From bd9b5a78887d344e5790a41832fb876cf2cf7900 Mon Sep 17 00:00:00 2001 From: AtomicQMS Service Date: Sat, 27 Dec 2025 11:24:16 -0500 Subject: [PATCH] Sync template from atomicqms-style deployment --- .gitea/workflows/atomicai.yml | 79 +++++ Forms/Competency/.gitkeep | 0 Forms/FRM-001-Document-Change-Request.md | 64 ++++ Forms/FRM-003-CAPA-Form.md | 91 ++++++ Forms/FRM-006-Audit-Checklist.md | 56 ++++ Forms/Grossing-Templates/.gitkeep | 0 Forms/Incident-Reports/.gitkeep | 0 Forms/QC-Records/.gitkeep | 0 Forms/Report-Templates/.gitkeep | 0 Forms/Requisition-Forms/.gitkeep | 0 .../FRM-PATH-001-Specimen-Receipt-Log.md | 196 ++++++++++++ Forms/Training/FRM-004-Training-Record.md | 72 +++++ Policies/POL-001-Quality-Policy.md | 57 ++++ README.md | 134 +++++++- SOPs/Autopsy/.gitkeep | 0 SOPs/Cytology/.gitkeep | 0 SOPs/General/SOP-001-Document-Control.md | 112 +++++++ SOPs/General/SOP-002-CAPA.md | 134 ++++++++ SOPs/General/SOP-003-Training.md | 123 ++++++++ SOPs/General/SOP-004-Internal-Audit.md | 136 ++++++++ SOPs/General/SOP-005-Management-Review.md | 114 +++++++ SOPs/Histology/.gitkeep | 0 SOPs/Molecular/.gitkeep | 0 SOPs/Safety/.gitkeep | 1 + SOPs/Specimen-Handling/.gitkeep | 0 .../SOP-PATH-001-Specimen-Accessioning.md | 293 ++++++++++++++++++ Templates/SOP-Template.md | 62 ++++ Work Instructions/WI-001-Template.md | 68 ++++ 28 files changed, 1790 insertions(+), 2 deletions(-) create mode 100644 .gitea/workflows/atomicai.yml create mode 100644 Forms/Competency/.gitkeep create mode 100644 Forms/FRM-001-Document-Change-Request.md create mode 100644 Forms/FRM-003-CAPA-Form.md create mode 100644 Forms/FRM-006-Audit-Checklist.md create mode 100644 Forms/Grossing-Templates/.gitkeep create mode 100644 Forms/Incident-Reports/.gitkeep create mode 100644 Forms/QC-Records/.gitkeep create mode 100644 Forms/Report-Templates/.gitkeep create mode 100644 Forms/Requisition-Forms/.gitkeep create mode 100644 Forms/Specimen-Tracking/FRM-PATH-001-Specimen-Receipt-Log.md create mode 100644 Forms/Training/FRM-004-Training-Record.md create mode 100644 Policies/POL-001-Quality-Policy.md create mode 100644 SOPs/Autopsy/.gitkeep create mode 100644 SOPs/Cytology/.gitkeep create mode 100644 SOPs/General/SOP-001-Document-Control.md create mode 100644 SOPs/General/SOP-002-CAPA.md create mode 100644 SOPs/General/SOP-003-Training.md create mode 100644 SOPs/General/SOP-004-Internal-Audit.md create mode 100644 SOPs/General/SOP-005-Management-Review.md create mode 100644 SOPs/Histology/.gitkeep create mode 100644 SOPs/Molecular/.gitkeep create mode 100644 SOPs/Safety/.gitkeep create mode 100644 SOPs/Specimen-Handling/.gitkeep create mode 100644 SOPs/Specimen-Handling/SOP-PATH-001-Specimen-Accessioning.md create mode 100644 Templates/SOP-Template.md create mode 100644 Work Instructions/WI-001-Template.md diff --git a/.gitea/workflows/atomicai.yml b/.gitea/workflows/atomicai.yml new file mode 100644 index 0000000..3b5850b --- /dev/null +++ b/.gitea/workflows/atomicai.yml @@ -0,0 +1,79 @@ +name: AtomicAI Pathology 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 Pathology 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 Pathology and Anatomic Pathology Quality Management. + + ## Your Expertise + - CAP (College of American Pathologists) accreditation + - CLIA laboratory standards + - Surgical pathology specimen handling + - Histology and tissue processing + - Immunohistochemistry protocols + - Cytology and FNA procedures + - Autopsy protocols and procedures + - Frozen section procedures + - Specimen identification and tracking + - Quality assurance and peer review + - Critical diagnosis communication + - Digital pathology and whole slide imaging + + ## Document Creation Guidelines + - Place Surgical Path SOPs in SOPs/Surgical-Pathology/ + - Place Histology SOPs in SOPs/Histology/ + - Place Cytology SOPs in SOPs/Cytology/ + - Place QA Forms in Forms/Quality-Assurance/ + - Place Specimen Forms in Forms/Specimen/ + - Place Policies in Policies/ + + ## Numbering Convention + - SOP-SP-XXX for Surgical Pathology SOPs + - SOP-HIS-XXX for Histology SOPs + - SOP-CYT-XXX for Cytology SOPs + - SOP-AUT-XXX for Autopsy SOPs + - POL-XXX for Policies + - FRM-XXX for Forms + + Always create branches and submit changes as Pull Requests for review. + Prioritize specimen integrity, diagnostic accuracy, and turnaround time. + allowed_tools: 'Read,Edit,Grep,Glob,Write' + disallowed_tools: 'Bash,WebSearch' diff --git a/Forms/Competency/.gitkeep