# Diagnostic Testing

## Overview

Often, [diagnostic tests](https://www.labii.com/diagnostic-testing) are used to examine a specific concern in order to determine whether it is caused by disease or not. [They are also often used to diagnose conditions in patients with symptoms or asymptomatic patients with a positive screening test.](https://www.labii.com/blogs/AOUEcvT5HX2oVZaXUIy-utilize-labii-lims-for-diagnostic-testing/)

Labii can be used as a [LIMS](https://www.labii.com/laboratory-information-management-system-lims) for documenting qPCR Cq values and calculating test results.

{% embed url="<https://youtu.be/5hjoOjgZYgI>" %}

## Configuration

In order to use the Diagnostic testing functions in Labii, you must first install the Diagnostic testing application. If Diagnostic testing application is selected when creating the account, then this step can be skipped.

1. Select Applications from **Settings -> Applications**
2. Click **Add application** and select **Add from a template**
3. Choose **Diagnostic testing** from the pop-out modal. A lack of such an option indicates that you have already installed it.

Following the configuration, you should have the following tables installed:

* qPCR CT Ranges
* qPCR Cq
* qPCR Reports

## Usage

### Before start: Prepare thresholds

In order to analyze or predict pathogen loads, thresholds or Ct ranges must first be created. It is only necessary to prepare threshold data once.

1. Click **Diagnostic Testing** app and then click **qPCR Ct Ranges** table.
2. Click **Add qPCR Ct Range** in the list view of qPCR Ct Ranges and choose **Add blank qPCR Ct Ranges**
3. Enter the pathogen's name in the **Name** field
4. Fill in the low, medium, and high Ct thresholds
5. If applicable, update the treatment and antibiotic resistance information

<figure><img src="https://3607108856-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-LHVg57XIRcjV-Vbubtn%2Fuploads%2Fgit-blob-a563b7715d7a55a2e89d7192013b410db32d1abc%2Fdiagnostic-testing-ct-range-form.webp?alt=media" alt=""><figcaption></figcaption></figure>

Thresholds can also be imported in bulk using the [**Import**](https://docs.labii.com/user-guide/list-view/import) function. Please find an example Excel file ready for import below.

<figure><img src="https://3607108856-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-LHVg57XIRcjV-Vbubtn%2Fuploads%2Fgit-blob-196e6a932e7a977b09e72bb8e3abed6e50ee59a1%2Fdiagnostic-testing-ct-range-import-template.webp?alt=media" alt=""><figcaption></figcaption></figure>

### Generate report with process management

Labii's process management for diagnostic testing streamlines the workflow into a seamless and efficient experience. This user-friendly system guides users through a well-defined flowchart, eliminating the need for manual navigation. The process involves three key steps: report creation, Cq value import, and report download. Users can effortlessly complete these tasks in a structured manner, ensuring precision and ease of use throughout the diagnostic testing procedure.

<figure><img src="https://www.labii.com/media/labii-diagnostic-testing-process.webp" alt=""><figcaption></figcaption></figure>

1. **Generate Report**
   1. To create a report, navigate to the "**Add**" menu, select "Report," and provide all the necessary details.
   2. Once added, the workflow's initial section will display, automatically marking the first step, "Create report," as complete.
2. **Import qPCR Cq Values**
   1. Proceed to the second step and click the "**Import**" button to upload qPCR Cq values.
   2. Choose the qPCR Cq values exported from your software. If it's a standard qPCR export file with the title row at row 20, you can simply click the "Submit" button. Otherwise, you have the option to adjust the "Title row's row number" to correspond with your title row's position. Refer to the image below for an example of qPCR Cq values.
   3. On the column matching page, the system will automatically match all columns. If your sheet contains different columns, be sure to align them with Labii's configuration.
   4. Click the "Submit" button to initiate the import process for all Cq values individually. Upon successful completion, the page will return to the report section, and the second step will be marked as completed automatically.
3. **Download Report**
   1. To obtain the report, select the "**Download**" button in the download report step. This step will execute result prediction, prepare the report, initiate the download, and close the new tab directly. Once the report is downloaded, the step will be marked as complete.

<figure><img src="https://3607108856-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-LHVg57XIRcjV-Vbubtn%2Fuploads%2Fgit-blob-a7f19b690c2cb5b6bfd2946894628c90d095f32f%2Fdiagnostic-testing-cq-import-template.webp?alt=media" alt=""><figcaption></figcaption></figure>

### Generate report manually

You can also genereate report manually:

#### 1. Import Cq values

You can import Cq values into Labii after preparing the threshold.

1. Export your RT-PCR data in **\*.tsv** or **\*.xlsx** format
2. Click **Diagnostic Testing** app and select **qPCR Cq** table in Labii
3. Once you've clicked **Import**, select the exported file, and click Submit
4. Match file headers with column names.
5. Importing can be started by clicking Submit.
6. Once imported, enable [editing mode](https://docs.labii.com/user-guide/list-view/table-list-view#edit-mode) to analyze data.
7. Disable editing once it has been completed.

<figure><img src="https://3607108856-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-LHVg57XIRcjV-Vbubtn%2Fuploads%2Fgit-blob-38a5d14fc108ce518b31957e1a0f7d619bf76c1d%2Fdiagnostic-testing-cq.webp?alt=media" alt=""><figcaption></figcaption></figure>

#### 2. Generate reports

You can start generating reports once the analysis is complete:

1. Click **Diagnostic Testing** app and then click **qPCR Reports** table.
2. Click **Add qPCR Report** in the list view of qPCR Reports and select **Add blank qPCR Report**.
3. Complete the Clinic Information, Laboratory Information, Patient Information, and Specimen Information fields
4. Click the **Submit** button
5. In the qPCR Cq table, simply select the Cqs you wish to include in the report from the list.
6. Then click **Bulk Edit**, select the **Report** column, and select the report you just created from the drop-down list
7. Submit the form by clicking the **Submit** button.
8. Open your newly created report once it has been created.
9. To generate the report, click the **Print** button.
10. If you don't want to see certain sections, you can hide them.
11. To print, click the **Print** button.

<figure><img src="https://3607108856-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-LHVg57XIRcjV-Vbubtn%2Fuploads%2Fgit-blob-0bbb37d7b9a4eb87ba65ba579aa40abdea66d31d%2Fdiagnostic-testing-report.webp?alt=media" alt=""><figcaption></figcaption></figure>