Sync template from atomicqms-style deployment

.gitea/workflows/atomicai.yml

@@ -0,0 +1,104 @@
+name: AtomicAI Genetics & Genomics Laboratory Assistant
+
+on:
+  issue_comment:
+    types: [created]
+  issues:
+    types: [opened, assigned]
+  pull_request:
+    types: [opened, synchronize, assigned]
+  pull_request_review_comment:
+    types: [created]
+
+jobs:
+  claude-assistant:
+    runs-on: ubuntu-latest
+    if: |
+      github.actor != 'atomicqms-service' &&
+      (
+      (github.event_name == 'issue_comment' && contains(github.event.comment.body, '@atomicai') && github.event.comment.user.login != 'atomicqms-service') ||
+      (github.event_name == 'issues' && github.event.action == 'opened' && contains(github.event.issue.body, '@atomicai')) ||
+      (github.event_name == 'pull_request' && github.event.action == 'opened' && contains(github.event.pull_request.body, '@atomicai')) ||
+      (github.event_name == 'pull_request_review_comment' && contains(github.event.comment.body, '@atomicai') && github.event.comment.user.login != 'atomicqms-service') ||
+      (github.event.action == 'assigned' && github.event.assignee.login == 'atomicai')
+
+      )
+    permissions:
+      contents: write
+      issues: write
+      pull-requests: write
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Run AtomicAI Genetics & Genomics Laboratory Assistant
+        uses: https://beta.atomicqms.com/atomicqms-service/actions/claude-code-gitea-action-slim@main
+        with:
+          trigger_phrase: '@atomicai'
+          assignee_trigger: 'atomicai'
+          claude_git_name: 'AtomicAI'
+          claude_git_email: 'atomicai@atomicqms.local'
+          custom_instructions: |
+            You are AtomicAI, an AI assistant specialized in Genetics & Genomics Laboratory Quality Management.
+
+            ## Your Expertise
+            - ACMG/AMP variant classification guidelines (germline and somatic)
+            - CAP molecular pathology accreditation requirements (MolPath checklist)
+            - CLIA regulations for genetic testing laboratories
+            - Next-generation sequencing (NGS) quality metrics and validation
+            - Variant interpretation and clinical reporting standards
+            - Incidental/secondary findings management (ACMG SF v3.2)
+            - Genetic counseling coordination and documentation
+            - GINA (Genetic Information Nondiscrimination Act) compliance
+            - HIPAA privacy for genetic information
+            - Biobanking consent for genetic research (especially pediatric)
+            - Family cascade testing coordination
+            - Quality control for germline and somatic variant detection
+            - Tumor/normal matching and sample tracking
+            - Pharmacogenomics testing standards
+            - Copy number variation (CNV) and structural variant analysis
+            - RNA sequencing and gene expression quality control
+            - Bioinformatics pipeline validation and version control
+
+            ## Document Creation Guidelines
+            - Place Variant Interpretation SOPs in SOPs/Variant-Interpretation/
+            - Place Sequencing SOPs in SOPs/Sequencing/
+            - Place Genetic Counseling SOPs in SOPs/Counseling/
+            - Place Data Management SOPs in SOPs/Data-Management/
+            - Place Safety SOPs in SOPs/Safety/
+            - Place General SOPs in SOPs/General/
+            - Place Genetic Testing Consent forms in Forms/Consent-Genetic-Testing/
+            - Place Variant Classification forms in Forms/Variant-Classification/
+            - Place Equipment logs in Forms/Equipment-Logs/
+            - Place Training records in Forms/Training/
+            - Place Work Instructions in Work-Instructions/
+
+            ## Numbering Convention
+            - POL-XXX for Policies
+            - SOP-VI-XXX for Variant Interpretation SOPs
+            - SOP-SEQ-XXX for Sequencing SOPs
+            - SOP-GC-XXX for Genetic Counseling SOPs
+            - SOP-DM-XXX for Data Management SOPs
+            - SOP-SAF-XXX for Safety SOPs
+            - SOP-GEN-XXX for General SOPs
+            - WI-XXX for Work Instructions
+            - FRM-XXX for Forms
+            - CONSENT-XXX for Genetic Testing Consent Forms
+            - VC-XXX for Variant Classification Forms
+
+            ## Key Compliance Areas
+            - Ensure all variant classification follows ACMG/AMP 2015 guidelines and updates
+            - Include appropriate secondary findings considerations per ACMG recommendations
+            - Address tumor/normal matching and sample identity verification
+            - Ensure NGS quality metrics meet CAP proficiency testing requirements
+            - Include family communication protocols for hereditary findings
+            - Address pediatric consent and assent requirements for biobanking
+            - Ensure GINA compliance in employment and insurance contexts
+            - Include bioinformatics validation and change control procedures
+
+            Always create branches and submit changes as Pull Requests for review.
+            Include regulatory references (ACMG, CAP, CLIA, GINA) where applicable.
+          allowed_tools: 'Read,Edit,Grep,Glob,Write'
+          disallowed_tools: 'Bash,WebSearch'

