CE_DNA_Vaccine_Purity_Checker

CE DNA Vaccine Purity Checker

Lumex QC URS & FS input.csv output.json rule-based LIMS-ready capillary electrophoresis

Utility description: CE DNA Vaccine Purity Checker

CE DNA Vaccine Purity Checker — Plasmid DNA Vaccine Purity Control (CE)

ℹ️ Utility checks plasmid DNA isoform distribution:
• Supercoiled form (CCC) ≥80.0% — ACTIVE
• Open Circular form (OC) ≤15.0%
• Linear form ≤5.0%
• RNA contamination ≤2.0%

⚠️ CRITICAL: Only the supercoiled form effectively transfects cells.
Presence of linear and OC forms reduces immunogenicity and may increase integration risk.

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

Input format:
BatchNumber,PlasmidName,SupercoiledPercent,OpenCircularPercent,LinearPercent,RnaContaminationPercent,TotalImpuritiesPercent

Example:
DNA-VAC-2026-001,pVAX1-AntigenX,85.5,10.2,2.1,0.5,14.5

— WHY IS THIS NEEDED?
DNA vaccines are plasmids encoding a target antigen.
The biological activity of the vaccine directly depends on the topological structure of the DNA:
• Supercoiled form (Covalently Closed Circular, CCC) — native, compact structure, most effectively penetrating the cell nucleus and expressing the antigen.
• Open Circular form (OC) — arises from a single-strand break (nick). Less active.
• Linear form — double-strand break. Can integrate into the host genome (mutagenesis risk), so its content is strictly limited.
• RNA — residue after bacterial lysis, must be removed during purification.

Capillary Electrophoresis (CE) allows rapid and accurate separation of these isoforms without intercalating dyes (unlike gel electrophoresis).

⚠️ CRITICAL:
• Supercoiled fraction must be ≥80% to ensure vaccine potency.
• Linear DNA ≤5% due to safety risks (integration).
• RNA control is important for product purity.
• Manufacturing process (fermentation, isolation, purification) must not cause significant plasmid damage.

Key features:
• Assessment of plasmid topological purity.
• Control of critical impurities (linear DNA, RNA).
• Compliance with WHO and FDA guidelines for DNA vaccines.
• LabWare LIMS integration.

Critical parameters:
• Supercoiled DNA (CCC): ≥80.0%
• Open Circular DNA (OC): ≤15.0%
• Linear DNA: ≤5.0%
• RNA: ≤2.0%
• Total impurities: ≤20.0%

💡 Usage tips:
1. Use specialized buffers for nucleic acid separation in CE.
2. Avoid mechanical stress (pipetting, freeze-thaw) that can convert CCC to OC or linear forms.
3. Store samples at low temperatures to maintain supercoiling.
4. Calibrate the system using molecular weight and topology standard markers.

⚠️ Note: Unlike protein drugs where amino acid sequence is key, for DNA vaccines, the physical form (topology) of the molecule is critical.

input.csv

BatchNumber,PlasmidName,SupercoiledPercent,OpenCircularPercent,LinearPercent,RnaContaminationPercent,TotalImpuritiesPercent
DNA-VAC-2026-001,pVAX1-AntigenX,85.5,10.2,2.1,0.5,14.5
DNA-FAIL-2026-002,pVAX1-AntigenX,75.0,18.0,5.5,1.0,25.5

URS & FS — User Requirements and Functional Specification

This document defines the controlled interface, validation behaviour and expected output of CE_DNA_Vaccine_Purity_Checker. The document is intended to reside inside the utility folder together with input.csv and the description file. Expected executable: CE_DNA_Vaccine_Purity_Checker.exe.

Purpose: the utility performs deterministic verification of QC input data against approved limits, generates machine-readable output.json, and supports QC/QA review, LIMS/ELN/MES integration and CSV/CSA preparation.

Scope

Utility class	Capillary electrophoresis
Main object/method	Plasmid DNA Vaccine Purity Control (CE)
Input	`input.csv` with a fixed header and controlled data types.
Output	`output.json` with `PASS`, `WARNING`, `FAIL` statuses, detailed checks and critical findings.
Exclusions	The utility does not replace the approved specification, analytical procedure, OOS/OOT investigation or Qualified Person / QA release decision.

