Author Archives: Anthony Rizzo

Click the titles below for a quick video on the subject:

Progeny Basics

Progeny Clinical Overview – An overview of Progeny.

The Learning Center – An overview of the Learning Center.

Navigation Overview – An overview of the navigation with the different modules in Progeny.

Workflows

High-Risk Colorectal Cancer Triage – Colorectal Cancer workflow.

High-Risk Breast Triage – Breast Cancer workflow.

Progeny Clinical For Cardio – Cardiology workflow.

Optimizing Progeny – Optimizing your Progeny usage, edit your default settings.

Profile Settings – Change the user profile settings.

Display All Individuals vs Only Probands – Switch your view to see only probands or all individuals.

Smart Lists – Columns that can be searched and filtered.

Switching IDS Formats – Switching between multiple IDS.

Pedigree Basics

Build a Pedigree – Build a pedigree by clicking to add individuals.

Build a Pedigree with Family Palette – Add individuals to a pedigree using the family palette tool.

Change Gender – Change the gender of an individual in a pedigree.

Change Vital Status – Change the vital status of an individual.

Mark Individual as Adopted – Mark an individual in a pedigree as adopted in or adopted out.

Change Proband – Change the proband of the pedigree to another individual.

Set Icon as Infertile or No Issue – Mark an individual on a pedigree as Infertile or No issue.

Mark Icon as asterisk plus minus – Mark an individual in a pedigree with an asterisk, plus, or minus sign.

Changing Attributes – Designate SAB – Mark the attribute of a specific individual to SAB on a pedigree.

Add Text Inside Icon – Add custom text inside an individual’s icon on a pedigree.

Add a Text-Box to Pedigree – Add your own custom free text box to a pedigree.

Edit Relationship Lines – Edit relationship lines on a pedigree to specify the type of relationship between two individuals.

Delete or Remove an Individual  – Delete or remove an individual from a pedigree.

Add a Patient – Adds a single patient with a pedigree in Progeny.

Select Individuals Meeting Query Criteria – Select and highlight individuals within a pedigree based on specified criteria.

Select and Move Individuals in a Pedigree – Select and move single or multiple individuals to any location within the same pedigree.

Print a Pedigree – Print a pedigree.

Save Pedigree as Image – Save a pedigree as an image to be used elsewhere.

Fit Pedigree to a Page – Makes the pedigree fit on a single page.

Copy a Pedigree – Copies a pedigree to be placed elsewhere.

Pedigree Settings

Pedigree Display Settings – Change the pedigree display settings.

Pedigree Dimensions – Change the pedigree dimensions.

Smartdraw Option Settings – Different settings for Smart Draw

Pedigree Format Settings – Change the different formats for the pedigree.

FHQ/Invites

Invite a new Patient to Complete a Questionnaire  – Invite a new patient to fill out a questionnaire.

Invite Patient to Complete a Questionnaire  – Invite a patient, new or existing, to fill out a questionnaire.

Launch a New Questionnaire from Full View on a Tablet – Invite a patient to fill out a questionnaire from your tablet.

Invite Status – The Invite Status module and the different features.

Move Pedigree Once FHQ is Submitted – Move pedigrees to a specified folder once the FHQ is submitted.

Lock or Unlock Questionnaires – Lock or unlock questionnaires.

Send Reminders – Send a reminder to patients.

Patient Forgot Username-Password – Reset a patients password for their FHQ.

FHQ Administrative Workflows

Edit Email Templates – Edit the Email Templates for the questionnaires.

Find Questionnaire Generic Link – The location of the Generic link for questionnaires.

Edit Questionnaire Datasheet – Customize the datasheet format for the questionnaires.

Edit Questionnaire Module Overview – The Edit Questionnaire module and the different features.

Edit Questionnaire Skip Logic – Edit the Skip Logic configuration for questionnaires.

Risk

Run Risk Models – Run the Bayes-Mendel, Tyrer-Cuzick, Gail, Premm, and Claus risk models on individuals within Progeny.

Competing Mortality – Enable the Competing Mortality function when running the Tyrer-Cuzick risk model.

Genetic Testing Results

Genetic Testing Results – Using the Genetics Testing Results table.

Genetic Test Results for Non-Ambry Lab – Using the Genetics Testing Results table for a lab other than Ambry.

Letter Generation

Progeny Letter Generation demo video – The Letter Generation feature.

Create Custom Letter Template – Create your very own custom letter template, which automatically updates when using this letter for different individuals.

Edit Letter Templates – Editing and updating Progeny letter templates to include other required fields and information.

Add an Image to a Letter – Incorporate a custom image into a letter.

Edit Individual Letter – Customize an individual’s letter to add information needed before saving or exporting as a file. If selecting an existing template, the changes will not be saved to the template.

Generate Letters and Consult Notes – Generate a letter for an individual in your database.

Generate Batched Letters – Generate a letter for multiple individuals in your database.

Spreadsheets

Run a Spreadsheet – The spreadsheet module and all its features.

