SampleIdentityConsistencyChecker

URS & FS — User Requirements and Functional Specification

This document describes the controlled interface and behaviour of SampleIdentityConsistencyChecker for Sample Identity Consistency Checker.

Domain limits and critical parameters

• Performs comprehensive identity verification per CAP/CLIA §GEN.48800, ISO 15189 §7.3.2, CLSI GP44-A2 and Joint Commission NPSG.01.01.01: demographics consistency (name, DOB, sex, MRN match between requisition and LIMS), barcode consistency across all workflow stages (tube → extraction → library → flow cell), genetic fingerprint (SNP concordance score ≥0.95 vs reference/prior sample), genetic sex determination vs declared sex, chain of custody completeness, metadata plausibility (collection date,
• ⚠️ Critical: Identification errors cause ~10% of serious lab incidents. ANY discrepancy = HOLD RELEASE pending investigation. SUSPECTED_SWAP = IMMEDIATE HALT + quarantine + director notification. Genetic fingerprint is most reliable verification method; use when possible. Manual barcode transcription increases error risk by order of magnitude. For germline tests, comparison with prior results mandatory when history available. Sex mismatch may be biological (DSD, transplant); not always error. To

URS — User Requirements Specification

input.csv contract

SampleID,PatientID,AssayName,Req_PatientName,Req_DateOfBirth,Req_Sex,Req_MRN,Req_OrderingProvider,LIMS_PatientName,LIMS_DateOfBirth,LIMS_Sex,LIMS_MRN,LIMS_AccessionNumber,Barcode_SampleTube,Barcode_ExtractionPlate,Barcode_LibraryPlate,Barcode_SequencingFlowCell,Barcode_AllMatch,Barcode_Readable_AllStages,GeneticFingerprint_Performed,GeneticFingerprint_MatchScore,MinGeneticFingerprint_MatchScore,GeneticSex_Determined,GeneticSex_MatchesDeclared,SNPs_Checked,SNPs_Concordant,ChainOfCustody_Complete,CustodyTransfers_Count,AllTransfers_Documented,CustodyGap_Description,CollectionDate_Plausible,AgeAtCollection_Plausible,SexConsistent_AcrossSources,DuplicateAccession_Detected,UnexpectedSampleType,PriorResults_Available,PriorGenotype_Concordant,PriorDiscordance_Details
ID-2026-001,PAT-LUNG-042,NSCLC_CGP,Ivanov Ivan,1965-03-15,M,MRN-12345,Dr. Petrov,Ivanov Ivan,1965-03-15,M,MRN-12345,ACC-2026-0891,BC-TUBE-0891,BC-EXT-0891,BC-LIB-0891,BC-FC-0891,true,true,true,0.998,0.95,XY,true,24,24,true,4,true,,true,true,true,false,false,true,true,
ID-2026-002,PAT-CRC-055,CRC_Panel,Smirnova Anna,1978-07-22,F,MRN-67890,Dr. Sidorova,Smirnova Anna,1978-07-22,F,MRN-67890,ACC-2026-0892,BC-TUBE-0892,BC-EXT-0892,BC-LIB-0893,BC-FC-0892,false,true,true,0.97,0.95,XY,false,24,23,true,4,true,,true,true,false,false,false,false,,
ID-2026-003,PAT-BRCA-061,BRCA1_2_Germline,Kozlova Maria,1985-11-03,F,MRN-11111,Dr. Ivanova,Kozlova Maria,1985-11-03,F,MRN-11111,ACC-2026-0893,BC-TUBE-0893,BC-EXT-0893,BC-LIB-0893,BC-FC-0893,true,true,true,0.72,0.95,XX,true,24,17,false,5,false,Missing transfer record between extraction and library prep,true,true,true,false,false,true,false,3/24 SNPs discordant with prior germline test from 2025-08

Input validation rules

FS — Functional Specification

Example output.json

{
  "utilityId": "sampleidentityconsistencychecker",
  "utilityFolder": "SampleIdentityConsistencyChecker",
  "package": "LiquidBiopsy",
  "overallStatus": "PASS|WARNING|FAIL",
  "sourceFile": "input.csv",
  "processedAtUtc": "2026-06-10T00:00:00Z",
  "checks": [
    {
      "parameter": "SampleID",
      "value": "ID-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": "AssayName",
      "value": "NSCLC_CGP",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-003"
    },
    {
      "parameter": "Req_PatientName",
      "value": "Ivanov Ivan",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-004"
    },
    {
      "parameter": "Req_DateOfBirth",
      "value": "1965-03-15",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-005"
    },
    {
      "parameter": "Req_Sex",
      "value": "M",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-006"
    },
    {
      "parameter": "Req_MRN",
      "value": "MRN-12345",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-007"
    },
    {
      "parameter": "Req_OrderingProvider",
      "value": "Dr. Petrov",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-008"
    },
    {
      "parameter": "LIMS_PatientName",
      "value": "Ivanov Ivan",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-009"
    },
    {
      "parameter": "LIMS_DateOfBirth",
      "value": "1965-03-15",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-010"
    },
    {
      "parameter": "LIMS_Sex",
      "value": "M",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-011"
    },
    {
      "parameter": "LIMS_MRN",
      "value": "MRN-12345",
      "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": "SampleIdentityConsistencyChecker.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.