QIAsymphony SP - AS User Manual Operating the AS ver 4.0 April 2012

April 2012

Trademarks QIAGEN®, QIAsymphony®, Rotor-Disc® (QIAGEN Group). Registered names, trademarks, etc. used in this document, even when not specifically marked as such, are not to be considered unprotected by law. © 2010–2012 QIAGEN, all rights reserved.

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1069307

04/2012

Sample & Assay Technologies

QIAsymphony® SP/AS User Manual - Operating the QIAsymphony AS

www.qiagen.com

QIAsymphony® SP/AS User Manual - Operating the QIAsymphony AS

For use with software version 4.0

Sample & Assay Technologies

Contents

Contents 1

Introduction

1-1

1.1

QIAsymphony SP/AS user manuals

1-1

1.2

About this user manual

1-2

1.3 General information 1.3.1 Technical assistance 1.3.2 Policy statement 1.3.3 Version management

1-2 1-2 1-3 1-3

1.4

Intended use of the QIAsymphony AS

1-3

2

Operating the QIAsymphony AS

2-1

2.1 Definitions 2.1.1 Integrated run 2.1.2 Independent run 2.1.3 Run with normalization 2.1.4 Standard curve

2-1 2-1 2-1 2-2 2-2

2.2 Things to do before defining a run 2.2.1 Transferring process files 2.2.2 Transferring work lists and rack files 2.2.3 Transferring concentration data file 2.2.4 Defining assay favorites

2-2 2-2 2-3 2-3 2-3

2.3 Recommended workflows 2.3.1 Recommended workflow for integrated run 2.3.2 Recommended workflow for independent run without normalization 2.3.3 Recommended workflow for independent run with normalization

2-5 2-5

2.4 Defining an integrated run 2.4.1 Assigning assays to sample positions 2.4.2 Creating AS batches 2.4.3 Defining internal controls

2-10 2-12 2-17 2-19

Operating the QIAsymphony AS 04/2012

2-7 2-9

Contents-1

Contents 2.4.4 2.4.5 2.5

Queuing an integrated run Modifying an integrated run Resolving errors regarding sample/internal control tubes or sample IDs

2-19 2-20 2-22

2.6 Loading an integrated run 2.6.1 Loading sample racks 2.6.2 Loading assay rack(s) 2.6.3 Loading reagents 2.6.4 Loading disposable filter-tips 2.6.5 Performing an inventory scan

2-22 2-23 2-26 2-33 2-37 2-39

2.7

2-41

Checking cooling temperatures

2.8 Starting an integrated run 2.8.1 Status of a run

2-43 2-43

2.9 Removing assays after an AS run 2.9.1 Procedure after run completion

2-43 2-45

2.10 Pausing, resuming and aborting an integrated run 2.10.1 Pausing a run 2.10.2 Resuming a run 2.10.3 Stopping a run

2-46 2-46 2-47 2-48

2.11 Switching from the sample preparation to the assay setup user interface

2-50

2.12 Defining an independent assay run 2.12.1 Defining ―Sample‖ slot(s) and assigning sample rack(s) 2.12.2 Defining/checking sample rack(s) 2.12.3 Defining assay(s) to be processed in the run 2.12.4 Import concentration data (only for assay run with normalization) 2.12.5 Assigning selected assays to sample positions 2.12.6 Modifying assay parameters 2.12.7 Queuing an independent assay run

2-51

2.13 Loading an independent run 2.13.1 Viewing loading information

2-87 2-87

Contents-2

2-52 2-58 2-69 2-74 2-76 2-83 2-86

Operating the QIAsymphony AS 04/2012

Contents 2.13.2

Loading a normalization rack (only for assay run with normalization)

2-88

2.14 Checking cooling temperatures

2-89

2.15 Starting an independent run 2.15.1 Status of a run

2-89 2-91

2.16 Removing assays after independent run 2.16.1 Unloading the worktable

2-91 2-92

2.17 Pausing, resuming, and aborting an independent run

2-93

2.18 Pipetting order 2-95 2.18.1 General pipetting scheme for an assay with internal control (IC) 2-95 2.18.2 General pipetting scheme for an assay without internal control (IC) 2-97 2.18.3 General pipetting scheme 2-98 2.18.4 Pipetting scheme for a multi-assay run 2-99 2.18.5 Pipetting scheme for standard curve 2-99 2.18.6 Pipetting scheme for assay with normalization 2-100 2.19 Protocol recovery 3

