Thermo Fisher Scientific CytoScan HD Assay Software Module User guide

Brand
Thermo Fisher Scientific
Model
CytoScan HD Assay Software Module
Type
User guide
For Research Use Only. Not for use in diagnostic procedures.
CytoScan™ HD Assay Software Module v1.2
USER GUIDE
Publication Number MAN0017903
Revision A.0
Manufacturer: Affymetrix Inc. | 3450 Central Expressway | Santa Clara, CA 95051 | USA
The information in this guide is subject to change without notice.
DISCLAIMER: TO THE EXTENT ALLOWED BY LAW, THERMO FISHER SCIENTIFIC INC. AND/OR ITS AFFILIATE(S) WILL NOT BE LIABLE FOR SPECIAL,
INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE, OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT,
INCLUDING YOUR USE OF IT.
Revision history: Pub. No. MAN0017903
Revision Date Description
A.0 26 October 2018 Initial release in Thermo Fisher Scientific document control system.
Supersedes legacy Affymetrix publication number 703055.
Updated to the current document template, with associated updates to trademarks, logos, licensing, and
warranty.
Removed Expression documents from reference document list.
Important Licensing Information: These products may be covered by one or more Limited Use Label Licenses. By use of these products, you accept
the terms and conditions of all applicable Limited Use Label Licenses.
Trademarks: All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. All other trademarks are
the property of their respective owners.
©2018 Thermo Fisher Scientific Inc. All rights reserved.
Contents
■CytoScan™ HD Assay Software Module v1.2 ............................. 4
Introduction .................................................................... 4
Nomenclature .............................................................. 4
Major features of the CytoScan™ HD Assay Software Module v1.2 ................. 4
Reagents .................................................................. 5
Installing the ASM ............................................................... 5
About an SSL server certificate ............................................... 5
Install a SSL server certificate ................................................ 6
Install the CytoScan™ HD Assay Software Module v1.2 ........................... 7
Create a Test Request .......................................................... 12
Add additional information to a specimen ......................................... 13
The Assay Home window ........................................................ 15
Add Reagent Information ................................................... 16
Reagent kit information .................................................... 17
Reagent entry information .................................................. 17
Reagent kit lot numbers and expiration dates ................................. 17
Viewing a Specimen Report ................................................. 18
Viewing a Test Request Log ................................................. 19
Edit additional Test Request information .......................................... 20
Manually grid your results ...................................................... 21
Transferring data .............................................................. 22
Review a Test Report ........................................................... 23
Ordering information ........................................................... 25
■Documentation and support ............................................. 26
Customer and technical support ................................................. 26
Limited product warranty ....................................................... 26
CytoScan
™
HD Assay Software Module v1.2 User Guide
3
CytoScan™ HD Assay Software
Module v1.2
Introduction
This user guide demonstrates how to create a CytoScan™ HD Assay Software Module
v1.2 RUO Assay Test Request.
This software is designed for use with the GeneChip™ System 3000Dx v.2 and is also
compatible with the CytoScan™ HD Array Kit and Reagent Kit Bundle (Cat. No.
901835). For your convenience, the kits within this bundle, the CytoScan™ HD Array
Kit (Cat. No. 901833) and the CytoScan™ Reagent Kit (Cat. No. 901808) are separately
available.
• The assay name is CytoScan HD Assay.
• The Assay display name is CytoScan HD v1.2.
• The term ASM refers to "assay software module".
The CytoScan™ HD Assay Software Module v1.2 allows you to perform the following
record keeping functions. This user guide discusses the use of these functions to help
set up an assay.
• Additional Information window
• Assay Home window (or Assay Landing window)
• Batch Edit window
• Report window
CytoScan™ HD v1.2, which is under the control of the Aymetrix™ Molecular
Diagnostics Software (AMDS), transfers all specimen information to the server.
IMPORTANT! It is not the purpose of this user guide to instruct you on how to run
the assay. This guide only provides instructions on how to create an RUO Test
Request and track associated information.
To complete an assay run, you must follow the standard AMDS assay protocols, then
process it through the workow to register, hybridize, wash/stain, and scan the array
(as part of the array cartridge). These specics are discussed in the Aymetrix™
Molecular Diagnostics Software User Guide.
IMPORTANT! Be thoroughly familiar with the following documents before using the
information in this supplement to run your assay.
