CfdnaExtractionYieldChecker

Cfdna Extraction Yield

Liquid Biopsy жидкостная биопсия cfDNA ctDNA CTC exosomes NGS qPCR

Utility description: Cfdna Extraction Yield

Cfdna Extraction Yield Checker — cfDNA Extraction Quality Control

ℹ️ Utility performs comprehensive assessment of circulating free DNA extraction quality according to CAP/CLIA standards for liquid biopsy:
• Material Yield: Verification of total cfDNA amount and concentration against minimum NGS thresholds.
• Efficiency Control: Assessment of exogenous spike-in recovery to exclude technical extraction errors.
• Sample Purity: Control of high molecular weight genomic DNA (HMW gDNA) level masking ctDNA signal.
• Fragmentation: Verification of characteristic nucleosomal peak (~167 bp) as true cfDNA marker.

⚠️ IMPORTANT:
• Low cfDNA yield (<5-10 ng) makes reliable detection of mutations with VAF <0.5% impossible.
• gDNA contamination >10% significantly reduces signal-to-noise ratio in sequencing.

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

Input format:
SampleID,ExtractionKit,InputPlasmaVolume_mL,ElutionVolume_uL,Concentration_ng_uL,MinConcentration_ng_uL,TotalYield_ng,MinTotalYield_ng,SpikeIn_Recovery_Percent,MinSpikeIn_Recovery_Percent,HMW_gDNA_Percent,MaxHMW_gDNA_Percent,FragmentSize_Peak_bp

Example:
CFDNA-001,QIAamp,2.0,50,0.8,0.2,40.0,5.0,85.0,50.0,3.5,10.0,167

📍 Scope of Application (Usage Where):
• Liquid Biopsy Laboratories: Incoming control before NGS library construction.
• Oncology Research: Ensuring sufficient material for rare variant detection.
• Non-Invasive Prenatal Testing (NIPT): Fetal DNA quality control.
• Method Development: Comparison of different extraction kit efficiencies.

— WHY IS THIS NEEDED?
cfDNA amount in plasma is limited and varies between patients.
Without strict yield and purity control, analytical test sensitivity cannot be guaranteed.
Automated verification prevents launching expensive sequencing on substandard material.

⚠️ CRITICAL:
• Spike-In Recovery: Low recovery (<50%) indicates DNA loss on column/magnetic beads.
• HMW gDNA: High level indicates double centrifugation protocol violation.
• Fragment Peak: Shift from 167 bp may indicate degradation or preparation artifacts.
• Input Volume: Insufficient plasma volume (<1-2 mL) is frequent cause of low yield.

Key features:
• Five-parameter extraction quality assessment
• Status differentiation (Pass/Low Yield Warning/Fail)
• Support for various commercial kits
• Structured QC report generation
• Compliance with CAP Molecular Pathology Checklist requirements

Critical parameters:
• Total Yield: ≥ Min Limit (typically 5-10 ng)
• Concentration: ≥ Min Limit (typically 0.2 ng/µL)
• Spike-In Recovery: ≥ 50%
• HMW gDNA: ≤ 10%
• Fragment Peak: 150-180 bp

💡 Usage tips:
1. Double Centrifugation: Mandatory for cell removal and gDNA reduction.
2. Plasma Freshness: Process blood within 2-4 hours or use stabilization tubes.
3. Spike-In: Add internal control before extraction start to monitor entire process.
4. Measurement: Use high-sensitivity methods (Qubit dsDNA HS, TapeStation) instead of NanoDrop.
5. Re-extraction: Upon low yield, consider re-extraction from remaining plasma.

⚠️ Note: This utility is a pre-analytical stage control tool. It does not replace bioinformatics analysis but guarantees that input data meets sensitivity requirements.

input.csv

SampleID,ExtractionKit,InputPlasmaVolume_mL,ElutionVolume_uL,Concentration_ng_uL,MinConcentration_ng_uL,TotalYield_ng,MinTotalYield_ng,SpikeIn_Recovery_Percent,MinSpikeIn_Recovery_Percent,HMW_gDNA_Percent,MaxHMW_gDNA_Percent,FragmentSize_Peak_bp
CFDNA-2026-001,QIAamp Circulating Nucleic Acid,2.0,50,0.8,0.2,40.0,5.0,85.0,50.0,3.5,10.0,167
CFDNA-2026-002,MagMAX Cell-Free DNA,1.0,30,0.1,0.2,3.0,5.0,40.0,50.0,25.0,10.0,165
CFDNA-2026-003,QIAamp Circulating Nucleic Acid,2.0,50,1.2,0.2,60.0,5.0,92.0,50.0,2.0,10.0,168

URS & FS — User Requirements and Functional Specification

This document describes the controlled interface and behaviour of CfdnaExtractionYieldChecker for Cfdna Extraction Yield 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.

