SequencingDepthGateChecker

Sequencing Depth Gate

Liquid Biopsy жидкостная биопсия cfDNA ctDNA CTC exosomes NGS qPCR

Utility description: Sequencing Depth Gate

Sequencing Depth Gate Checker — Per-Sample Sequencing Depth Adequacy Verification

Performs depth verification per CAP/CLIA §GEN.48800, FDA NGS guidance, AMP/ASCO/CAP Tiering and CLSI MM26-A: basic depth metrics (mean/median/min target depth, percent bases above minimum threshold), coverage uniformity (fold-80 penalty ≤2.0×, uniformity ≥80%, depth floor at 10% mean), critical region and hotspot coverage (100% required; any gap = potential false negative with explicit listing), UMI-adjusted molecular depth (unique molecular depth ≥ required, mean family size ≥3.0 for UMI assays), theoretical LOD calculation (3/effective_depth at 95% Poisson detection probability vs target assay LOD), and supplementary metrics (on-target rate ≥60%, GC bias correlation ≤0.3, duplicate rate ≤30%). Four-tier classification: DEPTH_SUFFICIENT / MARGINAL / INSUFFICIENT / CRITICAL_GAPS.

⚠️ Critical: Mean depth does NOT guarantee all-region coverage; uniformity and per-region analysis are mandatory. For UMI assays, raw depth may be 20,000× but unique molecular depth only 500× — the latter determines LOD. Fold-80 >2.0 means >20% of bases require disproportionate resequencing. Uncovered hotspot (e.g., EGFR T790M, BRAF V600E) = clinically unacceptable gap. Theoretical LOD is lower bound; actual LOD determined empirically during validation. GC bias >0.3 indicates enrichment/library issue, not just insufficient depth. High duplication without UMI = irreversible effective depth loss. Tool assesses DEPTH ADEQUACY only; does not evaluate variant quality. At CRITICAL_GAPS status, results may be released only with explicit disclosure of uncovered regions in report.

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

📍 Scope of Application:
• Clinical NGS laboratories: Mandatory per-sample check before variant calling.
• Resequencing decisions: Objective criteria for pool rebalancing.
• Panel validation: Confirmation of complete critical region coverage.
• CAP/ISO accreditation: Documentation of depth adequacy per sample.
• Research projects: QC filtering of insufficient-depth samples.

💡 Tips:
1. Assay-Specific Thresholds: Configure separate profiles for germline/somatic/cfDNA/amplicon.
2. Critical Region BED: Use annotated BED file with region priorities.
3. UMI Awareness: Always check unique molecular depth for UMI assays, not raw depth.
4. Pool Rebalancing: For INSUFFICIENT/MARGINAL, automatically calculate required resequencing volume.
5. Coverage Visualization: Integrate with IGV/Coverage plots for visual inspection of problematic regions.

⚠️ Note: This utility assesses DEPTH ADEQUACY, not variant quality. Variant calling QC is performed separately (VariantCallAcceptanceChecker). Depth is necessary but not sufficient for reliable variant detection; adequate base quality, mapping quality, and absence of artifacts are also required. For CRITICAL_GAPS status, results may be released only with explicit disclosure of uncovered regions in the clinical report.

input.csv

SampleID,PatientID,AssayName,AssayType,PanelName,MeanTargetDepth_X,MedianTargetDepth_X,MinTargetDepth_X,PercentBases_Above_MinDepth,RequiredMinDepth_X,RequiredMeanDepth_X,RequiredPercentAbove_MinDepth,Fold80_BasePenalty,MaxFold80_Allowed,Uniformity_Percent,MinUniformity_Percent,PercentBases_At10pctMean,MinPercentBases_At10pctMean,UMI_Assay,UniqueMolecularDepth_X,RequiredUniqueMolecularDepth_X,UMIDeduplication_Rate,MeanFamilySize,MinMeanFamilySize,TotalCriticalRegions,CriticalRegions_AtMinDepth,CriticalHotspots_Total,CriticalHotspots_AtMinDepth,UncoveredCriticalRegions,UncoveredHotspots,OnTargetRate_Percent,MinOnTargetRate_Percent,TotalReads_Million,OnTargetReads_Million,TargetLOD_VAF_Percent,GCBias_Correlation,MaxGCBias_Correlation,DuplicateRate_High,DuplicateRate_Percent,MaxDuplicateRate_Percent
DEP-2026-001,PAT-LUNG-042,OncoPanel_500,Somatic_Targeted,NSCLC_CGP,850,820,180,98.5,100,500,95,1.4,2.0,92.0,80,97.5,90,true,3200,1000,0.45,4.2,3.0,150,150,45,45,,,85.0,60,25,21,0.5,0.08,0.3,false,12.0,30
DEP-2026-002,PAT-CRC-055,CRC_Panel,Hybrid_Capture,CRC_200,320,180,15,72.0,100,500,95,3.8,2.0,62.0,80,75.0,90,false,0,0,0,0,0,80,68,25,22,"APC_exon15;SMAD4_exon2;TGFBR2_exon3","KRAS_G13D;BRAF_V600E",55.0,60,12,7,1.0,0.45,0.3,true,42.0,30
DEP-2026-003,PAT-BRCA-061,MRD_Panel,cfDNA_Panel,Breast_MRD,18000,15000,2500,94.0,5000,20000,95,1.8,2.0,85.0,80,92.0,90,true,1800,2000,0.72,8.5,3.0,60,58,20,20,ESR1_Y537S_region,,78.0,60,80,62,0.01,0.12,0.3,false,25.0,30

