InternationalSpecimenWorkflowChecker

International Specimen Workflow

Liquid Biopsy жидкостная биопсия cfDNA ctDNA CTC exosomes NGS qPCR

Utility description: International Specimen Workflow

International Specimen Workflow Checker — Cross-Border Biological Specimen Transfer Compliance

ℹ️ Utility performs comprehensive verification of cross-border specimen movement according to WHO Guidance, EU ABS Regulation 511/2014, IATA DGR and ISBER standards:
• Informed Consent: Confirmation of consent explicitly authorizing international transfer and overseas use.
• Material Transfer Agreement: Verification of executed MTA between partner institutions.
• Nagoya Protocol ABS: Check for access and benefit-sharing permit from competent authority.
• Export/Import Permits: Presence of origin country export license and destination country import permit.
• IATA DGR Compliance: Correct classification (UN3373/UN2814/Exempt), packaging, and Shipper's Declaration.
• Transit Integrity: Transit time within limits, active temperature monitoring, complete Chain of Custody.
• Ethics & Privacy: Ethics committee approval and GDPR compliance when EU is involved.

⚠️ IMPORTANT:
• Nagoya Protocol is legally binding for party countries. Violation = fines and publication ban.
• MTA must be signed BEFORE specimen shipment. Retroactive MTAs are invalid.
• IATA DGR violations lead to carrier rejection and customs confiscation.
• Informed consent must EXPLICITLY mention international transfer — general consent is insufficient.

Usage:
InternationalSpecimenWorkflowChecker.exe → demo mode (console output)
InternationalSpecimenWorkflowChecker.exe input.csv output.json → evaluate your data

Input format:
SpecimenID,StudyID,OriginCountry,DestinationCountry,SpecimenType,InformedConsent_IntlTransfer,ConsentDateValid,MTA_Executed,MTACounterparty,Nagoya_ABS_Permit,NagoyaPermitNumber,ExportLicense,ImportPermit,IATA_Classification,IATA_Packaging_Compliant,ShipperDeclaration_Present,ChainOfCustody_Complete,TemperatureMonitoring_Active,MaxAllowedTransit_Hours,EstimatedTransit_Hours,EthicsCommittee_Approval,DataPrivacy_GDPR_Compliant

Example:
SPEC-001,STUDY-X,Brazil,Germany,DNA,true,true,true,Charite,true,BR-ABS-001,true,true,UN3373,true,true,true,true,48,36,true,true

📍 Scope of Application (Usage Where):
• Multi-Center Clinical Trials: Control of specimen transfer between sites in different countries.
• Biobanks: Management of international specimen requests.
• Genomic Consortia (H3Africa, GA4GH): Ensuring compliant data and specimen exchange.
• Pharmaceutical Companies: Cross-border specimen transfer for R&D and regulatory purposes.

— WHY IS THIS NEEDED?
International specimen transfer is a high legal and reputational risk zone.
Customs confiscation due to missing documents = loss of irreplaceable specimens.
Nagoya Protocol violation = publication retractions, fines, exclusion from international consortia.
Automated verification prevents costly errors at logistics planning stage.

⚠️ CRITICAL:
• Informed Consent Intl Transfer: MANDATORY explicit authorization. General consent ≠ international.
• MTA Executed: BEFORE shipment. Without MTA, transfer is illegal.
• Nagoya ABS: For protocol party countries, missing permit = BLOCKED.
• IATA Packaging: Non-compliant packaging = carrier rejection.
• Ethics Approval: Missing approval = BLOCKED regardless of other documents.
• GDPR: When EU is involved, compliance confirmation is mandatory.

Key features:
• Nine-parameter international transfer check
• Automatic Nagoya Protocol applicability detection
• Integration of legal, logistical, and ethical requirements
• Four-tier classification (Compliant / Conditional / Non-Compliant / Blocked)
• Compliance with WHO, EU ABS 511/2014, IATA DGR, ISBER

Critical parameters:
• Informed Consent (International): True
• MTA Executed: True
• Nagoya ABS Permit: True (if applicable)
• Export + Import Permits: Both True
• IATA Packaging + Declaration: Both Compliant
• Transit Time: ≤ Max Allowed
• Ethics Committee Approval: True
• GDPR Compliance: True (if EU involved)

💡 Usage tips:
1. Planning: Start verification 4-8 weeks before planned shipment.
2. Nagoya Checkpoint: Check origin country status in ABS Clearing-House.
3. IATA Training: Ensure personnel holds valid IATA DGR Category 1 certificate.
4. MTA Templates: Use standardized templates (NIH, UBMTA) to accelerate negotiation.
5. Digital CoC: Use electronic tracking systems with GPS and temperature loggers.

