Referrals & Referral Test Data description

Referral data

Referral Data in the CIP-API represents the clinical data passed to the bioinformatics pipeline from TOMS

Field name	Type	Description
referralId	string	Unique human readable referral identifier e.g. r1234567890
referralUid	string	Referral internal unique identifier
referralTests	array	List of tests associated to the referral. See "Referral Test" below.
requester	OrganisationNgis	Requesting organisation of the referral. Example:  "requester":
orderingDate	null or Date	Date of referral being created. See Date. This is the date the "submit" button is pressed in TOMS
pedigree	null or Pedigree	Pedigree - note, this is the Pedigree data at the point the referral was created, therefore does not contain sample information
cancerParticipant	null or CancerParticipant	Only populated for cancer referrals. Contains participant information. For details see CancerParticipant
clinicalIndication	ClinicalIndication	Clinical Indication of the referral. See Clinical Indication Example:  "clinicalIndication":
collection	string	Optional field that can contain common identifier for research cohorts using GMS Framework. Only used for research cases.

Referral Test data

Field name	Type	Description
referralTestId	string	Test UID
referralTestOrderingDate	null or Date	The date of which the referralTest was sent to Bioinformatics. See Date
clinicalIndicationTest	ClinicalIndicationTest	Clinical indication and associated test type Example:  "clinicalIndicationTest": {  "clinicalIndicationTestTypeCode": "R98.2",  "testTypeId": "8a6f72ad-c4b7-4575-a654-34c9258f5e7c",  "technology": {  "testTechnologyId": "2ad3a7f4-e917-4688-a53b-a560892bc748",  "testTechnologyDescription": "WGS"  },  "clinicalIndicationTestTypeId": "5855bf27-6f9d-4c04-9d64-a163d618b234",  "testTypeName": "Inborn errors of metabolism WGS"  }
tumourSamples	null or array	Only populated for cancer referrals. See TumourSample  UPDATE: In GelReportModels release 7.7 (part of Anna NGIS release) labSampleId part of participant (v1.3.0) in the array of TumorSample is now a String, previously it was an integer
germlineSamples	null or array	Populated for rare disease samples and cancer samples where there is a matched germline sample. See GermlineSample  UPDATE: In GelReportModels release 7.7 (part of Anna NGIS release) labSampleId part of participant (v1.3.0) in the array of GermlineSamples is now a String, previously it was an integer
analysisPanels	null or array	Only populated for rare disease cases. Contains details of the PanelApp panel(s) applied for this test. See AnalysisPanel. Example:  "analysisPanels": [  {  "panelName": "Inborn errors of metabolism",  "multipleGeneticOrigins": "No",  "specificDisease": "R98",  "reviewOutcome": null,  "panelId": "467",  "panelVersion": "2.15"  }]
interpreter	OrganisationNgis	Organisation assigned for the interpretation of this test. See OrganisationNgis below.
processingLab	OrganisationNgis	Organisation assigned for the processing of the test. See OrganisationNgis below.
priority	Priority	Test priority as entered in TOMS. Either routine or urgent.  These map to the case_priority field returned from the interpretation request endpoint as follows:  ‘routine’ -> ‘medium’  ‘urgent’ -> ‘urgent’
pipelineStartDate	null or Date	Always null
diseasePenetrances	null or array	May be populated or null. Contains list of disease penetrances for this test. Includes the specificDisease name and the penetrance (either 'complete or 'incomplete')
matchedSamples	null or array	Only populated for cancer cases with matched tumour-germline samples. Contains list of matched sample IDs. Example:  "matchedSamples": [  {  "germlineSampleId": "LP5000071-DNA_C01",  "tumourSampleId": "LP5000063-DNA_C01"  }  ]

NGIS Organisation data

Field name	Data type	Value description
organisationId	string	Organisation id e.g. 823f68c3-ceb0-b44b-b3c7-0e45f66f4e2a
organisationCode	string	Organisation code e.g. RWH
organisationName	string	Organisation name e.g. East and North Hertfordshire NHS Trust
organisationNationalGroupingId	string	GLH ODS code e.g. 699M0
organisationNationalGroupingName	string	GLH name e.g. East Mids and East of England

Pedigree data

This is the pedigree data from TOMS

Field name	Type	Description
versionControl	null or VersionControl	Always null
LDPCode	null or string	Always null
familyId	string	Human readable referral ID e.g. r1234567890
members	array	List of members of a pedigree. See PedigreeMember.  UPDATE: In GelReportModels release 7.7 (part of Anna NGIS release) labSampleId part of participant (v1.3.0) in the array of GermlineSamples is now a String, previously and integer
analysisPanels	null or array	Always null in referral pedigree. Can be found in ReferralTest > analysisPanels (see above).
diseasePenetrances	null or array	Always null in referral pedigree. Can be found in ReferralTest > diseasePenetrances (see above).
readyForAnalysis	boolean	Flag indicating if a pedigree is ready for analysis
familyQCState	null or FamilyQCState	Only present for rare disease cases. See FamilyQCState for available options.

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Last update: 2022-04-01