PlasmaInputVolumeChecker

URS & FS — User Requirements and Functional Specification

This document describes the controlled interface and behaviour of PlasmaInputVolumeChecker for Plasma Input Volume Checker.

Domain limits and critical parameters

• Performs calculation-based volume adequacy assessment per CAP/CLIA, FDA NGS liquid biopsy guidance, IVD instructions and Blood Profiling Atlas standards: volume parameters (available vs protocol minimum, effective volume after dead volume loss, optimal volume), genome equivalent calculation (GE = cfDNA_conc × effective_vol × GE_factor), theoretical achievable LOD (LOD = 3 / [GE × extraction_eff × lib_prep_eff] based on Poisson statistics), quality modifiers (hemolysis ≤50, lipemia ≤100, time to
• ⚠️ Critical: LOD is INVERSELY PROPORTIONAL to volume. 1 mL instead of 4 mL = 4× worse LOD. MRD (LOD 0.01%) typically requires ≥2–4 mL plasma. Kit dead volume (0.2–0.5 mL) significantly impacts small volumes. Hemolysis >50 reduces effective cfDNA yield by 20–40%. When re-collection is impossible, discuss alternative assay or adjusted reporting threshold with clinician. Use MEASURED cfDNA concentration, not assumed. Tool performs THEORETICAL CALCULATION; actual LOD must be empirically validated. R

URS — User Requirements Specification

input.csv contract

SampleID,PatientID,OrderedTest,ClinicalContext,PlasmaVolumeAvailable_mL,ProtocolMinVolume_mL,OptimalVolume_mL,DeadVolume_mL,EffectiveVolume_mL,TargetLOD_VAF_Percent,CfDNA_Concentration_ng_mL,GenomeEquivalents_PerML,ExtractionEfficiency_Percent,LibraryPrepEfficiency_Percent,HemolysisIndex,MaxHemolysisIndex,LipemiaIndex,MaxLipemiaIndex,SampleRecollect_Possible,TubeType,TimeToProcessing_Hours,MaxTimeToProcessing_Hours,Priority,IsOnlyAvailableSample
PV-2026-001,PAT-LUNG-042,MRD_Signatera,MRD,4.0,2.0,4.0,0.2,3.8,0.01,18.0,660,75,55,5,50,8,100,true,Streck,2.0,72,Routine,false
PV-2026-002,PAT-CRC-055,MRD_Signatera,MRD,1.0,2.0,4.0,0.2,0.8,0.01,12.0,660,70,50,15,50,12,100,false,EDTA,3.0,4,STAT,true
PV-2026-003,PAT-BRCA-061,Guardant360,Resistance,2.5,2.0,4.0,0.3,2.2,0.5,22.0,660,65,45,48,50,25,100,true,Streck,18.0,72,Routine,false

Input validation rules

FS — Functional Specification

Example output.json

{
  "utilityId": "plasmainputvolumechecker",
  "utilityFolder": "PlasmaInputVolumeChecker",
  "package": "LiquidBiopsy",
  "overallStatus": "PASS|WARNING|FAIL",
  "sourceFile": "input.csv",
  "processedAtUtc": "2026-06-10T00:00:00Z",
  "checks": [
    {
      "parameter": "SampleID",
      "value": "PV-2026-001",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-001"
    },
    {
      "parameter": "PatientID",
      "value": "PAT-LUNG-042",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-002"
    },
    {
      "parameter": "OrderedTest",
      "value": "MRD_Signatera",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-003"
    },
    {
      "parameter": "ClinicalContext",
      "value": "MRD",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-004"
    },
    {
      "parameter": "PlasmaVolumeAvailable_mL",
      "value": "4.0",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-005"
    },
    {
      "parameter": "ProtocolMinVolume_mL",
      "value": "2.0",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-006"
    },
    {
      "parameter": "OptimalVolume_mL",
      "value": "4.0",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-007"
    },
    {
      "parameter": "DeadVolume_mL",
      "value": "0.2",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-008"
    },
    {
      "parameter": "EffectiveVolume_mL",
      "value": "3.8",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-009"
    },
    {
      "parameter": "TargetLOD_VAF_Percent",
      "value": "0.01",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-010"
    },
    {
      "parameter": "CfDNA_Concentration_ng_mL",
      "value": "18.0",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-011"
    },
    {
      "parameter": "GenomeEquivalents_PerML",
      "value": "660",
      "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": "PlasmaInputVolumeChecker.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.