Upload Genomic Data

This service allows Genomic Laboratory Hubs (GLHs) in the Genomic Medicine Service to upload patient files like FASTQs for analysis, using the Upload Genomic Data (UGD) API.

It helps you send genomic data in a way that is:

• secure
• standardised
• fast

It is created and maintained by Genomics England in partnership with the NHS. 

This service is for:

• bioinformaticians and clinical scientists working with genomic data in the NHS
• healthcare IT professionals developing applications for NHS services

Our users upload patient genomic data for further downstream processing. This happens as a part of the accredited Genomics England Whole Genome Sequencing pipeline. Access to this service is available where there is a legal basis.

To onboard to this API, you will need:

• an NHS API platform account
• approval from Genomics England (GEL)

The onboarding approval process can sometimes take a while, so it's worth starting 2-4 weeks in advance.

To get access

1. Sign in to or create a developer account.

2. Select Upload Genomic Data API.
3. Follow the steps.
4. Wait for approval via email.

The Upload Genomic Data API is currently in the beta stage of development. If your organisation has qualified as a sequencing genomic laboratory, you can use the digital onboarding service (DOS). You will need to get your software approved by Genomics England. This takes about 5 working days. To understand how the NHS API platform digital onboarding process works, see Digital assurances for APIs and services.

Uploading genomic data occurs in six stages:

1. Verify that genomic sequence data is expected. 
2. Make an upload request.
3. Upload the data.
4. Register the data.
5. Provide associated metadata.
6. Update the ServiceRequest to reference uploaded specimens.

Worked example: rare disease single-lane upload

This example walks through a complete upload of a single-lane, paired-end FASTQ dataset for a rare disease referral. It shows every HTTP request and response across all six stages.
Scenario

• referral ID: r123456789
• participant ID: p123456789
• ODS code for requesting lab: 69A70
• ODS code for sequencing lab: 69A50
• sequencing run ID: 251230_A00123_0001_3F159011F8
• lab sample ID (2D barcode identifier): 123456789 and local lab sample ID (e.g. from local LIMS): LIMS-123456
• lane: 1
• files:
  • sample1_S1_L001_R1_001.fastq.gz (31,457,280 bytes, SHA-256: a3f1b7c9d2e4f6a8b0c1d3e5f7a9b1c3d5e7f9a1b3c5d7e9f1a3b5c7d9e1f3a5)
  • sample1_S1_L001_R2_001.fastq.gz (32,505,856 bytes, SHA-256: b4e2c8d3f5a7b9c1d3e5f7a9b1c3d5e7f9a1b3c5d7e9f1a3b5c7d9e1f3a5b7c9)

The UGD API is intended to be a mandatory standard for supporting Sequencing Genomic Laboratory Pathfinders and supporting Pathfinder Laboratories in submitting genomic data to GEL.

It is expected that the UGD API will become mandatory for other organisations as and when they qualify as Sequencing Genomic Laboratories beyond the Pathfinder stage.

Consumers of the Upload Genomic Data API will be onboarded as and when they qualify as Sequencing Genomic Laboratories. Genomics England has put in place versioning for releases. Improvements will be agreed jointly with NHS England, documented and delivered iteratively as part of the Genomic Medicine Service.

This service is in beta.

The Service Desk is your point of contact if you need help. We support participants, researchers, and other users by:

• logging, prioritising, tracking and responding to all enquiries
• passing requests to the right team when needed
• keeping you updated on the progress of your request

We can help with questions about:

• questions about your participation in genomic research
• updating your email address
• submitting a Subject Access Request (SAR)
• withdrawing data from the National Genomic Research Library (NGRL)

Response time: 1-3 working days