Enter Data on a Spreadsheet – Entering data on a spreadsheet

The pedigree datasheet is used to enter and store information about pedigrees in your Progeny database. They function the same as Individual Datasheets, except a Pedigree Datasheet can contain only pedigree database fields.

Formatting a Pedigree Datasheet

You use a pedigree datasheet to enter and store data for a pedigree. When you create a new pedigree, a pedigree datasheet is automatically created for the pedigree. All the pedigrees that are assigned to a pedigree data folder can use the same datasheet format, or each pedigree in the folder can use a unique datasheet format. You can format a pedigree datasheet at the time that you add a pedigree to a data folder, or at a later date.
To format a pedigree datasheet

1. Create a pedigree data folder by clicking the New Folder button found in the upper left corner of the Main Progeny window.
2. If all the pedigrees that are assigned to the folder are to use the same pedigree datasheet format, make sure to select the Pedigree Datasheet template option shown in the image below; otherwise, keep this option unchecked. After typing in the new folder name in the Folder Name field and selecting the desired Template Options, click Save.
3. A message opens indicating the new folder was added successfully. Click OK.
4. Create a new pedigree by clicking on the New Ped button and add the pedigree to the desired data folder.
   
5. Once the new pedigree has been created, click Save. A message opens indicating the new pedigree was added successfully, click OK.
6. To edit the datasheet of your newly created pedigree, right-click on the pedigree in the pedigree window pane, and on the context menu that opens, click Open Pedigree Datasheet.Next click Form Design on this blank datasheet and format the datasheet as needed by utilizing Style, Fields, Add Text, Add Tab, and Properties buttons shown in the image below.
7. If the Pedigree Datasheet template option was selected for this folder when it was created, then all the pedigrees that you subsequently add to the folder will use the same datasheet format for entering and storing data; otherwise, you must manually format the datasheet for each pedigree that you add to the folder.
8. Add all the needed pedigrees to the folder. After you have added all of the needed pedigrees to the folder, right-click on any pedigree in the folder and on the context menu that opens, click Open Pedigree Datasheet. If during the creation of this folder, the Pedigree Datasheet template option was selected, then all pedigrees that are currently added to the folder or pedigrees that you continue to add to the folder will use this same datasheet format for entering and storing data; otherwise, you must format a datasheet for each pedigree in the folder.

Progeny Record-Level Database Fields

A database file is a collection of records. A database record is a set of fields. A database field is a single piece of information from a record. The Fields module displays the record-level fields that are contained in a Progeny database. To open this module, click the Fields button on the Navigation bar. There are four different types of record-level fields in Progeny:

1. Individual database fields – Individual database fields are stored at the individual record level. Individual database fields are displayed on the Fields module only if your organization has purchased and installed Progeny Clinical.
2. Pedigree database fields – Pedigree database fields are stored at the pedigree record level. Pedigree database fields are displayed on the Fields module only if your organization has purchased and installed Progeny Clinical.
3. Sample database fields – Sample database fields are stored at the sample record level. Sample database fields are displayed with all products of the Progeny Suite.
4. Marker database fields – Marker database fields are stored at the marker record level. Marker database fields are displayed on the Fields module only if your organization has purchased and installed Progeny Lab.

Database Field Types

When creating database fields in a Progeny database, you must specify the type for the field. The field type determines the type of data that a user can enter into the field (alphanumeric, numeric, date, and so on) or determines how the field functions in the database, for example, an image displays in the field when a user selects an image file for an image field, dropdown fields provide a custom pick list, and date fields provide a date and time picker when end users are doing data entry for those field types. By default, each field type is marked with a unique icon in the application. Not all field types are available for all record levels. The table below lists the field types that are available for each record level field in a Progeny database. It also provides a description of each field and the records for which the field type is applicable.

Text field

A text field is for alphanumeric data (all digits and printable characters). You can enter up to a maximum of 32,000 characters in a text field. A text field is the most generic and least restrictive of all the available field types. Examples of text fields include First Name, Last Name, Address, City, Notes and so on.

Date field

A date field contains a calendar. You can use the calendar to enter a date in a date field, or you can simply enter the date in the field. The first time that you click on a date field, the checkbox for the field is not selected, which means that the field is not editable. To make the field editable, you can do one of the following:

• Press the spacebar on your keyboard.
• Select the checkbox in the date field.
• Use the calendar by clicking on the drop-down arrow in the field, and then scrolling to and clicking on the appropriate date.

A date is stored in the database in a four digit format (M/D/YY) regardless of the date’s display when you use the calendar (MM/DD/YYYY) or if you manually entered a four-digit year. Dates are displayed in a date field based on the regional settings of the client workstation.

Numeric field

You can enter only the digits 0 through 9 in a numeric field. Decimals and negative numbers are allowed; however, no other characters, either alphabetic or special (such as commas) are allowed. If you want to sort data based on numeric values, then you must use a numeric field. You cannot sort based on numeric values if the data is entered in a text field.

