# Genetics & Genomics Laboratory Quality Management System

This repository contains template documents for implementing a Quality Management System (QMS) specifically designed for **Genetics and Genomics Laboratories** performing clinical genetic testing.

## 🧬 Designed For

- Clinical Genetics Laboratories
- Molecular Pathology Laboratories
- Cancer Genomics/Precision Oncology Labs
- Pharmacogenomics Testing Facilities
- Prenatal/Reproductive Genetics Labs
- Hereditary Disease Testing Centers
- NGS Core Laboratories (Clinical)
- Genetic Counseling Services

## Repository Structure

```
genetics-genomics/
├── Policies/                       # Quality policies and management commitment
├── SOPs/                           # Standard Operating Procedures
│   ├── Variant-Interpretation/     # ACMG/AMP classification, curation
│   ├── Sequencing/                 # NGS protocols, quality metrics
│   ├── Counseling/                 # Genetic counseling coordination
│   ├── Data-Management/            # Bioinformatics, variant databases
│   ├── Safety/                     # Biological safety, chemical hazards
│   └── General/                    # General lab operations
├── Work-Instructions/              # Detailed protocols
├── Forms/                          # Record forms and templates
│   ├── Consent-Genetic-Testing/    # Informed consent for genetic testing
│   ├── Variant-Classification/     # Classification worksheets, review forms
│   ├── Equipment-Logs/             # Sequencer maintenance, calibration
│   └── Training/                   # Competency assessment records
└── Templates/                      # Document templates
```

## Document Numbering Convention

- **POL-XXX**: Policies
- **SOP-VI-XXX**: Variant Interpretation SOPs
- **SOP-SEQ-XXX**: Sequencing SOPs
- **SOP-GC-XXX**: Genetic Counseling SOPs
- **SOP-DM-XXX**: Data Management SOPs
- **SOP-SAF-XXX**: Safety SOPs
- **SOP-GEN-XXX**: General SOPs
- **WI-XXX**: Work Instructions / Protocols
- **FRM-XXX**: Forms and Records
- **CONSENT-XXX**: Genetic Testing Consent Forms
- **VC-XXX**: Variant Classification Forms

## 🤖 AI-Powered Document Creation

This template includes **AtomicAI** integration. Create an issue and mention `@atomicai` to:
- Generate variant interpretation SOPs following ACMG/AMP guidelines
- Create NGS quality control procedures and metrics documentation
- Draft genetic testing consent forms with appropriate disclosures
- Develop secondary findings management protocols
- Create bioinformatics pipeline validation documentation
- Generate family cascade testing coordination procedures
- Draft pharmacogenomics reporting SOPs
- Create tumor/normal matching and sample identity verification procedures

## Getting Started

1. Create a new repository using this template
2. Customize documents with your laboratory's information
3. Create issues with `@atomicai` to generate new documents
4. Review and approve AI-generated content via Pull Requests

## Compliance & Standards

These templates support compliance with:
- **CAP Molecular Pathology Checklist** - Laboratory accreditation
- **CLIA** - Clinical Laboratory Improvement Amendments
- **ACMG/AMP Guidelines** - Variant classification standards (2015 and updates)
- **ACMG SF v3.2** - Secondary findings recommendations
- **CAP/ACMG Biochemical and Molecular Genetics Resource Committee** - Technical standards
- **GINA** - Genetic Information Nondiscrimination Act
- **HIPAA** - Health Information Privacy for genetic data
- **FDA Guidance** - Next Generation Sequencing-Based Oncology Panels
- **ISO 15189** - Medical laboratories quality and competence
- **NCCN Guidelines** - Genetic/Familial High-Risk Assessment
- **AMP/ASCO/CAP Guidelines** - Somatic variant interpretation in cancer
- **ClinGen** - Clinical Genome Resource curation standards
- **HGVS** - Variant nomenclature standards

## Key Quality Areas

### Variant Classification
- ACMG/AMP 5-tier classification system (Pathogenic, Likely Pathogenic, VUS, Likely Benign, Benign)
- Evidence-based classification using PM, PS, PP, BA, BS, BP criteria
- Variant curation and reclassification procedures
- ClinVar submission and variant sharing

### NGS Quality Metrics
- Coverage depth requirements (germline: >20x, somatic: >100x tumor, >30x normal)
- Quality score thresholds (Q30 >80%)
- Uniformity of coverage
- Variant allele frequency (VAF) thresholds
- Contamination and sample identity verification

### Secondary Findings
- ACMG SF v3.2 gene list management
- Patient opt-in/opt-out procedures
- Age-appropriate actionability
- Return of results protocols

### Genetic Counseling
- Pre-test and post-test counseling documentation
- Family history documentation (3-generation pedigree)
- Psychological impact assessment
- Cascade testing coordination

### Biobanking & Research
- Informed consent for genetic research use
- Pediatric assent and re-consent at age of majority
- Sample de-identification procedures
- Data sharing agreements

### Data Privacy
- GINA compliance in employment/insurance contexts
- Genetic information security measures
- Family member privacy considerations
- Research participant protections

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