Data in Participant Explorer¶

Data sources¶

Participant data¶

Participant clinical data is obtained from the source data in the most recent versions of the 100kGP data release, version 19 (31st October 2024), and NHS_GMS data release, version 4 (22nd August 2024), both of which can be viewed in LabKey. Some elements in the Participant Explorer UI provide deep links to the source data into LabKey.

The source data are imported into a Postgres database, and partially mapped to a standard data model (HL7 FHIR) using SQL. The Participant Explorer UI operates on top of the FHIR model, but hides the technical details of FHIR (such as element names and extension URLs) to create a user-friendly, intuitive interface. A detailed overview of the mapping from source tables and columns to elements in the UI is given below.

Reference data¶

Terminology reference data is provided by a FHIR terminology server, developed by the AEHRC. For details of the terminology server instance we are using, see the Terminology Server page.

Conceptual data model¶

The diagram below depicts the clinical data model used for representing participant data in the Participant Explorer. This model is based on the HL7 FHIR resource model.

Participant Explorer Label	FHIR Resource Type	Definition (from FHIR)	Meaning in terms of the 100kGP/NHS-GMS datasets
Participant	Patient	Demographics and other administrative information about an individual receiving care or other health-related services.	All consenting participants including probands and their relatives.
Referral	ServiceRequest	A record of a request for service such as diagnostic investigations, treatments, or operations to be performed	The referral to the Genomics Medicine Service for a genomic test for a specific clinical indication (NHS-GMS) or the recruitment to the 100kGP project for one of the eligible diseases.
Condition	Condition	A clinical condition, problem, diagnosis, or other event, situation, issue, or clinical concept that has risen to a level of concern.	Diagnoses from primary clinical data (including the recruited disease) and secondary data.
Observation	Observation	Measurements and simple assertions made about a patient	Phenotypic observations (HPO terms), Tumour morphology and stage observations
Procedure	Procedure	An action that is or was performed on or for a patient. This can be a physical intervention like an operation, or less invasive like long term services, counselling, or hypnotherapy.	Procedure and operation codes from primary and secondary data
Encounter	Encounter	An interaction between a patient and healthcare provider(s) for the purpose of providing healthcare service(s) or assessing the health status of a patient.	Grouping of conditions, observations and procedures by visit/event
Family Member	FamilyMemberHistory	Significant health conditions for a person related to the patient relevant in the context of care for the patient.	Key details and affected-status of family members of rare disease probands (Note: family members who are also participants will also have a patient/participant record)
Genome Sequence Report/ Family Case Report	DiagnosticReport	The findings and interpretation of diagnostic tests performed on patients, groups of patients, devices, and locations, and/or specimens derived from these.	Sequencing report meta information/ GMC exit questionnaire (case status and additional comments)
Drugs, Drug Group	MedicationAdministration	Describes the event of a patient consuming or otherwise being administered a medication.	SACT (chemotherapy) drug administrations

Code systems overview - using the right codes¶

The following table can help you select the code systems to use when searching by clinical concept, depending on your area of interest and scope. It also indicates whether the "include mapped concepts" feature may be of use. Below the table are examples involving each code system.

Note that the NHS-GMS Clinical Indications, OMIM and ORPHA codes are not yet searchable in Participant Explorer so are not described here. However, they are displayed in the Particpant Details and Download pages.