2-101

Assay Setup User Interface

3-1

3.1 Software features 3.1.1 Status bar 3.1.2 Drawer buttons 3.1.3 Help button

3-1 3-2 3-2 3-3

3.2

3-4

―Tools‖ tab

3.3 ―Integrated Run‖ tab 3.3.1 ―Integrated Setup‖ screen 3.3.2 ―Integrated Setup/Batch X/Define Samples‖ screen (tube carrier) 3.3.3 ―Integrated Setup/Batch X/Define Samples‖ screen (plate carrier) 3.3.4 ―Assay Assignment‖ screen 3.3.5 ―Assay Specifications‖ screen Operating the QIAsymphony AS 04/2012

3-7 3-15 3-18 3-25 3-27 3-29

Contents-3

Contents 3.3.6

―Sample Preparation/Internal Controls‖ screen

3-32

3.4 ―Assay Setup‖ tab 3-32 3.4.1 ―Assay Setup‖ tab - ―Assay Setup/Overview‖ screen 3-33 3.4.2 ―Assay Setup/Sample View‖ screen 3-39 3.4.3 ―Assay Setup/Parameter View‖ screen 3-41 3.4.4 ―Sample Rack(s)‖ screen 3-44 3.4.5 ―Sample Rack Layout‖ screen 3-48 3.4.6 ―Assay Selection‖ screen 3-54 3.4.7 ―Assay Assignment‖ screen 3-58 3.4.8 ―Assay Specifications‖ screen 3-62 3.4.9 ―Loading Information‖ screen 3-75 3.4.10 ―Temperature Status‖ screen 3-85 3.5 ―Maintenance AS‖ menu 3.5.1 ―Maintenance AS‖ screen

3-86 3-87

3.6 ―Service AS‖ menu 3.6.1 ―Script Execution‖ tab

3-89 3-89

3.7 ―Labware Browser‖ menu 3.7.1 ―Labware AS‖ tab

3-92 3-93

3.8 ―Rack Browser‖ menu 3.8.1 ―Assay Racks‖ tab

3-94 3-95

Appendix A

A-1

Index

Contents-4

Index-1

Operating the QIAsymphony AS 04/2012

Introduction

1

Introduction Thank you for choosing the QIAsymphony SP/AS instruments. We are confident they will become an integral part of your laboratory. Before using the QIAsymphony SP/AS instruments, it is essential that you read the user manuals carefully and pay particular attention to the safety information described in the General Description. The instructions and safety information in the user manuals must be followed to ensure safe operation of the instruments and to maintain the instruments in a safe condition.

WARNING/ CAUTION

Risk of personal injury and material damage [W1] Improper use of the QIAsymphony AS may cause personal injuries or damage to the instrument. The QIAsymphony AS must only be operated by qualified personnel who have been appropriately trained. Servicing of the QIAsymphony AS must only be performed by QIAGEN Field Service Specialists.

1.1

QIAsymphony SP/AS user manuals The QIAsymphony SP/AS instruments are provided with 4 user manuals, as outlined in the following table. QIAsymphony SP/AS User Manual - General Description

Provides a description of the instruments, and describes functions (e.g., handling files) that are the same for both instruments. Information about maintenance procedures and troubleshooting is also included.

QIAsymphony SP/AS User Manual - Operating the QIAsymphony SP

Provides details about how to operate the QIAsymphony SP instrument and a description of the QIAsymphony software required for operating the QIAsymphony SP.

Operating the QIAsymphony AS 04/2012

1-1

Introduction

1.2

QIAsymphony SP/AS User Manual - Operating the QIAsymphony AS

Provides details about how to operate the QIAsymphony AS instrument and a description of the QIAsymphony software required for operating the QIAsymphony AS.

