TumorInformedPanelQcChecker

Tumor-Informed Panel QC

Liquid Biopsy жидкостная биопсия cfDNA ctDNA CTC exosomes NGS qPCR

Utility description: Tumor-Informed Panel QC

Tumor-Informed Panel QC Checker — Quality Control for Personalized Tumor-Informed Panels

Performs design and quality verification per CAP/CLIA §GEN.48800, FDA tumor-informed assay guidance, ESMO MRD Guidelines and TRACERx standards: variant composition (total count ≥ minimum, clonal fraction ≥50%, driver inclusion), variant filtering (germline exclusion MANDATORY, CHIP exclusion, low-confidence exclusion, problematic region exclusion, matched normal verification), primer/probe design (success rate ≥95%, cross-reactivity check, off-target analysis with alignment score threshold), analytical performance (min depth per variant, uniformity across variants ≥70%, amplicon balance CV ≤30%), sensitivity estimation (theoretical LOD vs target, effective independent loci accounting for linkage), controls (positive, negative, NTC, synthetic reference), and documentation (tumor-normal pair verified, somatic pipeline validated, software version locked, manufacturing lot tracked). Four-tier classification: CLINICALLY_VALID / DESIGN_CONCERNS / INSUFFICIENT_SENSITIVITY / INVALID.

⚠️ Critical: Each tumor-informed panel is UNIQUE; standard QC metrics do not apply. Germline variant in panel = IRREMEDIABLE source of false positives in MRD monitoring. CHIP variants account for up to 30% of FPs in cfDNA for patients >60 years. Clonal fraction <50% means panel tracks minor clones; dominant clone may be missed. Theoretical LOD is lower bound; actual sensitivity determined empirically. Effective independent loci ≠ total variants; linked variants add no information. Off-target amplification can mimic rare variants at low VAF. Tool assesses DESIGN AND TECHNICAL QUALITY only; does not replace analytical validation (LoD, specificity, precision) or clinical interpretation. DESIGN_CONCERNS panels may be used with documented limitations; INVALID or INSUFFICIENT_SENSITIVITY requires redesign.

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

📍 Scope of Application:
• MRD/liquid biopsy laboratories: Acceptance of each personalized panel.
• Bespoke panel manufacturers: Design release QC.
• Clinical trials: Standardization of tumor-informed assays across sites.
• Regulatory inspections: Documentation of personalized assay QC.
• Panel developers: Design optimization based on QC feedback.

💡 Tips:
1. Clonal Priority: Always prioritize clonal variants; subclonal are supplementary.
2. CHIP Database: Use current CHIP gene list; update quarterly.
3. Sensitivity Modeling: Model LOD BEFORE panel manufacturing, not after.
4. Synthetic Controls: Create patient-specific synthetic references for each panel.
5. Version Control: Lock ALL versions: design software, primers, manufacturing lot.

⚠️ Note: This utility assesses DESIGN AND TECHNICAL QUALITY of the personalized panel. It does not replace analytical performance validation (LoD, specificity, precision) or clinical interpretation of monitoring results. Panels with DESIGN_CONCERNS status may be used with documented limitations; INVALID or INSUFFICIENT_SENSITIVITY status requires panel redesign before clinical use.

