ComprehensiveGenomicProfilingQcChecker

Comprehensive Genomic Profiling QC

Liquid Biopsy жидкостная биопсия cfDNA ctDNA CTC exosomes NGS qPCR

Utility description: Comprehensive Genomic Profiling QC

Comprehensive Genomic Profiling QC Checker — End-to-End CGP Quality Control

ℹ️  Utility performs multi-tier validation of comprehensive genomic profiling data according to CAP/CLIA and FDA PMA requirements:
     • Tier 1 — Sequencing QC: Coverage depth, uniformity, duplication rate.
     • Tier 2 — Tumor QC: Tumor purity, ploidy, TMB, MSI status.
     • Tier 3 — Clinical QC: Therapy recommendation completeness, report consistency, CDx IFU compliance.
     • Unified Verdict: Integration of all tiers into single PASS/FAIL/REVIEW_REQUIRED status.

⚠️  IMPORTANT: 
     • CGP test influences first-line therapy selection. Error at any level is unacceptable.
     • Technically quality sample with low tumor purity may yield false-negative result.
     • Clinically correct report based on invalid sequencing data is legally void.

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

Input format:
SampleID,PanelName,Mean_Target_Depth_X,Min_Mean_Depth_X,Uniformity_Percent,Min_Uniformity_Percent,Duplication_Rate_Percent,Max_Duplication_Rate_Percent,Tumor_Purity_Percent,Min_Tumor_Purity_Percent,Ploidy,TMB_Mut_Mb,MSI_Status,Actionable_Variants,Therapies_Listed,All_Actionable_Have_Therapy,Report_Consistent,CDx_Compliant

Example:
  CGP-001,OncoPanel,850,500,92,80,18,40,45,20,2.1,12.5,Stable,2,2,true,true,true

📍 Scope of Application (Usage Where):
     • Clinical NGS Laboratories: Final gatekeeper before CGP report release.
     • Pharmaceutical R&D: Quality control of stratification biomarkers in trials.
     • Regulatory Inspections: Demonstration of end-to-end QC system.
     • CAP Accreditation: Confirmation of Molecular Pathology Checklist compliance.

— WHY IS THIS NEEDED?
CGP test is a complex pipeline of dozens of steps.
Disparate QC checkers miss cross-stage inconsistencies (e.g., high depth but low purity → missed mutations).
Unified utility provides holistic assessment where each tier is checked in context of others.
This is the only way to guarantee physician receives reliable and complete genomic profile.

⚠️  CRITICAL:
• Tumor Purity: <20% requires special attention or re-sampling.
• Depth + Uniformity: Both parameters must be in spec simultaneously.
• Actionable-Therapy Link: 100% coverage mandatory for clinical report.
• CDx Compliance: Violation renders report illegitimate for approved therapy prescription.
• Report Consistency: Internal contradictions undermine trust in entire test.

Key features:
• Three-tier QC architecture (Sequencing → Tumor → Clinical)
• 9 verified parameters in single run
• Integrated technical and clinical assessment
• Automatic status classification
• Compliance with CAP Molecular Pathology and FDA PMA

Critical parameters:
• Mean Depth: ≥ Min Limit
• Uniformity: ≥ Min Limit
• Duplication Rate: ≤ Max Limit
• Tumor Purity: ≥ Min Limit
• Actionable-Therapy Link: 100%
• Report Consistency: True
• CDx Compliance: True

💡 Usage tips:
1. Integration: Connect to LIMS and bioinformatics pipeline for automatic metric collection.
2. Pre-signature Gate: Block pathologist signature upon FAIL status.
3. Trends: Monitor distribution of each parameter over time for early drift detection.
4. Thresholds: Customize limits per specific panel and sample type (FFPE vs fresh).
5. Documentation: Save JSON report as part of permanent laboratory record.