•Aymetrix™ Molecular Diagnostics Software User Guide (Pub. No. 703230)
•Aymetrix™ Molecular Diagnostics Software Quick Reference Guide (Pub. No. 08-0262)
Nomenclature
Major features of
the CytoScan™ HD
Assay Software
Module v1.2
4
CytoScan
™
HD Assay Software Module v1.2 User Guide
Reagents for the CytoScan™ HD Array Kit–single array (Cat. No. 520825) are
comprised of the following subkits:
• Restriction and Ligation Reagents (Part No. 901803)
• Ligation Adaptors and Fragmentation Reagents (Part No. 901749)
• GeneChip™ Hybridization Reagents (Part No. 901804)
• GeneChip™ Stain Reagents (Part No. 901805)
• Wash Buer A (Part No. 901680)
• Wash Buer B (Part No. 901681)
Installing the ASM
1. Install a certicate (only for secure transfers to a Data Transfer Server and not
required for CIFS transfers).
2. Install the CytoScan™ HD v1.2.
Note: In most cases, a eld service technician installs the certicate and the ASM.
Note: The steps in this section apply only if you are using a Data Transfer Server. If
you are transferring your data via CIFS, proceed directly to step 1 of the "Install the
CytoScan™ HD Assay Software Module v1.2" section.
As a security measure, AMDS requires that you or the eld service technician install a
SSL server certicate on your local workstation in order for your workstation to
communicate with the server. This certicate is required for the transfer of CytoScan™
HD v1.2 Test Request data to the Data Transfer Server.
A eld service technician should have installed a certicate at the time of the system's
installation. If for some reason the eld service technician did not install a certicate
or if the server has changed after the system's initial installation, the SSL server
certicate must be installed or reinstalled.
The SSL server certicate MUST be installed before installing the assay.
If a proper certicate has not been installed, you can still install the assay and process
Test Requests; however, you will not have permission to access the server and you
cannot transfer Test Request data to the server.
If you cannot access the server and have already installed a certicate, contact us at
[email protected]
Note: You must be logged in with either Laboratory Supervisor or System Maintainer
privileges to install a certicate.
Reagents
About an SSL
server certificate
CytoScan™ HD Assay Software Module v1.2
Installing the ASM
CytoScan
™
HD Assay Software Module v1.2 User Guide
5
The Administrator panel contains the Assay Management buon and provides the
starting point for installing a certicate (Figure 1).
Figure 1 Administrator panel (lower left).
1. Insert the CD into the drive.
2. Click Assay Management.
The Assay Management window appears.
3. Click Install Certicate.
The Server Certicate Browse window appears (Figure 2).
Figure 2 Server Certificate Browse window.
4. Make sure the Install from CD option is selected. Then, navigate to and click the
appropriate .cer le.
Install a SSL
server certificate
CytoScan™ HD Assay Software Module v1.2
Installing the ASM
6
CytoScan
™
HD Assay Software Module v1.2 User Guide
5. Click OK.
• If successful, you are notied by a message “You have successfully added
the server certicate “xxxxx.cer” to the AMDS trusted certicate store.”
• If the certicate installation fails, AMDS noties you with an error message.
The software prevents you from accessing the server and from transferring
data without the proper certicate installed. Contact
[email protected] for information to obtain a new certicate.
6. Click OK to return to the Assay Management window.
The ASM installation process is relatively simple. It requires the selection of a
manifest le and the selection of approved user access.
Note: You must be logged in with either Laboratory Supervisor or with System
Maintainer privileges to install an Assay Software Module.
1. Insert the CD into the drive.
2. Click Assay Management.
The Assay Management window appears.
3. Click Install Assay.
The Assay Installation window appears (Figure 3).
Figure 3 Assay Installation window.
Install the
CytoScan™ HD
Assay Software
Module v1.2
CytoScan™ HD Assay Software Module v1.2
Installing the ASM
CytoScan
™
HD Assay Software Module v1.2 User Guide
7
4. Click Browse.
The Assay Installation Browse window appears (Figure 4).
Figure 4 Assay Installation Browse window.
5. Make sure that the Install from CD option is selected. Then, navigate to and
click on D:\CytoScan_HD_v1.2\CytoScan_HD_v1.2.manifest
CytoScan™ HD Assay Software Module v1.2
Installing the ASM
8
CytoScan
™
HD Assay Software Module v1.2 User Guide
6. Click OK.
The Assay Installation Browse window appears (Figure 5).