URS & FS — User Requirements and Functional Specification

This document describes the controlled interface and behaviour of SequencingDepthGateChecker for Sequencing Depth Gate 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.

Performs depth verification per CAP/CLIA §GEN.48800, FDA NGS guidance, AMP/ASCO/CAP Tiering and CLSI MM26-A: basic depth metrics (mean/median/min target depth, percent bases above minimum threshold), coverage uniformity (fold-80 penalty ≤2.0×, uniformity ≥80%, depth floor at 10% mean), critical region and hotspot coverage (100% required; any gap = potential false negative with explicit listing), UMI-adjusted molecular depth (unique molecular depth ≥ required, mean family size ≥3.0 for UMI assays
⚠️ Critical: Mean depth does NOT guarantee all-region coverage; uniformity and per-region analysis are mandatory. For UMI assays, raw depth may be 20,000× but unique molecular depth only 500× — the latter determines LOD. Fold-80 >2.0 means >20% of bases require disproportionate resequencing. Uncovered hotspot (e.g., EGFR T790M, BRAF V600E) = clinically unacceptable gap. Theoretical LOD is lower bound; actual LOD determined empirically during validation. GC bias >0.3 indicates enrichment/library
• Panel validation: Confirmation of complete critical region coverage.
• CAP/ISO accreditation: Documentation of depth adequacy per sample.
2. Critical Region BED: Use annotated BED file with region priorities.
⚠️ Note: This utility assesses DEPTH ADEQUACY, not variant quality. Variant calling QC is performed separately (VariantCallAcceptanceChecker). Depth is necessary but not sufficient for reliable variant detection; adequate base quality, mapping quality, and absence of artifacts are also required. For CRITICAL_GAPS status, results may be released only with explicit disclosure of uncovered regions in the clinical report.

