UltraSensitiveMrdRunChecker

Ultra-Sensitive MRD Run

Liquid Biopsy жидкостная биопсия cfDNA ctDNA CTC exosomes NGS qPCR

Utility description: Ultra-Sensitive MRD Run

Ultra-Sensitive MRD Run Checker — Specialized QC for Ultra-Sensitive MRD Assay Runs

Performs MRD-specific run QC (LOD ≤0.01% VAF) per CAP/CLIA §GEN.48800, FDA MRD assay guidance, ESMO MRD Guidelines and Blood Profiling Atlas standards: UMI metrics (unique molecular depth ≥ required, mean family size ≥3.0, families ≥3 members ≥70%, consensus efficiency ≥60%, UMI collision rate ≤2%), positional background noise (mean ≤0.0005% VAF, max single position ≤0.001% VAF, error suppression factor ≥100×), ultra-low positive control (recovery ≥70% at LOD level), contamination controls (NTC zero false positives, index hopping ≤0.1%, UD indexes mandatory, cross-sample contamination ≤0.01%), limit of blank (LoB ≤0.005% VAF), and sensitivity verification (theoretical LOD ≤ declared LOD). Four-tier classification: MRD_RUN_ACCEPTED / SENSITIVITY_COMPROMISED / CONTAMINATION_SUSPECTED / MRD_RUN_REJECTED.

⚠️ Critical: Ultra-sensitive MRD operates at single-molecule level; every metric is critical. Raw depth is meaningless without UMI depth; 100,000× raw may yield only 2,000× unique. Family size <3 = consensus impossible; sequencing errors pass into final calls. Index hopping without UD indexes = guaranteed FPs in multiplexed runs. Any NTC contamination at MRD levels irreversibly compromises entire run. Positional background varies by position; per-position monitoring mandatory. LoB ≥ LOD = test cannot distinguish signal from noise; results meaningless. Tool assesses TECHNICAL SUITABILITY for ultra-sensitive MRD detection only; does not replace bioinformatic call validation or clinical MRD interpretation. For CONTAMINATION_SUSPECTED, all run results must be blocked pending investigation. For SENSITIVITY_COMPROMISED, results may be released only with explicit disclosure of reduced sensitivity and interpretation limitations.

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

📍 Scope of Application:
• MRD monitoring laboratories: Mandatory acceptance of every ultra-sensitive run.
• MRD-guided therapy clinical trials: QC of stratification biomarkers.
• MRD assay manufacturers: Release testing of reagents and pipelines.
• Regulatory inspections: Documentation of ultra-sensitive assay performance.
• CAP/ISO accreditation: Specialized QC for MRD testing.

💡 Tips:
1. UMI Design: Use ≥10 bp UMI with sufficient diversity for target depth.
2. NTC Multiplicity: Include ≥3 NTCs per run for reliable LoB estimation.
3. Positional Baselines: Maintain historical per-position background baselines; trends matter more than absolute values.
4. Ultra-Low Controls: Prepare aliquots; avoid freeze-thaw cycles.
5. Contamination Response Plan: Develop SOP for NTC contamination response (quarantine, investigation, re-run).

⚠️ Note: This utility assesses TECHNICAL SUITABILITY of the run for ultra-sensitive MRD detection. It does not replace bioinformatic variant call validation or clinical MRD result interpretation. For CONTAMINATION_SUSPECTED status, all run results must be blocked until investigation is complete. For SENSITIVITY_COMPROMISED status, results may be released only with explicit disclosure of reduced sensitivity and interpretation limitations.