Figure 5 Assay Installation Browse window.
7. Click each desired authorized Assay User or click Select All.
CytoScan™ HD Assay Software Module v1.2
Installing the ASM
CytoScan
™
HD Assay Software Module v1.2 User Guide
9
8. Click Install.
The Remote Device Seings window appears (Figure 6).
Figure 6 Remote Device Settings window.
Note: For AMDS versions 1.1.1 or newer, users can enter their transfer location
either as a WebDav URL (e.g., hps://dx2_webdav_server/dx2_ruo) or as a
Common Interface File System (CIFS) folder designation
(e.g., \\dx2_cifs_folder\dx2_ruo_les). For software releases prior to AMDS
1.1.1, only the WebDav option is available.
9. Locate and enter the NA Device URL. This location is where AMDS sends its
completed Assay data.
10. Enter the NA Device Server User Name. Use the existing server, workstation, or
network user name.
11. Enter the NA Device Server Password. Use the existing server, workstation, or
network password.
12. Conrm the password.
Note: Your NA Device Server Username and Password are not the user name
and password that you used to log into AMDS. You must enter your user name
and password that you use to access the server.
13. Conrm that the rewall is ON and your workstation is connected to the
network.
14. Click Install.
CytoScan™ HD Assay Software Module v1.2
Installing the ASM
10
CytoScan
™
HD Assay Software Module v1.2 User Guide
Firewall issues
If the software cannot connect through your system's rewall, the following error
message appears (Figure 7).
Figure 7 Error message.
There are 3 buons to acknowledge the Remote Device Seings Error message.
•Abort—Exits the ASM installation procedure.
•Retry—Aempts another ASM installation.
•Ignore—Continues the ASM installation.
Note: If you select Ignore, AMDS will install the ASM; however, you will not be
granted permission to communicate with any remote server.
Repair a currently installed ASM
If this ASM already exists on the system and it is reinstalled, the following message
appears (Figure 8).
Figure 8 Repair Assay window.
CytoScan™ HD Assay Software Module v1.2
Installing the ASM
CytoScan
™
HD Assay Software Module v1.2 User Guide
11
Any AMDS user with valid AMDS credentials and appropriate permissions can repair
the previously installed ASM.
1. Enter your User Name and Password. Then, click Continue.
The ASM Installation status window and progress bar appear (Figure 9).
Figure 9 Assay Installation window.
2. Click Finish to conclude the ASM installation and return to the Assay
Management window.
Installation of the ASM is complete and you may begin using the assay software
module.
Create a Test Request
Note: You must be a Laboratory Supervisor, Technician, or Technologist to create a
test request.
1. Click the Active Worklist buon if you are not already in the Active Worklist
window. The Active Worklist window appears (Figure 10).
Figure 10 Active Worklist window.
CytoScan™ HD Assay Software Module v1.2
Create a Test Request
12
CytoScan
™
HD Assay Software Module v1.2 User Guide
2. Click Create from the Active Worklist toolbar.
The Enter Test Request window appears (Figure 11).
Figure 11 Enter Test Request window.
3. Use the handheld barcode scanner to enter one or more Specimen ID. You may
also enter the Specimen ID manually.
4. Select the Assay Name from the drop-down menu for each Specimen ID.
Note: The current Assay Name for the CytoScan™ HD Assay Software Module
v1.2 is "CytoScan HD v1.2".
5. Click Submit when you have made your entries.
The Enter Test Request window closes. The software displays the Active
Worklist window with the newly created Test Request(s) on the window.
Note: After you have submied the Test Request, the procedures for
Registration, Hybridization, Fluidics Station processing and Scanning are the
same as those steps outlined in the Aymetrix™ Molecular Diagnostics Software
User Guide (Pub. No. 08-0261). Refer to this document for further instructions.
Add additional information to a specimen
After you create a Test Request and return to the Active Worklist, certain types of
pertinent information about the specimen can be added. This information can be
added here or in other worklists. This information is not necessary in order to run the
assay.
IMPORTANT! You cannot associate any additional information with Test Requests
after scanning has started. You will not be able to save your edits. If you aempt to
save, the software displays an error message.
CytoScan™ HD Assay Software Module v1.2
Add additional information to a specimen
CytoScan
™
HD Assay Software Module v1.2 User Guide
13
Note: Saving and editing specimen information requires an e-signature upon saving;
however, an e-signature is not required for initial data entry.