QIAsymphony Management Console User Manual

Provides details about how to use the QIAsymphony Management Console. This includes how to use the ―File Transfer‖, ―Checksum Validation‖, ―Process Definition‖ editor tool, ―CSV Conversion‖, and ―Automatic File Transfer‖ tools.

About this user manual This user manual describes how to operate the QIAsymphony AS and provides information in the following sections: 1. Introduction 2. Operating the QIAsymphony AS 3. QIAsymphony AS user interface

1.3

General information

1.3.1

Technical assistance At QIAGEN® we pride ourselves on the quality and availability of our technical support. Our Technical Services Departments are staffed by experienced scientists with extensive practical and theoretical expertise in molecular biology and the use of QIAGEN products. If you have any questions or experience any difficulties regarding the QIAsymphony SP/AS instruments or QIAGEN products in general, do not hesitate to contact us.

1-2

Operating the QIAsymphony AS 04/2012

Introduction QIAGEN customers are a major source of information regarding advanced or specialized uses of our products. This information is helpful to other scientists as well as to the researchers at QIAGEN. We therefore encourage you to contact us if you have any suggestions about product performance or new applications and techniques. For technical assistance and more information call one of the QIAGEN Technical Services Departments (for contact information, see back cover or visit www.qiagen.com).

1.3.2

Policy statement It is the policy of QIAGEN to improve products as new techniques and components become available. QIAGEN reserves the right to change specifications at any time. In an effort to produce useful and appropriate documentation, we appreciate your comments on this user manual. Please contact QIAGEN Technical Services.

1.3.3

Version management This document is the QIAsymphony User Manual - Operating the QIAsymphony AS, version 3.0 (for use with software version 4.0).

1.4

Intended use of the QIAsymphony AS The QIAsymphony AS instrument is designed to perform automated assay setup. If used in combination with QIAGEN Kits indicated for use with the QIAsymphony AS instrument it is intended for the applications described in the respective QIAGEN Kit handbooks. If the QIAsymphony AS instrument is used with kits other than QIAGEN kits, it is the user’s responsibility to validate the performance of such product combination for any particular application. The QIAsymphony AS instrument is intended for use by professional users trained in molecular biology techniques and the operation of the QIAsymphony AS instrument.

Operating the QIAsymphony AS 04/2012

1-3

Introduction Page left intentionally blank

1-4

Operating the QIAsymphony AS 04/2012

Operating the QIAsymphony AS

2

Operating the QIAsymphony AS This section describes how to operate the QIAsymphony AS. Before proceeding, we recommend that you familiarize yourself with the features of the instrument by referring to the corresponding sections of the General Description. The QIAsymphony operating software is described in detail in Section 3 of this user manual. The hood of the QIAsymphony AS must stay closed during operation of the instrument. Only open the hood when instructed to do so by the software or when carrying out maintenance procedures.

WARNING

Moving parts [W2] To avoid contact with moving parts during operation of the QIAsymphony AS, the instrument must be operated with the hood closed. If the hood sensor is not functioning correctly, contact QIAGEN Technical Services.

2.1

Definitions

2.1.1

Integrated run An integrated run consists of a sample preparation run on the QIAsymphony SP and then an assay setup run on the QIAsymphony AS. Eluates are automatically transferred from the QIAsymphony SP to the QIAsymphony AS via the transfer module. An integrated run is defined in the software for the complete workflow before starting the run.

2.1.2

Independent run The QIAsymphony SP and QIAsymphony AS can be operated independently of each other. It is possible to perform 2 independent runs (one on the QIAsymphony SP and one on the QIAsymphony AS) at the same time, where neither run influences the other.

Operating the QIAsymphony AS 04/2012

2-1

Operating the QIAsymphony AS It is also possible to perform an independent run on the QIAsymphony SP, and then transfer eluates via the transfer module to the QIAsymphony AS. Here samples can be processed using an independent assay setup run. In this case, sample preparation run definition must be performed first, and when the eluate rack is transferred to the QIAsymphony AS, assay setup run definition is performed.

2.1.3

Run with normalization The QIAsymphony AS can perform a normalization step (i.e., eluates of known concentration are diluted to target concentrations) before assay setup. This option is available for most assay definitions in combination with a normalization definition file, which is available on request from the QIAGEN Application Laboratory. Please contact QIAGEN for more information.