b/Forms/Competency/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/Forms/FRM-001-Document-Change-Request.md b/Forms/FRM-001-Document-Change-Request.md new file mode 100644 index 0000000..55c718a --- /dev/null +++ b/Forms/FRM-001-Document-Change-Request.md @@ -0,0 +1,64 @@ +# Document Change Request Form + +| Form ID | FRM-001 | Revision | 1.0 | +|---------|---------|----------|-----| + +--- + +## Section 1: Request Information + +| Field | Entry | +|-------|-------| +| Request Date | | +| Requested By | | +| Department | | + +## Section 2: Document Information + +| Field | Entry | +|-------|-------| +| Document Number | | +| Document Title | | +| Current Revision | | + +## Section 3: Change Description + +### Type of Change +- [ ] New Document +- [ ] Revision to Existing Document +- [ ] Document Obsolescence + +### Description of Change +*(Describe the proposed change in detail)* + + + + +### Reason for Change +*(Explain why this change is needed)* + + + + +## Section 4: Impact Assessment + +### Affected Areas +- [ ] Training Required +- [ ] Other Documents Affected +- [ ] Process Changes Required +- [ ] Validation Impact + +### List Affected Documents + + +## Section 5: Approvals + +| Role | Name | Signature | Date | +|------|------|-----------|------| +| Requester | | | | +| Document Owner | | | | +| Quality Assurance | | | | + +--- + +*Form FRM-001 Rev 1.0* diff --git a/Forms/FRM-003-CAPA-Form.md b/Forms/FRM-003-CAPA-Form.md new file mode 100644 index 0000000..6790a8f --- /dev/null +++ b/Forms/FRM-003-CAPA-Form.md @@ -0,0 +1,91 @@ +# Corrective and Preventive Action (CAPA) Form + +| Form ID | FRM-003 | Revision | 1.0 | +|---------|---------|----------|-----| + +--- + +## Section 1: CAPA Identification + +| Field | Entry | +|-------|-------| +| CAPA Number | | +| Date Initiated | | +| Initiated By | | +| CAPA Owner | | +| Target Closure Date | | + +## Section 2: Classification + +### Type +- [ ] Corrective Action +- [ ] Preventive Action + +### Source +- [ ] Customer Complaint +- [ ] Internal Audit +- [ ] External Audit +- [ ] Process Deviation +- [ ] Nonconforming Product +- [ ] Management Review +- [ ] Other: ____________ + +### Priority +- [ ] Critical (5 business days) +- [ ] Major (15 business days) +- [ ] Minor (30 business days) + +## Section 3: Problem Description + +*(Describe the nonconformity or potential nonconformity)* + + + + +## Section 4: Immediate Containment + +*(Actions taken to contain the immediate impact)* + + + + +## Section 5: Root Cause Investigation + +### Investigation Method Used +- [ ] 5 Whys +- [ ] Fishbone Diagram +- [ ] Fault Tree Analysis +- [ ] Other: ____________ + +### Root Cause Determination + + + + +## Section 6: Corrective/Preventive Actions + +| Action | Responsible | Due Date | Status | +|--------|-------------|----------|--------| +| | | | | +| | | | | +| | | | | + +## Section 7: Effectiveness Verification + +| Criteria | Method | Result | +|----------|--------|--------| +| | | | + +Verification Date: ____________ +Verified By: ____________ + +## Section 8: Closure + +| Role | Name | Signature | Date | +|------|------|-----------|------| +| CAPA Owner | | | | +| Quality Approval | | | | + +--- + +*Form FRM-003 Rev 1.0* diff --git a/Forms/FRM-006-Audit-Checklist.md b/Forms/FRM-006-Audit-Checklist.md new file mode 100644 index 0000000..45bf0b6 --- /dev/null +++ b/Forms/FRM-006-Audit-Checklist.md @@ -0,0 +1,56 @@ +# Internal Audit Checklist + +| Form ID | FRM-006 | Revision | 1.0 | +|---------|---------|----------|-----| + +--- + +## Audit Information + +| Field | Entry | +|-------|-------| +| Audit Number | | +| Audit Date | | +| Area/Process Audited | | +| Lead Auditor | | +| Auditee(s) | | + +--- + +## Checklist Items + +| # | Requirement/Question | Reference | C/NC/NA | Evidence/Notes | +|---|---------------------|-----------|---------|----------------| +| 1 | Are current versions of applicable procedures available? | SOP-001 | | | +| 2 | Are personnel trained on applicable procedures? | SOP-003 | | | +| 3 | Are training records current and complete? | SOP-003 | | | +| 4 | Are records properly maintained and retrievable? | SOP-001 | | | +| 5 | Are nonconformities being documented and addressed? | SOP-002 | | | +| 6 | Are CAPAs being completed on time? | SOP-002 | | | +| 7 | Is equipment calibrated and maintained? | | | | +| 8 | Are process controls being followed? | | | | +| 9 | Are quality objectives being monitored? | | | | +| 10 | | | | | + +**Legend:** C = Conforming, NC = Nonconforming, NA = Not Applicable + +--- + +## Findings Summary + +| Finding # | Type | Description | Clause Reference | +|-----------|------|-------------|------------------| +| | | | | +| | | | | + +--- + +## Auditor Signature + +| Auditor | Signature | Date | +|---------|-----------|------| +| | | | + +--- + +*Form FRM-006 Rev 1.0* diff --git a/Forms/Grossing-Templates/.gitkeep b/Forms/Grossing-Templates/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/Forms/Incident-Reports/.gitkeep b/Forms/Incident-Reports/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/Forms/QC-Records/.gitkeep b/Forms/QC-Records/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/Forms/Report-Templates/.gitkeep b/Forms/Report-Templates/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/Forms/Requisition-Forms/.gitkeep b/Forms/Requisition-Forms/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/Forms/Specimen-Tracking/FRM-PATH-001-Specimen-Receipt-Log.md b/Forms/Specimen-Tracking/FRM-PATH-001-Specimen-Receipt-Log.md new file mode 100644 index 0000000..92a5975 --- /dev/null +++ b/Forms/Specimen-Tracking/FRM-PATH-001-Specimen-Receipt-Log.md @@ -0,0 +1,196 @@ +# Specimen Receipt Log + +| Form ID | FRM-PATH-001 | Revision | 1.0 | +|---------|-------------|----------|-----| + +--- + +## Log Information + +| Field | Entry | +|-------|-------| +| Date | | +| Shift | ☐ Day ☐ Evening ☐ Night | +| Accessioning Technician | | +| Technician ID | | + +--- + +## Specimen Receipt Record + +### Specimen 1 + +| Field | Entry | +|-------|-------| +| Time Received | | +| Received From | ☐ OR ☐ Clinic ☐ Courier ☐ Transport ☐ Other: | +| Accession Number | | +| Patient Name | | +| MRN | | +| DOB | | +| Specimen Type | | +| Specimen Site | | +| Number of Containers | | +| Fixative | ☐ Formalin ☐ Fresh ☐ Other: | +| Collection Date/Time | | +| Container Labeled Correctly? | ☐ Yes ☐ No | +| Requisition Complete? | ☐ Yes ☐ No | +| Specimen Condition | ☐ Acceptable ☐ Compromised (see notes) | +| Priority | ☐ Routine ☐ Rush ☐ STAT | +| Discrepancy? | ☐ No ☐ Yes (Resolution: _______) | +| Received By (Initials) | | + +### Specimen 2 + +| Field | Entry | +|-------|-------| +| Time Received | | +| Received From | ☐ OR ☐ Clinic ☐ Courier ☐ Transport ☐ Other: | +| Accession Number | | +| Patient Name | | +| MRN | | +| DOB | | +| Specimen Type | | +| Specimen Site | | +| Number of Containers | | +| Fixative | ☐ Formalin ☐ Fresh ☐ Other: | +| Collection Date/Time | | +| Container Labeled Correctly? | ☐ Yes ☐ No | +| Requisition Complete? | ☐ Yes ☐ No | +| Specimen Condition | ☐ Acceptable ☐ Compromised (see notes) | +| Priority | ☐ Routine ☐ Rush ☐ STAT | +| Discrepancy? | ☐ No ☐ Yes (Resolution: _______) | +| Received By (Initials) | | + +### Specimen 3 + +| Field | Entry | +|-------|-------| +| Time Received | | +| Received From | ☐ OR ☐ Clinic ☐ Courier ☐ Transport ☐ Other: | +| Accession Number | | +| Patient Name | | +| MRN | | +| DOB | | +| Specimen Type | | +| Specimen Site | | +| Number of Containers | | +| Fixative | ☐ Formalin ☐ Fresh ☐ Other: | +| Collection Date/Time | | +| Container Labeled Correctly? | ☐ Yes ☐ No | +| Requisition Complete? | ☐ Yes ☐ No | +| Specimen Condition | ☐ Acceptable ☐ Compromised (see notes) | +| Priority | ☐ Routine ☐ Rush ☐ STAT | +| Discrepancy? | ☐ No ☐ Yes (Resolution: _______) | +| Received By (Initials) | | + +### Specimen 4 + +| Field | Entry | +|-------|-------| +| Time Received | | +| Received From | ☐ OR ☐ Clinic ☐ Courier ☐ Transport ☐ Other: | +| Accession Number | | +| Patient Name | | +| MRN | | +| DOB | | +| Specimen Type | | +| Specimen Site | | +| Number of Containers | | +| Fixative | ☐ Formalin ☐ Fresh ☐ Other: | +| Collection Date/Time | | +| Container Labeled Correctly? | ☐ Yes ☐ No | +| Requisition Complete? | ☐ Yes ☐ No | +| Specimen Condition | ☐ Acceptable ☐ Compromised (see notes) | +| Priority | ☐ Routine ☐ Rush ☐ STAT | +| Discrepancy? | ☐ No ☐ Yes (Resolution: _______) | +| Received By (Initials) | | + +### Specimen 5 + +| Field | Entry | +|-------|-------| +| Time Received | | +| Received From | ☐ OR ☐ Clinic ☐ Courier ☐ Transport ☐ Other: | +| Accession Number | | +| Patient Name | | +| MRN | | +| DOB | | +| Specimen Type | | +| Specimen Site | | +| Number of Containers | | +| Fixative | ☐ Formalin ☐ Fresh ☐ Other: | +| Collection Date/Time | | +| Container Labeled Correctly? | ☐ Yes ☐ No | +| Requisition Complete? | ☐ Yes ☐ No | +| Specimen Condition | ☐ Acceptable ☐ Compromised (see notes) | +| Priority | ☐ Routine ☐ Rush ☐ STAT | +| Discrepancy? | ☐ No ☐ Yes (Resolution: _______) | +| Received By (Initials) | | + +--- + +## Special Handling/Fresh Specimens + +*Document any specimens requiring immediate processing (frozen sections, special studies, etc.)