⚠️ Note: This utility is an end-to-end quality control tool. It does not replace molecular pathologist expert interpretation but guarantees that data for interpretation is technically reliable and clinically complete.

input.csv

SampleID,PanelName,Mean_Target_Depth_X,Min_Mean_Depth_X,Uniformity_Percent,Min_Uniformity_Percent,Duplication_Rate_Percent,Max_Duplication_Rate_Percent,Tumor_Purity_Percent,Min_Tumor_Purity_Percent,Ploidy,TMB_Mut_Mb,MSI_Status,Actionable_Variants,Therapies_Listed,All_Actionable_Have_Therapy,Report_Consistent,CDx_Compliant
CGP-2026-001,OncoPanel_500,850,500,92,80,18,40,45,20,2.1,12.5,Stable,2,2,true,true,true
CGP-2026-002,OncoPanel_500,320,500,65,80,55,40,12,20,3.8,4.2,Stable,1,0,false,false,false
CGP-2026-003,OncoPanel_500,620,500,85,80,35,40,30,20,2.4,8.7,Unstable,3,3,true,true,true

URS & FS — User Requirements and Functional Specification

This document describes the controlled interface and behaviour of ComprehensiveGenomicProfilingQcChecker for Comprehensive Genomic Profiling QC 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.

• Tier 2 — Tumor QC: Tumor purity, ploidy, TMB, MSI status.
• Technically quality sample with low tumor purity may yield false-negative result.
SampleID,PanelName,Mean_Target_Depth_X,Min_Mean_Depth_X,Uniformity_Percent,Min_Uniformity_Percent,Duplication_Rate_Percent,Max_Duplication_Rate_Percent,Tumor_Purity_Percent,Min_Tumor_Purity_Percent,Ploidy,TMB_Mut_Mb,MSI_Status,Actionable_Variants,Therapies_Listed,All_Actionable_Have_Therapy,Report_Consistent,CDx_Compliant
Disparate QC checkers miss cross-stage inconsistencies (e.g., high depth but low purity → missed mutations).
⚠️ CRITICAL:
• Tumor Purity: <20% requires special attention or re-sampling.
• Depth + Uniformity: Both parameters must be in spec simultaneously.
Critical parameters:
• Mean Depth: ≥ Min Limit
• Uniformity: ≥ Min Limit
• Duplication Rate: ≤ Max Limit
• Tumor Purity: ≥ Min Limit
4. Thresholds: Customize limits per specific panel and sample type (FFPE vs fresh).

URS — User Requirements Specification

ID	Requirement	Criticality	Acceptance criterion
URS-001	The utility shall accept an input.csv file for Comprehensive Genomic Profiling QC 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	`CGP-2026-001`	Sample or laboratory specimen identifier.
2	`PanelName`	string / controlled vocabulary	`OncoPanel_500`	Controlled input parameter for deterministic QC rules.
3	`Mean_Target_Depth_X`	string / controlled vocabulary	`850`	Controlled input parameter for deterministic QC rules.
4	`Min_Mean_Depth_X`	decimal	`500`	Controlled input parameter for deterministic QC rules.
5	`Uniformity_Percent`	decimal	`92`	Controlled input parameter for deterministic QC rules.
6	`Min_Uniformity_Percent`	decimal	`80`	Controlled input parameter for deterministic QC rules.
7	`Duplication_Rate_Percent`	decimal	`18`	Controlled input parameter for deterministic QC rules.
8	`Max_Duplication_Rate_Percent`	decimal	`40`	Controlled input parameter for deterministic QC rules.
9	`Tumor_Purity_Percent`	decimal	`45`	Purity or impurity profile; key QC parameter.
10	`Min_Tumor_Purity_Percent`	decimal	`20`	Purity or impurity profile; key QC parameter.
11	`Ploidy`	string / controlled vocabulary	`2.1`	Controlled input parameter for deterministic QC rules.
12	`TMB_Mut_Mb`	decimal	`12.5`	Controlled input parameter for deterministic QC rules.
13	`MSI_Status`	string / controlled vocabulary	`Stable`	Result/status used in final classification.
14	`Actionable_Variants`	decimal	`2`	Controlled input parameter for deterministic QC rules.
15	`Therapies_Listed`	decimal	`2`	Controlled input parameter for deterministic QC rules.
16	`All_Actionable_Have_Therapy`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
17	`Report_Consistent`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
18	`CDx_Compliant`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.