input.csv

RunID,AssayName,Platform,PanelType,RunDate,TotalSamples,TotalReads_Million,UniqueUMIs_Million,UMIDeduplication_Rate,UniqueMolecularDepth_X,RequiredUniqueMolecularDepth_X,MeanFamilySize,MinMeanFamilySize,MedianFamilySize,PercentFamilies_SizeGE3,MinPercentFamilies_SizeGE3,UMICollisionRate_Percent,MaxUMICollisionRate_Percent,ConsensusEfficiency_Percent,MinConsensusEfficiency_Percent,PositionalBackground_Mean_VAF,MaxPositionalBackground_VAF,PositionalBackground_MaxSingle_VAF,MaxAllowed_SinglePosition_Background_VAF,PositionsAboveBackground_Threshold,TotalMonitoredPositions,ErrorSuppression_Factor,MinErrorSuppression_Factor,UltraLowPositive_Control_Passed,UltraLowPos_Recovery_Percent,MinUltraLowPos_Recovery_Percent,UltraLowPos_ObservedVAF,UltraLowPos_ExpectedVAF,NegativeControl_Clean,NTC_PositiveSignals_Detected,MaxNTC_PositiveSignals_Allowed,NoTemplateControl_Pass,IndexHopping_Rate_Percent,MaxIndexHopping_Rate_Percent,UDIndexes_Used,CrossSampleContamination_Estimate_Percent,MaxCrossSampleContamination_Percent,PercentQ30_Read1,PercentQ30_Read2,MinPercentQ30,OnTargetRate_Percent,MinOnTargetRate_Percent,AssayDeclared_LOD_VAF,LimitOfBlank_VAF,MaxAcceptable_LoB_VAF,ReagentKit_Lot,ReagentLot_Verified,Calibration_Current,PipelineVersion,PipelineVersion_Validated
MRD-2026-0142,Signatera_NSCLC_v3,UMI_NGS,Tumor_Informed,2026-06-08,24,120,8.5,0.82,12500,5000,5.8,3.0,5.0,85.0,70,0.8,2.0,92.0,60,0.00008,0.0005,0.00035,0.001,0,32,850,100,true,94.5,70,0.0095,0.01,true,0,0,true,0.02,0.1,true,0.003,0.01,91.5,88.2,75,82.0,60,0.01,0.0002,0.005,RK-2026-0451,true,true,v4.2.1,true
MRD-2026-0143,Guardant_Reveal,UMI_NGS,Tumor_Agnostic,2026-06-09,24,95,4.2,0.78,3800,5000,2.4,3.0,2.0,42.0,70,3.5,2.0,48.0,60,0.0012,0.0005,0.0045,0.001,5,50,35,100,false,52.0,70,0.0052,0.01,false,3,0,false,0.35,0.1,false,0.08,0.01,82.0,76.5,75,65.0,60,0.01,0.008,0.005,RK-2026-0467,true,true,v4.2.1,true

URS & FS — User Requirements and Functional Specification

This document describes the controlled interface and behaviour of UltraSensitiveMrdRunChecker for Ultra-Sensitive MRD Run 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 MRD-specific run QC (LOD ≤0.01% VAF) per CAP/CLIA §GEN.48800, FDA MRD assay guidance, ESMO MRD Guidelines and Blood Profiling Atlas standards: UMI metrics (unique molecular depth ≥ required, mean family size ≥3.0, families ≥3 members ≥70%, consensus efficiency ≥60%, UMI collision rate ≤2%), positional background noise (mean ≤0.0005% VAF, max single position ≤0.001% VAF, error suppression factor ≥100×), ultra-low positive control (recovery ≥70% at LOD level), contamination controls (NTC
⚠️ Critical: Ultra-sensitive MRD operates at single-molecule level; every metric is critical. Raw depth is meaningless without UMI depth; 100,000× raw may yield only 2,000× unique. Family size <3 = consensus impossible; sequencing errors pass into final calls. Index hopping without UD indexes = guaranteed FPs in multiplexed runs. Any NTC contamination at MRD levels irreversibly compromises entire run. Positional background varies by position; per-position monitoring mandatory. LoB ≥ LOD = test c
• CAP/ISO accreditation: Specialized QC for MRD testing.
1. UMI Design: Use ≥10 bp UMI with sufficient diversity for target depth.
2. NTC Multiplicity: Include ≥3 NTCs per run for reliable LoB estimation.
⚠️ Note: This utility assesses TECHNICAL SUITABILITY of the run for ultra-sensitive MRD detection. It does not replace bioinformatic variant call validation or clinical MRD result interpretation. For CONTAMINATION_SUSPECTED status, all run results must be blocked until investigation is complete. For SENSITIVITY_COMPROMISED status, results may be released only with explicit disclosure of reduced sensitivity and interpretation limitations.