* + +| Accession # | Specimen Type | Special Handling Required | Time to Grossing | Pathologist Notified | +|-------------|---------------|---------------------------|------------------|---------------------| +| | | | | ☐ Yes | +| | | | | ☐ Yes | + +--- + +## Discrepancy Log + +| Time | Accession # | Discrepancy Type | Description | Resolution | Resolved By | +|------|-------------|------------------|-------------|------------|-------------| +| | | ☐ Labeling ☐ Requisition ☐ Condition ☐ Other | | | | +| | | ☐ Labeling ☐ Requisition ☐ Condition ☐ Other | | | | + +--- + +## Shift Summary + +| Field | Count | +|-------|-------| +| Total Specimens Received | | +| Surgical Pathology | | +| Cytology | | +| Frozen Sections | | +| STAT/Rush Cases | | +| Specimens with Discrepancies | | +| Specimens Held/Not Accessioned | | + +--- + +## Quality Notes + +*Document any quality issues, equipment problems, or unusual occurrences:* + +--- + +## Shift Handoff + +| Field | Entry | +|-------|-------| +| Pending Issues for Next Shift | | +| Outstanding Discrepancies | | +| Equipment Issues | | +| Shift Sign-Off | | +| Date/Time | | + +--- + +## Supervisor Review + +| Field | Entry | +|-------|-------| +| Reviewed By | | +| Date | | +| Comments | | +| Signature | | + +--- + +*Form FRM-PATH-001 Rev 1.0 - Specimen Receipt Log* diff --git a/Forms/Training/FRM-004-Training-Record.md b/Forms/Training/FRM-004-Training-Record.md new file mode 100644 index 0000000..b66164d --- /dev/null +++ b/Forms/Training/FRM-004-Training-Record.md @@ -0,0 +1,72 @@ +# Training Record Form + +| Form ID | FRM-004 | Revision | 1.0 | +|---------|---------|----------|-----| + +--- + +## Section 1: Employee Information + +| Field | Entry | +|-------|-------| +| Employee Name | | +| Employee ID | | +| Department | | +| Job Title | | + +## Section 2: Training Information + +| Field | Entry | +|-------|-------| +| Training Title | | +| Training Date | | +| Training Duration | | +| Trainer Name | | +| Trainer Qualification | | + +### Training Type +- [ ] Initial Training +- [ ] Retraining +- [ ] Refresher +- [ ] Procedure Update + +### Delivery Method +- [ ] Classroom +- [ ] On-the-Job +- [ ] Self-Study +- [ ] Computer-Based +- [ ] Other: ____________ + +## Section 3: Training Content + +*(List topics covered or attach training materials)* + + + + +## Section 4: Assessment + +### Assessment Method +- [ ] Written Test +- [ ] Practical Demonstration +- [ ] Verbal Assessment +- [ ] Observation + +### Assessment Results + +| Metric | Result | +|--------|--------| +| Score (if applicable) | | +| Pass/Fail | | + +## Section 5: Signatures + +| Role | Name | Signature | Date | +|------|------|-----------|------| +| Trainee | | | | +| Trainer | | | | +| Supervisor | | | | + +--- + +*Form FRM-004 Rev 1.0* diff --git a/Policies/POL-001-Quality-Policy.md b/Policies/POL-001-Quality-Policy.md new file mode 100644 index 0000000..ebd85dd --- /dev/null +++ b/Policies/POL-001-Quality-Policy.md @@ -0,0 +1,57 @@ +# Quality Policy + +| Document ID | POL-001 | +|-------------|---------| +| Title | Quality Policy | +| Revision | 1.0 | +| Effective Date | [DATE] | +| Author | [AUTHOR] | +| Approved By | [APPROVER] | + +--- + +## 1. Policy Statement + +[ORGANIZATION NAME] is committed to providing products and services that consistently meet customer requirements and applicable regulatory requirements. We strive for continual improvement of our Quality Management System to enhance customer satisfaction. + +## 2. Quality Objectives + +Our organization commits to: + +1. **Customer Focus**: Understanding and meeting customer needs and expectations +2. **Regulatory Compliance**: Maintaining compliance with all applicable regulations and standards +3. **Continuous Improvement**: Continually improving the effectiveness of our QMS +4. **Employee Engagement**: Ensuring all employees understand their role in quality +5. **Risk-Based Thinking**: Identifying and addressing risks and opportunities + +## 3. Management Commitment + +Top management demonstrates commitment to the QMS by: + +- Ensuring the quality policy is appropriate to the organization's