2.1.4

Standard curve The QIAsymphony AS can perform series dilutions of standards, using concentrated standard solution and dilution buffer, both provided by the user. This feature is only available when defined by an assay.

2.2

Things to do before defining a run Before defining a run, available adapter(s) and holder(s) must be configured in the software. If work list(s) and rack file(s) will be used in the run, these files must be transferred to the QIAsymphony SP/AS instruments.

2.2.1

Transferring process files Note: To transfer process files, the user must be logged in as ―Supervisor‖. Process files can be transferred directly using a USB stick, or by using the ―File Transfer‖ tool of the QIAsymphony Management Console. For an independent run, an Assay Definition and Assay Parameter Set must be transferred. For successful transfer of

2-2

Operating the QIAsymphony AS 04/2012

Operating the QIAsymphony AS the Assay Parameter Set, the Assay Definition must first be transferred. For an integrated run, a Protocol, Assay Control Set, Assay Definition, and Assay Parameter Set must be transferred. For successful transfer of the Assay Parameter Set, the Protocol, Assay Control Set, and Assay Definition must first be transferred.

2.2.2

Transferring work lists and rack files Work lists and rack files can be transferred directly using a USB stick, or by using the ―File transfer‖ tool of the QIAsymphony Management Console. Work list(s) and rack file(s) that are used on the QIAsymphony SP/AS instruments must be in *.xml format. Work list(s) and rack file(s) that are in *.csv format can be converted to *.xml format using the ―CSV Conversion‖ tool of the QIAsymphony Management Console. See Section 7 of the QIAsymphony Management Console User Manual for more details.

2.2.3

Transferring concentration data file For an assay run with a normalization step, a concentration data file in *.xml format must be transferred to the QIAsymphony SP/AS instruments before run definition. This file can be transferred directly using a USB stick, or by using the ―File transfer‖ tool of the QIAsymphony Management Console.

2.2.4

Defining assay favorites In the integrated mode, there is the possibility to define personalized assay favorites for quicker assignment within the ―Integrated Setup‖ screen. Define favorites by pressing ―Assay Favorites‖ within the ―Tools‖ screen.

Operating the QIAsymphony AS 04/2012

2-3

Operating the QIAsymphony AS

Press ―Assay Favorites‖ and the ―Define Assay Favorites‖ screen appears.

The dialog contains a list showing the available assays and a set of favorite buttons identical to the ones in the ―Integrated Setup‖ screen. 2-4

Operating the QIAsymphony AS 04/2012

Operating the QIAsymphony AS The buttons are labeled with the defined favorite assays if already assigned, otherwise the label is empty. To define the ―Favorites‖ buttons: 1. On the left side, select the assay to assign as a favorite. 2. Press the ―Favorite‖ button. Repeat steps 1 and 2 for all ‖Favorite‖ buttons to be defined. Using the ―Clear‖ button removes the assays from the checked ―Favorite‖ button. Confirm the favorites by pressing the ―Save‖ button. Changes are saved in the user data enabling a user-specific configuration of the ―Favorites‖ buttons. Pressing ―Cancel‖ displays a warning that all changes will be lost. By confirming the message with ―Yes‖ all changes are discarded and the dialog is left. Select ―No‖ to keep the changes and stay within the dialog.

2.3

Recommended workflows

2.3.1

Recommended workflow for integrated run 1. Switch on the QIAsymphony SP/AS instruments (see Section 5.1 of the General Description). 2. Log in (see Section 5.3 of the General Description). 3. Insert the tip chute into the QIAsymphony AS. 4. Insert an empty tip disposal bag into the QIAsymphony AS. 5. Switch to the ―Integrated Run‖ user interface (see Section 2.6). 6. Load the ―Waste drawer‖ according to section 2.3 ―Loading the ―Waste drawer‖‖ of Operating the QIAsymphony SP and start scan. 7. Load the ―Eluate‖ drawer with the correct rack inside the corresponding cooling adapter, together with the transfer frame on Elution slot 1. Assign the eluate rack to elution slot 1 on the touchscreen and start scan. (See Section 2.5 ―Loading the ―Eluate‖ drawer‖, in Operating the QIAsymphony SP.)

