Inhibition - Quantification Rule (PICQUANT)
Version: v3.0.0 Status: Normative (text), Illustrative (diagrams only) Scope: IC inhibition detection for quantification samples with error handling based on quant levels and test history Domain: RULES-INHQUANT Precedence: Within IC inhibition rule set
Statement
The system shall execute the PICQUANT rule to evaluate Internal Control (IC) inhibition for quantification samples and assign appropriate well errors based on the IC CT threshold, quantification level relative to LoD and 10,000 copies/mL, and whether the sample has been tested before.
When IC CT is elevated (>35), the rule determines outcome based on quantification results: high quantification (>10,000) compensates for inhibition and passes, positive but low quantification triggers either ICQUANT_FIRST_RUN or ICQUANT_INHP depending on test history, and negative quantification triggers either ICQUANT_FIRST_RUN or ICQUANT_INHN.
Quick Reference
| ID | Core Behavior | Priority | Status |
|---|---|---|---|
| REQ-RULES-INHQUANT-001 | Evaluate IC inhibition and assign errors based on CT, quant, and history | HIGH | Draft |
Key Integration Points: Analytics Rules Engine, Well Observation Data, Sample History Service, Error Management
Rule Summary
| Property | Value |
|---|---|
| Name | PICQUANT |
| Also Known As | IC for Quant |
| Triggers | When evaluating IC inhibition for quantification samples |
| Output | Sets well error codes (ICQUANT_INHN, ICQUANT_INHP, ICQUANT_FIRST_RUN) or passes |
Rule Flowchart (Illustrative)
This diagram illustrates the PICQUANT decision logic. The rule passes when IC CT is normal or when high quantification compensates for inhibition. Error codes vary based on test history and quantification status.
Definitions
| Term | Definition |
|---|---|
| CT | Cycle Threshold - the PCR cycle number at which fluorescence exceeds threshold |
| IC | Internal Control - a control target used to validate PCR amplification |
| LoD | Limit of Detection - the lowest concentration reliably detected |
| PICQUANT | Rule identifier for IC Inhibition Quantification check |
| Quant | Quantification value from PCR analysis (copies/mL) |
| ICQUANT_INHN | Error code for inhibition detected with negative quantification on retest |
| ICQUANT_INHP | Error code for inhibition detected with positive (low) quantification on retest |
| ICQUANT_FIRST_RUN | Error code for inhibition detected on first run requiring retest |
Assumptions
- The rule is executed within the analytics rules engine context
- Well observation data includes IC and non-IC target measurements
- Sample history service is available to determine prior test status
- LoD values are configured per mix/target combination
- Quantification values are available for non-IC observations
Requirements
IC Inhibition Quantification Validation (REQ-RULES-INHQUANT-001)
FR-INHQUANT-001: Evaluate IC Inhibition for Quantification Samples
The system shall execute the PICQUANT rule to evaluate IC inhibition for quantification samples and set appropriate well errors based on IC CT threshold, quantification level relative to LoD and 10,000, and prior testing status.
Inputs/Outputs
| Direction | Data | Source/Target |
|---|---|---|
| Input | IC observation with CT value | Well observation data |
| Input | Non-IC observations with quant values | Well observation data |
| Input | LoD values per mix/target | Kit configuration |
| Input | Sample testing history | Sample History Service |
| Output | Well error code | Error Management |
Acceptance Criteria
Pass Conditions:
- Given an observation with IC CT <= 35, when the PICQUANT rule is executed, then the rule shall pass with no error
- Given an observation with IC CT > 35 AND at least one non-IC observation with quant > LoD AND at least one non-IC observation with quant > 10,000, when the PICQUANT rule is executed, then the rule shall pass with no error
Negative Quantification Path:
- Given an observation with IC CT > 35 AND no non-IC observation with quant > LoD AND the sample/mix has been tested before, when the PICQUANT rule is executed, then the rule shall set well error ICQUANT_INHN
- Given an observation with IC CT > 35 AND no non-IC observation with quant > LoD AND the sample/mix has NOT been tested before (first run), when the PICQUANT rule is executed, then the rule shall set well error ICQUANT_FIRST_RUN
Positive Low Quantification Path:
- Given an observation with IC CT > 35 AND at least one non-IC observation with quant > LoD AND no non-IC observation with quant > 10,000 AND the sample/mix has been tested before, when the PICQUANT rule is executed, then the rule shall set well error ICQUANT_INHP
- Given an observation with IC CT > 35 AND at least one non-IC observation with quant > LoD AND no non-IC observation with quant > 10,000 AND the sample/mix has NOT been tested before (first run), when the PICQUANT rule is executed, then the rule shall set well error ICQUANT_FIRST_RUN
Threshold Configuration:
- The system shall use an IC CT inhibition threshold of 35
- The system shall use a high quantification compensation threshold of 10,000 copies/mL
- The system shall retrieve LoD values from the configured mix/target parameters
- The system shall evaluate all non-IC observations in the well when determining quantification status
Error Handling
- No IC observation in well: skip rule evaluation for the well
- IC CT value is null or invalid: skip rule evaluation for the well
- No non-IC observations in well: skip rule evaluation for the well
- Sample history service unavailable: treat the sample as first run
Trace: Source: 3.0.0-Inhibition - Quantification / Requirements Table (Rows 1-10), Objective, Flow Chart (image156.png) | Related: IC Inhibition rules | Tests: See scenarios
Configuration Options
| Option | Default | Description | Affects |
|---|---|---|---|
ic_ct_threshold | 35 | CT value above which IC is considered inhibited | REQ-RULES-INHQUANT-001 |
high_quant_threshold | 10,000 | Quantification level (copies/mL) that compensates for inhibition | REQ-RULES-INHQUANT-001 |
UI Detail (Illustrative)
[REVIEW REQUIRED: No UI specifications identified in source material. This is a backend analytics rule with no direct UI components.]