Domain limits and critical parameters

Key fragments from the source description are listed below. Before production use, limits shall be verified against the approved specification, registration dossier, current pharmacopoeial edition and local SOPs.

• Supercoiled form (CCC) ≥80.0% — ACTIVE
• Open Circular form (OC) ≤15.0%
• Linear form ≤5.0%
• RNA contamination ≤2.0%
⚠️ CRITICAL: Only the supercoiled form effectively transfects cells.
CE_DNA_Vaccine_Purity_Checker.exe input.csv output.json → evaluate your data
BatchNumber,PlasmidName,SupercoiledPercent,OpenCircularPercent,LinearPercent,RnaContaminationPercent,TotalImpuritiesPercent
• Supercoiled form (Covalently Closed Circular, CCC) — native, compact structure, most effectively penetrating the cell nucleus and expressing the antigen.
• Open Circular form (OC) — arises from a single-strand break (nick). Less active.
• Linear form — double-strand break. Can integrate into the host genome (mutagenesis risk), so its content is strictly limited.
• RNA — residue after bacterial lysis, must be removed during purification.
⚠️ CRITICAL:
• Supercoiled fraction must be ≥80% to ensure vaccine potency.
• Linear DNA ≤5% due to safety risks (integration).
• RNA control is important for product purity.
• Manufacturing process (fermentation, isolation, purification) must not cause significant plasmid damage.

Pharmacopoeial and regulatory references found in the description

#	Source	Note
1	FDA	Used as a source/context reference from the description; the current edition must be verified before implementation.

Production data flow

Step	Responsible object	Description	Control
1	LIMS/ELN/MES or QC analyst	Creates `input.csv` with measured values and batch identifier.	Header, mandatory-field and unit checks.
2	CE_DNA_Vaccine_Purity_Checker	Loads CSV, converts data types, applies domain rules and produces the result.	Deterministic rules; no ML/probabilistic conformance decision.
3	QC reviewer / QA	Reviews `output.json`, warnings, critical deviations and source values.	Review, deviation investigation and data-trail retention.
4	Archive / eQMS	Retains input, output, utility version, documentation and checksum.	Data integrity: ALCOA+, reproducibility and change control.

URS — User Requirements Specification

ID	Requirement	Criticality	Acceptance criterion
URS-001	The utility shall be supplied with `CE_DNA_Vaccine_Purity_Checker.documentation.html` in the same folder as the description and sample `input.csv`.	Medium	The documentation file exists in the `CE_DNA_Vaccine_Purity_Checker` folder and opens locally in a browser.
URS-002	The utility shall accept `input.csv` with the exact headers defined in the data contract.	High	A CSV file with the correct header is processed without manual editing.
URS-003	The utility shall validate mandatory fields, column count, data types and basic plausibility of values.	High	Schema and conversion errors are explicitly reported.
URS-004	The utility shall evaluate each critical and non-critical QC parameter against approved limits.	High	Each checked parameter receives a status and explanatory message.
URS-005	The utility shall produce a final record/batch status: `PASS`, `WARNING` or `FAIL`.	High	A critical deviation causes `FAIL`; a non-critical deviation causes `WARNING`.
URS-006	The utility shall generate `output.json` suitable for LIMS/ELN/MES integration and QA/QC review.	High	JSON contains source values, rules, statuses, warnings and critical findings.
URS-007	The utility shall preserve traceability between batch identifier, input values, applied rules and final status.	High	The output contains the batch/row identifier and list of checked parameters.
URS-008	The utility shall not use machine learning or probabilistic interpretation for conformance decisions.	Medium	The result is reproducible and based on explicit rules, thresholds and input values.
URS-009	The utility shall support the CLI scenario: `CE_DNA_Vaccine_Purity_Checker.exe input.csv output.json`.	High	With valid arguments, `output.json` is created; on error, a diagnostic message is returned.
URS-010	The documentation shall support IQ/OQ/PQ or equivalent CSV/CSA verification.	Medium	The document contains URS, FS, CSV contract, rules, test scenarios and traceability.
URS-011	The utility shall distinguish data errors, method warnings and critical specification failures.	High	`output.json` provides separate structures/fields for errors, warnings and critical findings.
URS-012	The utility shall support archival retention of unchanged input and output data.	Medium	`input.csv` and `output.json` can be retained as a batch record or OQ/PQ evidence.

