Sync template from atomicqms-style deployment

README.md

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-# genetics-genomics
+# 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.
+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
+
+---
+*Powered by AtomicQMS - AI-Enhanced Genetics & Genomics Laboratory Quality Management*