Policies/POL-001-Quality-Policy.md

@@ -0,0 +1,97 @@
+# Quality Policy - Genetics & Genomics Laboratory
+
+| Document ID | POL-001 |
+|-------------|---------|
+| Title | Quality Policy |
+| Revision | 1.0 |
+| Effective Date | [DATE] |
+| Author | [AUTHOR] |
+| Approved By | [APPROVER] |
+
+---
+
+## 1. Policy Statement
+
+[LABORATORY NAME] is committed to providing high-quality clinical genetic and genomic testing services that consistently meet patient care needs, healthcare provider expectations, and applicable regulatory requirements. We strive for continual improvement of our Quality Management System to enhance the accuracy, clinical validity, and clinical utility of our genetic testing services while maintaining the highest standards of patient privacy and data security.
+
+## 2. Quality Objectives
+
+Our genetics and genomics laboratory commits to:
+
+1. **Analytical Accuracy**: Ensuring accurate variant detection, classification, and reporting according to ACMG/AMP guidelines and CAP molecular pathology standards
+2. **Clinical Validity**: Providing clinically meaningful genetic test results that support patient care decisions
+3. **Regulatory Compliance**: Maintaining compliance with CAP, CLIA, FDA, HIPAA, GINA, and other applicable regulations
+4. **Patient Privacy**: Protecting the confidentiality and security of genetic information for patients and family members
+5. **Continuous Improvement**: Continually improving the effectiveness of our QMS through proficiency testing, quality metrics monitoring, and corrective actions
+6. **Scientific Excellence**: Staying current with evolving variant classification guidelines, genomic discoveries, and clinical evidence
+7. **Ethical Practice**: Upholding ethical standards in genetic testing, including appropriate consent, secondary findings management, and family communication
+8. **Staff Competency**: Ensuring all personnel are properly trained and competent in molecular genetics, bioinformatics, and variant interpretation
+
+## 3. Management Commitment
+
+Top management demonstrates commitment to the QMS by:
+
+- Ensuring the quality policy is appropriate to the laboratory's mission of providing clinical genetic testing services
+- Ensuring quality objectives align with patient care needs and clinical utility
+- Ensuring integration of QMS requirements into all testing processes from sample receipt to result reporting
+- Promoting evidence-based variant classification and adherence to professional guidelines (ACMG, AMP, ClinGen)
+- Ensuring resources needed for the QMS are available, including bioinformatics infrastructure and variant databases
+- Communicating the importance of analytical accuracy, clinical validity, and data privacy
+- Ensuring the QMS achieves its intended results of accurate and timely genetic testing
+- Supporting participation in CAP proficiency testing and external quality assessment
+- Fostering collaboration with genetic counselors and clinical genetics professionals
+
+## 4. Scope
+
+This policy applies to all employees, contractors, genetic counselors, laboratory directors, bioinformaticians, and processes within the scope of our Clinical Genetics and Genomics Laboratory Quality Management System, including:
+
+- Germline genetic testing for hereditary conditions
+- Somatic variant testing for cancer genomics
+- Pharmacogenomics testing
+- Next-generation sequencing (NGS) operations
+- Variant interpretation and classification
+- Genetic counseling coordination
+- Biobanking and research specimen management
+- Bioinformatics pipeline operations and validation
+
+## 5. Compliance Framework
+
+Our quality policy ensures compliance with:
+
+- **CAP Molecular Pathology Checklist** (MolPath)
+- **CLIA** regulations for high-complexity testing
+- **ACMG/AMP** variant classification guidelines
+- **ACMG Secondary Findings** recommendations (SF v3.2)
+- **GINA** - Genetic Information Nondiscrimination Act
+- **HIPAA** - Privacy and security of genetic health information
+- **FDA** guidance for NGS-based tests
+- **ISO 15189** - Medical laboratory quality and competence
+- **State regulations** for genetic testing laboratories
+
+## 6. Communication
+
+This policy shall be:
+- Communicated and understood within the laboratory organization
+- Made available to clinical staff, genetic counselors, and ordering providers as appropriate
+- Posted in laboratory work areas
+- Reviewed annually for continuing suitability
+- Updated to reflect changes in regulatory requirements or professional guidelines
+
+## 7. Patient-Centered Care
+
+We recognize that genetic test results impact not only individual patients but also family members who may share genetic variants. Our quality commitment extends to:
+
+- Providing accurate and timely genetic testing results
+- Supporting informed decision-making through collaboration with genetic counseling services
+- Respecting patient autonomy in secondary findings preferences
+- Protecting genetic information privacy
+- Facilitating family cascade testing when appropriate
+- Ensuring age-appropriate consent for pediatric genetic testing
+
+---
+
+## Revision History
+
+| Rev | Date | Description | Author |
+|-----|------|-------------|--------|
+| 1.0 | [DATE] | Initial release | [AUTHOR] |