Yes/No field

A Yes/No field is a checkbox field that holds a value of either 1 (to indicate Yes) or 0 (to indicate No). Progeny always stores a value in a database for a checkbox field whether or not the field is checked. If the field is checked, Progeny stores a value of “1” in the database. If the field is not checked, Progeny stores a value of “0”.

Dropdown field

A drop-down field displays a pre-defined list of items from which you can make a selection. To open the list, simply click in the field. You can scroll through the list and select one item at a time. The items are mutually exclusive. For example, you might create a dropdown field named “Race” and the available items are African American, American Indian, Asian, and so on. When you are adding/editing a drop-down field, the order in which you enter the items on the Add New Field/Edit Field dialog box is the order in which the items are displayed in the dropdown list. You can use the

arrow keys on your keyboard to move up and down the list of available values for the field. If you are selecting from a lengthy dropdown list on a datasheet, you can enter the first few letters of the name of the item that you want to select and the list is dynamically updated with the items that meet your search criteria.

Image field

An image field can display an image file in one of the following formats—.bmp, .gif, .png, .tiff, and .jpg/.jpeg. When you click on an image field, you are prompted to enter the type of image file that you want to display. You then navigate to the appropriate image file and select it. After you select the image file, the image is displayed in the Image field.

Table

A table allows you to enter multiple values for the same set of data fields. For example, you might add a table called Cancer History that would allow a user to enter cancer diagnosis information.

Lookup Table

A lookup table contains a dropdown list of fields that are related in some way. Each row within the drop-down contains a predefined “lookup” value which refers to a set of data fields that can be updated so as to remain current. For example, you might create a lookup table called Referring Physician that would allow a user to simply select a

physician’s name from the list, thereby associating all of the physician’s current contact information such as the physician’s phone number, the physician’s pager number, institution, and ID. To enter data in a lookup table field, simply click in the field to open the table, and select the appropriate value from the drop-down table.

Computed field

You cannot enter data into a computed field. Instead, a computed field contains an expression that yields a value that is automatically calculated each time the window that contains the field is opened. For example, a computed field for Current Age is defined as the difference in years between the date that is in the Current Date field and the date that is in the Date of Birth field.

Summary field

The purpose of a summary field is to summarize the data of object sub items (individuals or samples) of a database object (a pedigree, individual or sample). A summary field provides summary information for any selected data field and displays a summary value as a maximum value, minimum value, average, sum, or count. Summary functions can be carried out on all fields that are not contained in tables and conditional queries can be employed to populate precise summary values. Pedigree level summary fields summarize individual-level data of the individuals within each pedigree. Individual-level summary fields summarize sample level data of the samples associated with each individual. And sample level summary fields summarize sample level data of the sub-samples and aliquots of each sample. For example, a pedigree level summary field might provide a count for the total number of cancer diagnoses in the pedigree. An individual level might provide a count of the number of available DNA samples. And a sample level summary might provide a total available volume of all non-exhausted aliquots of each sample.

Table Summary field

Similar to a summary field, a table summary field is a computed field that summarizes a given column of a table. For example, you might create a table called Cancer Diagnosis with a field in it called Diagnosis Age and you want to see when the patient was diagnosed for the first time with a specific type of cancer. You can create a table summary field called Minimum age Colorectal or Minimum age Endometrial that displays the age of the patient when they were first diagnosed with these specific types of cancer.

Hyperlink field

A hyperlink field contains a hyperlink to an external file, program, or website. Simply click on the link in the field to open the file, program, or website. For example, a hyperlink field named Email Address could contain an individual’s email address. When you click on the email address in the field, an untitled email addressed to the individual opens in the available email client such as Microsoft Outlook. Hyperlink fields can also be used to load and view documents.

Adding, Editing, and Deleting Database Fields

You can add, edit, and delete record-level database fields only from the Fields module. When adding record-level fields in a Progeny database, you must specify the field type. You can set a default value for the field, add validation rules to the field, and set security for the field. You can create folders for storing and organizing database
fields. You can also delete a database field. When you delete a database field, it deletes not only the field but also, any data that is stored in the field.

To Add a Database Field

1. On the Progeny main window navigation bar, click the Fields module.
   • The Fields module opens.
2. Determine the record type for which you are creating the field (Individual, Pedigree, Sample, or Marker). In the left pane of the window, open the database folder to which you are adding the field.
   • A list of the fields that are already contained in the folder is displayed in the right pane of the Fields module.

3. On the Progeny toolbar, click the New Field button.
   • The New Data Field dialog box opens. The Settings tab is the active tab for the dialog box. All the fields that are contained in the selected folder are displayed alphabetically in the lower pane of the dialog box.

4. In the Field Name field, enter the name for the new field.
5. On the Type of Field drop-down list, select the field type for the new field.
   • The field type determines the type of data that a user can enter into the field and determines how the field functions in the database. Not all field types are available for all record types (see Database Field Types). In addition, if you are adding any of the following field types—Table, Lookup Table, Computed, Summary, or Table Summary field—then you must carry out additional steps to add the database field. For additional information refer to:

6. Optionally, do one or more of the following:
   1. If available, in the Default Value field, enter the default value for the field. A user can always edit this value.
   2. Open the Validations tab and set the validation rules for the field.
   3. Open the Security tab and set the security for the field.
7. Click Add. A message opens indicating that the new field was added successfully.
8. Click OK. The message closes. The Add New Field dialog box remains open in case you want to create another field. The new field is displayed in the lower pane of the dialog box.