purpose +- Ensuring quality objectives are established and compatible with strategic direction +- Ensuring integration of QMS requirements into business processes +- Promoting the use of the process approach and risk-based thinking +- Ensuring resources needed for the QMS are available +- Communicating the importance of effective quality management +- Ensuring the QMS achieves its intended results +- Engaging, directing, and supporting persons to contribute to QMS effectiveness + +## 4. Scope + +This policy applies to all employees, contractors, and processes within the scope of our Quality Management System. + +## 5. Communication + +This policy shall be: +- Communicated and understood within the organization +- Available to relevant interested parties as appropriate +- Reviewed for continuing suitability + +--- + +## Revision History + +| Rev | Date | Description | Author | +|-----|------|-------------|--------| +| 1.0 | [DATE] | Initial release | [AUTHOR] | diff --git a/README.md b/README.md index 8a4b65e..55660dd 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,133 @@ -# pathology +# Pathology & Laboratory Medicine Quality Management System -A comprehensive QMS template designed for anatomic pathology, clinical pathology, and laboratory medicine departments. \ No newline at end of file +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) + +--- + +*This template is maintained by AtomicQMS. For questions, open an issue in this repository.* diff --git a/SOPs/Autopsy/.gitkeep b/SOPs/Autopsy/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/SOPs/Cytology/.gitkeep b/SOPs/Cytology/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/SOPs/General/SOP-001-Document-Control.md b/SOPs/General/SOP-001-Document-Control.md new file mode 100644 index 0000000..b64ef52 --- /dev/null +++ b/SOPs/General/SOP-001-Document-Control.md @@ -0,0 +1,112 @@ +# Standard Operating Procedure: Document Control + +| Document ID | SOP-001 | +|-------------|---------| +| Title | Document Control | +| Revision | 1.0 | +| Effective Date | [DATE] | +| Author | [AUTHOR] | +| Approved By | [APPROVER] | +| Department | Quality Assurance | + +--- + +## 1. Purpose + +To establish a procedure for the creation, review, approval, distribution, and control of documents within the Quality Management System. + +## 2. Scope + +This procedure applies to all controlled documents including: +- Policies +- Standard Operating Procedures (SOPs) +- Work Instructions +- Forms and Templates +- Specifications +- External documents of external origin + +## 3. Responsibilities + +### 3.1 Document Owner +- Responsible for document content and accuracy +- Initiates document creation and revision +- Ensures periodic review is performed + +### 3.2 Quality Assurance +- Maintains the document control system +- Assigns document numbers +- Manages document distribution +- Archives obsolete documents + +### 3.3 Approvers +- Review and approve documents before release +- Ensure documents are adequate for intended purpose + +## 4. Procedure + +### 4.1 Document Creation + +1. Identify the need for a new document +2. Request document number from Quality Assurance +3. Draft document using appropriate template +4. Include all required header information +5. Submit for review and approval + +### 4.2 Document Review and Approval + +1. Route document to appropriate reviewers +2. Reviewers provide comments within 5 business days +3. Author addresses all comments +4. Final approval by designated approver +5. Quality Assurance releases document + +### 4.3 Document Numbering + +Documents shall be numbered according to the following convention: + +| Type | Prefix | Example | +|------|--------|---------| +| Policy | POL | POL-001 | +| SOP | SOP | SOP-001 | +| Work Instruction | WI | WI-001 | +| Form | FRM | FRM-001 | + +### 4.4 Revision Control + +1. All changes require documented justification +2. Changes follow same review/approval process as new documents +3. Revision number increments with each approved change +4. Revision history maintained in document footer + +### 4.5 Document Distribution + +1. Current versions available in document control system +2. Obsolete versions marked and archived +3. Training on new/revised documents as needed + +### 4.6 Periodic Review + +1. Documents reviewed at least every 2 years +2. Review documented even if no changes made +3. Reviews may result in revision or reaffirmation + +## 5. Related Documents + +- FRM-001 Document