NHS North West Genomics - Local Development build (v2.1.4) built by the FHIR (HL7® FHIR® Standard) Build Tools. See the Directory of published versions

Laboratory Analyte Result Introduction

Reference

1. openEHR Laboratory analyte result

Overview

BCR-ABL1 concentration testing is used to monitor the amount of the fusion gene (Philadelphia chromosome) in chronic myeloid leukemia (CML) patients, with results typically reported on an International Scale (%IS) to measure treatment response.

graph

analysis["Analytical Phase (Testing)"]
report["Post-Analytical Phase (Interpretation & Reporting)"]
placer[Order Placer]

analysis --> |Laboratory Analyte Result| report
report --> |Genomic Report| placer  

  classDef green fill:#D5E8D4;
  class placer green

Analytical Phase (Testing)

This is the core stage where the targeted substance (analyte) is actually measured.

• Calibration & Quality Control (QC): Before testing patient samples, laboratory technicians calibrate the instrument and run Quality Control materials with known values to ensure the equipment is operating perfectly.
• Analysis: The processed sample is placed into an automated analyzer. Depending on the analyte, the machine uses techniques like mass spectrometry, chromatography, or colorimetric spectroscopy to quantify or detect the substance.
• Validation: The instrument produces raw data which is processed and mathematically converted into a meaningful concentration.

​Output: Laboratory Analyte Result

Post-Analytical Phase (Interpretation & Reporting)

Once the analyzer generates a value, the results must be evaluated and distributed to the requesting physician or client.

• Verification: The laboratory scientist reviews the result against the laboratory's reference ranges (what is considered "normal") and validates the data quality.
• Reporting: The final validated result is transmitted to the clinician's health record or client file.
• Critical Action: If the analyte is at a dangerously abnormal level, immediate protocols (e.g., direct calls to the doctor) are enacted.Would you like to know more about how a specific clinical test (like a Comprehensive Metabolic Panel or Complete Blood Count) works, or are you interested in a specific analytical technology (like Mass Spectrometry)?

Output: Genomic Test Report Process Flow: Test Results Management (LAB-5)

Data Mapping

Laboratory Analyte Result

openEHR	Data Element	HL7 v2 R32	LOINC / SNOMED	HL7 FHIR	iGene	Example
	Patient Identifier	PID-3 Patient Identifier			P-Number
Specimen		Specimen Number (Order Filler)	SPM-2 Specimen ID	DiagnosticReport.specimen	S-Number
	Report Identifier			DiagnosticReport.identifier[PlacerNumber]	T-Number
	Order Number	ORC-2 Placer Order Number		DiagnosticReport.basedOn.identifier	R-Number
	Test Code	OBR-4 Universalserviceidentifier	Recommended	DiagnosticReport.code		BCRABL
Result Status	Result Status	OBR-25 ResultStatus		DiagnosticReport.status		F
Result				DiagnosticReport.result referencing Observation
Analysis performed time	- Test Start DateTime	TQ1-7 Startdatetime		Observation.effectivePeriod.start and DiagnosticReport.effectivePeriod
Analysis performed time	- Test End DateTime	TQ1-8 Enddatetime		Observation.effectivePeriod.end and DiagnosticReport.effectivePeriod
	- Performer	OBX-16 ResponsibleObserver		Observation.performer
	- Status
Analyte name	- Code	OBX-3 ObservationIdentifier	Recommended	Observation.code		BCRABL
Reference range guidance	- Reference Range	OBX-7 ReferenceRange		Observation.referenceRange		0.0030-55.00
Analyte result	- Value	OBX-5 Observation Value		Observation.valueQuantity.value	(IS)	0.011
	- Value Absent	OBX-5 Observation Value		Observation.dataAbsentReason.text	(Test Description)	INVALID [Too high ABL transcript]
	- Unit	OBX-6 Units		Obsevation.valueQuantity.unit		% (IS)
Analyte result detail	- Result Detail (see below)	OBX-4 ObservationSubID (when populated)	Recommended	Observation.component
	- Device Identifier	?? OBX-18 EquipmentInstanceIdentifier		Observation.device

Result Detail

These entries are expressed in Observation.component

BCRABL

Possible LOINC Codes for BCR-ABL:

• 69380-4 t(9;22)(q34.1;q11)(ABL1,BCR) b2a2+b3a2 fusion transcript/control transcript (International Scale) [# Ratio] in Blood or Tissue by Molecular genetics method

Data Element	Local Code	LOINC	SNOMED	iGene	Data Type	Unit	Example
MR	MR			MR	String		4.52
ABL_Analyte_Result	??			ABL_Analyte_Result	String		?? PASS
ABL_Ct	ABL&Ct			ABL_Ct	String		12.2
ABL_EndPt	ABL&EndPt			ABL_EndPt	String		434
ABL_Probe_Check_Result	ABL&			ABL_Probe_Check_Result	String		PASS
BCR-ABL_Analyte_Result	BCR-ABL&			BCR-ABL_Analyte_Result	String		POS
BCR-ABL_Ct	BCR-ABL&Ct			BCR-ABL_Ct	String		30.3
BCR-ABL_EndPt	BCR-ABL&EndPt			BCR-ABL_EndPt	String		164
BCR-ABL_Probe_Check_Result	??			BCR-ABL_Probe_Check_Result	String		?? PASS
BCR-ABL_Target_Delta_Ct	BCR-ABL&Delta Ct			BCR-ABL_Target_Delta_Ct	String		-18.1