input.csv

PatientID,PanelID,PrimaryTumorType,TumorSequencingID,MatchedNormalID,AssayPlatform,TotalVariants_Selected,MinVariants_Required,ClonalVariants_Count,SubclonalVariants_Count,ClonalFraction_InPanel,MinClonalFraction,DriverMutations_Included,PassengerMutations_Included,GermlineVariants_Excluded,CHIP_Variants_Excluded,LowConfidenceVariants_Excluded,VariantsInProblematicRegions_Excluded,VariantsRemoved_ByFilters,FilterFailure_Reasons,FailedPrimerDesign_Count,TotalPrimers_Designed,PrimerDesignSuccess_Rate,CrossReactivity_Check_Passed,OffTarget_Analysis_Completed,OffTarget_Sites_Identified,MaxOffTarget_AlignmentScore,MaxAllowed_OffTargetScore,MeanDepth_PerVariant_X,MinDepth_PerVariant_X,RequiredMinDepth_PerVariant_X,VariantsBelowMinDepth,Uniformity_AcrossVariants_Percent,MinUniformity_Percent,AmpliconBalance_CV_Percent,MaxAmpliconBalance_CV_Percent,TheoreticalLOD_VAF_Percent,TargetLOD_VAF_Percent,CurrentDesign_SupportsTargetLOD,EffectiveIndependentLoci,MinEffectiveLoci_ForTargetLOD,PositiveControl_Pass,NegativeControl_Pass,NoTemplateControl_Pass,SyntheticReference_Pass,TumorNormalPair_Verified,SomaticCalling_Pipeline_Validated,PanelDesign_Software_Version_Locked,DesignSoftware_Version,ManufacturingLot_Tracked,ManufacturingLot_Number
PAT-LUNG-042,TI-PNL-042-v1,NSCLC,WES-LUNG-042-T,WES-LUNG-042-N,Bespoke_Amplicon,32,16,26,6,0.81,0.5,3,29,true,true,true,true,45,,1,33,0.97,true,true,0,0.15,0.8,25000,8500,5000,0,88.0,70,18.5,30,0.005,0.01,true,28,10,true,true,true,true,true,true,true,v3.2.1,true,MFG-2026-0451
PAT-CRC-055,TI-PNL-055-v1,CRC,WES-CRC-055-T,WES-CRC-055-N,Bespoke_Amplicon,12,16,4,8,0.33,0.5,2,10,true,false,true,true,68,"CHIP_not_filtered;low_tumor_purity",5,17,0.71,false,true,3,0.92,0.8,12000,2800,5000,3,55.0,70,42.0,30,0.035,0.01,false,7,10,true,true,true,false,true,true,true,v3.2.1,true,MFG-2026-0467

URS & FS — User Requirements and Functional Specification

This document describes the controlled interface and behaviour of TumorInformedPanelQcChecker for Tumor-Informed Panel 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.

Performs design and quality verification per CAP/CLIA §GEN.48800, FDA tumor-informed assay guidance, ESMO MRD Guidelines and TRACERx standards: variant composition (total count ≥ minimum, clonal fraction ≥50%, driver inclusion), variant filtering (germline exclusion MANDATORY, CHIP exclusion, low-confidence exclusion, problematic region exclusion, matched normal verification), primer/probe design (success rate ≥95%, cross-reactivity check, off-target analysis with alignment score threshold), ana
⚠️ Critical: Each tumor-informed panel is UNIQUE; standard QC metrics do not apply. Germline variant in panel = IRREMEDIABLE source of false positives in MRD monitoring. CHIP variants account for up to 30% of FPs in cfDNA for patients >60 years. Clonal fraction <50% means panel tracks minor clones; dominant clone may be missed. Theoretical LOD is lower bound; actual sensitivity determined empirically. Effective independent loci ≠ total variants; linked variants add no information. Off-target amp
⚠️ Note: This utility assesses DESIGN AND TECHNICAL QUALITY of the personalized panel. It does not replace analytical performance validation (LoD, specificity, precision) or clinical interpretation of monitoring results. Panels with DESIGN_CONCERNS status may be used with documented limitations; INVALID or INSUFFICIENT_SENSITIVITY status requires panel redesign before clinical use.

