LibraryPrepBatchChecker

URS & FS — User Requirements and Functional Specification

This document describes the controlled interface and behaviour of LibraryPrepBatchChecker for Library Prep Batch Checker.

Domain limits and critical parameters

• ℹ️ Utility performs comprehensive assessment of library preparation quality at batch level according to CAP/CLIA, GATK Best Practices and ISO 15189:
• • PCR Cycles: Amplification cycles within limit (avoiding over-amplification).
• • Pass Rate: Fraction of samples passing all individual specifications (≥90%).
• • Concentration CV: Coefficient of variation of concentration within batch (≤30%).
• • Fragment Size CV: Coefficient of variation of fragment sizes (≤15%).
• • High concentration CV (>30%) leads to uneven pool representation.
• • Adapter dimers >5% compete with library during clustering, reducing data output.
• • Historical drift (|Z| > 2) indicates reagent degradation or protocol change.
• • Over-amplification (>15 cycles) increases duplicates and coverage bias.
• • CAP/ISO Accreditation: Documentation of sample preparation quality control system.
• ⚠️ CRITICAL:
• • Pass Rate ≥ 90%: Below = systematic preparation problem.
• • Concentration CV ≤ 30%: Exceedance = uneven pooling = data loss.
• • Fragment Size CV ≤ 15%: High CV = size selection or fragmentation issue.
• • Adapter Dimers ≤ 5%: Above = SPRI re-cleanup mandatory.
• • Historical |Z| ≤ 2.0: Exceedance = drift cause investigation.
• • Outliers ≤ 10%: High outlier % = unstable process.
• • PCR Cycles ≤ Max: Over-amplification irreversibly degrades quality.

URS — User Requirements Specification

input.csv contract

BatchID,SampleID,LibraryType,PrepKit,Concentration_ng_uL,MinConcentration,MaxConcentration,MeanFragmentSize_bp,MinFragmentSize,MaxFragmentSize,Molarity_nM,MinMolarity,AdapterDimer_Percent,MaxAdapterDimer_Percent,PCRCycles,MaxPCRCycles,InputDNA_ng,MinInputDNA_ng,HistoricalMean_Concentration,HistoricalSD_Concentration
BATCH-2026-045,S001,WES,KAPA HyperPrep,28.5,2.0,100.0,380,200,700,12.5,2.0,0.8,5.0,8,15,50,10,27.0,7.0
BATCH-2026-045,S002,WES,KAPA HyperPrep,32.1,2.0,100.0,395,200,700,14.2,2.0,0.5,5.0,8,15,50,10,27.0,7.0
BATCH-2026-045,S003,WES,KAPA HyperPrep,25.8,2.0,100.0,370,200,700,11.8,2.0,1.2,5.0,8,15,50,10,27.0,7.0

Input validation rules

FS — Functional Specification

Example output.json

{
  "utilityId": "libraryprepbatchchecker",
  "utilityFolder": "LibraryPrepBatchChecker",
  "package": "LiquidBiopsy",
  "overallStatus": "PASS|WARNING|FAIL",
  "sourceFile": "input.csv",
  "processedAtUtc": "2026-06-10T00:00:00Z",
  "checks": [
    {
      "parameter": "BatchID",
      "value": "BATCH-2026-045",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-001"
    },
    {
      "parameter": "SampleID",
      "value": "S001",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-002"
    },
    {
      "parameter": "LibraryType",
      "value": "WES",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-003"
    },
    {
      "parameter": "PrepKit",
      "value": "KAPA HyperPrep",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-004"
    },
    {
      "parameter": "Concentration_ng_uL",
      "value": "28.5",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-005"
    },
    {
      "parameter": "MinConcentration",
      "value": "2.0",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-006"
    },
    {
      "parameter": "MaxConcentration",
      "value": "100.0",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-007"
    },
    {
      "parameter": "MeanFragmentSize_bp",
      "value": "380",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-008"
    },
    {
      "parameter": "MinFragmentSize",
      "value": "200",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-009"
    },
    {
      "parameter": "MaxFragmentSize",
      "value": "700",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-010"
    },
    {
      "parameter": "Molarity_nM",
      "value": "12.5",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-011"
    },
    {
      "parameter": "MinMolarity",
      "value": "2.0",
      "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": "LibraryPrepBatchChecker.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.