Change Request Form +- FRM-002 Document Review Record + +## 6. Definitions + +| Term | Definition | +|------|------------| +| Controlled Document | Document managed under document control system | +| Obsolete | Document no longer valid for use | +| Revision | Updated version of a document | + +--- + +## Revision History + +| Rev | Date | Description | Author | +|-----|------|-------------|--------| +| 1.0 | [DATE] | Initial release | [AUTHOR] | diff --git a/SOPs/General/SOP-002-CAPA.md b/SOPs/General/SOP-002-CAPA.md new file mode 100644 index 0000000..8dace85 --- /dev/null +++ b/SOPs/General/SOP-002-CAPA.md @@ -0,0 +1,134 @@ +# Standard Operating Procedure: Corrective and Preventive Action (CAPA) + +| Document ID | SOP-002 | +|-------------|---------| +| Title | Corrective and Preventive Action | +| Revision | 1.0 | +| Effective Date | [DATE] | +| Author | [AUTHOR] | +| Approved By | [APPROVER] | +| Department | Quality Assurance | + +--- + +## 1. Purpose + +To establish a systematic process for identifying, investigating, correcting, and preventing nonconformities and potential nonconformities. + +## 2. Scope + +This procedure applies to: +- Product and process nonconformities +- Customer complaints +- Audit findings +- Process deviations +- Potential nonconformities identified through risk analysis + +## 3. Definitions + +| Term | Definition | +|------|------------| +| Corrective Action | Action to eliminate the cause of a detected nonconformity | +| Preventive Action | Action to eliminate the cause of a potential nonconformity | +| Root Cause | Fundamental reason for a nonconformity | +| Effectiveness Check | Verification that implemented actions achieved desired results | + +## 4. Responsibilities + +### 4.1 CAPA Owner +- Investigates the issue +- Identifies root cause +- Develops and implements corrective/preventive actions +- Verifies effectiveness + +### 4.2 Quality Assurance +- Manages CAPA system +- Assigns CAPA numbers +- Tracks CAPA status +- Reviews and approves CAPAs +- Reports CAPA metrics to management + +### 4.3 Management +- Provides resources for CAPA implementation +- Reviews CAPA trends +- Ensures timely closure + +## 5. Procedure + +### 5.1 CAPA Initiation + +1. Identify nonconformity or potential nonconformity +2. Document issue on CAPA Form (FRM-003) +3. Classify severity and priority +4. Assign CAPA owner + +### 5.2 Investigation + +1. Gather relevant data and evidence +2. Interview personnel involved +3. Review related documents and records +4. Use appropriate investigation tools: + - 5 Whys + - Fishbone Diagram + - Failure Mode Analysis + +### 5.3 Root Cause Analysis + +1. Identify potential root causes +2. Verify root cause through evidence +3. Document root cause determination +4. Consider systemic implications + +### 5.4 Action Development + +1. Develop corrective/preventive actions +2. Assign responsibilities and due dates +3. Assess actions for: + - Appropriateness to problem severity + - Impact on other processes + - Resource requirements + +### 5.5 Implementation + +1. Execute approved actions +2. Document implementation evidence +3. Update affected documents/processes +4. Provide training as needed + +### 5.6 Effectiveness Verification + +1. Define effectiveness criteria +2. Allow sufficient time for actions to take effect +3. Collect and analyze data +4. Document verification results +5. If ineffective, reopen CAPA for further action + +### 5.7 Closure + +1. Review all CAPA documentation +2. Verify all actions completed +3. Confirm effectiveness verified +4. Obtain approval for closure + +## 6. CAPA Metrics + +Quality Assurance shall track and report: +- Number of open CAPAs +- CAPA aging +- On-time closure rate +- Effectiveness rate +- CAPAs by category/source + +## 7. Related Documents + +- FRM-003 CAPA Form +- SOP-003 Nonconforming Product Control +- SOP-004 Customer Complaints + +--- + +## Revision History + +| Rev | Date | Description | Author | +|-----|------|-------------|--------| +| 1.0 | [DATE] | Initial release | [AUTHOR] | diff --git a/SOPs/General/SOP-003-Training.md b/SOPs/General/SOP-003-Training.md new file mode 100644 index 0000000..22538c1 --- /dev/null +++ b/SOPs/General/SOP-003-Training.md @@ -0,0 +1,123 @@ +# Standard Operating Procedure: Training and Competence + +| Document ID | SOP-003 | +|-------------|---------| +| Title | Training and Competence | +| Revision | 1.0 | +| Effective Date | [DATE] | +| Author | [AUTHOR] | +| Approved