SampleID,PanelName,Mean_Target_Depth_X,Min_Mean_Depth_X,Uniformity_Percent,Min_Uniformity_Percent,Duplication_Rate_Percent,Max_Duplication_Rate_Percent,Tumor_Purity_Percent,Min_Tumor_Purity_Percent,Ploidy,TMB_Mut_Mb,MSI_Status,Actionable_Variants,Therapies_Listed,All_Actionable_Have_Therapy,Report_Consistent,CDx_Compliant
CGP-2026-001,OncoPanel_500,850,500,92,80,18,40,45,20,2.1,12.5,Stable,2,2,true,true,true
CGP-2026-002,OncoPanel_500,320,500,65,80,55,40,12,20,3.8,4.2,Stable,1,0,false,false,false
CGP-2026-003,OncoPanel_500,620,500,85,80,35,40,30,20,2.4,8.7,Unstable,3,3,true,true,true

Input validation rules

ID	Field	Rule	Criticality
VR-001	`SampleID`	The field shall match an approved dictionary or accepted string representation.	High
VR-002	`PanelName`	The field shall match an approved dictionary or accepted string representation.	High
VR-003	`Mean_Target_Depth_X`	The field shall match an approved dictionary or accepted string representation.	High
VR-004	`Min_Mean_Depth_X`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-005	`Uniformity_Percent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-006	`Min_Uniformity_Percent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-007	`Duplication_Rate_Percent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-008	`Max_Duplication_Rate_Percent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-009	`Tumor_Purity_Percent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-010	`Min_Tumor_Purity_Percent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-011	`Ploidy`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-012	`TMB_Mut_Mb`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-013	`MSI_Status`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-014	`Actionable_Variants`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-015	`Therapies_Listed`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-016	`All_Actionable_Have_Therapy`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-017	`Report_Consistent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-018	`CDx_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 Comprehensive Genomic Profiling QC 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": "comprehensivegenomicprofilingqcchecker",
  "utilityFolder": "ComprehensiveGenomicProfilingQcChecker",
  "package": "LiquidBiopsy",
  "overallStatus": "PASS|WARNING|FAIL",
  "sourceFile": "input.csv",
  "processedAtUtc": "2026-06-10T00:00:00Z",
  "checks": [
    {
      "parameter": "SampleID",
      "value": "CGP-2026-001",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-001"
    },
    {
      "parameter": "PanelName",
      "value": "OncoPanel_500",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-002"
    },
    {
      "parameter": "Mean_Target_Depth_X",
      "value": "850",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-003"
    },
    {
      "parameter": "Min_Mean_Depth_X",
      "value": "500",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-004"
    },
    {
      "parameter": "Uniformity_Percent",
      "value": "92",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-005"
    },
    {
      "parameter": "Min_Uniformity_Percent",
      "value": "80",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-006"
    },
    {
      "parameter": "Duplication_Rate_Percent",
      "value": "18",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-007"
    },
    {
      "parameter": "Max_Duplication_Rate_Percent",
      "value": "40",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-008"
    },
    {
      "parameter": "Tumor_Purity_Percent",
      "value": "45",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-009"
    },
    {
      "parameter": "Min_Tumor_Purity_Percent",
      "value": "20",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-010"
    },
    {
      "parameter": "Ploidy",
      "value": "2.1",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-011"
    },
    {
      "parameter": "TMB_Mut_Mb",
      "value": "12.5",
      "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": "ComprehensiveGenomicProfilingQcChecker.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