URS — User Requirements Specification

ID	Requirement	Criticality	Acceptance criterion
URS-001	The utility shall accept an input.csv file for Tumor-Informed Panel 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	`PatientID`	string / controlled vocabulary	`PAT-LUNG-042`	Controlled input parameter for deterministic QC rules.
2	`PanelID`	string / controlled vocabulary	`TI-PNL-042-v1`	Controlled input parameter for deterministic QC rules.
3	`PrimaryTumorType`	string / controlled vocabulary	`NSCLC`	Controlled input parameter for deterministic QC rules.
4	`TumorSequencingID`	string / controlled vocabulary	`WES-LUNG-042-T`	Controlled input parameter for deterministic QC rules.
5	`MatchedNormalID`	string / controlled vocabulary	`WES-LUNG-042-N`	Controlled input parameter for deterministic QC rules.
6	`AssayPlatform`	string / controlled vocabulary	`Bespoke_Amplicon`	Controlled input parameter for deterministic QC rules.
7	`TotalVariants_Selected`	decimal	`32`	Controlled input parameter for deterministic QC rules.
8	`MinVariants_Required`	decimal	`16`	Controlled input parameter for deterministic QC rules.
9	`ClonalVariants_Count`	integer / decimal	`26`	Count parameter used for microbiological, particulate or cellular control.
10	`SubclonalVariants_Count`	integer / decimal	`6`	Count parameter used for microbiological, particulate or cellular control.
11	`ClonalFraction_InPanel`	decimal	`0.81`	Controlled input parameter for deterministic QC rules.
12	`MinClonalFraction`	integer / decimal	`0.5`	Controlled input parameter for deterministic QC rules.
13	`DriverMutations_Included`	decimal	`3`	Controlled input parameter for deterministic QC rules.
14	`PassengerMutations_Included`	decimal	`29`	Controlled input parameter for deterministic QC rules.
15	`GermlineVariants_Excluded`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
16	`CHIP_Variants_Excluded`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
17	`LowConfidenceVariants_Excluded`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
18	`VariantsInProblematicRegions_Excluded`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
19	`VariantsRemoved_ByFilters`	decimal	`45`	Controlled input parameter for deterministic QC rules.
20	`FilterFailure_Reasons`	string / controlled vocabulary		Controlled input parameter for deterministic QC rules.
21	`FailedPrimerDesign_Count`	integer / decimal	`1`	Count parameter used for microbiological, particulate or cellular control.
22	`TotalPrimers_Designed`	decimal	`33`	Controlled input parameter for deterministic QC rules.
23	`PrimerDesignSuccess_Rate`	decimal	`0.97`	Controlled input parameter for deterministic QC rules.
24	`CrossReactivity_Check_Passed`	string / controlled vocabulary	`true`	Potency/activity; critical efficacy-related parameter.
25	`OffTarget_Analysis_Completed`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
26	`OffTarget_Sites_Identified`	string / controlled vocabulary	`0`	Controlled input parameter for deterministic QC rules.
27	`MaxOffTarget_AlignmentScore`	decimal	`0.15`	Controlled input parameter for deterministic QC rules.
28	`MaxAllowed_OffTargetScore`	decimal	`0.8`	Controlled input parameter for deterministic QC rules.
29	`MeanDepth_PerVariant_X`	decimal	`25000`	Controlled input parameter for deterministic QC rules.
30	`MinDepth_PerVariant_X`	decimal	`8500`	Controlled input parameter for deterministic QC rules.
31	`RequiredMinDepth_PerVariant_X`	decimal	`5000`	Controlled input parameter for deterministic QC rules.
32	`VariantsBelowMinDepth`	decimal	`0`	Controlled input parameter for deterministic QC rules.
33	`Uniformity_AcrossVariants_Percent`	decimal	`88.0`	Controlled input parameter for deterministic QC rules.
34	`MinUniformity_Percent`	decimal	`70`	Controlled input parameter for deterministic QC rules.
35	`AmpliconBalance_CV_Percent`	decimal	`18.5`	Controlled input parameter for deterministic QC rules.
36	`MaxAmpliconBalance_CV_Percent`	decimal	`30`	Controlled input parameter for deterministic QC rules.
37	`TheoreticalLOD_VAF_Percent`	decimal	`0.005`	Controlled input parameter for deterministic QC rules.
38	`TargetLOD_VAF_Percent`	decimal	`0.01`	Controlled input parameter for deterministic QC rules.
39	`CurrentDesign_SupportsTargetLOD`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
40	`EffectiveIndependentLoci`	decimal	`28`	Controlled input parameter for deterministic QC rules.
41	`MinEffectiveLoci_ForTargetLOD`	decimal	`10`	Controlled input parameter for deterministic QC rules.
42	`PositiveControl_Pass`	string / controlled vocabulary	`true`	Control point/control sample for assay run validity.
43	`NegativeControl_Pass`	string / controlled vocabulary	`true`	Control point/control sample for assay run validity.
44	`NoTemplateControl_Pass`	string / controlled vocabulary	`true`	Temperature profile/MKT; storage, shipping and stability parameter.
45	`SyntheticReference_Pass`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
46	`TumorNormalPair_Verified`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
47	`SomaticCalling_Pipeline_Validated`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
48	`PanelDesign_Software_Version_Locked`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
49	`DesignSoftware_Version`	string / controlled vocabulary	`v3.2.1`	Controlled input parameter for deterministic QC rules.
50	`ManufacturingLot_Tracked`	string / controlled vocabulary	`true`	Batch or lot identifier used for traceability.
51	`ManufacturingLot_Number`	string / controlled vocabulary	`MFG-2026-0451`	Batch or lot identifier used for traceability.