URS — User Requirements Specification

ID	Requirement	Criticality	Acceptance criterion
URS-001	The utility shall accept an input.csv file for Ultra-Sensitive MRD Run 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	`RunID`	string / controlled vocabulary	`MRD-2026-0142`	Controlled input parameter for deterministic QC rules.
2	`AssayName`	string / controlled vocabulary	`Signatera_NSCLC_v3`	Controlled input parameter for deterministic QC rules.
3	`Platform`	string / controlled vocabulary	`UMI_NGS`	Controlled input parameter for deterministic QC rules.
4	`PanelType`	string / controlled vocabulary	`Tumor_Informed`	Controlled input parameter for deterministic QC rules.
5	`RunDate`	string / controlled vocabulary	`2026-06-08`	Controlled input parameter for deterministic QC rules.
6	`TotalSamples`	string / controlled vocabulary	`24`	Sample or laboratory specimen identifier.
7	`TotalReads_Million`	integer / decimal	`120`	Controlled input parameter for deterministic QC rules.
8	`UniqueUMIs_Million`	integer / decimal	`8.5`	Controlled input parameter for deterministic QC rules.
9	`UMIDeduplication_Rate`	string / controlled vocabulary	`0.82`	Controlled input parameter for deterministic QC rules.
10	`UniqueMolecularDepth_X`	decimal	`12500`	Controlled input parameter for deterministic QC rules.
11	`RequiredUniqueMolecularDepth_X`	decimal	`5000`	Controlled input parameter for deterministic QC rules.
12	`MeanFamilySize`	decimal	`5.8`	Controlled input parameter for deterministic QC rules.
13	`MinMeanFamilySize`	decimal	`3.0`	Controlled input parameter for deterministic QC rules.
14	`MedianFamilySize`	decimal	`5.0`	Controlled input parameter for deterministic QC rules.
15	`PercentFamilies_SizeGE3`	decimal	`85.0`	Controlled input parameter for deterministic QC rules.
16	`MinPercentFamilies_SizeGE3`	decimal	`70`	Controlled input parameter for deterministic QC rules.
17	`UMICollisionRate_Percent`	decimal	`0.8`	Controlled input parameter for deterministic QC rules.
18	`MaxUMICollisionRate_Percent`	decimal	`2.0`	Controlled input parameter for deterministic QC rules.
19	`ConsensusEfficiency_Percent`	decimal	`92.0`	Controlled input parameter for deterministic QC rules.
20	`MinConsensusEfficiency_Percent`	decimal	`60`	Controlled input parameter for deterministic QC rules.
21	`PositionalBackground_Mean_VAF`	decimal	`0.00008`	Controlled input parameter for deterministic QC rules.
22	`MaxPositionalBackground_VAF`	decimal	`0.0005`	Controlled input parameter for deterministic QC rules.
23	`PositionalBackground_MaxSingle_VAF`	decimal	`0.00035`	Controlled input parameter for deterministic QC rules.
24	`MaxAllowed_SinglePosition_Background_VAF`	decimal	`0.001`	Controlled input parameter for deterministic QC rules.
25	`PositionsAboveBackground_Threshold`	decimal	`0`	Controlled input parameter for deterministic QC rules.
26	`TotalMonitoredPositions`	decimal	`32`	Controlled input parameter for deterministic QC rules.
27	`ErrorSuppression_Factor`	decimal	`850`	Controlled input parameter for deterministic QC rules.
28	`MinErrorSuppression_Factor`	decimal	`100`	Controlled input parameter for deterministic QC rules.
29	`UltraLowPositive_Control_Passed`	string / controlled vocabulary	`true`	Control point/control sample for assay run validity.
30	`UltraLowPos_Recovery_Percent`	decimal	`94.5`	Recovery; indicator of analytical validity.
31	`MinUltraLowPos_Recovery_Percent`	decimal	`70`	Recovery; indicator of analytical validity.
32	`UltraLowPos_ObservedVAF`	decimal	`0.0095`	Controlled input parameter for deterministic QC rules.
33	`UltraLowPos_ExpectedVAF`	decimal	`0.01`	Controlled input parameter for deterministic QC rules.
34	`NegativeControl_Clean`	string / controlled vocabulary	`true`	Control point/control sample for assay run validity.
35	`NTC_PositiveSignals_Detected`	decimal	`0`	Controlled input parameter for deterministic QC rules.
36	`MaxNTC_PositiveSignals_Allowed`	flag / boolean	`0`	Controlled input parameter for deterministic QC rules.
37	`NoTemplateControl_Pass`	string / controlled vocabulary	`true`	Temperature profile/MKT; storage, shipping and stability parameter.
38	`IndexHopping_Rate_Percent`	decimal	`0.02`	Controlled input parameter for deterministic QC rules.
39	`MaxIndexHopping_Rate_Percent`	decimal	`0.1`	Controlled input parameter for deterministic QC rules.
40	`UDIndexes_Used`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
41	`CrossSampleContamination_Estimate_Percent`	decimal	`0.003`	Sample or laboratory specimen identifier.
42	`MaxCrossSampleContamination_Percent`	decimal	`0.01`	Sample or laboratory specimen identifier.
43	`PercentQ30_Read1`	decimal	`91.5`	Controlled input parameter for deterministic QC rules.
44	`PercentQ30_Read2`	decimal	`88.2`	Controlled input parameter for deterministic QC rules.
45	`MinPercentQ30`	decimal	`75`	Controlled input parameter for deterministic QC rules.
46	`OnTargetRate_Percent`	decimal	`82.0`	Controlled input parameter for deterministic QC rules.
47	`MinOnTargetRate_Percent`	decimal	`60`	Controlled input parameter for deterministic QC rules.
48	`AssayDeclared_LOD_VAF`	string / controlled vocabulary	`0.01`	Controlled input parameter for deterministic QC rules.
49	`LimitOfBlank_VAF`	decimal	`0.0002`	Approved limit applied during result evaluation.
50	`MaxAcceptable_LoB_VAF`	decimal	`0.005`	Controlled input parameter for deterministic QC rules.
51	`ReagentKit_Lot`	string / controlled vocabulary	`RK-2026-0451`	Batch or lot identifier used for traceability.
52	`ReagentLot_Verified`	string / controlled vocabulary	`true`	Batch or lot identifier used for traceability.
53	`Calibration_Current`	string / controlled vocabulary	`true`	Component ratio; structural or formulation CQA.
54	`PipelineVersion`	string / controlled vocabulary	`v4.2.1`	Controlled input parameter for deterministic QC rules.
55	`PipelineVersion_Validated`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.