⚠️ Note: This utility verifies DOCUMENTARY and PROCEDURAL aspects of transfer. It does not replace consultation with international law attorney or customs regulation specialist. For complex jurisdictions, always engage experts.

input.csv

SpecimenID,StudyID,OriginCountry,DestinationCountry,SpecimenType,InformedConsent_IntlTransfer,ConsentDateValid,MTA_Executed,MTACounterparty,Nagoya_ABS_Permit,NagoyaPermitNumber,ExportLicense,ImportPermit,IATA_Classification,IATA_Packaging_Compliant,ShipperDeclaration_Present,ChainOfCustody_Complete,TemperatureMonitoring_Active,MaxAllowedTransit_Hours,EstimatedTransit_Hours,EthicsCommittee_Approval,DataPrivacy_GDPR_Compliant
SPEC-INTL-001,MULTI-NAT-2026,Brazil,Germany,DNA,true,true,true,Charité Berlin,true,BR-ABS-2026-0451,true,true,UN3373,true,true,true,true,48,36,true,true
SPEC-INTL-002,MULTI-NAT-2026,Indonesia,USA,Tissue,true,true,false,,false,,true,false,UN2814,true,true,true,true,72,60,true,false
SPEC-INTL-003,AFRICA-GENOMICS,Kenya,UK,Blood,true,true,true,Wellcome Sanger Institute,true,KE-ABS-2026-112,true,true,UN3373,true,true,true,true,48,62,true,true

URS & FS — User Requirements and Functional Specification

This document describes the controlled interface and behaviour of InternationalSpecimenWorkflowChecker for International Specimen Workflow Checker.

Domain limits URS input.csv FS IQ/OQ/PQ

Domain limits and critical parameters

Key fragments from the source description are shown below. Before production use, limits must be verified against the approved specification, registration dossier and local SOPs.

ℹ️ Utility performs comprehensive verification of cross-border specimen movement according to WHO Guidance, EU ABS Regulation 511/2014, IATA DGR and ISBER standards:
• Transit Integrity: Transit time within limits, active temperature monitoring, complete Chain of Custody.
• MTA must be signed BEFORE specimen shipment. Retroactive MTAs are invalid.
• Informed consent must EXPLICITLY mention international transfer — general consent is insufficient.
⚠️ CRITICAL:
• Compliance with WHO, EU ABS 511/2014, IATA DGR, ISBER
Critical parameters:
• Transit Time: ≤ Max Allowed

URS — User Requirements Specification

ID	Requirement	Criticality	Acceptance criterion
URS-001	The utility shall accept an input.csv file for International Specimen Workflow Checker with headers defined in the data contract.	High	The file is processed without manual header editing.
URS-002	The utility shall perform deterministic QC evaluation without machine learning and without probabilistic conformance decisions.	High	Identical input data, rule version and configuration produce reproducible results.
URS-003	The utility shall validate mandatory fields, data types, ranges, units and domain plausibility.	High	Schema, conversion and range errors are explicitly reported.
URS-004	The utility shall apply domain limits and rules from the description, approved specification, registration dossier and local SOPs.	High	Each check has PASS/WARNING/FAIL and a clear message.
URS-005	The utility shall generate output.json with machine-readable results, source values, warnings, failures and critical findings.	High	JSON is suitable for LIMS/ELN/MES integration and QA/QC review.
URS-006	The utility shall preserve traceability between batch/sample, input file, applied rules and final status.	High	Output contains identifiers, checked parameters and audit metadata.
URS-007	The documentation shall support IQ/OQ/PQ, CSV/CSA and review by internal QA or inspectors.	Medium	URS, FS, input/output contract and test scenarios are supplied with the utility.
URS-008	The utility shall be used as a QC decision-support tool and not as a substitute for approved specifications and QA/QP release decision.	Medium	Documentation states change control and limit-verification expectations.

