VariantReportabilityRulesChecker

Variant Reportability Rules

Liquid Biopsy жидкостная биопсия cfDNA ctDNA CTC exosomes NGS qPCR

Utility description: Variant Reportability Rules

Variant Reportability Rules Checker — Variant Reporting Rules Validation

ℹ️ Utility performs independent verification of reportability rules application according to AMP/ASCO/CAP, ACMG/AMP, CLIA and EU IVDR:
• Technical Filters: Verification of minimum VAF and coverage depth thresholds for each variant.
• Population Filters: Context-dependent gnomAD filtering (different thresholds for somatic and germline).
• Clinical Significance: Verification of classification (ACMG/AMP Tier) alignment with reporting decision.
• Ethical Rules: Control of secondary findings handling and patient informed consent presence.
• Rule Engine Concordance: Comparison of expected decision with actual bioinformatics pipeline decision.

⚠️ IMPORTANT:
• Reportability rules must be DOCUMENTED in SOP BEFORE clinical testing begins.
• Any rule change requires revalidation and Change Control documentation.
• Discrepancy between rule engine and expected decision = potential pipeline error.
• Secondary findings without patient consent = ethical violation and legal risk.

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

Input format:
SampleID,VariantID,Gene,VariantType,Context,VAF_Percent,MinReportableVAF_Percent,ReadDepth,MinReportableDepth,ACMG_Classification,AMP_Tier,GnomAD_AF,MaxReportable_GNomAD_AF_Somatic,MaxReportable_GNomAD_AF_Germline,HasTherapeuticAssociation,HasDiagnosticSignificance,HasPrognosticSignificance,PatientConsent_SecondaryFindings,IsSecondaryFinding,IsOnGenePanel,RuleEngine_Pass,FilterReason

Example:
NGS-001,EGFR:c.2573T>G,EGFR,SNV,Somatic,28.5,5,850,100,,TierI,0.00001,0.01,0.001,true,true,true,false,false,true,true,

📍 Scope of Application (Usage Where):
• Clinical NGS Laboratories: Independent audit of rule engine decisions before report release.
• Bioinformatics Pipeline Validation: Confirmation of correct rules implementation.
• Regulatory Inspections: Demonstration of decision-making control system.
• CAP/CLIA Accreditation: Documentation of reporting standards compliance.

— WHY IS THIS NEEDED?
Bioinformatics pipelines contain hundreds of rules implemented in code.
Error in one condition may lead to inclusion of false-positive variant or missing pathogenic mutation.
Independent verification serves as second safety barrier after the pipeline itself.
This is critically important for patient safety and regulatory compliance.

⚠️ CRITICAL:
• Rule Engine Concordance: ANY discrepancy = CRITICAL. Requires immediate investigation.
• Secondary Findings: Without consent = BLOCKED. Ethics committee must be notified.
• gnomAD Context: Somatic and germline thresholds are DIFFERENT. Mixing = errors.
• ACMG/AMP Alignment: Benign/Likely Benign germline variants are NOT reportable.
• Tier IV Somatic: Without clinical significance = filtered. Do not clutter report.

Key features:
• Multi-tier verification (technical → population → clinical → ethical)
• Automatic rule engine discrepancy detection
• Context-dependent thresholds (somatic vs germline)
• Aggregated per-sample report with per-variant detail
• Compliance with AMP/ASCO/CAP + ACMG/AMP + CLIA + EU IVDR

Critical parameters:
• VAF ≥ Min Reportable Threshold
• Read Depth ≥ Min Reportable Depth
• gnomAD AF ≤ Context-specific Max
• ACMG/AMP Classification → Correct Reporting Decision
• Secondary Finding Consent: True if IsSecondaryFinding
• Rule Engine Concordance: 100%

💡 Usage tips:
1. Synchronization: Update checker thresholds simultaneously with pipeline updates.
2. Test Sets: Use reference datasets with known decisions for regression testing.
3. Audit: Run checker on EVERY clinical sample, not only during validation.
4. Documentation: Save JSON reports as part of each case's audit trail.
5. Escalation: Configure automatic notification upon CRITICAL_ISSUE detection.