URS — User Requirements Specification

ID	Requirement	Criticality	Acceptance criterion
URS-001	The utility shall accept an input.csv file for Sequencing Depth Gate 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	`DEP-2026-001`	Sample or laboratory specimen identifier.
2	`PatientID`	string / controlled vocabulary	`PAT-LUNG-042`	Controlled input parameter for deterministic QC rules.
3	`AssayName`	string / controlled vocabulary	`OncoPanel_500`	Controlled input parameter for deterministic QC rules.
4	`AssayType`	string / controlled vocabulary	`Somatic_Targeted`	Controlled input parameter for deterministic QC rules.
5	`PanelName`	string / controlled vocabulary	`NSCLC_CGP`	Controlled input parameter for deterministic QC rules.
6	`MeanTargetDepth_X`	string / controlled vocabulary	`850`	Controlled input parameter for deterministic QC rules.
7	`MedianTargetDepth_X`	string / controlled vocabulary	`820`	Controlled input parameter for deterministic QC rules.
8	`MinTargetDepth_X`	string / controlled vocabulary	`180`	Controlled input parameter for deterministic QC rules.
9	`PercentBases_Above_MinDepth`	decimal	`98.5`	Controlled input parameter for deterministic QC rules.
10	`RequiredMinDepth_X`	decimal	`100`	Controlled input parameter for deterministic QC rules.
11	`RequiredMeanDepth_X`	decimal	`500`	Controlled input parameter for deterministic QC rules.
12	`RequiredPercentAbove_MinDepth`	decimal	`95`	Controlled input parameter for deterministic QC rules.
13	`Fold80_BasePenalty`	decimal	`1.4`	Controlled input parameter for deterministic QC rules.
14	`MaxFold80_Allowed`	decimal	`2.0`	Controlled input parameter for deterministic QC rules.
15	`Uniformity_Percent`	decimal	`92.0`	Controlled input parameter for deterministic QC rules.
16	`MinUniformity_Percent`	decimal	`80`	Controlled input parameter for deterministic QC rules.
17	`PercentBases_At10pctMean`	integer / decimal	`97.5`	Controlled input parameter for deterministic QC rules.
18	`MinPercentBases_At10pctMean`	integer / decimal	`90`	Controlled input parameter for deterministic QC rules.
19	`UMI_Assay`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
20	`UniqueMolecularDepth_X`	decimal	`3200`	Controlled input parameter for deterministic QC rules.
21	`RequiredUniqueMolecularDepth_X`	decimal	`1000`	Controlled input parameter for deterministic QC rules.
22	`UMIDeduplication_Rate`	string / controlled vocabulary	`0.45`	Controlled input parameter for deterministic QC rules.
23	`MeanFamilySize`	decimal	`4.2`	Controlled input parameter for deterministic QC rules.
24	`MinMeanFamilySize`	decimal	`3.0`	Controlled input parameter for deterministic QC rules.
25	`TotalCriticalRegions`	decimal	`150`	Controlled input parameter for deterministic QC rules.
26	`CriticalRegions_AtMinDepth`	decimal	`150`	Controlled input parameter for deterministic QC rules.
27	`CriticalHotspots_Total`	decimal	`45`	Controlled input parameter for deterministic QC rules.
28	`CriticalHotspots_AtMinDepth`	decimal	`45`	Controlled input parameter for deterministic QC rules.
29	`UncoveredCriticalRegions`	string / controlled vocabulary		Controlled input parameter for deterministic QC rules.
30	`UncoveredHotspots`	string / controlled vocabulary		Controlled input parameter for deterministic QC rules.
31	`OnTargetRate_Percent`	decimal	`85.0`	Controlled input parameter for deterministic QC rules.
32	`MinOnTargetRate_Percent`	decimal	`60`	Controlled input parameter for deterministic QC rules.
33	`TotalReads_Million`	integer / decimal	`25`	Controlled input parameter for deterministic QC rules.
34	`OnTargetReads_Million`	string / controlled vocabulary	`21`	Controlled input parameter for deterministic QC rules.
35	`TargetLOD_VAF_Percent`	decimal	`0.5`	Controlled input parameter for deterministic QC rules.
36	`GCBias_Correlation`	integer / decimal	`0.08`	Controlled input parameter for deterministic QC rules.
37	`MaxGCBias_Correlation`	integer / decimal	`0.3`	Controlled input parameter for deterministic QC rules.
38	`DuplicateRate_High`	string / controlled vocabulary	`false`	Controlled input parameter for deterministic QC rules.
39	`DuplicateRate_Percent`	decimal	`12.0`	Controlled input parameter for deterministic QC rules.
40	`MaxDuplicateRate_Percent`	decimal	`30`	Controlled input parameter for deterministic QC rules.

SampleID,PatientID,AssayName,AssayType,PanelName,MeanTargetDepth_X,MedianTargetDepth_X,MinTargetDepth_X,PercentBases_Above_MinDepth,RequiredMinDepth_X,RequiredMeanDepth_X,RequiredPercentAbove_MinDepth,Fold80_BasePenalty,MaxFold80_Allowed,Uniformity_Percent,MinUniformity_Percent,PercentBases_At10pctMean,MinPercentBases_At10pctMean,UMI_Assay,UniqueMolecularDepth_X,RequiredUniqueMolecularDepth_X,UMIDeduplication_Rate,MeanFamilySize,MinMeanFamilySize,TotalCriticalRegions,CriticalRegions_AtMinDepth,CriticalHotspots_Total,CriticalHotspots_AtMinDepth,UncoveredCriticalRegions,UncoveredHotspots,OnTargetRate_Percent,MinOnTargetRate_Percent,TotalReads_Million,OnTargetReads_Million,TargetLOD_VAF_Percent,GCBias_Correlation,MaxGCBias_Correlation,DuplicateRate_High,DuplicateRate_Percent,MaxDuplicateRate_Percent
DEP-2026-001,PAT-LUNG-042,OncoPanel_500,Somatic_Targeted,NSCLC_CGP,850,820,180,98.5,100,500,95,1.4,2.0,92.0,80,97.5,90,true,3200,1000,0.45,4.2,3.0,150,150,45,45,,,85.0,60,25,21,0.5,0.08,0.3,false,12.0,30
DEP-2026-002,PAT-CRC-055,CRC_Panel,Hybrid_Capture,CRC_200,320,180,15,72.0,100,500,95,3.8,2.0,62.0,80,75.0,90,false,0,0,0,0,0,80,68,25,22,APC_exon15;SMAD4_exon2;TGFBR2_exon3,KRAS_G13D;BRAF_V600E,55.0,60,12,7,1.0,0.45,0.3,true,42.0,30
DEP-2026-003,PAT-BRCA-061,MRD_Panel,cfDNA_Panel,Breast_MRD,18000,15000,2500,94.0,5000,20000,95,1.8,2.0,85.0,80,92.0,90,true,1800,2000,0.72,8.5,3.0,60,58,20,20,ESR1_Y537S_region,,78.0,60,80,62,0.01,0.12,0.3,false,25.0,30

