From Tissue/Biospecimen Banking and Technology Tools

Chapter 7: Introduction to Clinical Annotations

The Clinical Annotations (CA) module allows you to collect clinical and pathological information of the participant, accession, and biospecimens. It is divided into:

• Pathology Information

• Clinical and Health Information

Pathology Information

This section outlines CAP-based (College of American Pathologists) pathology annotations. It involves collection of information on a broad spectrum of tumors. It captures information about various features associated with tumors such as TNM staging (tumor, node, and metastasis stage determination), histologic grading, histo-pathological examination, positive or negative margins, and other fundamental pathology details. The module consists of nine organ systems and data for these organ systems is independently captured. The nine organ systems are:

1. Prostate

2. Pancreas

3. Kidney

4. Lung

5. Blood/Bone Marrow (labeled as Heme in the UI)

6. CNS

7. Colon and Rectum

8. Breast

9. Skin (labeled as Melanoma in the UI)

To accommodate pathology data for tumors that do not fall under the nine organ systems, there is a generic annotation which can be used to capture information specific to that organ system. Clinical and Health Information

This section records clinical information about the participant‘s:

• Medical history

• Follow-up

• Medications administered (such as chemotherapy, radiation therapy, and so on)

• Social history (smoking and alcohol history)

• Environmental exposure history (for example: exposure to asbestos)

• Physical examinations

• Laboratory test details

• Family health history

The clinical annotations available in caTissue Suite can be found under the hook entities as outlined in the following table:

Table 23: Clinical Annotations under Various Hook Entities

Clinical Annotations Workflow

The clinical annotation workflow has three types of activities: assign annotations to protocols, enter annotations data, and query on annotation data. The following steps describe a typical clinical annotations workflow.

1. Administrator associates annotations to one or more than one relevant collection protocols.

2. Administrator, Supervisor, or Technician enters clinical data or pathological data for the annotations.

3. Administrator, Supervisor, Technician, or Scientist queries on the data entered for the specific annotations under specific collection protocols.

Assigning Annotations to a Collection Protocol

Various clinical annotations capture data that is specific to a particular collection protocol. For example: annotations related to prostrate cancer can be associated with only prostrate cancer protocol. Using the Conditions on Collection Protocol feature of DE, the Administrator can restrict specific annotations to specific protocols.

To assign clinical annotations, to a particular collection protocol, the Administrator will:

1. Click the Administrative Data tab.

2. Click Define under Local Extensions on the left pane of the screen. A warning message is displayed. It warns about the possible alterations to the database tables while creating or editing the dynamic extensions.

3. Click Next as shown in the following figure.

Figure97: Assign Clinical Annotations - Warning Page

4. Select the required CA group under Group on the Build Annotation Form page. All the forms created for the selected group are displayed under Form Title. For example: if you select the pathology_specimen group, all the CA forms created under this group are displayed under Form Title.

5. Click the Edit link under Conditions for the annotation on which collection protocol restrictions are to be set. Refer the following figure. For example, click Edit next to Colorectal Specimen Pathology Annotation.

Figure98: Assign Clinical Annotations – Edit Annotation

6. Select or update the required collection protocol in the Title list box to set restrictions on the availability of that annotation as shown in the following figure. For example: select C_C_P (Colon Cancer Protocol).

Figure99: Build Annotation Form

7. Click Submit to save the changes.

	Click Cancel to ignore the changes made to the collection protocol restrictions.

Similarly, you can assign other annotations to specific collection protocols. For example: the Local Excision Based Colorectal Pathology Annotation can be assigned to the Colon Cancer Protocol and the Generic Collection Protocol.

	You can select multiple collection protocols. Select the required collection protocol, press the [CTRL] key, and select another collection protocol.

Entering Clinical Data and Pathological Data for Annotation

Once an annotation is assigned to a collection protocol, you can enter the clinical and pathological data in the annotation. To enter data in the associated clinical annotation; the Administrator, Supervisor, or Technician performs the following steps:

1. Click the Biospecimen Data tab.

2. Select the required Collection Protocol from the drop-down list to which your annotation is restricted. The system displays the list of participants already registered to the selected collection protocol under Participant (Protocol ID).

3. Select one of the hook entities with which the CP is associated.

a. Participant

b. Specimen Collection Group

c. Specimen

4. Click the View Annotation tab to navigate to the Add New Annotation page as shown in the following figure.

Figure100: Add New Annotation

5. Select the required annotation form from the Annotation Forms drop-down list as shown in the following figure.

Figure 101: Annotation Forms

6. Click Go. The data entry page for the selected annotation form is displayed as shown in the following figure.

7. Enter the required details in the form.

Figure102: Annotation Forms: Data Entry Page

8. Click Submit.

For more information on default annotations in caTissue Suite, refer to Appendix 2: Clinical Annotations.

Querying on Annotations

Once you enter data in the annotations, all the users can search for the required annotations under specific collection protocols.

For more information on advance querying, refer to Advanced Query Wizard.

For more information on querying clinical annotations and viewing related examples, refer to Appendix 3, Queries on Annotations.