⚠️ Note: This utility verifies RULE APPLICATION, not clinical correctness of rules themselves. Rule correctness is determined by expert group (molecular pathologist, geneticist, bioinformatician) and documented in validation protocol. The utility guarantees that approved rules are applied consistently and without errors.

input.csv

SampleID,VariantID,Gene,VariantType,Context,VAF_Percent,MinReportableVAF_Percent,ReadDepth,MinReportableDepth,ACMG_Classification,AMP_Tier,GnomAD_AF,MaxReportable_GNomAD_AF_Somatic,MaxReportable_GNomAD_AF_Germline,HasTherapeuticAssociation,HasDiagnosticSignificance,HasPrognosticSignificance,PatientConsent_SecondaryFindings,IsSecondaryFinding,IsOnGenePanel,RuleEngine_Pass,FilterReason
NGS-2026-001,EGFR:c.2573T>G,EGFR,SNV,Somatic,28.5,5.0,850,100,,Tier I,0.00001,0.01,0.001,true,true,true,false,false,true,true,
NGS-2026-001,BRCA2:c.7868A>G,BRCA2,SNV,Germline,49.0,20.0,200,100,VUS,,0.0002,0.01,0.001,false,false,false,false,true,true,false,Secondary finding without patient consent
NGS-2026-001,TP53:c.215C>G,TP53,SNV,Somatic,8.0,5.0,500,100,,Tier IV,0.025,0.01,0.001,false,false,false,false,false,true,false,High population frequency
NGS-2026-001,MLH1:c.1852_1854del,MLH1,Indel,Germline,50.0,20.0,320,100,Pathogenic,,0.00005,0.01,0.001,false,true,true,true,false,true,true,

URS & FS — User Requirements and Functional Specification

This document describes the controlled interface and behaviour of VariantReportabilityRulesChecker for Variant Reportability Rules 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.

• Rule Engine Concordance: Comparison of expected decision with actual bioinformatics pipeline decision.
• Reportability rules must be DOCUMENTED in SOP BEFORE clinical testing begins.
SampleID,VariantID,Gene,VariantType,Context,VAF_Percent,MinReportableVAF_Percent,ReadDepth,MinReportableDepth,ACMG_Classification,AMP_Tier,GnomAD_AF,MaxReportable_GNomAD_AF_Somatic,MaxReportable_GNomAD_AF_Germline,HasTherapeuticAssociation,HasDiagnosticSignificance,HasPrognosticSignificance,PatientConsent_SecondaryFindings,IsSecondaryFinding,IsOnGenePanel,RuleEngine_Pass,FilterReason
NGS-001,EGFR:c.2573T>G,EGFR,SNV,Somatic,28.5,5,850,100,,TierI,0.00001,0.01,0.001,true,true,true,false,false,true,true,
This is critically important for patient safety and regulatory compliance.
⚠️ CRITICAL:
• Rule Engine Concordance: ANY discrepancy = CRITICAL. Requires immediate investigation.
• Secondary Findings: Without consent = BLOCKED. Ethics committee must be notified.
Critical parameters:
• VAF ≥ Min Reportable Threshold
• Read Depth ≥ Min Reportable Depth
• gnomAD AF ≤ Context-specific Max
5. Escalation: Configure automatic notification upon CRITICAL_ISSUE detection.

URS — User Requirements Specification

ID	Requirement	Criticality	Acceptance criterion
URS-001	The utility shall accept an input.csv file for Variant Reportability Rules 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	`SampleID`	string / controlled vocabulary	`NGS-2026-001`	Sample or laboratory specimen identifier.
2	`VariantID`	string / controlled vocabulary	`EGFR:c.2573T>G`	Controlled input parameter for deterministic QC rules.
3	`Gene`	string / controlled vocabulary	`EGFR`	Controlled input parameter for deterministic QC rules.
4	`VariantType`	string / controlled vocabulary	`SNV`	Controlled input parameter for deterministic QC rules.
5	`Context`	string / controlled vocabulary	`Somatic`	Controlled input parameter for deterministic QC rules.
6	`VAF_Percent`	decimal	`28.5`	Controlled input parameter for deterministic QC rules.
7	`MinReportableVAF_Percent`	decimal	`5.0`	Controlled input parameter for deterministic QC rules.
8	`ReadDepth`	decimal	`850`	Controlled input parameter for deterministic QC rules.
9	`MinReportableDepth`	decimal	`100`	Controlled input parameter for deterministic QC rules.
10	`ACMG_Classification`	string / controlled vocabulary		Controlled input parameter for deterministic QC rules.
11	`AMP_Tier`	string / controlled vocabulary	`Tier I`	Controlled input parameter for deterministic QC rules.
12	`GnomAD_AF`	decimal	`0.00001`	Controlled input parameter for deterministic QC rules.
13	`MaxReportable_GNomAD_AF_Somatic`	decimal	`0.01`	Controlled input parameter for deterministic QC rules.
14	`MaxReportable_GNomAD_AF_Germline`	decimal	`0.001`	Controlled input parameter for deterministic QC rules.
15	`HasTherapeuticAssociation`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
16	`HasDiagnosticSignificance`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
17	`HasPrognosticSignificance`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
18	`PatientConsent_SecondaryFindings`	string / controlled vocabulary	`false`	Controlled input parameter for deterministic QC rules.
19	`IsSecondaryFinding`	string / controlled vocabulary	`false`	Controlled input parameter for deterministic QC rules.
20	`IsOnGenePanel`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
21	`RuleEngine_Pass`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
22	`FilterReason`	string / controlled vocabulary		Controlled input parameter for deterministic QC rules.