To edit a database field

You can edit a database field only if no datasheets are open. If one or more is open, right-click on the tab(s) and click Close Tab. You can then continue with editing the database field.

1. On the navigation bar, click the Fields button. The Fields module opens.
2. In the left pane of the module, select the folder that contains the field that you wish to edit.
   • A list of the fields that are contained in the folder is displayed in the right pane.
3. Double-click the field that you wish to edit, or right-click it and select Edit Field….
   • The Edit Field dialog box opens. The dialog box displays all the current information for the field.
4. Click Change.
   • A message opens asking you if you are sure that you want to change the field. Click Yes. The message and Edit Field dialog box closes. You return to the Fields module with the fields listed in the right pane.

To delete a database field

You can delete a database field only if no datasheets are open. If one or more is open, right-click on the tab(s) and click Close Tab. You can then continue with deleting the database field.

1. On the navigation bar, click the Fields module. The Fields module opens.
2. In the left pane, select the folder that contains the field that you wish to delete. A list of the fields that are contained in the folder is displayed in the right pane of the Fields window.
3. Right-click on the field that you wish to delete and on the context menu that opens, click Delete Field, or CTRL-left click to select multiple fields, then right click and select Delete Field. A message opens asking if you are sure that you want to delete the selected fields and that the operation will delete the fields and the data.
4. Click OK. The message closes and the field (and the data stored in the field) is deleted from the database.

Adding a Table

Before you add a table, you must confirm that the fields that are to be added to the table already exist in the database, otherwise, you must add them. For example, before adding a table called Visit Information, you need to confirm that the fields Visit Date, Visit Type, and Visit Purpose already exists in the database, otherwise, you must add them.

To add a table

1. On the New Field dialog box, enter the name for the field and select Table for the field type.
2. In the Data Folders pane, open the folder that contains the fields that are to be added to the Table. The fields that are contained in the data folder are displayed in the Fields pane at the bottom of the dialog box.
3. Drag each field that you are adding to the table from the Fields pane into the Define the Table Structure pane (upper-right pane) of the dialog box.
4. In the Data Folders pane, select the folder where you would like to save your table.
   • Click Add. A message opens indicating that the new field was added successfully. Click OK. The message closes.
5. Click Close to close the dialog box and return to the Fields module.

Adding a Lookup Table

Before you add a lookup table, you must confirm that the fields that are to be added to the lookup table already exist in the database, otherwise, you must add them to the database. For example, before adding a lookup table called Referring Physician, you need to confirm that the fields Ref Phy Phone and Ref Phy Pager already exist in the database, otherwise, you must add them. After you add a lookup table, you can add the data to the fields in the table from scratch, or you can import data from a text file into the fields.

To add a lookup table

2. On the New Field dialog box, enter the name for the field and select Lookup Table for the field type.
3. In the Data Folders pane, open the folder that contains the fields that are to be added to the lookup table. The fields that are contained in the data folder are displayed in the Fields pane at the bottom of the dialog box.
4. Drag each field that you are adding to the lookup table from the Fields pane into the Define the Lookup Table Structure pane (upper-right pane) of the dialog box.
5. In the Data Folders pane, select the folder where you would like to save your lookup table.
6. Click Add to add the field the database. After you have added the lookup table, you can add data to the fields, either from scratch or by importing a text file that contains the necessary data.

To add data to an existing lookup table

1. On the navigation bar select the Fields module.
2. On the main menu, click Fields > Lookup Table Maintenance. The Lookup Maintenance tab opens. This tab displays every lookup table (by folder) that currently exists in the database.
3. In the left pane of the Lookup Maintenance tab, select the lookup table to which you are adding data.
4. On the Lookup Maintenance toolbar, click the Add Row button to enter data into the lookup table.

To import data into a lookup table

You can import data into a lookup table from a delimited file. The file can be a comma or tab delimited file, or you can specify another delimiter type.