Operating the QIAsymphony AS 04/2012

2-5

Operating the QIAsymphony AS 8.

Load the ―Reagent and Consumables‖ drawer according to the individual (assay) kit handbooks and Section 2.6, ‖Loading the Reagents and Consumables drawer‖, in Operating the QIAsymphony SP and start a full scan. 9. Press ―Define Run‖ to define an integrated run on the QIAsymphony SP/AS (see Section 2.4). 10. Load ―Sample‖ drawer with samples and optionally Internal Controls according to section 2.7 ―Loading the ―Sample‖ drawer‖ of Operating the QIAsymphony SP. 11. ―Edit Samples‖ to check or change sample tube types and inserts. The tubes are predefined for the inserts in the configuration and can be changed. See Section 6.1.2 ―Default tube types‖, in the General Description. 12. Press ―Define Assays‖ to assign assays to sample positions (see Section 2.4.1). 13. Create AS batch(es) using the defined SP batch(es) (Section 2.4.2). 14. Queue the integrated run by pressing ―OK‖ (see Section 2.4.2). 15. Optional: Define Internal Control(s) (see Section 2.4.3) 16. Start the integrated run by pressing ―Run‖ (see Section 2.4.2). 17. While the integrated run is being processed on the QIAsymphony SP, load the QIAsymphony AS (see Section 2.6, ―Loading an integrated run‖, in the QIAsymphony SP/AS User Manual - Operating the QIAsymphony AS); open the ―Eluate and Reagents‖ and ―Assays‖ drawers. 18. Load assay rack(s) into the appropriate precooled adapter(s) and place them onto the ―Assay‖ slot(s) (see Section 2.6.2). 19. Check the cooling temperatures of the cooling positions used (see Section 2.7). 20. Fill each reagent tubes with the required volume of appropriate reagent and place the reagent tubes, without lids, into the appropriate positions of precooled adapters

2-6

Operating the QIAsymphony AS 04/2012

Operating the QIAsymphony AS for reagents. Place the prepared assay adapter(s) onto the appropriate slot(s) (see Section 2.6.3) Note: Ensure that reagents are completely thawed. If desired, enter a kit bar code for each assay (see Section 2.6.1). 21. Load disposable filter-tips into the ―Eluate and Reagents‖ and ―Assays‖ drawers, according to the required number of each tip type (see Section 2.6.4). 22. Close the ―Eluate and Reagents‖ and ―Assays‖ drawers and start the inventory scan (see 2.6.5). 23. The assay setup will start automatically after the inventory scan was performed successfully and the sample preparation for the integrated batch was finished. 24. When running more than one integrated batch, remove the previous integrated batch in the ―Integrated Setup‖ overview (see Section 2.9). Reload the ―Eluate and Reagents‖ and ―Assays‖ drawers on QIAsymphony AS to continue the AS batch (i.e., repeat steps17–23).

2.3.2

Recommended workflow for independent run without normalization 1. Switch the QIAsymphony SP/AS instruments on (see Section 5.1, General Description). 2. Log in (see Section 5.3, General Description). 3. Insert the tip chute into the QIAsymphony AS. 4. Discard the QIAsymphony AS tip disposal bag. 5. Install an empty tip disposal bag into the QIAsymphony AS. 6. If available, transfer elution rack(s) from the QIAsymphony SP manually to the QIAsymphony AS (see Sections 2.19.1 and 2.20 of Operating the QIAsymphony SP). 7. Switch to the assay setup user interface (see Section 2.3). 8. Press ―New‖ to start the assay definition process (Section 2.4). The screens on the touchscreen guide the user through the assay definition process in a step-by-step fashion. Use of work lists and rack files are optional.