PatientID,PanelID,PrimaryTumorType,TumorSequencingID,MatchedNormalID,AssayPlatform,TotalVariants_Selected,MinVariants_Required,ClonalVariants_Count,SubclonalVariants_Count,ClonalFraction_InPanel,MinClonalFraction,DriverMutations_Included,PassengerMutations_Included,GermlineVariants_Excluded,CHIP_Variants_Excluded,LowConfidenceVariants_Excluded,VariantsInProblematicRegions_Excluded,VariantsRemoved_ByFilters,FilterFailure_Reasons,FailedPrimerDesign_Count,TotalPrimers_Designed,PrimerDesignSuccess_Rate,CrossReactivity_Check_Passed,OffTarget_Analysis_Completed,OffTarget_Sites_Identified,MaxOffTarget_AlignmentScore,MaxAllowed_OffTargetScore,MeanDepth_PerVariant_X,MinDepth_PerVariant_X,RequiredMinDepth_PerVariant_X,VariantsBelowMinDepth,Uniformity_AcrossVariants_Percent,MinUniformity_Percent,AmpliconBalance_CV_Percent,MaxAmpliconBalance_CV_Percent,TheoreticalLOD_VAF_Percent,TargetLOD_VAF_Percent,CurrentDesign_SupportsTargetLOD,EffectiveIndependentLoci,MinEffectiveLoci_ForTargetLOD,PositiveControl_Pass,NegativeControl_Pass,NoTemplateControl_Pass,SyntheticReference_Pass,TumorNormalPair_Verified,SomaticCalling_Pipeline_Validated,PanelDesign_Software_Version_Locked,DesignSoftware_Version,ManufacturingLot_Tracked,ManufacturingLot_Number
PAT-LUNG-042,TI-PNL-042-v1,NSCLC,WES-LUNG-042-T,WES-LUNG-042-N,Bespoke_Amplicon,32,16,26,6,0.81,0.5,3,29,true,true,true,true,45,,1,33,0.97,true,true,0,0.15,0.8,25000,8500,5000,0,88.0,70,18.5,30,0.005,0.01,true,28,10,true,true,true,true,true,true,true,v3.2.1,true,MFG-2026-0451
PAT-CRC-055,TI-PNL-055-v1,CRC,WES-CRC-055-T,WES-CRC-055-N,Bespoke_Amplicon,12,16,4,8,0.33,0.5,2,10,true,false,true,true,68,CHIP_not_filtered;low_tumor_purity,5,17,0.71,false,true,3,0.92,0.8,12000,2800,5000,3,55.0,70,42.0,30,0.035,0.01,false,7,10,true,true,true,false,true,true,true,v3.2.1,true,MFG-2026-0467