By | [APPROVER] | +| Department | Human Resources / Quality | + +--- + +## 1. Purpose + +To ensure personnel performing work affecting product quality are competent based on appropriate education, training, skills, and experience. + +## 2. Scope + +This procedure applies to: +- All employees performing quality-affecting activities +- Contractors and temporary personnel +- Personnel requiring GxP training + +## 3. Responsibilities + +### 3.1 Supervisors/Managers +- Identify training needs for their personnel +- Ensure training is completed before performing tasks +- Evaluate competence of personnel +- Maintain department training records + +### 3.2 Human Resources +- Coordinate training programs +- Maintain central training database +- Track training compliance +- Archive training records + +### 3.3 Quality Assurance +- Develop QMS-related training +- Approve training curricula for GxP activities +- Audit training compliance + +### 3.4 Employees +- Complete assigned training on time +- Maintain current qualifications +- Report training needs to supervisor + +## 4. Procedure + +### 4.1 Training Needs Assessment + +1. Identify competence requirements for each role +2. Document requirements in job descriptions +3. Assess current competence of personnel +4. Identify training gaps + +### 4.2 Training Curriculum Development + +1. Define learning objectives +2. Develop training materials +3. Identify delivery method: + - Classroom + - On-the-job + - Self-study + - Computer-based +4. Define assessment criteria +5. Obtain approval from Quality (for GxP training) + +### 4.3 Training Delivery + +1. Schedule training session +2. Document attendance +3. Deliver training per curriculum +4. Assess comprehension through: + - Written test (minimum 80% passing) + - Practical demonstration + - Supervisor observation + +### 4.4 Training Documentation + +Training records shall include: +- Employee name and ID +- Training title and date +- Trainer name and qualifications +- Assessment results +- Signatures + +### 4.5 Retraining Requirements + +Retraining is required when: +- Significant document revisions occur +- Performance deficiencies identified +- Extended absence from job function +- Periodic requalification due + +### 4.6 New Employee Orientation + +All new employees shall complete: +1. Company orientation +2. Quality system overview +3. Job-specific training +4. SOP read and understand for applicable procedures + +## 5. Training Records Retention + +- Training records maintained for duration of employment +- Records retained 3 years after employee departure +- Records available for regulatory inspection + +## 6. Related Documents + +- FRM-004 Training Record Form +- FRM-005 Training Assessment Form +- Job Descriptions + +--- + +## Revision History + +| Rev | Date | Description | Author | +|-----|------|-------------|--------| +| 1.0 | [DATE] | Initial release | [AUTHOR] | diff --git a/SOPs/General/SOP-004-Internal-Audit.md b/SOPs/General/SOP-004-Internal-Audit.md new file mode 100644 index 0000000..749d6a5 --- /dev/null +++ b/SOPs/General/SOP-004-Internal-Audit.md @@ -0,0 +1,136 @@ +# Standard Operating Procedure: Internal Audit + +| Document ID | SOP-004 | +|-------------|---------| +| Title | Internal Audit | +| Revision | 1.0 | +| Effective Date | [DATE] | +| Author | [AUTHOR] | +| Approved By | [APPROVER] | +| Department | Quality Assurance | + +--- + +## 1. Purpose + +To establish a systematic approach for conducting internal audits to verify the effectiveness of the Quality Management System. + +## 2. Scope + +This procedure covers: +- QMS process audits +- Compliance audits +- Product audits +- System audits + +## 3. Definitions + +| Term | Definition | +|------|------------| +| Audit | Systematic, independent examination to determine conformance | +| Auditor | Person qualified to perform audits | +| Finding | Observation of conformance or nonconformance | +| Observation | Noted item not rising to level of finding | + +## 4. Responsibilities + +### 4.1 Lead Auditor +- Plans and schedules audits +- Prepares audit checklists +- Conducts audit activities +- Reports audit findings + +### 4.2 Quality Manager +- Maintains audit program +- Qualifies auditors +- Reviews audit reports +- Reports to management + +### 4.3 Auditee +- Provides access to areas/records +- Responds to findings +- Implements corrective actions + +## 5. Procedure + +### 5.1 Annual Audit Schedule + +1. Develop annual audit schedule