Operating the QIAsymphony AS 04/2012

2-7

Operating the QIAsymphony AS Note: If elution rack(s) have been automatically transferred to the QIAsymphony AS, press ―Yes‖ in the message that appears. The ―Sample Rack(s)‖ screen of the assay setup user interface will then open. 9. Assign sample rack(s) and rack IDs to ―Sample‖ slots (Section 2.12.1). 10. Define and check sample rack type(s) for sample, EC+, and EC– positions, sample IDs, and volumes (see Section 2.12.2). 11. Define which Assay Parameter Set(s) to use in the run (see Section 2.12.3). 12. Assign Assay Parameter Set(s) to samples (see Section 2.12.5). If desired, assay parameters can be modified (Section 2.12.6). If a work list is being used, the Assay Parameter Set(s) are automatically assigned. 13. Assign rack IDs to assay rack(s). At this stage, assay rack(s) can be loaded onto the ―Assay‖ slot(s) (see Section 2.6.2). 14. Queue the assay run by pressing ―Queue‖. 15. Check the cooling temperatures of the used cooling positions (Section 2.7). 16. Fill each reagent tube with the required volume of appropriate reagent (Section 2.6.3). 17. Place the reagent tubes, without lids, into the appropriate positions of precooled adapters for reagents (see Section 2.6.3). Note: Ensure that reagents are completely thawed. 18. If not already done, place the appropriate assay rack(s) into the appropriate precooled adapter(s). 19. If not already done, place the appropriate sample rack(s) into the appropriate precooled adapter(s). 20. Open the ―Eluate and Reagents‖ drawer and load the prepared reagent adapter(s) into the appropriate slot(s). If desired, enter a kit bar code for each assay. 21. If not already done, place the prepared sample adapter(s) onto the appropriate slot(s). 22. Open the ―Assays‖ drawer.

2-8

Operating the QIAsymphony AS 04/2012

Operating the QIAsymphony AS 23. If not already done, place the prepared assay adapter(s) onto the appropriate slot(s). 24. Load disposable filter-tips into the ―Eluate and Reagents‖ and ―Assays‖ drawers, according to the required number of each tip type (Section 2.6.4). 25. Close the ―Eluate and Reagents‖ and ―Assays‖ drawers. 26. Upon closing drawers, press ―Scan‖ to start the inventory scan for each drawer. 27. The inventory scan checks the slots, adapters, and filtertips. If required, correct any errors. 28. Wait until the target cooling temperatures are reached. 29. Press ―Run‖ to start the run (Section 2.15).

2.3.3

Recommended workflow for independent run with normalization 1. Perform steps 1–29 of Section 2.3.2 to define and set up the quantification assay. 2. Transfer the assay rack to the thermal cycler. Transfer the cycler file to the cycler, and perform the quantification. 3. Convert the concentration data to a *.xml file using the ―Concentration Data Input Tool 4.0‖ and transfer the file to the system. 4. Transfer the concentration data file to the QIAsymphony SP/AS instruments. 5. Perform steps 1–29 of section 2.3.2 to define and set up the assays with normalization (e.g., STR assay). The system asks if you want to import the concentration data file (see Section 2.12.4).

Operating the QIAsymphony AS 04/2012

2-9

Operating the QIAsymphony AS

2.4

Defining an integrated run The following sections describe how to define an integrated run on the QIAsymphony SP/AS. The screens that appear on the touchscreen guide you through the steps. It is only possible to define an integrated run if an eluate rack and transfer frame have been loaded on eluate slot 1 of the QIAsymphony SP. To save time, the system checks for the transfer frame at the same as the rack carrier inventory scan. See Section 2.5 of Operating the QIAsymphony SP for more detailed information about how to load an eluate rack. Note: It is not possible to define a normalization step in an integrated run. An integrated run can be defined via the ―Integrated Run‖ tab in the overview screen. Select the ―Integrated Run‖ tab, and then press ―Define Run‖. Note: When ‖Define Run‖ is pressed, error messages can appear in the following situations:  If the bar code of the eluate rack is missing or unreadable  If the rack type loaded on eluate slot 1 of the QIAsymphony SP is not compatible with elution slot 2 on the QIAsymphony AS  If the eluate rack on slot 1 of the QIAsymphony SP has reserved columns  If there are still defined, running or completed independent runs present on QIAsymphony SP/AS Note: If required, refer to the troubleshooting section for details to solve the problems - see Section 10 of the General Description.

2-10

Operating the QIAsymphony AS 04/2012