Input validation rules

ID	Field	Rule	Criticality
VR-001	`PatientID`	The field shall match an approved dictionary or accepted string representation.	High
VR-002	`PanelID`	The field shall match an approved dictionary or accepted string representation.	High
VR-003	`PrimaryTumorType`	The field shall match an approved dictionary or accepted string representation.	High
VR-004	`TumorSequencingID`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-005	`MatchedNormalID`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-006	`AssayPlatform`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-007	`TotalVariants_Selected`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-008	`MinVariants_Required`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-009	`ClonalVariants_Count`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-010	`SubclonalVariants_Count`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-011	`ClonalFraction_InPanel`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-012	`MinClonalFraction`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-013	`DriverMutations_Included`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-014	`PassengerMutations_Included`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-015	`GermlineVariants_Excluded`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-016	`CHIP_Variants_Excluded`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-017	`LowConfidenceVariants_Excluded`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-018	`VariantsInProblematicRegions_Excluded`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-019	`VariantsRemoved_ByFilters`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-020	`FilterFailure_Reasons`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-021	`FailedPrimerDesign_Count`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-022	`TotalPrimers_Designed`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-023	`PrimerDesignSuccess_Rate`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-024	`CrossReactivity_Check_Passed`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-025	`OffTarget_Analysis_Completed`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-026	`OffTarget_Sites_Identified`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-027	`MaxOffTarget_AlignmentScore`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-028	`MaxAllowed_OffTargetScore`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-029	`MeanDepth_PerVariant_X`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-030	`MinDepth_PerVariant_X`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-031	`RequiredMinDepth_PerVariant_X`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-032	`VariantsBelowMinDepth`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-033	`Uniformity_AcrossVariants_Percent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-034	`MinUniformity_Percent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-035	`AmpliconBalance_CV_Percent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-036	`MaxAmpliconBalance_CV_Percent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-037	`TheoreticalLOD_VAF_Percent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-038	`TargetLOD_VAF_Percent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-039	`CurrentDesign_SupportsTargetLOD`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-040	`EffectiveIndependentLoci`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-041	`MinEffectiveLoci_ForTargetLOD`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-042	`PositiveControl_Pass`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-043	`NegativeControl_Pass`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-044	`NoTemplateControl_Pass`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-045	`SyntheticReference_Pass`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-046	`TumorNormalPair_Verified`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-047	`SomaticCalling_Pipeline_Validated`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-048	`PanelDesign_Software_Version_Locked`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-049	`DesignSoftware_Version`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-050	`ManufacturingLot_Tracked`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-051	`ManufacturingLot_Number`	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 Tumor-Informed Panel 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": "tumorinformedpanelqcchecker",
  "utilityFolder": "TumorInformedPanelQcChecker",
  "package": "LiquidBiopsy",
  "overallStatus": "PASS|WARNING|FAIL",
  "sourceFile": "input.csv",
  "processedAtUtc": "2026-06-10T00:00:00Z",
  "checks": [
    {
      "parameter": "PatientID",
      "value": "PAT-LUNG-042",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-001"
    },
    {
      "parameter": "PanelID",
      "value": "TI-PNL-042-v1",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-002"
    },
    {
      "parameter": "PrimaryTumorType",
      "value": "NSCLC",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-003"
    },
    {
      "parameter": "TumorSequencingID",
      "value": "WES-LUNG-042-T",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-004"
    },
    {
      "parameter": "MatchedNormalID",
      "value": "WES-LUNG-042-N",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-005"
    },
    {
      "parameter": "AssayPlatform",
      "value": "Bespoke_Amplicon",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-006"
    },
    {
      "parameter": "TotalVariants_Selected",
      "value": "32",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-007"
    },
    {
      "parameter": "MinVariants_Required",
      "value": "16",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-008"
    },
    {
      "parameter": "ClonalVariants_Count",
      "value": "26",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-009"
    },
    {
      "parameter": "SubclonalVariants_Count",
      "value": "6",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-010"
    },
    {
      "parameter": "ClonalFraction_InPanel",
      "value": "0.81",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-011"
    },
    {
      "parameter": "MinClonalFraction",
      "value": "0.5",
      "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": "TumorInformedPanelQcChecker.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