Code System Short Name	Description	Primary Clinical Data (cancer/rare diseases programme specific)	Secondary Data (longitudinal data for all participants)	Concept Maps Available?
Genomics England Rare Disease	Rare disease groups, subgroups and specific diseases for which participants were recruited in the Genomics England 100kGP	Rare diseases groups, subgroups and specific diseases	N/A	No
Genomics England Cancer Type	Cancer disease types for which participants were recruited in the Genomics England 100kGP	Cancer disease types	N/A	No
Genomics England Cancer Subtype	Cancer disease subtypes for which participants were recruited in the Genomics England 100kGP	Cancer disease subtypes	N/A	No
ICD10	ICD-10, WHO International Classification of Diseases	Cancer diagnoses	NHS inpatient/outpatient hospital diagnoses NHS mental health services diagnoses ONS causes of death NCRAS radiotherapy diagnoses NCRAS chemotherapy diagnoses	Yes, SNOMED to ICD10
HPO	Human Phenotype Ontology	Observed phenotypes (rare disease programme)	N/A	Yes, SNOMED to ICD10
ICDO	ICD-O-3, WHO International Classification of Diseases for Oncology	Tumour morphology and topography	NCRAS chemotherapy tumour morphology	No
OPCS	OPCS-4 Classification of Interventions and Procedures	N/A	Cancer imaging (body site) Cancer surgery procedures NHS inpatient/outpatient hospital operations NCRAS radiotherapy procedures and body site NCRAS chemotherapy procedures	Yes, SNOMED to OPCS
SNOMED	SNOMED CT (UK Edition)	Cancer tumour morphology and topography Imaging procedures (rare disease and cancer)	NHS emergency care NHS imaging procedures and body site	Yes, SNOMED to ICD10, OPCS and HPO.
SACT Drug Group	Drugs used in treatments recorded in the SACT data	N/A	Systemic Anti-Cancer Therapy (SACT) drugs from the `Drug Analysis` treatment data	No

Examples¶

Rare Diseases | Intellectual Disability: selects rare disease participants who were recruited for intellectual disability (including relatives).

Cancer Type | Lung: selects cancer participants who were recruited for lung cancer.

HPO | HP:0012622: Chronic kidney disease: selects rare disease participants with an observed phenotype of chronic kidney disease (including relatives).

ICD10 | C50: Malignant neoplasm of breast: selects any participant with a diagnosis of breast cancer in their medical history (including rare disease probands and relatives, as well as cancer participants recruited for other cancer types).

OPCS | J01: Transplantation of liver: selects _any participant_with a liver transplantation record in their medical history.

SCT | 241620005: Cardiac MRI: selects any participant with a record of a cardiac MRI in their Genomics England data or general medical history.

SCT | 38341003: Hypertensive disorder (with mapped concepts DISABLED): selects no participants, because SNOMED codes are only available in our data sets for cancer diseases and imaging procedures.

SCT | 38341003: Hypertensive disorder (with mapped concepts ENABLED): adds equivalent ICD10 and HPO codes for hypertensive disorder to the search criteria, and consequently selects any participant with a record of hypertension in their medical history plus rare disease participants with a hypertension phenotype. Disclaimer: the concept maps underlying this feature are not complete and can be inaccurate. Please review the included mapped concepts carefully, when using this feature.

ICDO | 80109: Carcinomatosis plus SCT | 307593001: Carcinomatosis: selects cancer participants with this tumour morphology plus any participant with a record of chemotherapy for this tumour morphology in their medical history (including rare disease probands and relatives, as well as cancer participants recruited for other cancer types). Because tumour morphology/topography may be coded with ICD-O or SNOMED, it is advised to include both code systems when searching for morphology or topography.

Mapping of 100kGP and NHS-GMS data release¶

For detailed information on 100kGP and NHS-GMS source tables and columns, please refer to the relevant data dictionaries of the 100kGP Data Release / NHS_GMS data release. The tables below show how the value in Participant Explorer is mapped from the (sometimes several) source table/columns in Labkey.

Participant¶

Participant Explorer	Dataset	Source Table	Source Column	Notes
Participant ID	Both	participant	participant_id
Year of Birth	100kGP	participant	year_of_birth
	NHS-GMS	participant	participant_year_of_birth
Stated Gender	100kGP	participant	participant_stated_gender
	NHS-GMS	participant	administrative_gender
Phenotypic Sex	100kGP	participant	participant_phenotypic_sex
	NHS-GMS	participant	phenotypic_sex
Ethnic Category	100kGP	participant	participant_ethnic_category
	NHS-GMS	participant	ethnicity_description
Life Status	100kGP	death_details	death_date	if different from mortality, the value from mortality is used
	NHS-GMS	participant	participant_year_of_death	if different from mortality, the value from mortality is used
	Both	mortality	date_of_death	takes precendence

