ProteinDnaPanelBatchChecker

URS & FS — User Requirements and Functional Specification

This document describes the controlled interface and behaviour of ProteinDnaPanelBatchChecker for Protein/DNA Panel Batch Checker.

Domain limits and critical parameters

• Performs three-tier quality assessment per CAP/CLIA, FDA multi-omics guidance, HUPO-PSI and CPTAC standards: proteomics layer (detection rate ≥80%, intra-batch CV ≤15%, FDR ≤1%, controls, sample QC fail rate ≤10%), genomics layer (depth ≥500×, uniformity ≥80%, on-target ≥60%, Q30 ≥75%, controls), cross-layer concordance (mutation-proteoform agreement ≥85%, protein-mRNA correlation ≥0.4, sample identity verification), batch effects (PCA variance ≤15%, plate position effects, reagent lot tracking)
• ⚠️ Critical: Proteogenomic panels require QC at THREE LEVELS: proteomic, genomic, integration. Cross-layer concordance is unique and critical; without it, multi-omics is meaningless. Protein-mRNA correlation ~0.4–0.7 is biological norm; r<0.3 indicates technical issue. Batch effects typically stronger in proteomics than genomics. Sample identity verification MANDATORY between layers. CROSS_LAYER_FAIL means individual layers may be usable separately but NOT together. Tool assesses TECHNICAL QUALI

URS — User Requirements Specification

input.csv contract

BatchID,PanelName,Platform_Protein,Platform_DNA,RunDate,TotalSamples,ProteinTargets_Total,ProteinTargets_Detected_Mean,ProteinDetection_Rate_Percent,MinProteinDetection_Rate_Percent,ProteinCV_IntraBatch_Percent,MaxProteinCV_IntraBatch_Percent,Protein_FDR_Percent,MaxProtein_FDR_Percent,Protein_LOD_Normalized_Mean,NPX_ScaleFactor_Mean,Protein_PositiveControl_Pass,Protein_NegativeControl_Pass,Protein_SamplesFailedQC,DNA_MeanDepth_X,MinDNA_MeanDepth_X,DNA_Uniformity_Percent,MinDNA_Uniformity_Percent,DNA_OnTargetRate_Percent,MinDNA_OnTargetRate_Percent,DNA_Q30_Percent,MinDNA_Q30_Percent,DNA_PositiveControl_Pass,DNA_NegativeControl_Pass,DNA_SamplesFailedQC,ProteinMRNA_Correlation_Mean,MinProteinMRNA_Correlation,MutationProteoform_Concordant_Count,MutationProteoform_Total_Checked,CrossLayer_Concordance_Rate_Percent,MinCrossLayer_Concordance_Percent,SampleIdentity_Verified_CrossLayer,Protein_BatchEffect_PCA_VarPercent,DNA_BatchEffect_PCA_VarPercent,MaxBatchEffect_VarPercent,PlatePosition_Effect_Protein,PlatePosition_Effect_DNA,ReagentLot_Protein,ReagentLot_DNA,Normalization_Completed_BothLayers,BatchCorrection_Applied,IntegrationPipeline_Completed,PipelineVersion
PG-BATCH-2026-001,OncoProteogenomic_300,Olink_Explore,NovaSeq_6000,2026-06-08,48,2940,2750,93.5,80,8.2,15,0.5,1.0,0.85,1.02,true,true,1,850,500,91.0,80,85.0,60,89.0,75,true,true,0,0.62,0.4,18,20,92.0,85,true,5.2,3.8,15,false,false,OLK-2026-089,LOT-2026-0451,true,true,true,v4.2.1
PG-BATCH-2026-002,ImmunoProteogenomic_200,SomaLogic,NextSeq_2000,2026-06-09,48,1800,1520,84.4,80,18.5,15,0.8,1.0,1.15,0.88,true,true,5,620,500,82.0,80,72.0,60,82.0,75,true,false,3,0.28,0.4,8,15,62.0,85,true,22.5,8.0,15,true,false,SL-2026-112,LOT-2026-0467,true,false,true,v4.2.1

Input validation rules

FS — Functional Specification

Example output.json

{
  "utilityId": "proteindnapanelbatchchecker",
  "utilityFolder": "ProteinDnaPanelBatchChecker",
  "package": "LiquidBiopsy",
  "overallStatus": "PASS|WARNING|FAIL",
  "sourceFile": "input.csv",
  "processedAtUtc": "2026-06-10T00:00:00Z",
  "checks": [
    {
      "parameter": "BatchID",
      "value": "PG-BATCH-2026-001",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-001"
    },
    {
      "parameter": "PanelName",
      "value": "OncoProteogenomic_300",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-002"
    },
    {
      "parameter": "Platform_Protein",
      "value": "Olink_Explore",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-003"
    },
    {
      "parameter": "Platform_DNA",
      "value": "NovaSeq_6000",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-004"
    },
    {
      "parameter": "RunDate",
      "value": "2026-06-08",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-005"
    },
    {
      "parameter": "TotalSamples",
      "value": "48",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-006"
    },
    {
      "parameter": "ProteinTargets_Total",
      "value": "2940",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-007"
    },
    {
      "parameter": "ProteinTargets_Detected_Mean",
      "value": "2750",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-008"
    },
    {
      "parameter": "ProteinDetection_Rate_Percent",
      "value": "93.5",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-009"
    },
    {
      "parameter": "MinProteinDetection_Rate_Percent",
      "value": "80",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-010"
    },
    {
      "parameter": "ProteinCV_IntraBatch_Percent",
      "value": "8.2",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-011"
    },
    {
      "parameter": "MaxProteinCV_IntraBatch_Percent",
      "value": "15",
      "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": "ProteinDnaPanelBatchChecker.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.