1. On the navigation bar, select the Fields module.
2. On the main menu, click Fields > Lookup Table Maintenance. The Lookup Maintenance tab opens. This tab displays every lookup table (by folder) that currently exists in the selected database.
3. In the left pane of the Lookup Maintenance tab, select the lookup table into which you are importing the data.
4. On the Lookup Maintenance toolbar, click the Import button. The Import Lookup Data dialog box opens. Comma Delimited is selected by default.
5. Select the type of delimited file that you are importing. (If the file is not comma or tab delimited, then you must specify the delimiter that the file uses.)
6. Specify the values for the following:
   1. The number of Matched Columns – Enter the number of columns in the text file that you are importing that match the number of columns in the lookup table. No data in the matched columns is overwritten. Only data from the matched point forward is overwritten. For example, if your lookup table and import text file have three columns, and you indicate “1” for the number of matched columns, then when the data is imported into the lookup table, the data in Column 1 of the lookup table is not overwritten; however, the data in Columns 2 and 3 of the lookup table is overwritten by the data in Columns 2 and 3 of the import file.
   2. Ignore column headings—The first row of the import file is treated as a column heading row during the import process. If you do not want the first row to be treated as a column heading row, then select Ignore column headings.
   3. Allow import to add additional rows—Importing from an import file does not over-write existing rows. It either adds all rows in the import file to the existing lookup table or adds the additional number of rows in the import file above the number of rows in the lookup table.
7. Click Import. The Open File dialog box opens.
8. In the Open File dialog box, browse and select the file that you are importing, and then click Open. A message opens indicating the Import operation was successful.
9. Click OK. The message closes. You return to the Lookup Maintenance tab. The imported information is displayed in the lookup table.
10. Adjust the column widths as you would like them to appear during data entry and select File | Save Format from the Main Menu.

Adding a Computed Field

You cannot enter data into a computed field. Instead, when you add a computed field, you must define an expression for the field that yields a non-editable value that is automatically calculated each time the window that contains the field is opened. For example, a computed field for Current Age is defined as the difference in years between

the dates in the Current Date field and the Date of Birth field. The expression can use functions, constants, and values in other fields for the calculation of the value. For example, a computed field can display the Body Mass Index (BMI) for an individual by calculating BMI based on the values in the Height and Weight fields. You can also specify the parameters for a computed field so that the field displays data only if another field is null (no data has been entered in the field). A computed field can be displayed in spreadsheets, pedigrees, and datasheets without displaying the fields on which its

calculation is based. For example, the Current Age field can be displayed without displaying the Current Date and/or Date of Birth fields.

Computed field expressions

An expression is a group of characters or symbols that represent either a quantity/value or an operation. Table 2-2 lists the expressions that are allowed for a computed field.

You can include other computed fields, summary fields, and/or system fields when you are defining the expression for a computed field. An example of including system fields when you are defining the expression for a computed field is the expression {Global ID} + 1000, which is a computed field that would display the value in the system field {Global ID} plus 1000 in the field. When you are defining the expression for a computed field, all references to database fields must be enclosed in curly brackets {}. For example, the sum (SUM) of the two database fields NUM1 and NUM2 is defined as {NUM1} + {NUM2}. To make data entry easier, you can drag a database field from the Fields pane at the bottom of the Add New Field dialog box into its correct location in the expression. The database field is automatically enclosed in curly brackets when you add it to the expression.

NULL values in computed field expressions

A NULL field is a field in which no data has been entered. Any expression that receives a NULL parameter returns NULL, and this is often not an acceptable result. For example, the following expression returns the sum of three numeric fields:

{Field1} + {Field2} + {Field3}

However, if either Field1 or Field2 and/or Field3 is null, the expression returns NULL.

You can use the IFNULL function to return a value of one of the fields in the expression, or a zero value. For example, if you use the IFNULL function to define the allowed returned value:

IFNULL({Field1},0,{Field1}) + IFNULL({Field2},0,{Field2}) + IFNULL({Field3},0,{Field3})

then the field will return an acceptable result.

To add a computed field

The following example is simply a high-level example of the typical approach used to define a computed field expression.

1. On the New Field dialog box, enter the name for the computed field and select Computed for the field type.
2. In the Computed Field Definition pane, enter the expression for the computed field that results in the difference between the Date of Birth and the Current Date (in years) being displayed in the Current Age field. For example:
   1. Enter the YEARDIF function followed by an open left parenthesis: YEARDIF (
   2. In the Data Folder pane, open the Demographics folder, and drag and drop the Date of Birth field after the open left parenthesis. The expression now looks like this: YEARDIF ({Demographics\Date of Birth}
   3. After the right curly bracket, enter a comma followed by a space and then the system constant CURRENT DATE. Complete the expression with a closing right parenthesis. The complete expression now looks like this: YEARDIF ({Demographics\Date of Birth}, CURRENT DATE)
3. Click Test.
   1. If the definition is acceptable, then a message opens stating that the expression is OK.
   2. If the definition is not acceptable, then a message opens indicating that there is an error in the expression.
   3. Click OK to close the message.
4. If the expression is acceptable, then continue to any other necessary tasks for the field, or click Add to add the field to the database.
5. If the expression has an error, continuing modifying and testing the expression until it is acceptable, then continue to any other necessary tasks for the field, or click Add to add the field to the database.