Referral¶

Participant Explorer	Dataset	Source Table	Source Column	Notes
Referral ID / Family ID	100kGP	participant	rare_diseases_family_id / gel_case_reference	Rare Disease / Cancer
	NHS-GMS	referral	referral_id	Both Rare Disease and Cancer
Proband/Relative	100kGP	participant	participant_type
	NHS-GMS	referral_participant	referral_participant_is_proband
Disease Category/ Programme	100kGP	participant	programme
	NHS-GMS	referral	category
Clinical Indication/ Recruited Disease	100kGP	rare_diseases_participant_disease	normalised_specific_disease
	100kGP	cancer_participant_disease	cancer_disease_type + cancer_disease_sub_type
	NHS-GMS	referral	clinical_indication_full_name
Family Case Solved	100kGP	gmc_exit_questionnaire	case_solved_family
	NHS-GMS	report_outcome_questionnaire	case_solved_family
Referral Date	100kGP	N/A		Not populated for 100k, as for families the choice of date is unclear. In practice other registration events on the timeline show the likely period for the referral.
	NHS-GMS	referral	date_submitted
Family Members Tested	100kGP	rare_diseases_family	family_group_type
	NHS-GMS	referral_test	referral_test_expected_number_of_participants
Family Members Available	100kGP	participant	N/A	count of participants with family id
	NHS-GMS	referral	N/A	count of participants with referral id

Referral Members/Family Details¶

Participant Explorer	Dataset	Source Table	Source Column	Notes
Relationship to Proband	100kGP	rare_diseases_pedigree_member	father_id, mother_id	First-degree relationships are derived from father_id and mother_id. Others are displayed as "Family Member".
	NHS-GMS	referral_participant	relationship_to_proband
Affection Status	100kGP	rare_diseases_pedigree_member	affection_status
	NHS-GMS	referral_participant	disease_status
Stated Gender	100kGP	participant	participant_stated_gender	not available for non-participants
	NHS-GMS	participant	administrative_gender
Phenotypic Sex	100kGP	participant / rare_diseases_pedigree_member	phenotypic_sex, father_id, mother_id	rare_diseases_pedigree_member entry is used for non-participants, otherwise participant table participant_phenotypic_sex overrides.
	NHS-GMS	participant	phenotypic_sex
Participant ID	100kGP	rare_diseases_pedigree_member	participant_id
	NHS-GMS	referral_participant	participant_id
Pedigree Member ID	100kGP	rare_diseases_pedigree_member	rare_diseases_pedigree_member_id	only available for 100kGP

Rare disease family case report¶

Participant Explorer	Dataset	Source Table	Source Column
Family Case Comments	100kGP	gmc_exit_questionnaire	additional_comments
	NHS-GMS	report_outcome_questionnaire	additional_comments
Position of "Family case report" on the timeline	Both	gmc_exit_questionnaire or report_outcome_questionnaire	event_date
Medical Review Date	100kGP	rare_diseases_family	family_medical_review_date

Genome sequence report¶

Participant Explorer	Dataset	Source Table	Source Column	Notes
Delivery ID	Both	sequencing_report	delivery_id
Plate Key	Both		plate_key
Type	Both		type
Delivery Version	Both		delivery_version
Genome Build	Both		genome_build
Delivery Date	Both		delivery_date
Path	Both		path
Sample Date	100kGP	clinic_sample	clinic_sample_datetime	sequencing_report is linked to clinic_sample via the lab_sample_id and clinic_sample_sk in the laboratory_sample table
	NHS-GMS	sample	collection_date	sequencing_report is linked to sample via the referral_id

Condition¶

Shows how condition codes are mapped from multiple source tables.

