NHS North West Genomics
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Use Case: BCR-ABL Monitoring

References

  1. Laboratory Analyte Result - Data Mapping
  2. Test Results Management (LAB-5)
  3. 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

Clinical Pathway Overview

What is being tested

BCR-ABL1 fusion transcript (Philadelphia chromosome) quantification is used to monitor how well a patient with Chronic Myeloid Leukaemia (CML) is responding to tyrosine kinase inhibitor (TKI) treatment. The result is reported as a ratio on the International Scale (%IS), so results from different laboratories can be compared directly.

The end-to-end clinical journey

  1. Patient on treatment - a patient diagnosed with CML is established on TKI therapy and needs regular monitoring of their response.
  2. Sample taken - a blood sample is collected at the scheduled monitoring interval.
  3. Order sent - the requesting clinician's EPR sends the monitoring request to the laboratory.
  4. Testing performed - the sample is analysed on a Cepheid GeneXpert analyser. (LAB-5, Automation Manager → Order Filler.)
  5. Result reported - the %IS result reaches the requesting clinician. (LAB-3.)
  6. Clinical decision - the clinician tracks the %IS trend over successive tests to confirm the treatment is working, or to detect early signs of resistance/relapse and consider a change of therapy.
flowchart LR
    A[Patient established<br/>on TKI treatment] --> B[Sample taken at<br/>monitoring interval]
    B --> C[Order sent to<br/>laboratory]
    C --> D[BCR-ABL1<br/>quantification]
    D --> E[%IS result reported<br/>to clinician]
    E --> F[Trend reviewed -<br/>continue or<br/>change treatment]

Why this matters for developers

  • The result is a %IS ratio (LOINC 69380-4), carried as a Laboratory Analyte Result Observation, not a plain numeric value on its own - see Result Detail below for how the underlying BCR-ABL/BCR-ABL Ct/ABL/%MR components map onto it.
  • Because clinicians compare each result against previous ones to judge the trend, consistent mapping of the %IS value (rather than raw Ct/control values) is what actually drives the clinical decision.

Actors

IHE Actor Role System
Automation Manager Performs the analytical phase (testing) Cepheid GeneXpert (ASTM-communicating)
Intermediary Converts Cepheid's ASTM result to the NW Standard, routes it, and converts it to a CSV for iGene's import Regional Integration Engine (RIE)
Order Filler Laboratory Information Management System iGene
Order Placer Requesting clinician (treatment response monitoring) Requesting Trust EPR

Transactions

Transaction Description
LAB-5 Automation Manager → Order Filler (analytical result), via the RIE (ASTM → HL7 v2 R32 NW Standard → FHIR Message R32 → CSV)
LAB-3 Order Filler → Order Placer (validated report)

Current Process

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.

This use case reflects BCR-ABL1 quantification performed on an ASTM-communicating analyser (e.g. Cepheid GeneXpert) with results ultimately consumed by iGene, following the generic Analytical/Post-Analytical phases below.

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

Technical Process (Cepheid to iGene)

Between the analyser and iGene, the Regional Integration Engine (RIE) converts and routes the result:

  1. Cepheid sends an ASTM Result message to the RIE.
  2. The RIE converts this to an HL7 v2 R32 message (NW Standard).
  3. The RIE transforms this into a FHIR Message R32.
  4. The RIE routes the message.
  5. The RIE's Cepheid handler converts this into a CSV file for iGene to import.
sequenceDiagram
    participant Cepheid as Cepheid GeneXpert<br/>Automation Manager
    participant RIE as Regional Integration Engine (RIE)<br/>Intermediary
    participant iGene as iGene<br/>Order Filler

    Cepheid ->> RIE: ASTM Result message
    RIE ->> RIE: Convert to HL7 v2 R32 message (NW Standard)
    RIE ->> RIE: Transform to FHIR Message R32
    RIE ->> RIE: Route message
    RIE ->> RIE: Cepheid handler converts to CSV
    RIE ->> iGene: CSV import

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.

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

Future Process

No distinct future-state changes are currently defined for this pathway - this section will be populated as further Cepheid/ASTM analyser integrations are brought onto the same pattern.

Data Models

Result Detail

See Laboratory Analyte Result - Data Mapping for the full field mapping (openEHR / HL7 v2 / LOINC-SNOMED / FHIR / iGene) this use case populates. These entries are expressed in Observation.component, structured as the BCR-ABL Monitoring Result Panel Questionnaire - its item.definition/item.code values are inferred directly from this IG's own Observation-BCRABL-Valid/Observation-BCRABL-Invalid examples.

BCRABL

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

Examples

Example Description
Observation-BCRABL-Valid A normal result - valueQuantity populated
Observation-BCRABL-Invalid An out-of-range result - dataAbsentReason populated instead of valueQuantity

Security Considerations

Includes:

Developer Guides

No Developer Guides notebook covers this use case yet.