RunID,AssayName,Platform,PanelType,RunDate,TotalSamples,TotalReads_Million,UniqueUMIs_Million,UMIDeduplication_Rate,UniqueMolecularDepth_X,RequiredUniqueMolecularDepth_X,MeanFamilySize,MinMeanFamilySize,MedianFamilySize,PercentFamilies_SizeGE3,MinPercentFamilies_SizeGE3,UMICollisionRate_Percent,MaxUMICollisionRate_Percent,ConsensusEfficiency_Percent,MinConsensusEfficiency_Percent,PositionalBackground_Mean_VAF,MaxPositionalBackground_VAF,PositionalBackground_MaxSingle_VAF,MaxAllowed_SinglePosition_Background_VAF,PositionsAboveBackground_Threshold,TotalMonitoredPositions,ErrorSuppression_Factor,MinErrorSuppression_Factor,UltraLowPositive_Control_Passed,UltraLowPos_Recovery_Percent,MinUltraLowPos_Recovery_Percent,UltraLowPos_ObservedVAF,UltraLowPos_ExpectedVAF,NegativeControl_Clean,NTC_PositiveSignals_Detected,MaxNTC_PositiveSignals_Allowed,NoTemplateControl_Pass,IndexHopping_Rate_Percent,MaxIndexHopping_Rate_Percent,UDIndexes_Used,CrossSampleContamination_Estimate_Percent,MaxCrossSampleContamination_Percent,PercentQ30_Read1,PercentQ30_Read2,MinPercentQ30,OnTargetRate_Percent,MinOnTargetRate_Percent,AssayDeclared_LOD_VAF,LimitOfBlank_VAF,MaxAcceptable_LoB_VAF,ReagentKit_Lot,ReagentLot_Verified,Calibration_Current,PipelineVersion,PipelineVersion_Validated
MRD-2026-0142,Signatera_NSCLC_v3,UMI_NGS,Tumor_Informed,2026-06-08,24,120,8.5,0.82,12500,5000,5.8,3.0,5.0,85.0,70,0.8,2.0,92.0,60,0.00008,0.0005,0.00035,0.001,0,32,850,100,true,94.5,70,0.0095,0.01,true,0,0,true,0.02,0.1,true,0.003,0.01,91.5,88.2,75,82.0,60,0.01,0.0002,0.005,RK-2026-0451,true,true,v4.2.1,true
MRD-2026-0143,Guardant_Reveal,UMI_NGS,Tumor_Agnostic,2026-06-09,24,95,4.2,0.78,3800,5000,2.4,3.0,2.0,42.0,70,3.5,2.0,48.0,60,0.0012,0.0005,0.0045,0.001,5,50,35,100,false,52.0,70,0.0052,0.01,false,3,0,false,0.35,0.1,false,0.08,0.01,82.0,76.5,75,65.0,60,0.01,0.008,0.005,RK-2026-0467,true,true,v4.2.1,true