Participant Explorer	Dataset	Source Table	Source Column(s)	Code System	Notes
Condition Code (and Condition Source Code)	Both	av_tumour	site_icd10_o2	ICD-10	Normalised¹
	100kGP	cancer_invest_sample_pathology	primary_diagnosis_icd_code	ICD-10	Normalised¹
	100kGP	cancer_participant_disease	cancer_disease_type cancer_disease_sub_type	Genomics England
	100kGP	cancer_participant_tumour	diagnosis_icd_code	ICD-10	Normalised¹
	100kGP	cancer_registry	cancer_site	ICD-10	Normalised¹
	NHS-GMS	condition	code	OMIM or ORPHANET
	Both	ecds	diagnosis_code_1 - diagnosis_code_12	SNOMED CT	if diagnosis_qualifier_n /!= '415684004' ("suspected")
	Both	hes_apc	diag_01 - diag_20	ICD-10	Normalised¹
	Both	hes_op	diag_01 - diag_12	ICD-10	Normalised¹
	100kGP	mhmd_v4_event mhldds_event	ic_eve_primarydiagnosis ic_eve_secondarydiagnosis	ICD-10 ICD-10	Normalised¹
	100kGP	mhsds_medical_history_previous_diagnosis	prevdiag diagschemeinuse	ICD-10 / SNOMED	Normalised¹ If diagschemeinuse is 1, 2, 02, ID, 4, 6 or 06
	100kGP	mhsds_provisional_diagnosis	provdiag diagschemeinuse	ICD-10 / SNOMED	Normalised¹ If diagschemeinuse is 1, 2, 02, ID, 4, 6 or 06
	100kGP	mhsds_primary_diagnosis	primdiag diagschemeinuse	ICD-10 / SNOMED	Normalised¹ If diagschemeinuse is 1, 2, 02, ID, 4, 6 or 06
	100kGP	mhsds_secondary_diagnosis	secdiag diagschemeinuse	ICD-10 / SNOMED	Normalised¹ If diagschemeinuse is 1, 2, 02, ID, 4, 6 or 06
	100kGP	mhsds_care_activity mhsds_indirect_activity	codefind findschemeinuse	ICD-10/ SNOMED	If diagschemeinuse is 1, 2, 02, ID, 4, 6 or 06
	100kGP	rare_diseases_participant_disease	normalised_disease_group normalised_disease_sub_group normalised_specific_disease	Genomics England
	Both	mortality	icd10_underlying_cause	ICD-10	Normalised¹
	Both	mortality	icd10_multiple_cause_code_1 ... 15	ICD-10	Normalised¹
	Both	rtds	radiotherapydiagnosisicd	ICD-10	Normalised¹
	Both	sact	primary_diagnosis	ICD-10	Normalised¹
Body Site Code	100kGP	cancer_invest_sample_pathology	topography_snomed_ct_code	SNOMED CT
TNM Stage Group	100kGP	cancer_participant_tumour	integrated_tnm_stage_grouping
	100kGP	cancer_participant_tumour	ajcc_stage
	Both	sact	sact_stage_at_start
Stage Best	Both	av_tumour	stage_best
Stage Best System	Both	av_tumour	stage_best_system
T Stage	Both	av_tumour	t_best
	100kGP	cancer_participant_tumour	component_tnm_t
M Stage	Both	av_tumour	m_best
	100kGP	cancer_participant_tumour	component_tnm_m
N Stage	Both	av_tumour	n_best
	100kGP	cancer_participant_tumour	component_tnm_n
Dukes	Both	av_tumour	dukes
	100kGP	cancer_participant_tumour	modified_dukes_stage
FIGO	Both	av_tumour	figo
	100kGP	cancer_participant_tumour	final_figo

Observation¶

Shows how observation codes are mapped from multiple source tables.