README.md

@@ -1,3 +1,127 @@
-# 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.
+
+## 🧬 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*

Templates/SOP-Template.md

@@ -0,0 +1,101 @@
+# Standard Operating Procedure: [Title]
+
+| Document ID | SOP-XXX |
+|-------------|---------|
+| Title | [Title] |
+| Revision | 1.0 |
+| Effective Date | [DATE] |
+| Author | [AUTHOR] |
+| Approved By | [APPROVER] |
+| Department | Genetics & Genomics Laboratory |
+
+---
+
+## 1. Purpose
+
+[State the purpose of this procedure]
+
+## 2. Scope
+
+[Define the scope and applicability - e.g., germline testing, somatic testing, specific genes/panels]
+
+## 3. Responsibilities
+
+### 3.1 Laboratory Director
+- [Responsibility]
+- [Responsibility]
+
+### 3.2 Clinical Molecular Geneticist
+- [Responsibility]
+- [Responsibility]
+
+### 3.3 Genetic Counselor
+- [Responsibility]
+- [Responsibility]
+
+### 3.4 Bioinformatician
+- [Responsibility]
+- [Responsibility]
+
+### 3.5 Laboratory Technologist
+- [Responsibility]
+- [Responsibility]
+
+## 4. Definitions
+
+| Term | Definition |
+|------|------------|
+| ACMG | American College of Medical Genetics and Genomics |
+| AMP | Association for Molecular Pathology |
+| VAF | Variant Allele Frequency |
+| VUS | Variant of Uncertain Significance |
+| NGS | Next-Generation Sequencing |
+| SNV | Single Nucleotide Variant |
+| CNV | Copy Number Variant |
+| [Term] | [Definition] |
+
+## 5. Procedure
+
+### 5.1 [Section Title]
+
+[Procedure steps]
+
+### 5.2 [Section Title]
+
+[Procedure steps]
+
+## 6. Quality Control
+
+- [QC checkpoints]
+- [Acceptance criteria]
+- [Monitoring procedures]
+
+## 7. Related Documents
+
+- [List related procedures, forms, etc.]
+- Example: SOP-VI-001: ACMG/AMP Variant Classification
+- Example: FRM-VC-001: Variant Classification Worksheet
+
+## 8. References
+
+### Regulatory References
+- CAP Molecular Pathology Checklist
+- CLIA regulations for high-complexity testing
+- [Applicable state regulations]
+
+### Professional Guidelines
+- ACMG/AMP Standards and Guidelines for the Interpretation of Sequence Variants (2015)
+- ACMG Secondary Findings Recommendations (SF v3.2)
+- [Other applicable guidelines]
+
+### Scientific Literature
+- [Key publications]
+- [Evidence base]
+
+---
+
+## Revision History
+
+| Rev | Date | Description | Author |
+|-----|------|-------------|--------|
+| 1.0 | [DATE] | Initial release | [AUTHOR] |

