128 lines
5.3 KiB
Markdown
128 lines
5.3 KiB
Markdown
# Genetics & Genomics Laboratory Quality Management System
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This repository contains template documents for implementing a Quality Management System (QMS) specifically designed for **Genetics and Genomics Laboratories** performing clinical genetic testing.
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## 🧬 Designed For
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- Clinical Genetics Laboratories
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- Molecular Pathology Laboratories
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- Cancer Genomics/Precision Oncology Labs
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- Pharmacogenomics Testing Facilities
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- Prenatal/Reproductive Genetics Labs
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- Hereditary Disease Testing Centers
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- NGS Core Laboratories (Clinical)
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- Genetic Counseling Services
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## Repository Structure
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```
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genetics-genomics/
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├── Policies/ # Quality policies and management commitment
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├── SOPs/ # Standard Operating Procedures
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│ ├── Variant-Interpretation/ # ACMG/AMP classification, curation
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│ ├── Sequencing/ # NGS protocols, quality metrics
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│ ├── Counseling/ # Genetic counseling coordination
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│ ├── Data-Management/ # Bioinformatics, variant databases
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│ ├── Safety/ # Biological safety, chemical hazards
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│ └── General/ # General lab operations
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├── Work-Instructions/ # Detailed protocols
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├── Forms/ # Record forms and templates
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│ ├── Consent-Genetic-Testing/ # Informed consent for genetic testing
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│ ├── Variant-Classification/ # Classification worksheets, review forms
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│ ├── Equipment-Logs/ # Sequencer maintenance, calibration
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│ └── Training/ # Competency assessment records
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└── Templates/ # Document templates
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```
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## Document Numbering Convention
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- **POL-XXX**: Policies
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- **SOP-VI-XXX**: Variant Interpretation SOPs
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- **SOP-SEQ-XXX**: Sequencing SOPs
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- **SOP-GC-XXX**: Genetic Counseling SOPs
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- **SOP-DM-XXX**: Data Management SOPs
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- **SOP-SAF-XXX**: Safety SOPs
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- **SOP-GEN-XXX**: General SOPs
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- **WI-XXX**: Work Instructions / Protocols
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- **FRM-XXX**: Forms and Records
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- **CONSENT-XXX**: Genetic Testing Consent Forms
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- **VC-XXX**: Variant Classification Forms
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## 🤖 AI-Powered Document Creation
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This template includes **AtomicAI** integration. Create an issue and mention `@atomicai` to:
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- Generate variant interpretation SOPs following ACMG/AMP guidelines
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- Create NGS quality control procedures and metrics documentation
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- Draft genetic testing consent forms with appropriate disclosures
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- Develop secondary findings management protocols
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- Create bioinformatics pipeline validation documentation
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- Generate family cascade testing coordination procedures
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- Draft pharmacogenomics reporting SOPs
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- Create tumor/normal matching and sample identity verification procedures
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## Getting Started
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1. Create a new repository using this template
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2. Customize documents with your laboratory's information
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3. Create issues with `@atomicai` to generate new documents
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4. Review and approve AI-generated content via Pull Requests
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## Compliance & Standards
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These templates support compliance with:
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- **CAP Molecular Pathology Checklist** - Laboratory accreditation
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- **CLIA** - Clinical Laboratory Improvement Amendments
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- **ACMG/AMP Guidelines** - Variant classification standards (2015 and updates)
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- **ACMG SF v3.2** - Secondary findings recommendations
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- **CAP/ACMG Biochemical and Molecular Genetics Resource Committee** - Technical standards
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- **GINA** - Genetic Information Nondiscrimination Act
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- **HIPAA** - Health Information Privacy for genetic data
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- **FDA Guidance** - Next Generation Sequencing-Based Oncology Panels
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- **ISO 15189** - Medical laboratories quality and competence
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- **NCCN Guidelines** - Genetic/Familial High-Risk Assessment
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- **AMP/ASCO/CAP Guidelines** - Somatic variant interpretation in cancer
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- **ClinGen** - Clinical Genome Resource curation standards
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- **HGVS** - Variant nomenclature standards
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## Key Quality Areas
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### Variant Classification
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- ACMG/AMP 5-tier classification system (Pathogenic, Likely Pathogenic, VUS, Likely Benign, Benign)
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- Evidence-based classification using PM, PS, PP, BA, BS, BP criteria
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- Variant curation and reclassification procedures
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- ClinVar submission and variant sharing
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### NGS Quality Metrics
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- Coverage depth requirements (germline: >20x, somatic: >100x tumor, >30x normal)
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- Quality score thresholds (Q30 >80%)
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- Uniformity of coverage
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- Variant allele frequency (VAF) thresholds
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- Contamination and sample identity verification
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### Secondary Findings
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- ACMG SF v3.2 gene list management
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- Patient opt-in/opt-out procedures
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- Age-appropriate actionability
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- Return of results protocols
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### Genetic Counseling
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- Pre-test and post-test counseling documentation
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- Family history documentation (3-generation pedigree)
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- Psychological impact assessment
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- Cascade testing coordination
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### Biobanking & Research
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- Informed consent for genetic research use
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- Pediatric assent and re-consent at age of majority
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- Sample de-identification procedures
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- Data sharing agreements
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### Data Privacy
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- GINA compliance in employment/insurance contexts
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- Genetic information security measures
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- Family member privacy considerations
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- Research participant protections
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---
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*Powered by AtomicQMS - AI-Enhanced Genetics & Genomics Laboratory Quality Management*
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