OncomineCfnaRunQcChecker

URS & FS — User Requirements and Functional Specification

This document describes the controlled interface and behaviour of OncomineCfnaRunQcChecker for Oncomine cfNA Run QC Checker.

Domain limits and critical parameters

• Performs comprehensive quality verification of Oncomine cfNA sequencing runs per FDA CDx guidance, CAP/CLIA and Thermo Fisher User Guide: Ion Torrent chip metrics (ISP density 200–1200 K/mm², polyclonal rate ≤30%, AQ20 ≥70%), AmpliSeq enrichment (on-target ≥70%, uniformity ≥80%, mean depth ≥20,000×, amplicon dropout ≤5%), UMI/molecular tag processing (deduplication ≤90%, unique molecular depth ≥2,000×, consensus family size ≥3.0, collision rate ≤5%), cfRNA-specific metrics (RT efficiency ≥0.7, f
• ⚠️ Critical: Polyclonality >30% on Ion Torrent is IRREVERSIBLE. AQ20 (not Q30) is correct quality metric for Ion Torrent. UMI depth <2,000× makes VAF <0.5% detection unreliable regardless of total depth. Homopolymer errors are Ion Torrent Achilles' heel. For cfRNA+cfDNA panels, both components must pass QC independently. Amplicon dropout >5% may miss critical variants. Tool assesses RUN QUALITY only; does not replace bioinformatic variant analysis or clinical interpretation. Thresholds based on

URS — User Requirements Specification

input.csv contract

RunID,PanelVersion,ChipType,NucleicAcidType,ISP_Density_K_mm2,MinISP_Density,MaxISP_Density,PolyclonalRate_Percent,MaxPolyclonalRate_Percent,PercentAQ20_Reads,MinAQ20_Percent,TotalReads_Million,MinTotalReads_Million,OnTargetRate_Percent,MinOnTargetRate_Percent,Uniformity_Percent,MinUniformity_Percent,MeanAmpliconDepth_X,MinMeanAmpliconDepth_X,AmpliconsWithLowCoverage_Count,TotalAmplicons_Count,MaxLowCoverageAmplicon_Fraction,UMIDeduplication_Rate,MaxUMIDeduplication_Rate,UniqueMolecularDepth_X,MinUniqueMolecularDepth_X,ConsensusFamilySize_Mean,MinConsensusFamilySize,UMICollisionRate_Percent,MaxUMICollisionRate_Percent,RNA_Component_Present,RT_Efficiency_Score,MinRT_Efficiency_Score,FusionPanel_Coverage_Percent,MinFusionCoverage_Percent,BackgroundNoise_VAF,MaxBackgroundNoise_VAF,HomopolymerError_Rate,MaxHomopolymerError_Rate,StrandBias_Artifacts_Detected,PositiveControl_Pass,NegativeControl_Pass,NoTemplateControl_Pass,InternalAmplification_Control_Pass,CriticalHotspots_Total,CriticalHotspots_AtMinDepth,MinHotspotCoverage_Fraction
OC-CFNA-2026-001,Comprehensive_v3,550,cfDNA,850,200,1200,18.0,30,85.0,70,120,50,92.0,70,88.0,80,35000,20000,3,280,0.05,0.78,0.90,7700,2000,4.5,3.0,1.5,5.0,false,0,0.7,0,80,0.0003,0.001,0.008,0.02,false,true,true,true,true,190,188,0.95
OC-CFNA-2026-002,Lung_cfDNA,540,cfDNA+cfRNA,1350,200,1200,42.0,30,68.0,70,85,50,65.0,70,72.0,80,12000,20000,25,190,0.05,0.93,0.90,840,2000,2.1,3.0,8.5,5.0,true,0.55,0.7,62.0,80,0.002,0.001,0.035,0.02,true,true,true,true,true,190,155,0.95

Input validation rules

FS — Functional Specification

Example output.json

{
  "utilityId": "oncominecfnarunqcchecker",
  "utilityFolder": "OncomineCfnaRunQcChecker",
  "package": "LiquidBiopsy",
  "overallStatus": "PASS|WARNING|FAIL",
  "sourceFile": "input.csv",
  "processedAtUtc": "2026-06-10T00:00:00Z",
  "checks": [
    {
      "parameter": "RunID",
      "value": "OC-CFNA-2026-001",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-001"
    },
    {
      "parameter": "PanelVersion",
      "value": "Comprehensive_v3",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-002"
    },
    {
      "parameter": "ChipType",
      "value": "550",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-003"
    },
    {
      "parameter": "NucleicAcidType",
      "value": "cfDNA",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-004"
    },
    {
      "parameter": "ISP_Density_K_mm2",
      "value": "850",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-005"
    },
    {
      "parameter": "MinISP_Density",
      "value": "200",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-006"
    },
    {
      "parameter": "MaxISP_Density",
      "value": "1200",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-007"
    },
    {
      "parameter": "PolyclonalRate_Percent",
      "value": "18.0",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-008"
    },
    {
      "parameter": "MaxPolyclonalRate_Percent",
      "value": "30",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-009"
    },
    {
      "parameter": "PercentAQ20_Reads",
      "value": "85.0",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-010"
    },
    {
      "parameter": "MinAQ20_Percent",
      "value": "70",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-011"
    },
    {
      "parameter": "TotalReads_Million",
      "value": "120",
      "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": "OncomineCfnaRunQcChecker.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.