input.csv contract

#	Field	Type	Sample	Purpose
1	`BatchNumber`	string	`DNA-VAC-2026-001`	Batch or lot identifier used for traceability.
2	`PlasmidName`	string	`pVAX1-AntigenX`	Controlled input parameter used by the deterministic QC rules.
3	`SupercoiledPercent`	controlled string	`85.5`	Controlled category used to apply the correct rule set.
4	`OpenCircularPercent`	decimal	`10.2`	Controlled input parameter used by the deterministic QC rules.
5	`LinearPercent`	decimal	`2.1`	Controlled input parameter used by the deterministic QC rules.
6	`RnaContaminationPercent`	decimal	`0.5`	Controlled input parameter used by the deterministic QC rules.
7	`TotalImpuritiesPercent`	decimal	`14.5`	Specified, unspecified or total impurity parameter controlled against an approved limit.

BatchNumber,PlasmidName,SupercoiledPercent,OpenCircularPercent,LinearPercent,RnaContaminationPercent,TotalImpuritiesPercent
DNA-VAC-2026-001,pVAX1-AntigenX,85.5,10.2,2.1,0.5,14.5
DNA-FAIL-2026-002,pVAX1-AntigenX,75.0,18.0,5.5,1.0,25.5

Input validation rules

ID	Field	Type	Check	Criticality
VR-001	`BatchNumber`	string	not empty; unique within file where applicable	Medium
VR-002	`PlasmidName`	string	not empty where mandatory	Medium
VR-003	`SupercoiledPercent`	controlled string	not empty; value belongs to controlled set or is reported as warning	Medium
VR-004	`OpenCircularPercent`	decimal	parse as invariant decimal; finite value; no NaN/Infinity; evaluate against approved % limit	Medium
VR-005	`LinearPercent`	decimal	parse as invariant decimal; finite value; no NaN/Infinity; evaluate against approved % limit	Medium
VR-006	`RnaContaminationPercent`	decimal	parse as invariant decimal; finite value; no NaN/Infinity; evaluate against approved % limit	Medium
VR-007	`TotalImpuritiesPercent`	decimal	parse as invariant decimal; finite value; no NaN/Infinity; evaluate against approved % limit	Medium

FS — Functional Specification

ID	Function	Implementation	URS link
FS-001	Local HTML documentation	Provide a bilingual `CE_DNA_Vaccine_Purity_Checker.documentation.html` file with RU/EN switch, source description, URS, FS, contracts and tests.	URS-001, URS-010
FS-002	CSV import	Read `input.csv` in UTF-8/CSV-compatible format and identify the header row and data records.	URS-002, URS-009
FS-003	Schema validation	Compare actual columns against the expected contract; missing key fields are recorded as schema errors.	URS-002, URS-003
FS-004	Type conversion	Convert decimal, flag/boolean and controlled string values. Invalid values are recorded at row and field level.	URS-003
FS-005	Domain rule engine	Apply rules for CE DNA Vaccine Purity Checker, including critical limits from the description and approved specification.	URS-004, URS-008
FS-006	Status aggregation	Aggregate parameter statuses: `FAIL` for critical failure, `WARNING` for non-critical deviation, `PASS` for conformance.	URS-005, URS-011
FS-007	JSON export	Write `output.json` with utility identifier, source values, check results, warnings and critical findings.	URS-006, URS-007
FS-008	Error handling	Separate execution errors, schema errors, conversion errors and domain-limit failures.	URS-003, URS-011
FS-009	Audit support	Keep result structure suitable for review, OOS/OOT investigation, calculation reproduction and inspection discussion.	URS-007, URS-012
FS-010	Integration contract	Support the standard scenario: LIMS/ELN/MES creates `input.csv`, the utility returns `output.json`, and the portal displays description and documentation.	URS-006, URS-009
FS-011	Configuration/change control	Any change to limits, column names or rule logic requires versioning, review, regression tests and documentation update.	URS-010, URS-012
FS-012	Data integrity	Do not modify the source `input.csv`; save results separately in `output.json` for archival retention.	URS-007, URS-012

