How to add a variant to Curate

The Curate module allows you to store, organize, and manage variants for long-term reference and knowledge sharing across your organization. Variants can be added to Curate manually (single or batch) or exported directly from the Variant Page.

1. Add a new variant in Curate

To manually add a new variant:

1. Click on the Add new variant/gene button,

2. Select a desired human genome assembly,

3. Fill the variant's description in the format "chr1:123456 A>G",

4. Click Save. You will be directed to the variant's Curate Variant page.

2. Export from the Variant page

For customers using Emedgene Analyze, it is possible to export a variant from the Variant page directly to Curate:

1. Tag the variant.

2. Set a Pathogenicity classification (Pathogenic, Likely Pathogenic, VUS, Likely Benign, or Benign).

3. Open the variant in the variant page.

4. Click on the Curate dropdown on the Variant page top bar and select Add. You will be directed to the variant's Curate Variant page in a new browser tab.

Note: Only users with a specific role have permission to export variants to Curate.

3. Batch upload variants to Curate (v37.0+)

The batch upload feature allows you to add large sets of variants at once via a validated CSV template.

1. Go to Curate and click Add New.

2. Switch to Batch Mode to enable bulk upload.

3. Download the sample CSV template provided.

4. Fill in variant details following the format in the template.

5. Upload the file back into Curate.

• Emedgene will automatically validate the file to ensure compatibility and accuracy.

• Once uploaded, a toaster notification (bottom-left) will confirm progress and report any errors.

• If you attempt to leave the page before the upload is complete, a message will appear stating that any unsaved changes will be lost.

• If batch variant creation fails due to a timeout, a toaster notification appears with an option to download a summary file. The summary file results:

  • Success – Variant created with all details.

  • Fail – Variant not created due to overlap or intergenic status.

  • Partial Success – Variant created but missing details (e.g., transcript, notes, interpretation, disease info).

  • Duplication – Variant already exists in Curate.

Tip: Review the summary file, correct errors, and re-upload.

Batch upload limits:

• Maximum 5,000 variants per upload or 10 MB file size.

• Multiple concurrent uploads are supported.

• If an upload fails or partially validates, you must start a new upload after correcting the error file.

• CNV uploads currently do not support transcript selection, though the field can be passed through in the template.

• Gene lists can include gene symbols or NCBI IDs—both are accepted without further formatting.

Notes:

• If you navigate away from Curate, the toaster will disappear, and the upload report cannot be accessed from the UI. You will need to contact Illumina Support for assistance.

• Use batch upload for large variant sets to save time and reduce manual input.

• Always validate your CSV file to prevent upload errors.

• Keep track of uploaded variants via the toaster until completion.

• Use manual entry for one-off variants or smaller edits.

Warnings:

• Do not exceed file limits (5,000 variants or 10 MB) to avoid processing errors.

• CNVs require additional review, as transcript selection is not fully supported.

• Uploading via APIs has format restrictions (NCBI IDs not supported).

• Once the toaster is closed or page is refreshed, upload status cannot be recovered via the UI.