Participant Explorer	Dataset	Source Table	Source Column(s)	Code System	Notes
Observation Code	Both	av_tumour	histology_coded	ICD-O-3
	Both	av_tumour	stage_best	STAGE
	Both	av_tumour	figo	STAGE
	Both	av_tumour	dukes	STAGE
	Both	av_tumour	t_best n_best m_best	TNM STAGE	Concatenated
	100kGP	cancer_analysis	histology_coded	ICD-O-3	Removing the / character for technical reasons
	100kGP	cancer_participant_tumour	morphology_snomed_ct_code morphology_icd_code	SNOMED CT ICD-O-3
	100kGP	cancer_participant_tumour	integrated_tnm_stage_grouping	STAGE
	100kGP	cancer_participant_tumour	ajcc_stage	STAGE
	100kGP	cancer_participant_tumour	final_figo	STAGE
	100kGP	cancer_participant_tumour	modified_dukes_stage	STAGE
	100kGP	cancer_participant_tumour	component_tnm_t component_tnm_n component_tnm_m	TNM STAGE	Concatenated
	Both	cancer_registry	cancer_type cancer_behaviour	ICD-O-3	Concatenated
	100kGP	mhsds_care_activity	codeobs obsschemeinuse	SNOMED	if obsschemeinuse = 3
	NHS-GMS	observation	normalised_hpo_id	HPO	filter value_code = present
	100kGP	rare_diseases_participant_phenotype	hpo_id	HPO	filter hpo_present = true
	Both	sact	morphology_clean	ICD-O-3
	Both	sact	sact_stage_at_start	STAGE
	NHS-GMS	tumour	tumour_type, presentation	-	date from tumour_diagnosis_day, tumour_diagnosis_month, tumour_diagnosis_year
	NHS-GMS	tumour_morphology	morphology	SNOMED CT	date from parent tumour table
	NHS-GMS	tumour_topography	actual_body_site	SNOMED CT	date from parent tumour table
	NHS-GMS	tumour_topography	primary_body_site	SNOMED CT	date from parent tumour table
Observation Code Description	Both	av_tumour	histology_coded_desc	ICD-O-3
Body Site Code	Both	av_tumour	site_coded	ICD-O-3	if coding_system_desc starts with "ICD-O-3"
	100kGP	cancer_participant_tumour	topography_snomed_ct_code topography_snomed_code, topography_snomed_version topography_icd_code	SNOMED CT SNOMED CT ICD-O-3
Body Site Description	Both	av_tumour	site_coded_desc	ICD-O-3

Procedure¶

Participant Explorer	Dataset	Source Table	Source Column(s)	Code System	Notes
Procedure Code	Both	av_treatment	eventcode	NCRAS
	Both		opcs4_code	OPCS-4
	Both		radiocode	NCRAS
	Both		imagingcode	NCRAS
	Both		imagingsite	OPCS-4
	100kGP	cancer_invest_imaging	imaging_code_snomed_ct_code	SNOMED CT
	100kGP	cancer_surgery	primary_procedure	OPCS-4	Ignore '.'
	100kGP	rare_diseases_imaging	procedure_other_snomed_ct	SNOMED CT
	Both	ecds	treatment_code_1 - treatment_code_12	SNOMED CT
	Both	hes_apc	opertn_01-24	OPCS-4	Z-chapter codes mapped to body site and grouped with preceding non-Z-chapter code
	Both	hes_op	opertn_01-24	OPCS-4	Z-chapter codes mapped to body site and grouped with preceding non-Z-chapter code
	Both	rtds	primaryprocedureopcs	OPCS-4
	Both	sact	opcs_procurement_code opcs_delivery_code	OPCS-4	If 3 digits: prefix with "X" Uppercase ignore "N/A"
	100kGP	did	did_snomedct_code	SNOMED CT
Procedure Code Description	Both	av_treatment	eventdesc	NCRAS
	Both		radiodesc	NCRAS
	Both		imagingdesc	NCRAS
Body Site Code	100kGP	cancer_invest_imaging	anatomical_site	OPCS-4	Split comma-separated values into multiple codes for the same procedure
	Both	hes_apc	opertn_01-24	OPCS-4	Z-chapter codes mapped to body site and grouped with preceding non-Z-chapter code
	Both	hes_op	opertn_01-24	OPCS-4	Z-chapter codes mapped to body site and grouped with preceding non-Z-chapter code
	Both	rtds	rttreatmentanatomicalsite	OPCS-4
	100kGP	did	ic_sub_syscomp_id ic_sub_sys_id ic_system_id ic_sub_region_id ic_region_id	SNOMED CT	Only using the most specific system code and the most specific region code. I.e., when both a region_id and sub_region_id are present, only include the sub_region_id in the body site coding.
Source Code	Both	sact		OPCS-4
	100kGP	cancer_surgery		OPCS-4

Medication administration¶

Participant Explorer	Dataset	Source Table	Source Column(s)	Code System	Notes
Code	Both	sact	drug_group	SACT Drug Group	Convert to title-case
Source Code	Both

