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

Create a new repository using this template
Customize documents with your laboratory's information
Create issues with @atomicai to generate new documents
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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