2025)¶

Purpose¶

This document provides a description of the NHS GMS data release v5 dated 28th August 2025.

Each progressive release incorporates new content, enhances existing content, and enables more effective use of the data.

This data are presented within the Genomics England Research Environment, accessed via the AWS virtual desktop interface and subject to all Genomics England data protection and privacy principles.

Please see the Research Environment User Guide for detailed documentation on how to use and query the Genomics England dataset. This page also includes instructional videos which can not be viewed from within the Research Environment.

Release overview¶

The NHS Genomic Medicine Service (GMS) Data Release Version 5 provides clinical data for 38,728 participants which are part of 22,980 referrals. In summary, this release includes 40,968 genomes from 38,728 participants. There are 36,500 genomes from 36,500 rare disease programme participants and 4,468 genomes from 2,228 cancer programme participants.

We further provide tiering data from 18,351 referrals, and 18,291 interpretations are represented in the Report Outcome Questionnaire of which 24.5% have a case_solved status of "yes". Within the Report Outcome Questionnaire, cases are included up to 01/08/2025. This release includes 20,746 interpretation requests from the Rare Disease program and 2,234 interpretation requests from the Cancer program.

The secondary clinical data (historic records) from NHSE, NCRAS and ONS contains data up to 11/04/2025 (this is variable between datasets, see the 'Activity period coverage for the longitudinal secondary data tables' table below for dates for each).

Table overview of genomic data:

Type	Genomes count	Participant count
Rare Disease	36,500	36,500
Cancer Germline	2,234	2,228
Cancer Tumour	2,234	2,228
Cancer Total	4,468	2,228
Genomes Total	40,968	38,728

Participants by program(*) breakdown:

Programme	Participants	Referrals
Rare Disease	36,500	20,746
Cancer	2,228	2,234

(*) Participants can be part of multiple referrals and across programs.

Clinical data in this release¶

NHS Genomic Medicine Service (GMS) Data Release clinical data is organised into tables found in LabKey. You can find details of these tables and their contents in our common clinical data documentation, cancer clinical data documentation and data dictionary.

Activity period coverage for the longitudinal secondary data tables¶

Source	Category	Dataset	Start	End
NHSE	Hospital Episode Statistics	op	01/04/2003	31/01/2025
NHSE	Hospital Episode Statistics	apc	13/09/1995	31/01/2025
NHSE	Hospital Episode Statistics	ae	01/04/2007	31/03/2020
NHSE	Hospital Episode Statistics	ecds	05/04/2017	01/02/2025
NHSE	Hospital Episode Statistics	cc	05/04/2008	31/01/2025
NHSE	Other	cancer_registry	09/01/1981	13/08/2024
NHSE	Office of National Statistics Mortality	mortality	25/02/2010	11/04/2025
NCRAS	NCRAS	sact	20/02/2013	23/08/2022
NCRAS	NCRAS	rtds	19/08/2009	28/02/2022
NCRAS	NCRAS	av_treatment	01/04/1995	09/05/2022
NCRAS	NCRAS	av_tumour	05/05/1995	28/12/2019

Change Summary¶

New table¶

Cancer variant tiering information is now available in the cancer_tier_and_domain_variants table.

Changes to existing tables¶

The participant table now includes the column programme_consent_status. This field includes the up-to-date consent status (Consenting, Withdrawn (Partial) or Withdrawn (Full)) of the participant. When you start a new research project, you must filter your list of participants to remove any non-consenting participants.

The cancer_analysis table now includes a referral_type column, which describes whether a cancer case included both germline and somatic samples (matched_normal) or only the tumour sample (tumour_only). In this release all cases are matched normal.

Audience¶

The intended audience for this document is researchers that have access to the Genomics England Research Environment.

Identifying this data release¶

The clinical data and tabulated bioinformatic data for this data release, and the paths to the applicable genome files, are found in the following LabKey folder:

nhs-gms-release_v5_2025-08-28

Subsequent releases will be identified by an incremental increase in the version number and the date of data release. Relevant genomic data produced by the Genomics England Bioinformatics pipeline (i.e. joint-called VCFs, annotated somatic VCFs) can be found in your home directory, under the folder gel_data_resources and then gms. Use the genome_file_paths_and_types table to identify the files.

Scope¶

For release v5, the inclusion criteria are as follows:

Participant has been through a manual consent validation and passed
Only those participants who had all of their consent documents validated, and all documents consistently confirmed that they were eligible (they had both discussed and consented to inclusion in the NGRL, and were consented as an adult or child) are included.
Any participants who were consented as children but were already 16 at the time of consent, or have since turned sixteen (but are not deceased) are deemed ineligible. Unless they have been reconsented as an adult.
Participant is part of an eligible referral
Eligible referrals refer to closed cases that contain at least one eligible participant.

In scope¶

Below we provide an overview of the data in scope for this release. By definition, this relates to cancer and rare disease data for participants enrolled in NHS GMS that consented for research. These data include:

Genomic data for participants when available.
This data contains closed case data only. This means that all referrals have gone through interpretation.
Whole genome sequencing (WGS) family-based quality control for rare disease.
Outputs of the Genomics England Bioinformatics rare diseases interpretation pipeline
Tiering data – rare disease
Exomiser results for interpreted genomes – rare disease
Report outcome data ("report outcome questionnaire data") – rare disease - up until 01/08/2025.
Outputs of the Genomics England Bioinformatics cancer interpretation pipeline
'Gold standard' cancer genomes which have been through interpretation and passed quality checks
Annotation and tiering of small variants
Primary clinical data, including recruited disease and primary tumour types
Secondary datasets (medical history) from National Cancer Registration and Analysis Service (NCRAS)

Out of scope¶

Additional time is required to update the applications/tools that are available in the RE to the current data release, e.g. IVA, Participant Explorer. Please refer to the Application Data Versions page for the data release version used in the RE products and services.

Data out of scope for this release:

Clinical and genomic data for participants that have withdrawn from research after enrolment to the Genomic Medicine Service, or were otherwise ineligible.
Participant data from the pilot phases of the 100,000 Genomes Project (i.e. not main programme).
Participant data from the 100,000 Genomes Project (main programme).

Quality notes¶

This section will be amended for future releases as more documentation becomes available.

Note on Labkey platekey query limitations¶

Aggregation or Distinct queries including specifically the platekey column (e.g. SELECT DISTINCT participant_id, platekey FROM <table_name>) in Labkey will intentionally fail with a 'Status code = 500' error , UnauthorizedException or 'Unable to locate required logging column Key'. This can initially be circumvented by pulling in the entire data with SELECT * FROM <table_name> and subsetting or filtering your data downstream. We will continue to monitor the impact of the issue.

Terms of use for specific cohorts¶

For NHS GMS Data Release Version 5, no cohort has been formally linked to the data. This will change in future releases and the Terms of Use for Specific Cohorts will be amended.

Data release description¶

For an overview of the tables available in LabKey please see: NHS GMS dataset overview

The Genomics England data are organised into data views (displayed within LabKey as tables) categorised into common, bioinformatics and cancer. The data dictionary describes the table structure and provides data definitions for this release.

Contact and support¶

For all queries relating to this data release please contact the Genomics England Service Desk portal: Service Desk (accessible from outside the Research Environment). The Service Desk is supported by dedicated Genomics England staff for all relevant questions.