement time
• sample identifier
• reporter dye setting
• target DNA description
• well plate identifier
• device type
• total partition count
• number concentration - this corresponds to counts/uL
• positive partition count
• device control identifier

The group file can contain the following columns (if available within the data):

• device identifier
• model number
• device serial number
• data system instance identifier
• asset management identifier - this represents the computer from which the data was retrieved
• file name
• UNC path - this corresponds to the complete file path of data file 
• software name
• software version
• product manufacturer
• ASM converter
• ASM converter version
• target DNA description <reporter dye>
• sample identifier
• sample role type <reporter dye>
• calculated data name/result

Configure Run Schema to employ QIAGEN QIAcuity Connection

The Run schema can be created from the menu under Feature Settings.

As part of the Run schema creation, the user should specify 'QIAGEN QIAcuity' as the Connection Schema.

Configure the Output File Processor

For details on configuring the Output File Processor within the Run schema, please refer to these articles.

• Configure the Output File Config of a Benchling Connect Run
• Configure the Output File Processor to Create New Entities
• Configure the Output File Processor to Capture Results

QIAGEN QIAcuity Connector Requirements

* This is the version of QIAcuity with which the connector has been developed and tested. The connector may work with other versions of QIAcuity, but that must be verified by the user.

Revision History

2024/07/11

Initial Version

2024/09/03

Update link to referenced schemas in Github

2024/09/18

Added Github testdata link

2024/09/27

Added description of measurement data file .CSV including expected column headers (if available within the data)