PathIQ ImmunoQuery 2.8 User s Guide

Transcription

1 PathIQ ImmunoQuery 2.8 User s Guide Welcome to the PathIQ ImmunoQuery 2.8 User s Guide, designed to assist you in maximizing use of this important decision-support tool. CTRL-Click on subject headings in the following Table of Contents to jump to the subject you are interested in. LOGIN PAGE Login Forgot User Name Forgot Password Free Test Drive Purchase or Renew ImmunoQuery or CustomSync HOME PAGE SMART SEARCH BUILDING A DIAGNOSIS PANEL Single Diagnosis Panel Multiple Diagnoses Panel Set Sensitivity Set Minimum Refs Comprehensive Panel Suggested Panel ASK AN EXPERT SAVE CASE BUILD ANTIBODY PANEL Single Antibody Panel Multi-Antibody Panel Printing Your Results ANALYZE RESULTS PAGE LEARN ABOUT Learn About a Diagnosis Group PathIQ ImmunoQuery User s Guide 2.8 v

2 Learn About an Antibody USING CUSTOMSYNC TO FILTER PANELS Comprehensive Panels without Filtering Only Lab-Available Antibody Filter Lab Antibody Names Filter Ordering Antibodies PURCHASING/RENEWAL CAP Members BUTTONS, TABS, BOXES, ICONS AND LINKS PathIQ ImmunoQuery User s Guide 2.8 v

3 LOGIN PAGE This is the login page. From this page you can: login to ImmunoQuery sign up for a free test drive purchase or renew a subscription to ImmunoQuery purchase a subscription to CustomSync PathIQ ImmunoQuery User s Guide 2.8 v

4 Login If you already have an account, enter your User Name and Password and click the Login button. You must have a user account to get past the Login Page of PathIQ ImmunoQuery. Forgot User Name If you have an account but can t remember your Username, click Forgot User Name and fill in the following form. We ll your password to you quickly. PathIQ ImmunoQuery User s Guide 2.8 v

5 Forgot Password If you can t remember your password, click Forgot Password and complete the following form. We ll you a new password quickly. When you receive your new password, please change it, by going to the Change Password prompt on the Home Page. Free Test Drive If you are interested in reviewing ImmunoQuery and this is your first visit, click on the Free Test Drive red go button to create a two week subscription. You must have a user account in order to use PathIQ ImmunoQuery. Purchase or Renew ImmunoQuery or CustomSync If you want to renew your PathIQ ImmunoQuery subscription, click the Purchase Now/Renew button and enter your login credentials. If you are a CAP member and want a discount for PathIQ ImmunoQuery, click the Sign Up Now button under the CAP logo and follow the on-screen prompts. If you are already an ImmunoQuery user and want to upgrade to CustomSync, click the red Upgrade button and follow the on-screen prompts. PathIQ ImmunoQuery User s Guide 2.8 v

6 HOME PAGE The Home page is where you begin your queries. The design of PathIQ ImmunoQuery helps pathologists: find antibodies that identify a diagnosis find diagnoses that match staining results analyze results of previous immunohistochemical investigations learn about diagnoses and antibodies by accessing the database information. In the left column are the three main search function tabs: Build Dx Panel Build Ab Panel Analyze Results PathIQ ImmunoQuery User s Guide 2.8 v

7 In the center column are the sections for: saved results of previous database queries that you can easily link to for analyzing your results when the staining is done Learn About text fields for retrieving information about diagnoses and antibodies included in the system SMART SEARCH To start a smart search: 1. Select the Build DX Panel, Build AB Panel or Analyze Results tab. 2. Enter a full or partial diagnosis keyword or antibody name into the relevant search box. 3. Try entering only three letters if you are unsure of the spelling or correct name. In this example, we are searching for a diagnosis that contains the letters adeno. PathIQ ImmunoQuery User s Guide 2.8 v

8 Click View All to see all diagnoses or antibodies in ImmunoQuery. Click the green plus sign to add a correct name to the relevant query Selected box. Click the red minus sign to remove a name from the Selected box. Mouse over the blue information icon to display associated discrete diagnosis names or clone names. PathIQ ImmunoQuery User s Guide 2.8 v

