UrineBiofluidSampleGateChecker

URS & FS — User Requirements and Functional Specification

This document describes the controlled interface and behaviour of UrineBiofluidSampleGateChecker for Urine Biofluid Sample Gate Checker.

Domain limits and critical parameters

• Performs urine suitability verification per CAP/CLIA §GEN.48800, CLSI GP44-A2, FDA urine biomarker guidance and urinary liquid biopsy consensus recommendations: stabilization timing (≤2h to stabilizer, validated stabilizer required, no-stabilizer + >4h delay = significant degradation), physicochemical parameters (pH 5.0–8.0, specific gravity 1.005–1.030, volume ≥ minimum), analyte yield (cfDNA yield ≥ minimum, concentration ≥0.5 ng/mL, fragment peak ~170±30 bp, DIN ≥1.5), inhibition testing (spi
• ⚠️ Critical: Urine is the most variable biofluid; every parameter affects results. Without stabilizer, cfDNA degrades at ~20%/hour at RT. Diluted urine (SG <1.005, creatinine <20) may cause false negatives. Hematuria >2+ makes quantitative tumor DNA interpretation impossible. PCR inhibition is the most common technical failure cause for urine. First-catch urine contains more urethral/bladder cells/DNA than midstream. UTI is not absolute contraindication but requires documentation and cautious in
• • CAP/ISO accreditation: Documentation of pre-analytical QC for non-traditional matrices.
• ⚠️ Note: This utility assesses PRE-ANALYTICAL URINE SAMPLE SUITABILITY. It does not replace post-extraction QC or analytical assay validation. For ACCEPTABLE_WITH_LIMITATIONS status, results must be accompanied by a comment describing identified limitations. For DILUTED_DEGRADED status, re-collection is recommended before issuing a negative result.

URS — User Requirements Specification

input.csv contract

SampleID,PatientID,TargetAnalyte,ClinicalIndication,CollectionType,CollectionDateTime,StabilizationDateTime,ProcessingDateTime,TimeToStabilization_Hours,MaxTimeToStabilization_Hours,TimeToProcessing_Hours,MaxTimeToProcessing_Hours,StabilizerUsed,Stabilizer_Validated_ForAnalyte,Volume_mL,MinVolume_mL,pH_Value,MinAcceptable_pH,MaxAcceptable_pH,SpecificGravity,MinSpecificGravity,MaxSpecificGravity,Dipstick_Performed,Hematuria_Score,MaxHematuria_Score,Proteinuria_mg_dL,MaxProteinuria_mg_dL,Pyuria_Detected,LeukocyteEsterase_Score,Nitrite_Positive,Bacteriuria_Detected,CfDNA_Yield_ng,MinCfDNA_Yield_ng,CfDNA_Concentration_ng_mL,MinCfDNA_Concentration_ng_mL,CfDNA_FragmentPeak_bp,ExpectedFragmentPeak_bp,FragmentTolerance_bp,DIN_Score,MinDIN_Score,InhibitionTest_Performed,InhibitionTest_Recovery_Percent,MinInhibitionRecovery_Percent,PCR_Inhibition_Detected,Urea_Concentration_mM,MaxUrea_Concentration_mM,Creatinine_mg_dL,MinCreatinine_mg_dL,CreatinineNormalized_Reporting,StorageCondition,RequiredStorageCondition,StorageCondition_Met,FreezeThawCycles,MaxFreezeThawCycles
UR-2026-001,PAT-BLADDER-042,Urine_cfDNA,Bladder_Monitoring,First_Catch,2026-06-08T07:00:00,2026-06-08T07:30:00,2026-06-08T14:00:00,0.5,2.0,7.0,24.0,EDTA,true,45.0,10.0,6.2,5.0,8.0,1.018,1.005,1.030,true,0.5,2.0,8.0,30.0,false,0,false,false,28.5,5.0,0.63,0.5,168,170,30,2.8,1.5,true,92.0,70,false,280,500,85.0,20,true,-80C,-80C,true,0,2
UR-2026-002,PAT-PROSTATE-055,Urine_cfDNA,Prostate_Cancer,Midstream,2026-06-07T14:00:00,,2026-06-08T10:00:00,0,2.0,20.0,24.0,None,false,120.0,10.0,8.5,5.0,8.0,1.002,1.005,1.030,true,3.0,2.0,45.0,30.0,true,2,true,true,2.1,5.0,0.018,0.5,220,170,30,1.2,1.5,true,35.0,70,true,620,500,8.0,20,true,4C,-80C,false,3,2

Input validation rules

FS — Functional Specification

Example output.json

{
  "utilityId": "urinebiofluidsamplegatechecker",
  "utilityFolder": "UrineBiofluidSampleGateChecker",
  "package": "LiquidBiopsy",
  "overallStatus": "PASS|WARNING|FAIL",
  "sourceFile": "input.csv",
  "processedAtUtc": "2026-06-10T00:00:00Z",
  "checks": [
    {
      "parameter": "SampleID",
      "value": "UR-2026-001",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-001"
    },
    {
      "parameter": "PatientID",
      "value": "PAT-BLADDER-042",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-002"
    },
    {
      "parameter": "TargetAnalyte",
      "value": "Urine_cfDNA",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-003"
    },
    {
      "parameter": "ClinicalIndication",
      "value": "Bladder_Monitoring",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-004"
    },
    {
      "parameter": "CollectionType",
      "value": "First_Catch",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-005"
    },
    {
      "parameter": "CollectionDateTime",
      "value": "2026-06-08T07:00:00",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-006"
    },
    {
      "parameter": "StabilizationDateTime",
      "value": "2026-06-08T07:30:00",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-007"
    },
    {
      "parameter": "ProcessingDateTime",
      "value": "2026-06-08T14:00:00",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-008"
    },
    {
      "parameter": "TimeToStabilization_Hours",
      "value": "0.5",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-009"
    },
    {
      "parameter": "MaxTimeToStabilization_Hours",
      "value": "2.0",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-010"
    },
    {
      "parameter": "TimeToProcessing_Hours",
      "value": "7.0",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-011"
    },
    {
      "parameter": "MaxTimeToProcessing_Hours",
      "value": "24.0",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-012"
    }
  ],
  "criticalFindings": [],
  "warnings": [],
  "audit": {
    "inputHash": "sha256:<calculated at runtime>",
    "rulesVersion": "<utility executable version>",
    "documentation": "UrineBiofluidSampleGateChecker.documentation.html"
  }
}

Traceability matrix

IQ/OQ/PQ test scenarios

QA/QC and change control

• Do not rename columns without updating validator, documentation and test set.
• Retain input.csv, output.json, executable version and checksum.
• Before production use, perform IQ/OQ/PQ or equivalent CSV/CSA verification.
• Critical limits shall be verified against the approved specification, registration dossier and local SOPs.
• The utility provides structured QC decision support; final release decision remains with QA/QP and approved procedures.