Adding a Summary Field

A summary field provides summary information for a given column on a per pedigree basis. Summary functions can be carried out on all fields that are not contained in tables. (The fields can be contained in lookup tables). When you add a summary field, you must specify the type of summary value (Average, Count, Maximum, Minimum, or Sum) that is to be returned in the field. Summary fields allow you to summarize data from the database field type directly below it – for example:

• Pedigree-level fields summarize Individual-level data
• Individual-level fields summarize Sample-level data
• Sample-level fields summarize Sample-level data (for sub-samples)

To add a summary field

1. On the New Field dialog box, enter the name for the summary field and select Summary for the field type.

2. In the Define the Summary Field pane, do the following:
   1. Select the Summary type. All summaries are calculated on a per pedigree basis. Available values are:
      • Avg—Calculate the average value of a field.
      • Count—Return the total count of items in a field.
      • Max—Return the maximum value in a field.
      • Min—Return the minimum value in a field.
      • Sum—Return the sum total of a numeric field.
   2. Select the field in the pedigree that you are summarizing.
3. Define a query to filter the data:
   1. Right-click the dark grey area inside the query window and choose Add Row. A field chooser window will open.
   2. Select the desired field and choose OK.
   3. Back in the query window, choose the query function and enter the query value.
   4. Add additional rows to the query window as needed.
4. Continue to any other necessary tasks for the field, or click Add to add the field the database.

Adding a Table Summary Field

A table summary field is a computed field that summarizes the data for a given column in a given table. For example, you might add a table called Visit Record with a field in it called Visit Date and you want to see what the most recent visit date is for a specific patient. You can add a table summary field called Most Recent Visit Date that displays the most recent visit date for a patient who has five distinct visit date entries in the Visit Record table.

To add a table summary field

1. On the New Field dialog box, enter the name for the table summary field and select Table Summary for the field type. Choose the table field you want to summarize and click OK.
2. In the Define Table Summary field pane, select the Summary Function. Available values are:
   • Avg – Calculate the average value of a field.
   • Count – Return the total count of items in a field.
   • Max – Return the maximum value in a field.
   • Min – Return the minimum value in a field.
   • Sum – Return the sum total of a numeric field.
3. Select the field in the table that you are summarizing from the Based on Field drop-down.
   • If you choose the Count function, this dropdown will disappear. Count functions are configured entirely in the Query window.
4. Optionally you can define a query to further filter the data:
   • Drag a field (you can select multiple subfields by using CTRL + click) from the Table SubFields pane to the Query pane then choose a Query Operator type and enter the Query Value.
5. Continue to any other necessary tasks for the field, or click Add to add the field the database.

Copying Fields between Databases

When you are creating a new database or modifying an existing database, you have the option of adding new fields “from scratch” to the database; however, if an existing database already contains the needed fields, you can simply copy these fields. When you copy fields between databases, if any fields have the same name and are of the same or different type, then a prompt opens asking you if you want to overwrite the original field and all of the data in the field. You can select to overwrite the original field and all its data, or you can leave the original field and its data as is.

To copy fields between databases

1. Log in to the database from which you are copying the fields.
2. On the Progeny main window navigation bar, click the Fields button. The Fields module opens.
3. If you are copying all the data fields for all the record types, go to Step 4; otherwise, do one of the following:
   1. To copy only selected fields, in the left pane of the Fields window, open the folder that contains the fields that are to be copied, and then in the right pane of the main window, select the fields (CTRL-click to select multiple fields).
   2. To copy all the fields for a level (pedigree, individual, sample, marker), in the left pane of the Fields window, select the record type. For example, to copy all the Individual data fields, then select Individual Data Fields.
4. On the main menu, click Fields > Save Fields as Text, and then select one of the following:
   1. Save Selected Fields.
   2. Save All < > Data Fields, where < > can be Individual, Pedigree, Sample Data, or Marker Data, for example, Save All Individual Data Fields.
   3. Save All Data Fields.
5. In the Open dialog box, browse to the location where the copied fields are to be saved, enter a name for the file that contains the copied fields, and then click Open. A pop-up window will confirm the fields were successfully saved.
6. Log out of the database from which you are copying the fields, and then log in to the database into which you are copying the fields.
7. On the navigation bar, click the Fields button. The Fields module opens.
8. On the main menu, click Fields > Load Fields from Text. The Open dialog box opens.
9. Browse to and select the text file that you saved, and then click Open.
   • If none of the fields in the text file has the same name as any of the fields in the database into which you are importing the fields, then the Import Fields dialog box opens. The dialog box indicates the number and type of fields that were successfully imported into the database; otherwise, for each matching field, a prompt opens that asks you if you want to overwrite the original field and all its data. Click Yes to overwrite the original field and all its data, or click No to leave the original field and all its data as-is. After you have responded to the prompt for each matching field, the Import Fields dialog box opens.
10. When the import is complete, click Close to close the Import Fields dialog box.

Setting Validations for a Database Field

When you are adding or editing a database field, you have the option of setting validations for the field. Validations guarantee that every data value that is entered into the field is correct and accurate. Three types of field-level validations are available—data entry rules, field validation settings, and dependent validations. If field validation settings and/or dependent validations are violated when you attempt to save data, then validation errors are generated.