9 BUILDING A DIAGNOSIS PANEL Single Diagnosis Panel A single diagnosis panel lets you see the success of antibodies in identifying a diagnosis, as reported in the current literature. To run a single Diagnosis panel: 1. Type in a diagnosis name in the search box to display corresponding matches (in this example, Adenocarcinoma, NOS). 2. Click on either the green plus sign or the diagnosis name to select a diagnosis. 3. You can modify the search sensitivity or minimum reference settings by clicking the radio buttons below the Selected Dxs box (or on the next screen). 4. Click the Build Panel button. The single diagnosis panel displays a comprehensive list of: antibodies (sorted by percent positive) the number of cases included in the references the confidence interval (CI) range the number of references. From this panel you can: display bibliographic information of associated references by clicking the # of Refs hyperlink. open an associated Learn About page by clicking on either the diagnostic group name or antibody name modify the search sensitivity or minimum reference settings by clicking the radio buttons above the right column PathIQ ImmunoQuery User s Guide 2.8 v

10 sort results alphabetically by clicking the Antibody hyperlink at the top of the column. sort results by percent positivity by clicking on the Positive hyperlink at the top of the column. (By default, the display shows search results sorted by decreasing percent positive.) rebuild the panel by setting the sensitivity or minimum number of references. Click the Return button to return to the home page. Multiple Diagnoses Panel A multiple diagnoses panel helps you determine which antibodies to use to distinguish between diagnoses. You can select up to three diagnoses for comparison. 1. Begin typing a diagnosis (for example, mesothelioma) in the diagnosis smart search field. 2. Scroll down until you find the diagnosis group name Mesothelia, All. 3. Click the diagnosis name to have it added under Selected Dxs. 4. Go through the same steps with adenoca. (The NOS diagnosis group includes the broadest range of antibodies for adenocarcinoma and helps distinguish most adenocarcinomas from mesothelioma.) 5. Use the Set Sensitivity radio buttons to define how sensitive the staining search criteria should be, on a scale of 1 to Use the Set Minimum Refs radio buttons to specify the number of references you want included in the analysis. 7. When you have selected the diagnosis groups, sensitivity, and minimum references, click the Build Panel button to bring up the expanded Comprehensive Panel and the collapsed Suggested Panels. You expand or collapse each panel by clicking the plus and minus signs. PathIQ ImmunoQuery User s Guide 2.8 v

11 Set Sensitivity The Set Sensitivity radio buttons let you define how sensitive the staining search criteria should be, on a scale of 1 to 3. The buttons work as shown: Set Minimum Refs The Set Minimum Refs radio buttons let you specify the number of references you want included in the analysis. Some antibodies are associated with a particular diagnosis in only one reference, while others have many associated references. Increasing the number of minimum references narrows the list of antibodies, but increases the confidence for your search. Changing the minimum references includes or excludes suggested antibodies based on the number of references. Using the default setting of >1 provides moderate confidence. If you build a Dx panel and see no antibody results, check to see which Set Minimum Refs radio button is clicked. If only one reference includes the diagnosis you are researching, then the default setting of >1 will not be helpful and you should click the All radio button PathIQ ImmunoQuery User s Guide 2.8 v

12 Comprehensive Panel The Comprehensive Panel is an inclusive list of antibodies that may be useful in differentiating the diagnoses you selected in this example Mesothelioma, All and Adenocarcinoma, NOS. By default, the Build Panel results display as a collapsed Suggested Panel and an expanded Comprehensive Panel. Clicking the plus or minus sign next to each panel will expand or collapse the associated panel. The selected diagnosis groups are in the columns and the antibodies are in the rows. The display shows: the % positive for each antibody the number of cases included in references the images associated with that antibody a visual marker that helps you discern whether the antibody differentiates one diagnosis group from the other. From this panel you can: Click any antibody name to learn about the antibody. Click a diagnosis name to learn about the diagnosis. Mouse over the blue information icon to display associated discrete diagnosis names or clone names. PathIQ ImmunoQuery User s Guide 2.8 v