Input validation rules

ID	Field	Rule	Criticality
VR-001	`SampleID`	The field shall match an approved dictionary or accepted string representation.	High
VR-002	`PatientID`	The field shall match an approved dictionary or accepted string representation.	High
VR-003	`AssayName`	The field shall match an approved dictionary or accepted string representation.	High
VR-004	`AssayType`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-005	`PanelName`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-006	`MeanTargetDepth_X`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-007	`MedianTargetDepth_X`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-008	`MinTargetDepth_X`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-009	`PercentBases_Above_MinDepth`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-010	`RequiredMinDepth_X`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-011	`RequiredMeanDepth_X`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-012	`RequiredPercentAbove_MinDepth`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-013	`Fold80_BasePenalty`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-014	`MaxFold80_Allowed`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-015	`Uniformity_Percent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-016	`MinUniformity_Percent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-017	`PercentBases_At10pctMean`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-018	`MinPercentBases_At10pctMean`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-019	`UMI_Assay`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-020	`UniqueMolecularDepth_X`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-021	`RequiredUniqueMolecularDepth_X`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-022	`UMIDeduplication_Rate`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-023	`MeanFamilySize`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-024	`MinMeanFamilySize`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-025	`TotalCriticalRegions`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-026	`CriticalRegions_AtMinDepth`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-027	`CriticalHotspots_Total`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-028	`CriticalHotspots_AtMinDepth`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-029	`UncoveredCriticalRegions`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-030	`UncoveredHotspots`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-031	`OnTargetRate_Percent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-032	`MinOnTargetRate_Percent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-033	`TotalReads_Million`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-034	`OnTargetReads_Million`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-035	`TargetLOD_VAF_Percent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-036	`GCBias_Correlation`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-037	`MaxGCBias_Correlation`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-038	`DuplicateRate_High`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-039	`DuplicateRate_Percent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-040	`MaxDuplicateRate_Percent`	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 Sequencing Depth Gate 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": "sequencingdepthgatechecker",
  "utilityFolder": "SequencingDepthGateChecker",
  "package": "LiquidBiopsy",
  "overallStatus": "PASS|WARNING|FAIL",
  "sourceFile": "input.csv",
  "processedAtUtc": "2026-06-10T00:00:00Z",
  "checks": [
    {
      "parameter": "SampleID",
      "value": "DEP-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": "OncoPanel_500",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-003"
    },
    {
      "parameter": "AssayType",
      "value": "Somatic_Targeted",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-004"
    },
    {
      "parameter": "PanelName",
      "value": "NSCLC_CGP",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-005"
    },
    {
      "parameter": "MeanTargetDepth_X",
      "value": "850",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-006"
    },
    {
      "parameter": "MedianTargetDepth_X",
      "value": "820",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-007"
    },
    {
      "parameter": "MinTargetDepth_X",
      "value": "180",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-008"
    },
    {
      "parameter": "PercentBases_Above_MinDepth",
      "value": "98.5",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-009"
    },
    {
      "parameter": "RequiredMinDepth_X",
      "value": "100",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-010"
    },
    {
      "parameter": "RequiredMeanDepth_X",
      "value": "500",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-011"
    },
    {
      "parameter": "RequiredPercentAbove_MinDepth",
      "value": "95",
      "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": "SequencingDepthGateChecker.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