To set validations for a database field

1. If the field is already open in the Add New Field dialog box, then go to Step 3; otherwise, on the navigation bar, click the Fields button to open the Fields module.
2. In the left pane of the Fields module, open the folder that contains the field for which you are setting the validations, and then in the right pane of the window, double-click the field to open the field in the Edit Field dialog box.
3. Open the Validations tab on the Add New Field/Edit Field dialog box.
4. Set the validations for the field.
   • Data Entry Rules—these rules are applied only at data entry time. (Data entry in a datasheet, spreadsheet, and the Update Workflow window.)
   • Required Field—you must enter a value in the field before you can save the data for the individual.
   • Must Confirm Data Entry—You are prompted to re-enter the data in the field before you can save the data. If a field has the Must Confirm Data Entry validation assigned to it, then a Confirm New Value dialog box opens for repeating the entry.
   • Field Validation Settings—these settings are applied at the database level and are applied at all times (data entry, imports, and so on).
   • Unique value—you must enter a unique value in the field wherever it is used (pedigree, individual, or sample).
   • Within Specific Range—Indicates the allowed range of values (numbers, dates, and so on) for the field.
   • Specific Mask—Defines how you must enter data into the field maintain consistency and to make your database easier to manage. For example, with the underscore character (_) representing a single character, an input mask of (___) ___-____ would require a phone number like this: (574) 968-0822.
   • Maximum Number of Characters—indicates the maximum number of characters that you can enter into the field.
   • Dependent Validation Settings—these settings are applied at the database level and are applied at all times (data entry, imports, and so on).
   • Use Dependent-Validation – specify the relation that the field must have with another field of the same type.
5. Continue to any other necessary tasks for the field, or click Add to add the field the database.

Data validation errors

If field validation settings and/or dependent validations are violated when you attempt to save data, then the fields with the validation errors are highlighted in red on the affected datasheet and spreadsheet and a Validation Errors dialog box opens. This dialog box lists the validation errors on a field by field basis. You can double-click on a field that is listed in error to go the field in the open datasheet or spreadsheet.

Adding, Editing and Deleting Database Folders

Folders provide a means of organizing your database fields. You can add as many folders and subfolders as needed to support your business needs. After you add a folder, you can set the security for the folder as well as for fields that are in the folder. You can also edit the security for a database folder. The default security settings for a folder are set to Read and Write for All Users. You can add more classes if needed. After you add additional user classes, all the user classes will be displayed. You can delete a folder only if the folder is empty (contains no database fields).

To add a database folder

1. On the navigation bar, click the Fields button to open the Fields module.
2. On the Fields module toolbar, click the New Folder icon. The New Folder dialog box opens.
3. In the Folder Name field, enter the name for the new folder.
4. Select the location for the new folder. For example, to create a folder at the root level for Individual data, select Individual Data Fields. To create a folder that is a subfolder of Individual Demographic data, under Individual Data Fields, select the Demographics folder.
5. Click Save. A message opens indicating that the folder was successfully added.
6. Click OK. The message closes. You return to the Fields module. The newly added folder is displayed in the window.
   • When you create database fields, you typically set the security for the fields on a field by field basis; however, if you want to apply the same security settings for every single field that is contained in the same database folder in a single step, then you can apply the settings at the folder level.

To edit a folder

You can rename a folder, and you can change the security settings for a folder.

• To rename a folder, triple-click on the folder in the Fields window to select it, or right-click the folder and select Edit Folder Security…, and then modify the name as needed.

To delete a database folder

You can delete a selected database folder only if the folder is empty (contains no database fields). If you want to delete a database folder that contains fields, you must first delete all of the fields in the folder.

1. On the navigation bar, click the Fields button to open the Fields module.
2. In the left pane of the Fields window, right-click on the folder that you are deleting, and on the context menu that opens, select Delete Folder.
   • A message opens asking you to confirm the deletion of the folder.
3. Click OK to close the message and delete the folder

Setting Database Field Security for New Fields

1. From the Fields module, click the New Field menu button
2. On the New Data Field dialog box, select the Security
3. Do one or more of the following:
   • Modify the security for All Users or for the different classes of users.
   • Click Add Class to open the New User Class dialog box to create a new user class, and then set the security for the class.
     

Setting Database Field Security for Existing Fields

Using database field security we can specify which users will have access to certain fields. It gives us the flexibility to differentiate between the users that can view and enter data into fields for which they have been given permission.

1. On the navigation bar, select the Fields
2. In the left pane open the folder that contains the field for which you are setting the security, right-click on the field, then click Field Security Level on the context menu that opens up.
3. The Field Security dialog box opens.
4. Do one or more of the following:
   • Modify the security for All Users or for the different classes of users.
   • Click Add Class to open the New User Class dialog box to create a new user class, and then set the security for the class.

To set database Field folder security

1. On the navigation bar, select the Fields module button to open the Fields
2. On the Fields window toolbar, right-click on the folder for which you are setting the security, and on the context menu that opens, click Edit Folder Security.
3. The Modify Data Folder Settings dialog box opens. The name of the selected database folder is displayed in the Folder Name field.
4. Do one or more of the following:
   • Modify the security settings for All Users or for the different classes of users.
     • Read D Folder?—Open and view the contents of the database folder.
     • Add Field?—Add database fields to the folder.
     • Del Field?—Delete database fields from the folder.
     • Modify Field?—Modify database fields in the folder.
   • Click Add Class… to open the New User Class dialog box to create a new user class, and then set the folder security for the new class being added.
     
