Attaching a PON to a kit

Users can attach a PON to an existing Kit BED.

A new PON Management section is available in the Organization Settings page: PON Management.

This section includes a table displaying:

  • Kit Name

  • Kit ID

  • GC Corrected Status

  • Human Reference

  • DRAGEN Version

  • Maximum Interval Size

Additionally, there is an ‘Add PON’ button to initiate the PON addition process.

Prerequisites

Before adding a PON, ensure the following requirements are met:

  • The PON file must be a combined counts file.

  • The file must be stored in a supported cloud storage (AWS S3, ICA, or BaseSpace Storage). Direct uploads are not allowed.

  • Users must have the “Manage PON” role.

  • The Enrichment Kit and its human reference BED must already exist. The BED file must match the one used to generate the PON.

  • Only one PON per unique combination of Enrichment Kit, Human Reference BED, and DRAGEN Main Version is allowed.

  • PONs cannot be added for DRAGEN sub-versions.

Compatibility

To use the PON for CNV calling, the sample pipeline version must be set to 37.0 or higher. Otherwise, CNV calling will not use the newly added PON.

Existing PONs

Previously existing PONs will not appear in the PON table. However, a notification will indicate the presence of existing PONs within the workgroup.

PON Migration

Previously existing PONs will continue to function, and CNV calling will remain unaffected. If migration to the new PON table is required, please contact [email protected] or your bioinformatics support team.

Adding a new PON

  1. Click ‘Add PON’ to open a pop-up window.

  2. Select values for the required fields:

    1. Enrichment Kit: Lists all unique kits within the organization (excluding common kits). To add a PON for a common Kit BED, create a separate Kit with the same Kit BED (refer to Kit Management for details).

    2. DRAGEN Version: Only versions 3.6 and later are supported.

    3. Human Reference: Choose GRCh37 or GRCh38.

  3. Based on the selected DRAGEN version, the system will display the expected maximum interval size:

    1. DRAGEN 4.2 and below: 250bp

    2. DRAGEN 4.3 and above: 500bp (default for DRAGEN 4.3)

  4. Click Next go to file selection window:\

  1. On next window select a combined counts file from a supported cloud storage service (AWS S3, ICA, or BaseSpace Storage). Ensure the file is available in storage before proceeding.

  2. Only one file with the extension “.combined.counts.txt.gz” can be selected.

  3. Click ‘Next’ to validate the file.\

Automated Validations

Before adding a PON, the system performs the following checks:

1. Maximum Interval Size Validation

  • The system inspects the first 1000 rows of the combined counts file to ensure that no target exceeds the threshold interval size.

  • Using a combined counts file with the expected maximum interval size is strongly recommended.

2. GC Correction Validation

  • The system determines GC correction status by checking the cnv-enable-gcbias-correction field in the file headers:

    • 0: Non-GC corrected

    • 1: GC corrected

  • If this field is missing, the system analyzes target value types:

    • Integer values: Non-GC corrected

    • Float values: GC corrected

  • Users must ensure the combined counts file has the intended GC correction status.

Viewing Added PONs

Once a PON is successfully added, it appears in the PON table with details based on the selected inputs. Value for Maximum Interval Size and GC Corrected Status are inferred from validation results.\

Deleting PON from table

If user wants to delete a PON for a combination listed in table for any reasons, then user with role “Manage Pon” shall be able to delete it. This deletion will be a soft deletion i.e. linkage between combined counts file and Kit BED will be removed and there will be no impact on combined counts file itself.

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