13 Click on the View References hyperlink to access the references used for data on the antibody. The hyperlink shows up to the right of an antibody as you mouse over its name. Use your Internet browser s print command to print the Comprehensive Panel search results. Save the panel for future analysis by clicking Suggested Panel Applying further analysis to the data shown in the Comprehensive Panel, ImmunoQuery produces a brief Suggested Panel listing the antibodies most likely to provide the strongest differentiation between the diagnosis groups. The Suggested Panel displays: diagnosis groups in columns antibodies in rows color-coded reactivity icons that show an antibody s reactivity, located at each diagnosis group-antibody intersection In this example, MOC-31 and CK5 are the best differentiators for these diagnoses. PathIQ ImmunoQuery User s Guide 2.8 v

14 From this panel you can: Click Exclude this Antibody if you don t want to include the antibody in the analysis. For example, if you exclude MOC-31, ImmunoQuery recalibrates and provides another best differentiating antibody, in this example MUC4. Add an antibody by mousing down the list of antibodies on the Comprehensive Panel and clicking where this icon appears. You might want to do this for an antibody that you use in your lab. Set the staining sensitivity or minimum references to different values to recalculate the Suggested Panel. PathIQ ImmunoQuery User s Guide 2.8 v

15 Click on View References for any antibody to see which references support the selected antibody. Click the associated article s reference hyperlink to access its PubMed information. Click on the antibody name to learn about the antibody. Click on the diagnosis name to learn about the diagnosis. PathIQ ImmunoQuery User s Guide 2.8 v

16 Click on Panel History to track changes made to the Suggested panels and restore the panel to its initial state. Click the Ask An Expert box to get additional information on your query. ASK AN EXPERT Amirsys asked 13 acclaimed experts in their respective fields to suggest which antibodies they would use to confirm a diagnosis. The result is the Ask An Expert feature. These customized panels offer at least 500 distinct two diagnoses and three diagnoses queries. Compare our meta-analysis with what a world-renowned expert suggests and improve patient care through increased diagnostic effectiveness. To access an expert panel, click the Ask An Expert check box in both a one diagnosis and 2+ diagnoses searches. In general, a combination of empirical and evidentiary information weighs in when determining which antibodies will be used to diagnosis a specimen. The Ask An Expert feature provides the pathologist with the first and only source for simultaneously viewing empirical and evidentiary support. PathIQ ImmunoQuery User s Guide 2.8 v

17 Plus (+) and minus (-) signs signify the reactivity that the expert attributes to a particular antibody and diagnosis combination. This information is juxtaposed with data from the meta-analysis for comparative purposes. To return to the Comprehensive Panel, click Ask An Expert again to remove the check mark. SAVE CASE After you ve built a panel, you can save it. If you built only a Comprehensive Panel, you can save it to view later, for example if you haven t the time immediately to finish studying it. If you have also opened a Suggested Panel, you can save it to view later or until any immunohistochemical tests you ordered are ready for analysis. You can save a suggested panel containing up to five antibodies for further analysis. If you don t want to save a panel, click the Return button to go back to the Home screen. 1. Save your panel by clicking the Save Panel for Analysis button. 2. Complete the Save Case popup by entering a HIPPA-compliant description. PathIQ ImmunoQuery User s Guide 2.8 v

18 3. Click the Save button. You will return to the home screen where the saved panel is listed under Open Cases. PathIQ ImmunoQuery User s Guide 2.8 v

19 To compare the saved panel with your staining results: 1. Click the check box next to the case you saved. 2. Click Analyze Results to advance to the Analyze Results page. In the following example, we have added three antibodies to the original list. 3. Compare your results by clicking one of the My Staining Results radio buttons over each antibody column. Depending on the combination of results you enter, ImmunoQuery calculates the strength of the possibility that one of the diagnoses is the correct one. 4. To view diagnosis details, click view diagnosis details under a diagnosis. You will see a table that has all the information that the system contains on the diagnosis group. 5. Click the Return button to return to the Home page. The system returns you to the Analyze Results tab. All the antibodies and diagnoses in the saved Suggested Panel are listed under Selected Abs and Selected Dxs. You can add or subtract diagnoses and antibodies to build another Analyze Results panel. PathIQ ImmunoQuery User s Guide 2.8 v

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21 BUILD ANTIBODY PANEL Building an antibody panel in PathIQ ImmunoQuery provides a comparison of up to three antibodies and suggests possible differential diagnoses based on the antibodies reactivities You use the same smart search techniques as in the diagnosis panel. To select an antibody: 1. Begin typing the antibody name, or clone name or view the entire list by clicking View All 2. Find the antibody of interest in the list. 3. Click either the green plus sign, or the antibody name to add it to Selected Abs. 4. Click the Build Panel button. PathIQ ImmunoQuery User s Guide 2.8 v

