IC Qualitative Serum Rule (PICQUAL_SERUM)

Version: v3.0.0 Status: Normative (text), Illustrative (diagrams only) Scope: IC validity evaluation for qualitative patient samples with Serum specimen type Domain: RULES-ICQUALSERUM Precedence: Part of IC validation rule family

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Statement

The system shall evaluate qualitative serum wells for suspected inhibition by analyzing Internal Control (IC) cycle threshold values and non-IC observation status using the PICQUAL_SERUM rule.

The rule implements a two-stage evaluation: first checking if the IC CT is within an acceptable threshold (<=35), then examining non-IC target results when IC CT exceeds the threshold. This approach prevents false-positive inhibition errors when positive targets demonstrate successful PCR despite IC failure (due to reagent competition).

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Quick Reference

ID	Core Behavior	Priority	Status
REQ-RULES-ICQUALSERUM-001	Evaluate IC validity for qualitative serum samples	HIGH	Draft

Key Integration Points: Analytics Engine, Well data processing, Error reporting subsystem

Rule Summary

Property	Value
Name	PICQUAL_SERUM
Specimen Type	Serum
Sample Type	Qualitative
IC CT Threshold	35 cycles
Error Code	ICQUAL_INHN

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Rule Flowchart (Illustrative)

This diagram illustrates the two-stage IC validation logic. Positive non-IC observations override high IC CT because they prove successful PCR amplification despite IC failure.

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Definitions

Term	Definition
IC	Internal Control - a target used to validate PCR amplification success
CT	Cycle Threshold - the PCR cycle number at which fluorescence exceeds baseline
Cutoff	Assay-defined CT value above which an observation is considered negative
Qualitative Assay	An assay that determines presence/absence rather than quantity
Serum	Blood specimen type without cellular components
Inhibition	PCR amplification failure due to interfering substances in the sample

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Assumptions

• Wells being evaluated contain qualitative samples with Serum specimen type
• IC target observation is present with a valid CT value
• Assay-specific cutoff value is configured for determining positive/negative status
• The rule is invoked within the analytics rule execution framework

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Requirements

IC Validation (REQ-RULES-ICQUALSERUM-001)

FR-ICQUALSERUM-001: Evaluate IC Validity for Qualitative Serum Samples

The system shall evaluate qualitative serum wells for suspected inhibition by analyzing Internal Control (IC) cycle threshold values and non-IC observation status using the PICQUAL_SERUM rule.

Inputs/Outputs

Direction	Data	Source/Target
Input	Well observation data (IC CT, non-IC CT values)	PCR analysis
Input	Assay-configured cutoff value	Kit configuration
Output	Pass/Fail status	Well record
Output	Error code (ICQUAL_INHN)	Well error record

Acceptance Criteria

IC CT Threshold Evaluation:

• The rule shall terminate without error when the IC CT value is less than or equal to 35
• The rule shall use an IC CT threshold value of 35 cycles
• The rule shall evaluate the IC target observation CT value as the primary determination factor

Non-IC Observation Evaluation:

• The rule shall terminate without error when the IC CT value is greater than 35 AND at least one non-IC observation is positive (CT less than or equal to cutoff)
• The rule shall generate an inhibition error when the IC CT value is greater than 35 AND all non-IC observations are negative (CT greater than cutoff)
• The rule shall evaluate all non-IC observations in the well to determine collective status

Classification Logic:

• The rule shall classify non-IC observations as negative when CT is greater than the assay-configured cutoff value
• The rule shall classify non-IC observations as positive when CT is less than or equal to the assay-configured cutoff value

Scope:

• The rule shall apply only to wells containing qualitative samples with Serum specimen type

Error Handling

• IC CT > 35 AND all non-IC observations negative: Generate error code ICQUAL_INHN indicating suspected inhibition
• IC observation missing: Not applicable - mixes without IC observation are not recognized by the system

Trace: Source: 3.0.0-IC for qual Serum (Requirements Table Rows 1-2, Objective Section) | Jira: BT-674 | Tests: See scenarios | Related: PICQUAL rule family (other specimen types)

