User Manual for Illumina Local Run Manager CF 139-Variant 2.0 Analysis Module

Quick guide from the manual

The Local Run Manager CF 139-Variant 2.0 Analysis Module is designed for use with the TruSight Cystic Fibrosis 139-Variant Assay. Key operational requirements include:

• Controls: Every run must include at least one positive and one negative control sample to be saved.
• Sample Validation: Proceeding with fewer than 24 samples is not validated by Illumina.
• System Requirements: Requires a Windows operating system and a web browser-based interface.

Overview

This module performs secondary analysis and report generation for sequencing runs using the TruSight Cystic Fibrosis kit. It evaluates short regions of amplified DNA (amplicons) to detect 139 clinically relevant cystic fibrosis mutations and variants in the CFTR gene.

Setting Up a Run

1. Log in to the Local Run Manager.
2. Select Create Run and choose CF 139-Variant 2.0.
3. Enter a unique run name (up to 40 characters).
4. Enter the lot number and expiration date for the library prep kit.
5. Specify samples using manual entry or by importing a CSV file.

Managing Samples

You can add samples manually or import them via a template file:

• Manual Entry: Enter a unique sample name, right-click to select positive and negative controls, and optionally add a description.
• Importing: Use the Import Samples feature to upload a comma-separated values (*.csv) file. A template is available for download on the Create Run screen.

After adding samples, select the Print icon to display and print the plate layout for library preparation reference. Select Save Run to finalize.

Viewing Run and Results

To review analysis results:

1. Click the run name on the main screen.
2. Use the Run Overview tab to review sequencing metrics.
3. Use the Sequencing Information tab to review run parameters.
4. Use the Samples and Results tab to view the sample list, call rates, and control information.

Detailed variant information is displayed below the sample list when a sample is selected. Changes saved to the sample list generate a new analysis results file in the Alignment folder.

Analysis Reports

The module generates a tab-delimited text file named TruSightCF139VariantAssay.txt. This file contains three sections: file header, sample information, and sample variants information. You can view this file by clicking Export Data on the Samples and Results tab or by opening it directly in the Alignment folder.

Technical Assistance

For technical support, visit www.illumina.com or email [email protected]. Safety data sheets and additional product documentation are available at support.illumina.com.