22 Single Antibody Panel You can perform a one-antibody panel search for a comprehensive list of discrete diagnoses. 1. Select an Antibody from the drop down menu. 2. Click the Build Panel button to advance to the single antibody search page. This panel shows: A comprehensive list of discrete diagnoses The corresponding percent positive when stained with the antibody The number of cases found in the references used The confidence interval (CI) range The number of references used in the meta-analysis PathIQ ImmunoQuery User s Guide 2.8 v

23 From this panel you can: Click the # of Refs hyperlink to view the associated references for the discrete diagnosis. Click the antibody name to access its Learn About page. Sort by positivity by clicking the top of the Positive column (default sorting is highest to lowest percent). Sort alphabetically by clicking the top of the Discrete Diagnosis panel. Click the Return button to return to the home page. PathIQ ImmunoQuery User s Guide 2.8 v

24 Multi-Antibody Panel You can build an antibody panel that shows the reactivity of up to three antibodies to all diagnoses mentioned in the literature used in the meta-analysis. 1. Begin typing the antibody name, or clone name or view the entire list by clicking View All. 2. Find up to three antibodies of interest in the list. 3. Click either the green plus sign, or the antibody name, of an antibody to add it to Selected Abs. To remove an antibody from Selected Abs, click the red minus sign. PathIQ ImmunoQuery User s Guide 2.8 v

25 4. Click the Build Panel button to bring up the Ab Panel page. This panel contains: A number of rows determined by the permutations of the reactivity icons. Rows with (0) after Discrete Diagnosis indicating no diagnosis with the shown reactivity combination Rows preceded by an arrow icon indicating they can expand to show a table with the diagnoses that correspond to the shown reactivity combination. The number in parentheses following Discrete Diagnosis indicates the number of diagnoses included in the expanded table. Expand All and Collapse All arrows in the upper right corner that expand or collapse all the tables. Return button which takes you back to the home page. Printing Your Results Use your Internet browsers print command to print all of the tables in the expanded view. PathIQ ImmunoQuery User s Guide 2.8 v

26 ANALYZE RESULTS PAGE The analyze results tab lets you compare up to 5 antibodies with suspected diagnoses groups. There are two ways to get to the Analyze Results page. Enter and select Antibodies and Diagnosis Groups in their respective boxes. Select a case to analyze from one you saved earlier. Let s start from an empty Analyze Results page. 1. Select the antibodies you want to see, in this case we ll use Moc-31, Podoplanin and Calretinin. 2. Select the diagnoses you are considering, such as mesothelia and adenocarcinoma. PathIQ ImmunoQuery User s Guide 2.8 v

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28 3. Click the Analyze Results button. 4. Below the My Staining Results header, select the radio buttons consistent with your laboratory s immunohistochemical results for each antibody. In this example, MOC-31 is positive, Podoplanin is negative and Calretinin is inconclusive. This page shows: rows showing the diagnoses you selected columns showing the antibodies you selected the reactivity of each antibody with each diagnosis PathIQ ImmunoQuery User s Guide 2.8 v

29 summary rows highlighting all statistical information available for the specific diagnosis group and antibody relationship star-ranking for each diagnosis group suggesting the correct diagnosis group based on the comparison between your reported results and the meta-data analysis (If the results are inconclusive, build another panel with additional or different antibodies.) specific details of a diagnoses that belong to a group (click view diagnosis details to expand the row) references to antibodies that pertain to a specific diagnosis (click the red numerical Ref to open the References pop-up window) In this screen shot, the green circles indicate that the reference covers the antibody and the diagnosis. The first reference covers only MOC-31 and Mesothelioma Nos. The second and third references discuss the antibody and both diagnoses. PathIQ ImmunoQuery User s Guide 2.8 v

30 LEARN ABOUT ImmunoQuery provides several ways to learn about diagnoses and antibodies and their relationships. Learn About a Diagnosis Group To learn more about a diagnosis group: 1. Enter a diagnosis name into the Learn About a Diagnosis Group area in the center column on the HOME page. Smart search operates the same here as in other areas of the product. PathIQ ImmunoQuery User s Guide 2.8 v