Implementation (Illustrative)
| Component | Location |
|---|---|
| BicRule | Analyzer/Rules/BicRule.php |
| PicquantRule | Analyzer/Rules/PicquantRule.php |
Traceability Matrix
| Requirement | Title | Verification | Implementation | Test Cases | Status |
|---|---|---|---|---|---|
| REQ-RULES-INHQUANT-001 | Evaluate IC Inhibition for Quantification Samples | Test | BicRule, PicquantRule | PICQUANT-001 to PICQUANT-006 | Draft |
Notes
- Rule ID: PICQUANT
- Also Known As: IC for Quant
- Flow diagram reference: See
media/image156.pngfor original rule execution flow - The 10,000 threshold distinguishes between definitive positive results (quant > 10,000 passes) and borderline positive results that warrant error flagging
- ICQUANT_FIRST_RUN is used in both negative and positive quantification paths to indicate first-time inhibition detection requiring retest
- IC inhibition can suppress PCR amplification, potentially causing false negatives or inaccurate quantification
Acceptance Tests
Test: REQ-RULES-INHQUANT-001
Test: PICQUANT-001 - Pass When IC CT Normal
Given: A well with IC and non-IC observations
And: IC CT value is 30
And: Target A quantification is 500
When: The PICQUANT rule is executed
Then: The rule shall pass with no error
And: No well error shall be set
Test: PICQUANT-002 - Pass When High Quantification Compensates
Given: A well with elevated IC CT but high quantification
And: IC CT value is 38
And: Target A quantification is 15,000
When: The PICQUANT rule is executed
Then: The rule shall pass with no error
And: No well error shall be set
Test: PICQUANT-003 - ICQUANT_FIRST_RUN on First Test with Low Positive Quant
Given: A well with elevated IC CT and low quantification
And: IC CT value is 37
And: Target A quantification is 5,000 (above LoD, below 10,000)
And: The sample/mix has NOT been tested before
When: The PICQUANT rule is executed
Then: The rule shall set well error ICQUANT_FIRST_RUN
Test: PICQUANT-004 - ICQUANT_INHP on Retest with Positive Low Quant
Given: A well with elevated IC CT and positive but low quantification
And: IC CT value is 36
And: Target A quantification is 500 (above LoD, below 10,000)
And: The sample/mix has been tested before
When: The PICQUANT rule is executed
Then: The rule shall set well error ICQUANT_INHP
Test: PICQUANT-005 - ICQUANT_INHN on Retest with Negative Quant
Given: A well with elevated IC CT and negative quantification
And: IC CT value is 40
And: Target A quantification is 0 (below LoD)
And: The sample/mix has been tested before
When: The PICQUANT rule is executed
Then: The rule shall set well error ICQUANT_INHN
Test: PICQUANT-006 - ICQUANT_FIRST_RUN on First Test with Negative Quant
Given: A well with elevated IC CT and negative quantification
And: IC CT value is 39
And: Target A quantification is 0 (below LoD)
And: The sample/mix has NOT been tested before
When: The PICQUANT rule is executed
Then: The rule shall set well error ICQUANT_FIRST_RUN
Related Design Documents
| Design Document | Relevant Sections |
|---|---|
| SDD Algorithms | IC Inhibition Rules |
Appendix: Process Artifacts
Completion Checklist
- All requirements are capability-level (describe behavior, not UI)
- Requirement variants consolidated (no requirement explosion) - N/A, single requirement
- UI details are fully demoted to Illustrative section
- Configuration options are not encoded as requirements
- Acceptance criteria describe behavior, not UI mechanics
- Every requirement has acceptance criteria and source traceability
- Error handling addressed for I/O, validation, and external system requirements
- Open questions documented with owners assigned - None identified
- Consolidations documented in Reviewer Notes with reversibility info
- Module can survive a full UI redesign unchanged
- Threshold-type acceptance criteria do not introduce new capabilities
- Traceability matrix is complete
Reviewer Notes
No Consolidation Required
The source file contains a single requirement (REQ-RULES-INHQUANT-001) representing one cohesive rule capability. No consolidation was performed.
Source Structure:
- 1 requirement with 6 detailed Given/When/Then acceptance criteria
- Decision tree logic preserved in acceptance criteria
- Error codes and thresholds preserved as acceptance criteria (grouped by concern)
Readability Improvements:
- Added Statement section for quick understanding
- Added Mermaid decision flowchart illustrating the rule logic
- Grouped acceptance criteria by concern (Pass Conditions, Negative Path, Positive Low Path, Threshold Configuration)
- Added blank lines before bullet lists for PDF rendering
- Moved tests to end with back-link to requirement
- Changed "Non-normative" to "Illustrative"
- Added Quick Reference and Rule Summary tables
Reversibility: Not applicable - no consolidation performed.
Source Reference:
- Source:
output/srs/rules/rule-inhibition-quantification.md - Original SDD:
output/pilot/rules/rule-inhibition-quantification/sdd/rule-inhibition-quantification-design.md