   • If you have assigned field-level security to one more field in the folder, and you want to override the security settings for these fields based on the security settings at the folder level, click Override Field Level Security, and then set the appropriate field-level security for the different classes of users.
     • Field Read? – View the data in the field.
     • Field Write? – Write data to the field.
5. Click Save once the proper security settings have been assigned in the Modify Data Folder Settings window, then a message opens indicating the settings for the folder were successfully changed. Click OK to close the message and return to the Fields window.

System Fields

Individual Fields

•  Adopted
  • 0 = not adopted
  • 1 = adopted in
  • 2 = adopted out
• Deceased Status – the vital status of the individual
  • 0 = living
  • 1 = deceased
• Degree of Relation – degree of relation to the proband
  • 0 = infinity
  • 1 = 1st degree
  • 2 = 2nd degree
  • [3-x] = 3 to xth degree, depending on the number
• Degree of Relation2
  • 0 = unknown
  • 1 = proband
  • 2 = sibling
  • 3 = child
  • 4 = parent
  • 5 = paternal grandparent
  • 6 = paternal uncle/aunt
  • 7 = maternal grandparent
  • 8 = maternal uncle/aunt
  • 13 = nephew/niece
  • 14 = spouse
  • 15 = brother/sister in law
  • 16 = identical twin
• Father ID – the UPN of the father
• Folder – the folder that the individual is saved in
• Folder Path – the full path of the folder that the individual is saved in
• G:P – generation number:person number
• Gender
  • M = male
  • F = female
  • U = unknown
• Gender Unknown
  • 0 = gender is known
  • 1 = gender is unknown
• Genotyped – Genotype data; whether genotypes have been imported for this individual (LAB feature)
  • 0 = no genotype data for individual
  • 1 = yes
• Global ID – the unique number given by Progeny to each individual in the database
• Individual Created By – the user who created the individual
• Individual Created Date – the date the individual was created
• Individual Last Modified –  the date the individual was last modified
• Individual Modified By – the user who last modified the individual
• Individual Name – the default individual name; pedigreename_UPN
• Invite Count – counts the number of invitations that were sent to the individual
• Marked By – the Marked by symbol of the individual
  • 0 = none
  • 1 = Plus (+)
  • 2 = Minus (-)
  • 3 = Asterisk (*)
• Maternal-Paternal – maternal/paternal relation
  • Both
  • Pat = Paternal
  • Mat = Maternal
• Mother ID – the UPN of the mother
• No Issues – no children by choice vs because of infertility
  • 0 = no data
  • 2 = no issue
  • 3 = infertile
• Pedigree name – the name of the pedigree
• Primary Sample – the name of the primary sample for the individual
• Proband status
  • 0 = not proband
  • 1 = proband
• SAB – Spontaneous Abortion
  • 0 = no spontaneous abortion
  • 1 = spontaneous abortion
• Sample Count – the number of samples that are attached to the individual
• Twin Relationship
  • Dizygotic
  • Monozygotic
  • Unknown
• Twin status – value for identifying twins/multiples
  • 0 = not twin/multiple
  • 1 = 1st set
  • 2 = 2nd set
  • [3-x] = 3rd or xth set
• UPN – unique person number within a pedigree

Pedigree Fields

• Audit Status – Whether or not this pedigree and its individuals are being audited
  • 0 – audit if off
  • 1 – audit is on
• FHQ Completed Date – the date the questionnaire was completed
• FHQ Last Invite Created By – the user who last sent a questionnaire to the proband
• FHQ Last Invite Sent Date – the date the last questionnaire was sent
• FHQ Num Invites Sent –  the number of invites that have been sent
• FHQ Status – the status of the questionnaire
  • In Progress
  • Complete
• Folder – the family that the pedigree is located in
• Folder Path – the full path for the location of the pedigree
• Last Modified – the date the pedigree was last modified
• Modified By – the user who last modified the pedigree
• Pedigree Created By – the user who created the pedigree
• Pedigree Created Date – the date the pedigree was created
• Pedigree name – the name of the pedigree

Sample Fields

• Barcode
• Container Barcode
• Container Name – the name of the container that the sample is located
• Container Path –  the full location of where the sample is located
• Container Type
• Order Number
• Parent Sample Name
• Position – the well position of the sample
• Sample Audit Status
  • On
  • Off
• Sample Created By – the user who created the sample
• Sample Created Date – the date the sample was created
• Sample Folder – the folder where the sample is located
• Sample Folder Path – the full folder path where the sample is located
• Sample Last Modified –  the date the sample was last modified
• Sampled Modified By – the user who last modified the sample
• Sample Name – the name of the sample
• Volume
• Workflow – the name of the workflow that the sample is located
• Workflow Stage – the specific stage of a workflow that the sample is located