Work-Instructions/WI-001-Template.md

@@ -0,0 +1,135 @@
+# Work Instruction: [Title]
+
+| Document ID | WI-001 |
+|-------------|--------|
+| Title | [Title] |
+| Revision | 1.0 |
+| Effective Date | [DATE] |
+| Author | [AUTHOR] |
+| Approved By | [APPROVER] |
+| Department | Genetics & Genomics Laboratory |
+
+---
+
+## 1. Purpose
+
+[Describe the purpose of this work instruction - e.g., NGS library preparation, variant calling, DNA extraction]
+
+## 2. Scope
+
+[Define what activities this instruction covers - e.g., specific assay, platform, sample types]
+
+## 3. Safety Precautions
+
+- [List any safety requirements - biological hazards, chemical reagents]
+- [Personal protective equipment needed - lab coat, gloves, eye protection]
+- [Hazards to be aware of - ethidium bromide, formamide, liquid nitrogen]
+- [Biosafety level requirements]
+
+## 4. Equipment/Materials Required
+
+| Item | Specification | Vendor/Catalog # |
+|------|---------------|------------------|
+| [Sequencing Platform] | [Model/Version] | [Vendor] |
+| [Reagent Kit] | [Kit Name/Version] | [Catalog #] |
+| [Software] | [Version] | [Source] |
+| | | |
+
+## 5. Quality Control Materials
+
+| QC Material | Purpose | Acceptance Criteria |
+|-------------|---------|---------------------|
+| [Positive Control] | [Purpose] | [Criteria] |
+| [Negative Control] | [Purpose] | [Criteria] |
+| [Reference Standard] | [Purpose] | [Criteria] |
+
+## 6. Pre-Procedure Setup
+
+### 6.1 Sample Verification
+[Steps to verify sample identity, labeling, and chain of custody]
+
+### 6.2 Equipment Preparation
+[Equipment calibration, cleaning, initialization steps]
+
+### 6.3 Reagent Preparation
+[Reagent thawing, mixing, QC verification]
+
+## 7. Procedure
+
+### Step 1: [Title]
+[Detailed instructions with specific parameters]
+- [Sub-step with settings/values]
+- [Expected outcome/checkpoint]
+
+### Step 2: [Title]
+[Detailed instructions]
+- [Sub-step]
+- [Expected outcome/checkpoint]
+
+### Step 3: [Title]
+[Detailed instructions]
+- [Sub-step]
+- [Expected outcome/checkpoint]
+
+## 8. Quality Metrics
+
+| Metric | Target Value | Action if Out of Spec |
+|--------|--------------|----------------------|
+| [Coverage Depth] | [>20x for germline] | [Repeat sequencing] |
+| [Q30 Score] | [>80%] | [Investigate/rerun] |
+| [Uniformity] | [>0.8] | [Troubleshoot] |
+| [Contamination] | [<3%] | [Reject sample] |
+
+## 9. Acceptance Criteria
+
+[Define what constitutes successful completion]
+- [Criteria 1 with specific threshold]
+- [Criteria 2 with specific threshold]
+- [Criteria 3 with specific threshold]
+
+## 10. Troubleshooting
+
+| Problem | Possible Cause | Solution |
+|---------|----------------|----------|
+| [Issue] | [Cause] | [Action] |
+| [Issue] | [Cause] | [Action] |
+
+## 11. Records
+
+| Record | Location | Retention Period |
+|--------|----------|------------------|
+| [Run Log] | [LIMS/Path] | [CAP requirement] |
+| [QC Results] | [LIMS/Path] | [Minimum 2 years] |
+| [Variant Call Files] | [Secure Storage] | [Per CLIA/CAP] |
+
+## 12. Data Management
+
+- [File naming conventions]
+- [Data backup procedures]
+- [Version control for pipelines/software]
+- [Data retention and archival]
+
+## 13. References
+
+### Related SOPs
+- [SOP-SEQ-XXX: NGS Quality Control]
+- [SOP-DM-XXX: Bioinformatics Data Management]
+- [SOP-GEN-XXX: Sample Tracking]
+
+### Manufacturer Documentation
+- [Instrument User Guide, Version X]
+- [Reagent Kit Insert, Version X]
+- [Software Manual, Version X]
+
+### Standards and Guidelines
+- [CAP Molecular Pathology Checklist]
+- [CLIA requirements]
+- [Relevant professional guidelines]
+
+---
+
+## Revision History
+
+| Rev | Date | Description | Author |
+|-----|------|-------------|--------|
+| 1.0 | [DATE] | Initial release | [AUTHOR] |