NovaSeq 6000Dx Run Set Up

The following instructions describe steps to set up a run on NovaSeq 6000Dx Analysis Application.

Use the following steps to configure a TruSight™ Oncology 500 run in Illumina Run Manager.

1. Go to the "Runs" section of Illumina Run Manager by selecting "Runs" on the left-hand side.

2. Enter sample data manually or by importing a sample sheet

3. To enter sample data run manually, select “Create Run”.

4. Choose "DRAGEN TruSight™ Oncology 500 (with HRD) Analysis Application" from the "Create Run" screen to set-up and analyze runs for TruSight Oncology 500 assay with or without HRD add-on.

   • If you are a customer in Japan, choose "DRAGEN TruSight™ Oncology 500 Analysis Application"

Run Settings

1. On the "Run Settings" screen, enter a run name with the following criteria:

   1. 1 - 40 characters.

   2. Alphanumeric characters, underscores, or dashes only.

   3. Unique across all runs on the instrument.

   The run name identifies the run from sequencing through analysis.

2. [Optional] Enter a run description. The run description must have the following criteria:

   1. 1 - 50 characters.

   2. Alphanumeric characters or spaces only.

   3. Spaces must be preceded and followed by an alphanumeric character.

3. Select kit used during library preparation:

   1. TruSight Oncology 500

   2. TruSight Oncology 500 High-Throughput

4. Index adapter kit will be automatically selected based on the library prep kit selection

5. [Optional] Enter a library tube ID.

Depending on the library prep kit selected, additional fields will be populated for run settings and are not editable. Read and index lengths will differ between library prep kit type.

Sample Data

Use the table on the "Sample Data" screen to enter sample information manually.

Alternately, select Import Samples to upload sample information. Refer to NovaSeq 6000Dx Analysis Application: Sample Sheet Requirements for sample sheet requirements.

1. Select lane information. Options include one to four, or all lanes.

2. Enter a unique sample ID in the sample ID field with the following criteria:

   1. Controls should be added first.

   2. 1 - 40 characters.

   3. Alphanumeric characters, underscores, or dashes only.

   4. Underscores and dashes must be preceded and followed by an alphanumeric character.

3. Select an index set ID for the DNA / RNA library prepared from the sample.

4. [Optional] Enter a library name.

Depending on the options selected for index set ID, additional fields will be auto-populated for sample data and are not editable.

Sample Settings

Use the table on the "Sample Settings" screen to enter additional sample information.

1. Enter Pair ID with the following criteria:

   1. 1 - 40 characters.

   2. Alphanumeric characters, underscores, or dashes only.

   3. Underscores and dashes must be preceded and followed by an alphanumeric character.

   4. Pairs at most one DNA and one RNA samples from the same biological sample from the same individual.

2. Select Sample Type: DNA or RNA

3. Enter Sample Feature: Select HRD for DNA samples with HRD probes. For all other samples, leave the field blank.

   1. Note: This only applies to DRAGEN TruSight™ Oncology 500 (with HRD) analysis application

4. [Optional] Enter a sample name with the following criteria:

   1. 1 - 50 characters.

   2. Alphanumeric characters, dashes, underscores, or spaces.

   3. Spaces, underscores, and dashes must be preceded and followed by an alphanumeric character.

5. [Optional] Enter a sample description with the following criteria:

   1. 1 - 50 characters.

   2. Alphanumeric characters, dashes, underscores, or spaces.

   3. Spaces, underscores, and dashes must be preceded and followed by an alphanumeric character.

Additional fields will be auto-populated based on selections made in the Sample Data screen, which are not editable.

Before starting your run, review that the information entered is correct in the “Run Review” page before saving.