SampleID,VariantID,Gene,VariantType,Context,VAF_Percent,MinReportableVAF_Percent,ReadDepth,MinReportableDepth,ACMG_Classification,AMP_Tier,GnomAD_AF,MaxReportable_GNomAD_AF_Somatic,MaxReportable_GNomAD_AF_Germline,HasTherapeuticAssociation,HasDiagnosticSignificance,HasPrognosticSignificance,PatientConsent_SecondaryFindings,IsSecondaryFinding,IsOnGenePanel,RuleEngine_Pass,FilterReason
NGS-2026-001,EGFR:c.2573T>G,EGFR,SNV,Somatic,28.5,5.0,850,100,,Tier I,0.00001,0.01,0.001,true,true,true,false,false,true,true,
NGS-2026-001,BRCA2:c.7868A>G,BRCA2,SNV,Germline,49.0,20.0,200,100,VUS,,0.0002,0.01,0.001,false,false,false,false,true,true,false,Secondary finding without patient consent
NGS-2026-001,TP53:c.215C>G,TP53,SNV,Somatic,8.0,5.0,500,100,,Tier IV,0.025,0.01,0.001,false,false,false,false,false,true,false,High population frequency

Input validation rules

ID	Field	Rule	Criticality
VR-001	`SampleID`	The field shall match an approved dictionary or accepted string representation.	High
VR-002	`VariantID`	The field shall match an approved dictionary or accepted string representation.	High
VR-003	`Gene`	The field shall match an approved dictionary or accepted string representation.	High
VR-004	`VariantType`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-005	`Context`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-006	`VAF_Percent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-007	`MinReportableVAF_Percent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-008	`ReadDepth`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-009	`MinReportableDepth`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-010	`ACMG_Classification`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-011	`AMP_Tier`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-012	`GnomAD_AF`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-013	`MaxReportable_GNomAD_AF_Somatic`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-014	`MaxReportable_GNomAD_AF_Germline`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-015	`HasTherapeuticAssociation`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-016	`HasDiagnosticSignificance`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-017	`HasPrognosticSignificance`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-018	`PatientConsent_SecondaryFindings`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-019	`IsSecondaryFinding`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-020	`IsOnGenePanel`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-021	`RuleEngine_Pass`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-022	`FilterReason`	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 Variant Reportability Rules 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": "variantreportabilityruleschecker",
  "utilityFolder": "VariantReportabilityRulesChecker",
  "package": "LiquidBiopsy",
  "overallStatus": "PASS|WARNING|FAIL",
  "sourceFile": "input.csv",
  "processedAtUtc": "2026-06-10T00:00:00Z",
  "checks": [
    {
      "parameter": "SampleID",
      "value": "NGS-2026-001",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-001"
    },
    {
      "parameter": "VariantID",
      "value": "EGFR:c.2573T>G",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-002"
    },
    {
      "parameter": "Gene",
      "value": "EGFR",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-003"
    },
    {
      "parameter": "VariantType",
      "value": "SNV",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-004"
    },
    {
      "parameter": "Context",
      "value": "Somatic",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-005"
    },
    {
      "parameter": "VAF_Percent",
      "value": "28.5",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-006"
    },
    {
      "parameter": "MinReportableVAF_Percent",
      "value": "5.0",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-007"
    },
    {
      "parameter": "ReadDepth",
      "value": "850",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-008"
    },
    {
      "parameter": "MinReportableDepth",
      "value": "100",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-009"
    },
    {
      "parameter": "ACMG_Classification",
      "value": "",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-010"
    },
    {
      "parameter": "AMP_Tier",
      "value": "Tier I",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-011"
    },
    {
      "parameter": "GnomAD_AF",
      "value": "0.00001",
      "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": "VariantReportabilityRulesChecker.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