31 2. Select the diagnosis you want to learn about from the drop down list. This screen shows: You can: a list of all the discrete diagnoses antibody staining patterns (when available) a comprehensive list of antibodies a list of all the referenced articles for this diagnosis group. sort the antibodies by alphabetical order by clicking on ABC sort the antibodies by percent positive by clicking on Positivity learn about an antibody by clicking on its name jump to the abstract of an article on PubMed by clicking on the title of the article PathIQ ImmunoQuery User s Guide 2.8 v

32 see pitfalls associated with an image To see pitfalls: Pitfall 1. Click on the image that is has Pitfall listed next to it. In the above example, this is the image for RCC. PathIQ ImmunoQuery User s Guide 2.8 v

33 Pitfall tab 2. Click the Pitfall tab to see the areas that are considered pitfalls and an explanation of them. PathIQ ImmunoQuery User s Guide 2.8 v

34 Pitfall areas Pitfall explanation 3. Click Close to return to the LEARN DX screen. 4. Click HOME to return to the HOME page. You also can learn about a diagnosis by clicking on its name whenever the name is underlined. Learn About an Antibody To learn about an antibody: 1. Enter an antibody name into the Learn About an Antibody area in the center column on the HOME page. Smart search operates the same here as in other areas of the product. PathIQ ImmunoQuery User s Guide 2.8 v

35 2. Click on the name of the antibody in the drop down list. PathIQ ImmunoQuery User s Guide 2.8 v

36 This screen shows you: You can: an image of the tissue stained with the antibody (if available) a list of clones the name of the company that developed the antibody a list of all the referenced articles for this antibody a list of diagnosis groups that can be identified using the antibody. learn about a diagnosis by clicking on its name jump to the abstract of an article on PubMed by clicking on the title of the article return to the HOME page by clicking the HOME tab PathIQ ImmunoQuery User s Guide 2.8 v

37 USING CUSTOMSYNC TO FILTER PANELS You can customize ImmunoQuery panels by upgrading your ImmunoQuery license to ImmunoQuery/CustomSync. When you purchase a CustomSync upgrade: 1. Amirsys sends you a list of the antibodies the standard program currently uses. 2. You enter the names of the antibodies your lab uses next to the corresponding ImmunoQuery antibody name. 3. You return the list to Amirsys Customer Support. 4. Our pathology experts check your entries to make sure they are acceptable replacements. If we have questions, we contact you. 5. We enter your antibody list into our database and give you access to ImmunoQuery customized for your lab. CustomSync gives you three options for viewing Dx panels: no filtering (classic ImmunoQuery) lab-available antibody filter lab antibody names filter. Comprehensive Panels without Filtering No filtering is classic ImmunoQuery, with the Comprehensive and Suggested Panels using meta-analysis (no boxes beside the word Filter are checked). In addition: an icon to the left of an antibody name ( ) in the results panel means the antibody is not available in your lab. no icon next to an antibody name identifies the antibody as available in your lab. The Suggested Panel and Ask An Expert panel operate the same way. PathIQ ImmunoQuery User s Guide 2.8 v

38 No boxes checked Antibody available No antibody available Only Lab-Available Antibody Filter To display a panel that shows only antibodies available in-house, click the Available in Lab Inventory check box. Unavailable antibodies do not display. This filter also works with the Suggested Panel and Ask An Expert Panel. PathIQ ImmunoQuery User s Guide 2.8 v

39 Lab Antibody Names Filter When you check the Show Lab AB Names, your laboratory-specific names replace those used by vanilla ImmunoQuery. Notice that in the following example, D2-40 replaces Podoplanin. This filter also works with the Suggested Panel and Ask An Expert panel. PathIQ ImmunoQuery User s Guide 2.8 v

40 Ordering Antibodies Antibody ordering allows you to select only antibodies available in your lab to be used in your testing. This helps keep costs down by reducing the number of send-outs. To order an antibody in the Suggested Panel click on Add to Order. PathIQ ImmunoQuery User s Guide 2.8 v

