OncoBEAMRasCrcMutationChecker

URS & FS — User Requirements and Functional Specification

This document describes the controlled interface and behaviour of OncoBEAMRasCrcMutationChecker for OncoBEAM RAS CRC Mutation Checker.

Domain limits and critical parameters

• Performs comprehensive quality verification of OncoBEAM KRAS/NRAS mutation analysis per ESMO CRC Guidelines, NCCN Colon Cancer, CAP/CLIA and FDA CDx guidance: compartmentalization metrics (total droplets ≥50K, lambda ≤0.3, empty droplets ≥70%, multiple occupancy ≤5%), fluorescence separation (SNR ≥10, separation index ≥5.0, rain fraction ≤2.0%), triple control verification (positive recovery ≥80%, negative FP rate ≤0.01%, NTC pass), DNA input quality (≥5 ng, amplifiable fraction ≥10%), and clini
• ⚠️ Critical: Lambda >0.3 = QUANTITATIVE RESULT INVALID (Poisson assumption violated). Rain events may mimic rare mutations. Single positive droplets near LOD require confirmation. RAS status determines FIRST-LINE therapy choice in metastatic CRC. Testing must cover ALL clinically relevant KRAS (exons 2,3,4) and NRAS (exons 2,3,4) exons. Technical QC does not replace clinical decision-making by oncologist.

URS — User Requirements Specification

input.csv contract

SampleID,PatientID,Gene,Exon,SpecificMutation,SampleType,TotalDroplets_Analyzed,MinTotalDroplets,PositiveDroplets_Count,WildTypeDroplets_Count,MutantFraction_Percent,AssayLOD_Percent,AssayLOQ_Percent,Lambda_Value,MaxLambda,EmptyDroplet_Percent,MinEmptyDroplet_Percent,MultipleOccupancy_Percent,MaxMultipleOccupancy_Percent,SignalToNoise_Ratio,MinSignalToNoise,FluorescenceSeparation_Index,MinFluorSeparation,RainEvents_Detected,RainFraction_Percent,MaxRainFraction_Percent,PositiveControl_Pass,PosControl_Recovery_Percent,MinPosControl_Recovery,NegativeControl_Pass,NegControl_FalsePositive_Rate,MaxNegControl_FP_Rate,NoTemplateControl_Pass,InputDNA_ng,MinInputDNA_ng,AmplifiableDNA_Fraction,MinAmplifiableDNA_Fraction,IsAntiEGFR_Eligible,ClinicalInterpretation
OB-CRC-2026-001,PAT-CRC-042,KRAS,Exon2,G12D,Plasma_cfDNA,125000,50000,375,124625,0.30,0.02,0.05,0.15,0.3,86.0,70,1.2,5,45.0,10,12.5,5.0,false,0.3,2.0,true,95.0,80,true,0.002,0.01,true,25.0,5,0.45,0.1,false,KRAS G12D mutant. Anti-EGFR therapy NOT recommended.
OB-CRC-2026-002,PAT-CRC-055,NRAS,Exon3,Q61H,FFPE_Tissue,62000,50000,18,61982,0.03,0.02,0.05,0.45,0.3,63.5,70,8.5,5,6.0,10,3.2,5.0,true,4.5,2.0,true,72.0,80,true,0.008,0.01,true,8.0,5,0.08,0.1,false,NRAS Q61H detected but QC concerns.
OB-CRC-2026-003,PAT-CRC-061,KRAS,Exon2,None,Plasma_cfDNA,150000,50000,2,149998,0.001,0.02,0.05,0.12,0.3,88.7,70,0.8,5,52.0,10,14.0,5.0,false,0.1,2.0,true,98.0,80,true,0.001,0.01,true,30.0,5,0.52,0.1,true,KRAS Exon2 WT. Anti-EGFR therapy may be considered.

Input validation rules

FS — Functional Specification

Example output.json

{
  "utilityId": "oncobeamrascrcmutationchecker",
  "utilityFolder": "OncoBEAMRasCrcMutationChecker",
  "package": "LiquidBiopsy",
  "overallStatus": "PASS|WARNING|FAIL",
  "sourceFile": "input.csv",
  "processedAtUtc": "2026-06-10T00:00:00Z",
  "checks": [
    {
      "parameter": "SampleID",
      "value": "OB-CRC-2026-001",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-001"
    },
    {
      "parameter": "PatientID",
      "value": "PAT-CRC-042",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-002"
    },
    {
      "parameter": "Gene",
      "value": "KRAS",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-003"
    },
    {
      "parameter": "Exon",
      "value": "Exon2",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-004"
    },
    {
      "parameter": "SpecificMutation",
      "value": "G12D",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-005"
    },
    {
      "parameter": "SampleType",
      "value": "Plasma_cfDNA",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-006"
    },
    {
      "parameter": "TotalDroplets_Analyzed",
      "value": "125000",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-007"
    },
    {
      "parameter": "MinTotalDroplets",
      "value": "50000",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-008"
    },
    {
      "parameter": "PositiveDroplets_Count",
      "value": "375",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-009"
    },
    {
      "parameter": "WildTypeDroplets_Count",
      "value": "124625",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-010"
    },
    {
      "parameter": "MutantFraction_Percent",
      "value": "0.30",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-011"
    },
    {
      "parameter": "AssayLOD_Percent",
      "value": "0.02",
      "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": "OncoBEAMRasCrcMutationChecker.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.