• Sample Purity: Control of high molecular weight genomic DNA (HMW gDNA) level masking ctDNA signal.
• Low cfDNA yield (<5-10 ng) makes reliable detection of mutations with VAF <0.5% impossible.
• gDNA contamination >10% significantly reduces signal-to-noise ratio in sequencing.
• Method Development: Comparison of different extraction kit efficiencies.
cfDNA amount in plasma is limited and varies between patients.
Without strict yield and purity control, analytical test sensitivity cannot be guaranteed.
⚠️ CRITICAL:
• Spike-In Recovery: Low recovery (<50%) indicates DNA loss on column/magnetic beads.
• Input Volume: Insufficient plasma volume (<1-2 mL) is frequent cause of low yield.
Critical parameters:
• Total Yield: ≥ Min Limit (typically 5-10 ng)
• Concentration: ≥ Min Limit (typically 0.2 ng/µL)
• Spike-In Recovery: ≥ 50%
• HMW gDNA: ≤ 10%

URS — User Requirements Specification

ID	Requirement	Criticality	Acceptance criterion
URS-001	The utility shall accept an input.csv file for Cfdna Extraction Yield 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	`CFDNA-2026-001`	Sample or laboratory specimen identifier.
2	`ExtractionKit`	string / controlled vocabulary	`QIAamp Circulating Nucleic Acid`	Controlled input parameter for deterministic QC rules.
3	`InputPlasmaVolume_mL`	decimal	`2.0`	Volume/dose used for load, limit or release calculation.
4	`ElutionVolume_uL`	decimal	`50`	Volume/dose used for load, limit or release calculation.
5	`Concentration_ng_uL`	decimal	`0.8`	Component ratio; structural or formulation CQA.
6	`MinConcentration_ng_uL`	decimal	`0.2`	Component ratio; structural or formulation CQA.
7	`TotalYield_ng`	decimal	`40.0`	Controlled input parameter for deterministic QC rules.
8	`MinTotalYield_ng`	decimal	`5.0`	Controlled input parameter for deterministic QC rules.
9	`SpikeIn_Recovery_Percent`	decimal	`85.0`	Recovery; indicator of analytical validity.
10	`MinSpikeIn_Recovery_Percent`	decimal	`50.0`	Recovery; indicator of analytical validity.
11	`HMW_gDNA_Percent`	decimal	`3.5`	Biological/molecular component controlled as a CQA.
12	`MaxHMW_gDNA_Percent`	decimal	`10.0`	Biological/molecular component controlled as a CQA.
13	`FragmentSize_Peak_bp`	decimal	`167`	Controlled input parameter for deterministic QC rules.

SampleID,ExtractionKit,InputPlasmaVolume_mL,ElutionVolume_uL,Concentration_ng_uL,MinConcentration_ng_uL,TotalYield_ng,MinTotalYield_ng,SpikeIn_Recovery_Percent,MinSpikeIn_Recovery_Percent,HMW_gDNA_Percent,MaxHMW_gDNA_Percent,FragmentSize_Peak_bp
CFDNA-2026-001,QIAamp Circulating Nucleic Acid,2.0,50,0.8,0.2,40.0,5.0,85.0,50.0,3.5,10.0,167
CFDNA-2026-002,MagMAX Cell-Free DNA,1.0,30,0.1,0.2,3.0,5.0,40.0,50.0,25.0,10.0,165
CFDNA-2026-003,QIAamp Circulating Nucleic Acid,2.0,50,1.2,0.2,60.0,5.0,92.0,50.0,2.0,10.0,168

Input validation rules

ID	Field	Rule	Criticality
VR-001	`SampleID`	The field shall match an approved dictionary or accepted string representation.	High
VR-002	`ExtractionKit`	The field shall match an approved dictionary or accepted string representation.	High
VR-003	`InputPlasmaVolume_mL`	The field shall match an approved dictionary or accepted string representation.	High
VR-004	`ElutionVolume_uL`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-005	`Concentration_ng_uL`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-006	`MinConcentration_ng_uL`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-007	`TotalYield_ng`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-008	`MinTotalYield_ng`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-009	`SpikeIn_Recovery_Percent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-010	`MinSpikeIn_Recovery_Percent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-011	`HMW_gDNA_Percent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-012	`MaxHMW_gDNA_Percent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-013	`FragmentSize_Peak_bp`	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 Cfdna Extraction Yield 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": "cfdnaextractionyieldchecker",
  "utilityFolder": "CfdnaExtractionYieldChecker",
  "package": "LiquidBiopsy",
  "overallStatus": "PASS|WARNING|FAIL",
  "sourceFile": "input.csv",
  "processedAtUtc": "2026-06-10T00:00:00Z",
  "checks": [
    {
      "parameter": "SampleID",
      "value": "CFDNA-2026-001",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-001"
    },
    {
      "parameter": "ExtractionKit",
      "value": "QIAamp Circulating Nucleic Acid",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-002"
    },
    {
      "parameter": "InputPlasmaVolume_mL",
      "value": "2.0",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-003"
    },
    {
      "parameter": "ElutionVolume_uL",
      "value": "50",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-004"
    },
    {
      "parameter": "Concentration_ng_uL",
      "value": "0.8",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-005"
    },
    {
      "parameter": "MinConcentration_ng_uL",
      "value": "0.2",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-006"
    },
    {
      "parameter": "TotalYield_ng",
      "value": "40.0",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-007"
    },
    {
      "parameter": "MinTotalYield_ng",
      "value": "5.0",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-008"
    },
    {
      "parameter": "SpikeIn_Recovery_Percent",
      "value": "85.0",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-009"
    },
    {
      "parameter": "MinSpikeIn_Recovery_Percent",
      "value": "50.0",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-010"
    },
    {
      "parameter": "HMW_gDNA_Percent",
      "value": "3.5",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-011"
    },
    {
      "parameter": "MaxHMW_gDNA_Percent",
      "value": "10.0",
      "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": "CfdnaExtractionYieldChecker.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