1. Click the desired Specimen ID eld.
The Additional Information window appears (Figure 12).
Figure 12 Additional Information window.
2. Add the following information into the Field Values column:
•Sample_ID—Enter manually or from a barcode.
•Family_ID—Enter manually or from a barcode.
•Individual_ID—Enter manually or from a barcode.
•Father_ID—Enter manually or from a barcode.
•Mother_ID—Enter manually or from a barcode.
•Individual Record Name—Enter manually or from a barcode.
•Individual Family Name—Enter manually.
•Individual Given Name—Enter manually.
•Sex—Select: Male - Female - Unknown - Blank Field
•Aection Status—Select: Unknown - Unaected - Aected - Blank Field
•Date of Birth—Enter manually using a dened format. The format MUST be
entered in an ISO 8601 format: 4-digit year rst, then month, then day.
(Example: 2012-11-09 for November 9, 2012). No other date format is
allowed.
•Sample_Type—Enter manually.
CytoScan™ HD Assay Software Module v1.2
Add additional information to a specimen
14
CytoScan
™
HD Assay Software Module v1.2 User Guide
•Sample Size Unit—Select: mL - μL - oz - mg - g - inch - cm - mm - Blank
Field
•Sample Size Value—Enter manually using a oating-point numeric value.
•Method of Collection—Enter manually.
•Collection Date—Enter manually using an ISO 8601 approved date format.
•Collection Time—Enter manually using either a 12 or 24-hour time format.
Twenty-four hour entries are automatically converted to 12-hour. (Example:
13:15 -> 1:15 pm)
•Requestor Family Name—Enter manually.
•Requestor Given Name—Enter manually.
•Requesting Institution—Enter manually.
•Request Date—Enter manually using an ISO 8601 approved date format.
•Additional Info 1-5—Manually enter up to 5 elds.
3. Click Save and Close or Close (to exit without saving).
After clicking Close, the following events may occur:
• If no edits were made, the window will close.
• If you made edits, a pop-up asks if you would you like to save any changes
with Yes, No, and Cancel options.
– Click Yes and the software collects an e-signature and then saves and
closes the window.
– Click No and the software discards changes and closes the window.
– Click Cancel and the software returns to the Additional Information
screen with edits preserved.
The Assay Home window
The Assay Home window (also known as the Assay Information window) provides a
summary of all specimen information, Test Request logs, and pertinent reagent
information for each assay type.
The Assay Home window allows you to perform the following functions:
• Add Reagent Information
• View a Specimen Report
• View a Test Request Log
CytoScan™ HD Assay Software Module v1.2
The Assay Home window
CytoScan
™
HD Assay Software Module v1.2 User Guide
15
In any worklist window, click on the Assay Name in the Assay Name eld.
•The Assay Home window appears (Figure 13). The Reagent Information screen is
the default tab.
Figure 13 Assay Home window.
1. Click the Reagent Information tab (Figure 13), if not already open, to view
current reagent information.
2. Click to select each appropriate Specimen ID from the list (left pane).
3. Use the handheld barcode scanner to scan each reagent kit barcode.
Note: You can also enter the reagent kit information manually by selecting test
requests in the left side of the window, then placing the cursor in to the lot
number and expiration date elds for the appropriate kits and typing in the
correct information. This method should be used for all reagents manufactured
by companies other than Thermo Fisher Scientic.
The scanner parses the Reagent Information and then enters its lot number and
expiration date into the correct elds (for all selected test requests). Using the
barcode scanner eliminates manual entry errors.
4. Click Save.
Add Reagent
Information
CytoScan™ HD Assay Software Module v1.2
The Assay Home window
16
CytoScan
™
HD Assay Software Module v1.2 User Guide
The Assay Home (Assay Information) window contains the following reagent kit
information:
•Reagent kit names:
– Restriction and Ligation Reagents (Part No. 901803)
– Ligation Adaptors and Fragmentation Reagents (Part No. 901749)
– GeneChip™ Hybridization Reagents (Part No. 901804)
– GeneChip™ Stain Reagents (Part No. 901805)
– Wash Buer A (Part No. 901680)
– Wash Buer B (Part No. 901681)
• Reagent Kit Manufacturer information
• Reagent Lot Number
• Reagent Expiration Date
Note: The Reagent Kit Lot Number and Expiration Date are NOT required to run the
assay.
