Sample Sheet Creation in BaseSpace Run Planning tool

How to Create TSO 500 ctDNA Sample Sheets in BaseSpace Run Planning tool

The BaseSpace Sequence Hub Run Planning tool is available, and is used to generate a valid sample sheet in v2 format for use on a TSO 500 ctDNA supported sequencer for both ICA and Standalone DRAGEN Server analysis options. Filling out the form on the user interface will produce a exportable sample sheet with the required fields filled in. Refer to ICA Auto-launch Sample Sheet Requirements for descriptions of fields that appear in ICA sample sheets.

The sections below represent each step in the BaseSpace Run Planning tool.

Note that NovaSeq X Series has a different run set up configuration screen than other instrument platforms. TSO 500 ctDNA does not support multi analysis, and in order to run TSO 500 ctDNA on NovaSeq X Series, enter the appropriate Read 1, Read 2, Index 1 and Index 2 described in the instructions below.

BaseSpace Run Planning tool cannot generate a valid sample sheet for the NovaSeq 6000Dx TSO 500 ctDNA Analysis Application on Illumina Run Manager. Refer to Sample Sheet Requirements page to create a valid sample sheet.

Step 1: Run Settings

Parameter Name	Required	Description
Run Name	Required	Run Name can contain 255 alphanumeric characters, dashes, underscores, periods, and spaces; and must start with an alphanumeric, a dash or an underscore.
Run Description	Optional	Run Description can contain 255 characters except square brackets, asterisks, and commas.
Instrument Platform	Required	Choose from TSO 500 ctDNA supported instruments: NovaSeq 6000/6000Dx NovaSeq X Series
Secondary Analysis	Required	BaseSpace/Illumina Connected Analytics (to generate sample sheet for cloud analysis) Local
Read 1	Required on Instrument Platform NovaSeq X Series	Fill with value 101 for TSO 500 ctDNA analysis
Index 1	Required on Instrument Platform NovaSeq X Series	Fill with value 10 for TSO 500 ctDNA analysis
Index 2	Required on Instrument Platform NovaSeq X Series	Fill with value 10 for TSO 500 ctDNA analysis
Read 2	Required on Instrument Platform NovaSeq X Series	Fill with value 101 for TSO 500 ctDNA analysis
Sample Container ID	Optional	Unique Identifier for the container that holds the sample

Step 2: Configuration

Note: On NovaSeq X Series, this page is called "Configuration 1". The right hand corner of the UI displays the Read 1, Read 2, Index 1 and Index 2 entered on the previous run settings screen.

Parameter Name	Required	Description
Application	Required	DRAGEN TruSight Oncology 500 ctDNA Analysis Software - 2.6.1
Description	Optional	Optional text field
Library Prep Kit	Required	TruSight Oncology 500 ctDNA (only for NovaSeq 6000/6000Dx instruments) TruSight Oncology 500 ctDNA v2
Index Adapter Kit	Required	TSO 500 ctDNA: TruSight Oncology 500 ctDNA (NovaSeq6000Dx) TruSight Oncology 500 ctDNA (NovaSeq6000) TSO 500 ctDNA v2: TruSight Oncology 500 ctDNA Index Set A and B (UDP 1-192) (NovaSeq6000Dx, NovaSeqX Series) TruSight Oncology 500 ctDNA Index Set A and B (UDP 1-192) (NovaSeq6000)

Step 3: Sample Settings

Users can manually enter sample information, or download a template file to bulk upload sample information. Users can import the completed template or a compatible sample sheet.

Parameter Name	Required	Description
Read Lengths: Read 1 and Read 2	Required Not applicable on NovaSeq X Series	Auto filled with the standard values, but can be optionally overwritten.
Override Cycles	Required on NovaSeq X Series	Entered based on Run Settings read lengths & index 1 / index 2
Lane Usage	Not applicable on NovaSeq X Series	Checkbox allows users to apply the same lane across samples.
Lane	Required if Lane Usage is unchecked	Specify lanes for each sample. The unmarked checkbox at the top of the dropdown selects all lanes.
Index ID	Required	Index set ID options are based on selected Index Adapter Kit
Project	Optional	Optional field to describe the associated project
Starts from Fastq	Required	True or False If auto-launching TSO 500 ctDNA from BCL files, set the value to False. If auto-launching TSO 500 ctDNA from FASTQ after auto-launching BCL Convert, set the value to True.
DNA Barcode Mismatches Index 1 DNA Barcode Mismatches Index 2	Required on NovaSeq X	Default value is set to 1. These fields are required by NovaSeq X and represent BCL Convert settings for index diversity checks when demultiplexing. These values are not used in TSO 500 ctDNA analysis.

Step 4: Run Review

Once all details are captured and pass validation, the user can review the details on the Run Review screen. From here they can choose to edit details in previous screens or export the sample sheet. Once completed, press the Cancel button to finish run planning.

Note: once leaving this screen, the run and sample sheet will not be accessible.

For NovaSeqX Plus users, the run can be saved as a draft or as a planned run (via “Save as Draft” and “Save as Planned” buttons respectively). Either selection will save the run to the Planned Runs screen on BaseSpace. There is no option to export the sample sheet on this screen.

Planned Runs Screen (NovaSeq X Series only)

The Planned Runs screen lists all planned or drafted runs. Users can set drafted runs to planned, export the sample sheet, and edit or delete a run on this screen.

Once the run is saved as Planned, it will appear on the NovaSeq X Series instrument where it can be selected for sequencing.

For more information on run planning, refer to the BaseSpace Sequence Hub support site page.

Guided Examples

Please review these guided examples of analysis workflows that include a step of setting up a run in BaseSpace Run Planning tool:

• NovaSeq 6000Dx: TSO 500 Auto-launch Analysis in Cloud