pathology/README.md

# Pathology & Laboratory Medicine Quality Management System

A comprehensive QMS template designed for anatomic pathology, clinical pathology, and laboratory medicine departments.

## 🔬 Designed For

- **Anatomic Pathology** - Surgical pathology, cytopathology, autopsy
- **Clinical Pathology** - Chemistry, hematology, microbiology, transfusion medicine
- **Reference Laboratories** - Specialized testing services
- **Molecular Pathology** - Genetic and molecular diagnostics
- **Forensic Pathology** - Medical examiner and coroner services
- **Dermatopathology** - Skin biopsy interpretation
- **Neuropathology** - Brain and nervous system pathology

## 📋 Regulatory Framework

This template supports compliance with:

- **CAP** - College of American Pathologists accreditation
- **CLIA** - Clinical Laboratory Improvement Amendments
- **The Joint Commission** - Hospital accreditation (laboratory chapter)
- **FDA** - IVD and LDT regulations
- **AABB** - Blood bank standards (if applicable)
- **State Clinical Laboratory Licensing** - State-specific requirements
- **OSHA** - Bloodborne pathogens, chemical safety
- **HIPAA** - Patient information privacy
- **ASCP** - Pathologist and technologist standards
- **CAP Biorepository** - Tissue banking requirements (if applicable)

## Repository Structure

```
├── SOPs/
│   ├── Specimen-Handling/     # Accessioning, processing, storage
│   ├── Histology/             # Tissue processing, embedding, sectioning, staining
│   ├── Cytology/              # Cytology preparation and screening
│   ├── Autopsy/               # Post-mortem examination procedures
│   ├── Molecular/             # Molecular testing, NGS, PCR
│   └── General/               # Document control, training, CAPA
├── Forms/
│   ├── Requisition-Forms/     # Specimen submission, clinical history
│   ├── Grossing-Templates/    # Specimen dictation templates
│   ├── QC-Records/            # Staining QC, reagent logs, instrument checks
│   ├── Report-Templates/      # Synoptic and narrative report templates
│   ├── Competency/            # Technologist and pathologist assessments
│   └── Incident-Reports/      # Specimen quality, labeling errors
├── Policies/                  # Department policies
├── Work-Instructions/         # Step-by-step procedures
└── Templates/                 # Document templates
```

## Document Numbering Convention

- **POL-XXX**: Policies
- **SOP-SP-XXX**: Specimen Handling SOPs
- **SOP-HIS-XXX**: Histology SOPs
- **SOP-CYT-XXX**: Cytology SOPs
- **SOP-AUT-XXX**: Autopsy SOPs
- **SOP-MOL-XXX**: Molecular SOPs
- **WI-XXX**: Work Instructions
- **FRM-XXX**: Forms and Records

## 🤖 AI-Powered Assistance

This repository includes **AtomicAI**, your pathology QMS assistant. Mention `@atomicai` in any issue or pull request to:

- Draft specimen handling and processing SOPs
- Create histology and staining procedures
- Generate grossing templates for specimen types
- Develop molecular testing protocols
- Create quality control procedures
- Review documents for CAP/CLIA compliance

### Example Prompts

- "@atomicai create an SOP for surgical specimen grossing and sampling"
- "@atomicai draft a tissue processor validation procedure"
- "@atomicai write an immunohistochemistry staining and QC protocol"
- "@atomicai create a synoptic report template for breast cancer"
- "@atomicai develop a frozen section procedure with turnaround time standards"
- "@atomicai create a specimen labeling and identification policy"

## Getting Started

1. **Establish Specimen Policies** - Define accessioning and handling requirements
2. **Standardize Processing** - Document histology and cytology procedures
3. **Implement QC Programs** - Set up staining, reagent, and instrument QC
4. **Define Reporting Standards** - Create synoptic and narrative templates
5. **Train Staff** - Use competency assessment forms

## Key Documents to Create First

1. **Specimen Accessioning SOP** - Receiving, labeling, and logging specimens
2. **Tissue Processing SOP** - Fixation, processing, embedding procedures
3. **H&E Staining Protocol** - Routine hematoxylin and eosin procedure
4. **Immunohistochemistry SOP** - IHC staining and controls
5. **Frozen Section SOP** - Intraoperative consultation procedure
6. **Grossing Manual** - Specimen-specific grossing guidelines
7. **Critical Values Policy** - Urgent result communication

## Special Considerations for Pathology

### Specimen Integrity
- Specimen identification and labeling
- Fixation timing and adequacy
- Cold ischemia documentation
- Tissue banking considerations
- Chain of custody (legal cases)

### Quality Control
- H&E and special stain QC
- IHC positive and negative controls
- Reagent expiration and storage
- Instrument calibration and maintenance
- Proficiency testing participation

### Reporting
- Turnaround time standards
- Synoptic reporting (CAP protocols)
- Critical/unexpected results
- Amendment and addendum procedures
- Second opinion and consultation

### Safety
- Formalin handling and exposure limits
- Xylene substitutes and ventilation
- Infectious specimen handling
- Sharps safety (microtome blades)
- Prion precautions (CJD)

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*This template is maintained by AtomicQMS. For questions, open an issue in this repository.*