AMDS provides the ability to transfer the Reagent Kit Name, Manufacturer, Part
Number, Lot No. and Expiration Date to the server, along with other test request
information.
Reagents marked with Thermo Fisher Scientic as the manufacturer can be entered
using a barcode scanner. The corresponding lot number and expiration date (for ALL
selected test requests) are automatically entered into their appropriate eld.
Reagent information manufactured by other companies must be entered manually.
Note: You cannot make any edits to a test request after the array associated with that
particular test request has started scanning on the GeneChip™ System 3000Dx v.2.
If you click Close only, the following events may occur:
• If no edits were performed, the window will close.
• If you made edits, a pop-up asks if you would you like to save any changes with
Yes, No, and Cancel options.
– Click Yes and the software collects an e-signature, and then saves and closes
the window.
– Click No and the software discards changes and closes the window.
– Click Cancel and the software returns to the Additional Information window
with edits preserved.
The CytoScan™ HD v1.2 retains the association between a reagent kit lot number and
its expiration date.
Expiration date scenarios
• If you enter a lot number already associated with another test request, AMDS will
auto-populate the Expiration Date eld.
Click Save to save all associated test requests.
• If you enter a date change to modify an AMDS auto-populated Expiration Date
eld, then click Save.
Reagent kit
information
Reagent entry
information
Reagent kit lot
numbers and
expiration dates
CytoScan™ HD Assay Software Module v1.2
The Assay Home window
CytoScan
™
HD Assay Software Module v1.2 User Guide
17
The following message appears: Do you want to save this expiration date for all
other test requests with this lot number?.
– Click Cancel to return to the window without modifying the original
expiration date.
– Click OK to save this expiration date for ALL test requests.
Clicking OK generates the following message: You have changed the
expiration date for <reagent kit name> Lot <lot number> from <old date> to
<new date>.
This change aects <count> Test Requests.
After saving, the new expiration dates are retained. ALL pre-scanned test
requests and lot numbers now include their new expiration dates.
The Specimen Report tab (Figure 14) allows you to view all the Specimen IDs
associated with that assay type (in this case the CytoScan™ HD v1.2).
Figure 14 Specimen Report tab.
The Specimen Report tab includes the following elds:
• Specimen ID
• Individual Record Number
• Individual Family Name
• Individual Given Name
• Sex
•Aection Status
• Sample_ID
• Sample_Type
• Requestor Family Name
• Requestor Given Name
Viewing a
Specimen Report
CytoScan™ HD Assay Software Module v1.2
The Assay Home window
18
CytoScan
™
HD Assay Software Module v1.2 User Guide
Test Request Log tab (Figure 15) allows you to view all the Test Requests associated
with an assay type.
Figure 15 Test Request Log tab.
Each Test Request includes the following log entry information:
• Date (of the log entry)
• Time (user logged in when the log entry was created)
• User (user logged in when the log entry was created)
• Type (of log entry)
• Subsystem (associated with the log entry)
• Short Message (associated with the log entry)
• Long Message (related to the selected short message)
Viewing a Test
Request Log
CytoScan™ HD Assay Software Module v1.2
The Assay Home window
CytoScan
™
HD Assay Software Module v1.2 User Guide
19
Edit additional Test Request information
The Batch Edit feature allows you to enter or edit the identical information over
multiple test requests at the same time.
IMPORTANT! To ensure data accuracy, changes must be saved before scanning. You
cannot add or edit information after scanning is complete.
1. Select your Test Requests from the Active Worklist or any of the worklist
windows.
2. Click the Batch Edit buon.
The Assay Batch Information window appears (Figure 16) listing Specimen IDs
(left pane).
Figure 16 Assay Batch Information window.
3. Use the Field Value column (right pane) to enter or change the following:
• Sex
•Aection Status
• Sample_Type
• Method of Collection
• Collection Date
• Collection Time
• Requestor Family Name
• Requestor Given Name
• Requesting Institution
• Request Date
• Additional Info 1-5 (ve user-dened elds)
CytoScan™ HD Assay Software Module v1.2
Edit additional Test Request information
20
CytoScan
™
HD Assay Software Module v1.2 User Guide
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Thermo Fisher Scientific CytoScan HD Assay Software Module User guide

Brand
Thermo Fisher Scientific
Model
CytoScan HD Assay Software Module
Type
User guide
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