41 Two things happen: A green checkmark appears next to the antibody name. The antibody is added to your antibody cart. Place your cursor over the cart to show the list of ordered antibodies. Remove antibodies from your order by: selecting Exclude this Antibody under the antibody name in the Suggested Panel clicking on the red minus sign next to the antibody name in the cart clicking remove all. PathIQ ImmunoQuery User s Guide 2.8 v

42 To order an antibody in the Comprehensive Panel: Click on the Add to Order icon that appears when you mouse over an in-house antibody name. Click on the icon again to remove the antibody from the Abs in Order list. All antibodies in the cart are listed with your lab's preferred name. To print the list, click Print Order. ImmunoQuery generates a form listing the antibodies in your order that you can print out, fill in the relevant information and attach to your requisition and specimen bound for the lab. PathIQ ImmunoQuery User s Guide 2.8 v

43 PURCHASING/RENEWAL To purchase or renew a license for PathIQ ImmunoQuery, click the Purchase/Renew hyperlink in the lower left-hand portion of the login screen. CAP Members CAP members receive special pricing for PathIQ ImmunoQuery. Please click on the CAP Discount button located on the PathIQ ImmunoQuery login page to ensure you receive this discounted price. PathIQ ImmunoQuery User s Guide 2.8 v

44 BUTTONS, TABS, BOXES, ICONS AND LINKS Or Return Prepares a form that includes patient information and immunostains to be used. Can be printed using your web browser print command and attached to sample for delivery to lab. Returns you to the Home Page. If you are in a window with no return symbol, use your browser s back button to go back one screen. Takes you to a panel that helps you determine the strength of a diagnosis based on your staining results compared to the metaanalysis of ImmunoQuery. Displays a single Dx panel which shows a comprehensive list of antibodies and their staining results for that DX. Displays a multiple Dx panel showing the usefulness of antibodies in differentiating between the Dxs. Displays a single Ab panel that identifies the Dxs the antibody is effective in identifying. Displays a panel of up to three Abs, all the Dxs they have been tested against and the strength of the results. This button is inactive when gray. Pops up a window that lets you begin the process of renewing an ImmunoQuery subscription or purchasing a new subscription. Pops up a window that lets you select the kind of ImmunoQuery subscription you want to order. Sends information you have entered to ImmunoQuery for action by our support staff. Starts the process of implementing CustomSync, a product that uses the names of your lab s antibodies in the ImmunoQuery panels. Takes you to the ImmunoQuery Home Page after you have entered your User Name and Password Begins the process of signing up for a free two-week test drive of ImmunoQuery. Takes you to this guide. Other help symbols in the product will pop up an form for contacting our Support staff. Pops up a form that lets you enter comments on ImmunoQuery. Pops up a form that lets you change your password. You should change your password from the one ed to you by Support. Logs you off of the ImmunoQuery product. In a multi-user subscription, logging off frees up your seat for another user. If you do not log off, but only close your browser, the seat will not be available for 60 minutes. PathIQ ImmunoQuery User s Guide 2.8 v

45 One of the tabs at the top of the window that identifies your location within the program. This tab turns gray when you are not on the HOME page. Four of the tabs at the top of the window that identify your location within the program. Other tables are LEARN DX and LEARN AB Expands the panel it is next to. Collapses the panel it is next to. Clicking on any check box causes the described action to occur. To return to the original screen, uncheck the box. For example, if you click the Ask An Expert check box, you will see only Ask An Expert Panels, until you uncheck it. Provides an information box about the item it is next to. Expands or collapses information about the item it is next to. When this icon appears next to an antibody as you mouse over the name, you can add the antibody to the Suggested Panel. If you have subscribed to CustomSync, this icon does not appear next to antibodies that are not in your lab. When this icon appears next to an antibody as you mouse over the name, you can open the list of references used to supply information about the antibody. When this icon appears next to an antibody as you mouse over the name, you can put this antibody in the Abs in Order list. This icon appears only in CustomSync. This icon indicates that the antibody it is next to is not available in your laboratory. This icon appears only in CustomSync. This icon, which only appears in Ask An Expert panels, indicates the presence of information about the stain it s pointing to. Mouse over the icon to see the information. This icon indicates that an antibody can be used to differentiate one diagnosis from another. This icon indicates that an antibody does not differentiate one diagnosis from another. This icon indicates that an antibody is neutral in its ability to differentiate among diagnoses. PathIQ ImmunoQuery User s Guide 2.8 v