input.csv contract

#	Field	Type	Sample	Purpose
1	`SpecimenID`	string / controlled vocabulary	`SPEC-INTL-001`	Controlled input parameter for deterministic QC rules.
2	`StudyID`	string / controlled vocabulary	`MULTI-NAT-2026`	Controlled input parameter for deterministic QC rules.
3	`OriginCountry`	string / controlled vocabulary	`Brazil`	Count parameter used for microbiological, particulate or cellular control.
4	`DestinationCountry`	string / controlled vocabulary	`Germany`	Count parameter used for microbiological, particulate or cellular control.
5	`SpecimenType`	string / controlled vocabulary	`DNA`	Controlled input parameter for deterministic QC rules.
6	`InformedConsent_IntlTransfer`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
7	`ConsentDateValid`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
8	`MTA_Executed`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
9	`MTACounterparty`	string / controlled vocabulary	`Charité Berlin`	Count parameter used for microbiological, particulate or cellular control.
10	`Nagoya_ABS_Permit`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
11	`NagoyaPermitNumber`	string / controlled vocabulary	`BR-ABS-2026-0451`	Controlled input parameter for deterministic QC rules.
12	`ExportLicense`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
13	`ImportPermit`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
14	`IATA_Classification`	string / controlled vocabulary	`UN3373`	Controlled input parameter for deterministic QC rules.
15	`IATA_Packaging_Compliant`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
16	`ShipperDeclaration_Present`	string / controlled vocabulary	`true`	Component ratio; structural or formulation CQA.
17	`ChainOfCustody_Complete`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
18	`TemperatureMonitoring_Active`	string / controlled vocabulary	`true`	Temperature profile/MKT; storage, shipping and stability parameter.
19	`MaxAllowedTransit_Hours`	integer / decimal	`48`	Time parameter for process, incubation, storage or analytical workflow.
20	`EstimatedTransit_Hours`	integer / decimal	`36`	Time parameter for process, incubation, storage or analytical workflow.
21	`EthicsCommittee_Approval`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
22	`DataPrivacy_GDPR_Compliant`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.

SpecimenID,StudyID,OriginCountry,DestinationCountry,SpecimenType,InformedConsent_IntlTransfer,ConsentDateValid,MTA_Executed,MTACounterparty,Nagoya_ABS_Permit,NagoyaPermitNumber,ExportLicense,ImportPermit,IATA_Classification,IATA_Packaging_Compliant,ShipperDeclaration_Present,ChainOfCustody_Complete,TemperatureMonitoring_Active,MaxAllowedTransit_Hours,EstimatedTransit_Hours,EthicsCommittee_Approval,DataPrivacy_GDPR_Compliant
SPEC-INTL-001,MULTI-NAT-2026,Brazil,Germany,DNA,true,true,true,Charité Berlin,true,BR-ABS-2026-0451,true,true,UN3373,true,true,true,true,48,36,true,true
SPEC-INTL-002,MULTI-NAT-2026,Indonesia,USA,Tissue,true,true,false,,false,,true,false,UN2814,true,true,true,true,72,60,true,false
SPEC-INTL-003,AFRICA-GENOMICS,Kenya,UK,Blood,true,true,true,Wellcome Sanger Institute,true,KE-ABS-2026-112,true,true,UN3373,true,true,true,true,48,62,true,true

Input validation rules

ID	Field	Rule	Criticality
VR-001	`SpecimenID`	The field shall match an approved dictionary or accepted string representation.	High
VR-002	`StudyID`	The field shall match an approved dictionary or accepted string representation.	High
VR-003	`OriginCountry`	The field shall match an approved dictionary or accepted string representation.	High
VR-004	`DestinationCountry`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-005	`SpecimenType`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-006	`InformedConsent_IntlTransfer`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-007	`ConsentDateValid`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-008	`MTA_Executed`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-009	`MTACounterparty`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-010	`Nagoya_ABS_Permit`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-011	`NagoyaPermitNumber`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-012	`ExportLicense`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-013	`ImportPermit`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-014	`IATA_Classification`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-015	`IATA_Packaging_Compliant`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-016	`ShipperDeclaration_Present`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-017	`ChainOfCustody_Complete`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-018	`TemperatureMonitoring_Active`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-019	`MaxAllowedTransit_Hours`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-020	`EstimatedTransit_Hours`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-021	`EthicsCommittee_Approval`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-022	`DataPrivacy_GDPR_Compliant`	The field shall match an approved dictionary or accepted string representation.	Medium