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Configuration Options

Option	Default	Description	Affects
ic_ct_threshold	35	Maximum acceptable CT value for IC to be considered valid	REQ-RULES-ICQUALSERUM-001
cutoff	Assay-defined	CT value above which an observation is considered negative	REQ-RULES-ICQUALSERUM-001

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UI Notes (Illustrative)

REQ-RULES-ICQUALSERUM-001 UI Specifications

• Flow diagram available: image157.png
• Rule mapped to IC (Internal Control) target in rule configuration
• Error display follows standard analytics error presentation format

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Implementation (Illustrative)

Component	Location	Purpose
PicqualSerumRule	Analyzer/Rules/PicqualSerumRule.php	IC qualitative serum validation - two-stage IC CT and non-IC positive check

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Traceability Matrix

Requirement	Title	Verification	Implementation	Test Cases	Status
REQ-RULES-ICQUALSERUM-001	Evaluate IC Validity for Qualitative Serum Samples	Test	PicqualSerumRule.php	[Pending]	Draft

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Notes

• This is a serum specimen-specific variant of the PICQUAL rule family
• Other specimen types may use different IC validation rules with different parameters
• The two-stage evaluation approach prevents false-positive inhibition errors when positive targets demonstrate successful PCR despite IC failure (likely due to reagent competition)
• The IC CT threshold of 35 is the standard cutoff for Internal Control validation in this assay type

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Acceptance Tests

Test: REQ-RULES-ICQUALSERUM-001

Back to requirement

Test: IC CT Within Threshold (Pass)

Given:
  well A1:
    specimen_type: Serum
    sample_type: Qualitative
    observation IC:
      target: IC
      ct: 32

When:
  Execute PICQUAL_SERUM rule on well A1

Then:
  well A1:
    error: null
    status: Pass

Test: IC CT At Threshold Boundary (Pass)

Given:
  well A1:
    specimen_type: Serum
    sample_type: Qualitative
    observation IC:
      target: IC
      ct: 35

When:
  Execute PICQUAL_SERUM rule on well A1

Then:
  well A1:
    error: null
    status: Pass

Test: IC CT Above Threshold with All Non-IC Negative (Error)

Given:
  well A1:
    specimen_type: Serum
    sample_type: Qualitative
    observation IC:
      target: IC
      ct: 38
    observation Target1:
      target: Non-IC
      ct: 45
      cls: Neg
    observation Target2:
      target: Non-IC
      ct: 42
      cls: Neg

When:
  Execute PICQUAL_SERUM rule on well A1

Then:
  well A1:
    error: ICQUAL_INHN
    status: Fail

Test: IC CT Above Threshold with Some Non-IC Positive (Pass)

Given:
  well A1:
    specimen_type: Serum
    sample_type: Qualitative
    observation IC:
      target: IC
      ct: 38
    observation Target1:
      target: Non-IC
      ct: 28
      cls: Pos
    observation Target2:
      target: Non-IC
      ct: 42
      cls: Neg

When:
  Execute PICQUAL_SERUM rule on well A1

Then:
  well A1:
    error: null
    status: Pass

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Related Design Documents

Design Document	Relevant Sections
SDD Algorithms	IC Validation Rules

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Appendix: Process Artifacts

Completion Checklist

• All requirements are capability-level (describe behavior, not UI)
• Requirement variants consolidated (no requirement explosion)
• 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
• Consolidations documented in Reviewer Notes with reversibility info
• Module can survive a full UI redesign unchanged
• Refinements folded into Acceptance Criteria
• Traceability matrix is complete

Reviewer Notes

No Consolidation Required

This domain contains a single requirement (REQ-RULES-ICQUALSERUM-001) representing the complete PICQUAL_SERUM rule behavior. No consolidation was necessary as the source material already represents a single coherent capability.

Source Reference:

• Source: /home/aron/code/req_docs/output/pilot/rules/rule-ic-qual-serum/rule-ic-qual-serum-restructured.md
• SDD: /home/aron/code/req_docs/output/pilot/rules/rule-ic-qual-serum/sdd/rule-ic-qual-serum-design.md
• Confluence: 3.0.0-IC for qual Serum

Design Rationale Preserved

The two-stage evaluation logic (IC CT check followed by non-IC status check) is documented in the SDD. The error suppression logic prevents false positives when positive targets indicate successful PCR despite high IC CT.