Input validation rules

ID	Field	Rule	Criticality
VR-001	`RunID`	The field shall match an approved dictionary or accepted string representation.	High
VR-002	`AssayName`	The field shall match an approved dictionary or accepted string representation.	High
VR-003	`Platform`	The field shall match an approved dictionary or accepted string representation.	High
VR-004	`PanelType`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-005	`RunDate`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-006	`TotalSamples`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-007	`TotalReads_Million`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-008	`UniqueUMIs_Million`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-009	`UMIDeduplication_Rate`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-010	`UniqueMolecularDepth_X`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-011	`RequiredUniqueMolecularDepth_X`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-012	`MeanFamilySize`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-013	`MinMeanFamilySize`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-014	`MedianFamilySize`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-015	`PercentFamilies_SizeGE3`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-016	`MinPercentFamilies_SizeGE3`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-017	`UMICollisionRate_Percent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-018	`MaxUMICollisionRate_Percent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-019	`ConsensusEfficiency_Percent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-020	`MinConsensusEfficiency_Percent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-021	`PositionalBackground_Mean_VAF`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-022	`MaxPositionalBackground_VAF`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-023	`PositionalBackground_MaxSingle_VAF`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-024	`MaxAllowed_SinglePosition_Background_VAF`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-025	`PositionsAboveBackground_Threshold`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-026	`TotalMonitoredPositions`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-027	`ErrorSuppression_Factor`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-028	`MinErrorSuppression_Factor`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-029	`UltraLowPositive_Control_Passed`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-030	`UltraLowPos_Recovery_Percent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-031	`MinUltraLowPos_Recovery_Percent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-032	`UltraLowPos_ObservedVAF`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-033	`UltraLowPos_ExpectedVAF`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-034	`NegativeControl_Clean`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-035	`NTC_PositiveSignals_Detected`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-036	`MaxNTC_PositiveSignals_Allowed`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-037	`NoTemplateControl_Pass`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-038	`IndexHopping_Rate_Percent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-039	`MaxIndexHopping_Rate_Percent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-040	`UDIndexes_Used`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-041	`CrossSampleContamination_Estimate_Percent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-042	`MaxCrossSampleContamination_Percent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-043	`PercentQ30_Read1`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-044	`PercentQ30_Read2`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-045	`MinPercentQ30`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-046	`OnTargetRate_Percent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-047	`MinOnTargetRate_Percent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-048	`AssayDeclared_LOD_VAF`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-049	`LimitOfBlank_VAF`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-050	`MaxAcceptable_LoB_VAF`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-051	`ReagentKit_Lot`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-052	`ReagentLot_Verified`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-053	`Calibration_Current`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-054	`PipelineVersion`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-055	`PipelineVersion_Validated`	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 Ultra-Sensitive MRD Run 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": "ultrasensitivemrdrunchecker",
  "utilityFolder": "UltraSensitiveMrdRunChecker",
  "package": "LiquidBiopsy",
  "overallStatus": "PASS|WARNING|FAIL",
  "sourceFile": "input.csv",
  "processedAtUtc": "2026-06-10T00:00:00Z",
  "checks": [
    {
      "parameter": "RunID",
      "value": "MRD-2026-0142",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-001"
    },
    {
      "parameter": "AssayName",
      "value": "Signatera_NSCLC_v3",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-002"
    },
    {
      "parameter": "Platform",
      "value": "UMI_NGS",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-003"
    },
    {
      "parameter": "PanelType",
      "value": "Tumor_Informed",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-004"
    },
    {
      "parameter": "RunDate",
      "value": "2026-06-08",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-005"
    },
    {
      "parameter": "TotalSamples",
      "value": "24",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-006"
    },
    {
      "parameter": "TotalReads_Million",
      "value": "120",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-007"
    },
    {
      "parameter": "UniqueUMIs_Million",
      "value": "8.5",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-008"
    },
    {
      "parameter": "UMIDeduplication_Rate",
      "value": "0.82",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-009"
    },
    {
      "parameter": "UniqueMolecularDepth_X",
      "value": "12500",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-010"
    },
    {
      "parameter": "RequiredUniqueMolecularDepth_X",
      "value": "5000",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-011"
    },
    {
      "parameter": "MeanFamilySize",
      "value": "5.8",
      "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": "UltraSensitiveMrdRunChecker.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