FS — Functional Specification

ID	Function	Implementation
FS-001	CLI execution	Support execution modes: demo mode without arguments and production mode input.csv output.json.
FS-002	CSV import	Read input.csv in UTF-8/CSV-compatible format and validate header and expected columns.
FS-003	Schema validation	Check mandatory fields, column count, unknown key fields and empty mandatory values.
FS-004	Type conversion	Convert numeric, flag and text values; invalid format is recorded as a row-level error.
FS-005	Domain rule engine	Apply rules for International Specimen Workflow Checker, including critical limits from the description and approved specification.
FS-006	Status aggregation	Produce final status: FAIL for critical failure, WARNING for non-critical deviation, PASS for conformance.
FS-007	JSON export	Write output.json with detailed checks, source values, warnings, failures and critical findings.
FS-008	Audit support	Keep result structure suitable for review, deviation investigation and calculation reproduction.
FS-009	Integration contract	Support the scenario LIMS/ELN/MES → input.csv → utility → output.json → portal/admin review.
FS-010	Error handling	Return explicit messages for missing file, empty CSV, invalid schema, output write failure and invalid format.

Example output.json

{
  "utilityId": "internationalspecimenworkflowchecker",
  "utilityFolder": "InternationalSpecimenWorkflowChecker",
  "package": "LiquidBiopsy",
  "overallStatus": "PASS|WARNING|FAIL",
  "sourceFile": "input.csv",
  "processedAtUtc": "2026-06-10T00:00:00Z",
  "checks": [
    {
      "parameter": "SpecimenID",
      "value": "SPEC-INTL-001",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-001"
    },
    {
      "parameter": "StudyID",
      "value": "MULTI-NAT-2026",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-002"
    },
    {
      "parameter": "OriginCountry",
      "value": "Brazil",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-003"
    },
    {
      "parameter": "DestinationCountry",
      "value": "Germany",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-004"
    },
    {
      "parameter": "SpecimenType",
      "value": "DNA",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-005"
    },
    {
      "parameter": "InformedConsent_IntlTransfer",
      "value": "true",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-006"
    },
    {
      "parameter": "ConsentDateValid",
      "value": "true",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-007"
    },
    {
      "parameter": "MTA_Executed",
      "value": "true",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-008"
    },
    {
      "parameter": "MTACounterparty",
      "value": "Charité Berlin",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-009"
    },
    {
      "parameter": "Nagoya_ABS_Permit",
      "value": "true",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-010"
    },
    {
      "parameter": "NagoyaPermitNumber",
      "value": "BR-ABS-2026-0451",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-011"
    },
    {
      "parameter": "ExportLicense",
      "value": "true",
      "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": "InternationalSpecimenWorkflowChecker.documentation.html"
  }
}

Traceability matrix

URS	FS	Test	Evidence
URS-001	FS-001, FS-002	OQ-001	Verify execution and import of valid input.csv.
URS-002	FS-005, FS-006	OQ-004	Repeat the same dataset and compare output.json.
URS-003	FS-003, FS-004, FS-010	OQ-002, OQ-003	Verify missing columns and invalid types.
URS-004	FS-005, FS-006	OQ-004, PQ-001	Verify critical deviations on real/boundary data.
URS-005	FS-007, FS-009	OQ-005	Verify JSON schema and downstream-system suitability.
URS-006	FS-008	OQ-006	Verify identifiers and audit metadata.
URS-007	FS-008, FS-010	IQ-001, OQ-007	Verify documentation completeness and control evidence.
URS-008	FS-005, FS-008	PQ-002	Verify review workflow and no replacement of QA decision.

IQ/OQ/PQ test scenarios

ID	Scenario	Expected result
IQ-001	Verify executable, input.csv, documentation and checksum availability.	Delivery set is complete; version is recorded.
OQ-001	Valid sample row from input.csv.	PASS or acceptable WARNING according to rules.
OQ-002	Remove a mandatory CSV column.	Schema error or FAIL with missing-column reference.
OQ-003	Place a non-numeric value into a numeric field.	Type-conversion error with row/field reference.
OQ-004	Set a critical parameter outside the limit.	FAIL and critical finding.
OQ-005	Verify output.json structure.	All mandatory sections are present and JSON is valid.
OQ-006	Verify batch/sample traceability.	Input and result identifiers match.
PQ-001	Verify 3–5 real user batches/samples.	Result is confirmed by QC/QA review.
PQ-002	Verify deviation workflow and manual QA decision.	Utility supports review but does not replace approved decision.

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.

Included in packages

Liquid Biopsy QC Suite

QC and pre-analytical control package for liquid biopsy workflows: cfDNA/ctDNA, CTC, EV/exosomes, methylation, NGS/qPCR/ddPCR, sample quality, contamination, sensitivity and reporting checks.

Open