Example output.json structure

{
  "utilityId": "ce-dna-vaccine-purity-checker",
  "utilityName": "CE_DNA_Vaccine_Purity_Checker",
  "object": "CE DNA Vaccine Purity Checker",
  "overallStatus": "PASS|WARNING|FAIL",
  "sourceFile": "input.csv",
  "recordCount": 2,
  "checks": [
    {
      "parameter": "BatchNumber",
      "value": "DNA-VAC-2026-001",
      "status": "PASS|WARNING|FAIL",
      "message": "Rule-based check result",
      "ruleReference": "VR-001"
    },
    {
      "parameter": "PlasmidName",
      "value": "pVAX1-AntigenX",
      "status": "PASS|WARNING|FAIL",
      "message": "Rule-based check result",
      "ruleReference": "VR-002"
    },
    {
      "parameter": "SupercoiledPercent",
      "value": "85.5",
      "status": "PASS|WARNING|FAIL",
      "message": "Rule-based check result",
      "ruleReference": "VR-003"
    },
    {
      "parameter": "OpenCircularPercent",
      "value": "10.2",
      "status": "PASS|WARNING|FAIL",
      "message": "Rule-based check result",
      "ruleReference": "VR-004"
    },
    {
      "parameter": "LinearPercent",
      "value": "2.1",
      "status": "PASS|WARNING|FAIL",
      "message": "Rule-based check result",
      "ruleReference": "VR-005"
    },
    {
      "parameter": "RnaContaminationPercent",
      "value": "0.5",
      "status": "PASS|WARNING|FAIL",
      "message": "Rule-based check result",
      "ruleReference": "VR-006"
    },
    {
      "parameter": "TotalImpuritiesPercent",
      "value": "14.5",
      "status": "PASS|WARNING|FAIL",
      "message": "Rule-based check result",
      "ruleReference": "VR-007"
    }
  ],
  "criticalFindings": [],
  "warnings": [],
  "metadata": {
    "executionMode": "CLI",
    "interface": "CSV to JSON",
    "documentationFile": "CE_DNA_Vaccine_Purity_Checker.documentation.html"
  }
}

Traceability matrix URS → FS → OQ/PQ

URS	FS	Verification	Expected result
URS-001	FS-001	Check that `CE_DNA_Vaccine_Purity_Checker.documentation.html` exists in the utility folder.	The file exists, opens, and the RU/EN switch works.
URS-002/003	FS-002/003/004	Run the utility with a correct CSV, a CSV missing a mandatory column and a CSV with an invalid data type.	Correct CSV is processed; schema and type errors are explicit.
URS-004/005	FS-005/006	Submit values within limits, at warning level and beyond a critical limit.	`PASS`, `WARNING` and `FAIL` are produced according to rules.
URS-006/007	FS-007/009/012	Verify `output.json` structure and batch traceability.	JSON contains batch identifier, values, rules, statuses and critical findings.
URS-008	FS-005	Repeat execution with the same `input.csv`.	The result is identical; no probabilistic behaviour is present.
URS-009/010/012	FS-010/011/012	Execute the CLI scenario and archive input/output/version.	Artefacts are suitable for OQ/PQ and change-control records.

OQ/PQ test scenarios

ID	Scenario	Input data	Expected result
OQ-001	Positive path	Sample CSV with valid values.	`output.json` is created; final status is `PASS` or acceptable `WARNING` according to rules.
OQ-002	Mandatory column missing	Remove one key column from the header.	Schema error; the row shall not be treated as passed.
OQ-003	Invalid type	Put text into a numeric field.	Type-conversion error with field and row identification.
OQ-004	Critical limit	Critical parameter value outside the approved limit.	`FAIL` and an entry in `criticalFindings`.
OQ-005	Warning	Non-critical deviation or unknown controlled category.	`WARNING` without hiding the source value.
PQ-001	User real batch	Real `input.csv` from the QC process.	Reviewed result with `input.csv`, `output.json`, version and checksum retained.

QA/QC, CSV/CSA and change control

Do not rename columns without updating the validator, test set and documentation.
Retain input.csv, output.json, executable version, checksum and a copy of the documentation.
Before production use, perform IQ/OQ/PQ or equivalent risk-based CSV/CSA verification.
Critical limits shall be approved by the process owner and verified against the registration dossier, pharmacopoeia and local SOPs.
Any change to rules, thresholds or status interpretation shall go through change control and regression testing.

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