Encounter¶

Participant Explorer	Dataset	Source Tables	Source Column	Notes
Encounter Date	Both	av_treatment	eventdate
Encounter Type	Both		"National Cancer Registration"
Encounter Date	Both	av_tumour	diagnosisdatebest
Encounter Type	Both		"National Cancer Registration"
Encounter Date	Both	participant	registration_date date_of_consent	registration_date if available; otherwise date_of_consent Also used for recruited diseases
Encounter Type	Both		"Genomics England"
Encounter Date	100kGP	cancer_participant_tumour	diagnosis_date
Encounter Type	100kGP		"Genomics England"
Encounter Date	100kGP	cancer_invest_sample_pathology	event_date
Encounter Type	100kGP		"Genomics England"
Encounter Date	100kGP	cancer_invest_imaging	imaging_date
Encounter Type	100kGP		"Genomics England"
Encounter Date	100kGP	cancer_invest_sample_pathology	event_date
Encounter Type	100kGP		"Genomics England"
Encounter Date	100kGP	cancer_surgery	procedure_date
Encounter Type	100kGP		"Genomics England"
Encounter Date	Both	cancer_analysis	tumour_clinical_sample_time
Encounter Type	Both		"Genomics England"
Encounter Date	Both	cancer_registry	event_date
Encounter Type	Both		"National Cancer Registration"
Encounter Date	100kGP	rare_diseases_participant_phenotype	phenotype_report_date
Encounter Type	100kGP		"Genomics England"
Encounter Date	100kGP	rare_diseases_imaging	date
Encounter Type	100kGP		"Genomics England"
Encounter Date	Both	ecds	arrival_date arrival_time
Encounter Date	Both		departure_date departure_time
Encounter Type	Both		"Emergency"
Encounter Date	Both	hes_apc	admidate
Encounter Type	Both		"Inpatient"
Encounter Type	Both	hes_op	"Outpatient"
Encounter Date	Both		apptdate
Encounter Type	100kGP	did	"Diagnostic Imaging"
Encounter Date	100kGP		did_date3
Encounter Date	100kGP	mhmd_v4_event mhldds_event	mhd_eventdate
Encounter Type	100kGP		"Mental Health Services"
Encounter Date	100kGP	mhsds_medical_history_previous_diagnosis mhsds_primary_diagnosis mhsds_secondary_diagnosis	diagdate
Encounter Type	100kGP		"Mental Health Services"
Encounter Date	100kGP	mhsds_provisional_diagnosis	provdiagdate
Encounter Type	100kGP		"Mental Health Services"
Encounter Date	100kGP	mhsds_indirect_activity	indirectactdate
Encounter Type	100kGP		"Mental Health Services"
Encounter Date	100kGP	mhsds_care_activity	carecontdate
Encounter Type	100kGP		"Mental Health Services"
Encounter Date	Both	mortality	event_date
Encounter Type	Both		"Office of National Statistics"
Encounter Type	Both	rtds	"Radiotherapy"
Encounter Date	Both		decisiontotreatdate	For diagnosis codes
Encounter Type	Both	rtds	"Radiotherapy"
Encounter Date	Both		proceduredate
Encounter Date	Both	sact	date_decision_to_treat	For diagnosis, morphology and staging codes
Encounter Type	Both		"Chemotherapy"
Encounter Date	Both	sact	administration_date
Encounter Type	Both		"Chemotherapy"
Encounter Date	NHS-GMS	observation	observation_effective_from
Encounter Type	NHS-GMS		"Genomics England"
Encounter Date	NHS-GMS	tumour tumour_morphology tumour_topography	tumour date fields (see notes)	tumour_diagnosis_day/tumour_diagnosis_month/tumour_diagnosis_year. If day not present then 01 is used. If month not present, data point is not used on the timeline.
Encounter Type	NHS-GMS		"Genomics England"

ICD-10 codes are normalised so that they match the ICD-10 reference data. This includes the removal of any non-numeric characters other than the first character, and inserting a dot at the fourth position (for example, a coded value of "E149D" is normalised to "E14.9"). The original values can be obtained via the "Source Code" column. ↩↩↩↩↩↩↩↩↩↩↩↩↩↩↩