considering: + - Previous audit results + - Process criticality + - Regulatory requirements + - Changes to processes +2. Ensure all QMS processes audited at least annually +3. Obtain management approval +4. Communicate schedule to affected areas + +### 5.2 Auditor Qualification + +Auditors shall: +- Complete auditor training course +- Conduct at least 2 audits under supervision +- Be independent of area being audited +- Maintain competence through ongoing audits + +### 5.3 Audit Preparation + +1. Review applicable procedures and standards +2. Review previous audit reports +3. Prepare audit checklist +4. Notify auditee of audit scope and schedule +5. Confirm auditor availability + +### 5.4 Conducting the Audit + +1. Hold opening meeting with auditee +2. Execute audit checklist +3. Gather objective evidence: + - Document review + - Personnel interviews + - Process observation +4. Document findings with evidence +5. Classify findings: + - Major Nonconformance + - Minor Nonconformance + - Observation +6. Hold closing meeting + +### 5.5 Audit Reporting + +1. Complete audit report within 5 business days +2. Report shall include: + - Audit scope and criteria + - Personnel interviewed + - Findings with evidence + - Recommendations +3. Distribute report to auditee and management + +### 5.6 Finding Resolution + +1. Auditee responds with corrective action plan within 10 business days +2. Quality reviews and approves plan +3. Auditee implements corrective actions +4. Auditor verifies effectiveness +5. Close finding upon verification + +## 6. Audit Records + +Maintain for 5 years: +- Audit schedules +- Checklists +- Reports +- Corrective action records + +## 7. Related Documents + +- FRM-006 Audit Checklist Template +- FRM-007 Audit Report Template +- SOP-002 CAPA + +--- + +## Revision History + +| Rev | Date | Description | Author | +|-----|------|-------------|--------| +| 1.0 | [DATE] | Initial release | [AUTHOR] | diff --git a/SOPs/General/SOP-005-Management-Review.md b/SOPs/General/SOP-005-Management-Review.md new file mode 100644 index 0000000..dd82006 --- /dev/null +++ b/SOPs/General/SOP-005-Management-Review.md @@ -0,0 +1,114 @@ +# Standard Operating Procedure: Management Review + +| Document ID | SOP-005 | +|-------------|---------| +| Title | Management Review | +| Revision | 1.0 | +| Effective Date | [DATE] | +| Author | [AUTHOR] | +| Approved By | [APPROVER] | +| Department | Quality Assurance | + +--- + +## 1. Purpose + +To ensure top management reviews the Quality Management System at planned intervals to ensure its continuing suitability, adequacy, and effectiveness. + +## 2. Scope + +This procedure applies to the periodic management review of the QMS, including all processes and quality objectives. + +## 3. Frequency + +Management reviews shall be conducted: +- At least annually +- More frequently if significant changes occur +- As needed based on quality performance + +## 4. Responsibilities + +### 4.1 Quality Manager +- Prepares management review agenda and materials +- Facilitates the meeting +- Documents meeting minutes and action items +- Tracks completion of action items + +### 4.2 Top Management +- Attends management review meetings +- Reviews QMS performance data +- Makes decisions on QMS improvements +- Allocates resources as needed + +### 4.3 Department Managers +- Provides input data for their areas +- Attends management review +- Implements assigned action items + +## 5. Management Review Inputs + +The following shall be considered: + +### 5.1 Actions from Previous Reviews +- Status of action items +- Effectiveness of implemented actions + +### 5.2 Changes in Context +- Internal changes (organization, resources) +- External changes (regulations, market) + +### 5.3 QMS Performance +- Customer satisfaction and feedback +- Quality objectives achievement +- Process performance metrics +- Nonconformities and corrective actions +- Audit results +- Supplier performance + +### 5.4 Resource Adequacy +- Personnel +- Infrastructure +- Work environment + +### 5.5 Risk and Opportunities +- Risk assessment results +- Effectiveness of risk controls +- New opportunities identified + +### 5.6 Improvement Opportunities +- Process improvements +- Product improvements +- QMS enhancements + +## 6. Management Review Outputs + +Decisions and actions related to: +- Improvement of QMS and processes +- Product improvement +- Resource needs +- Changes to quality policy or objectives + +## 7. Documentation + +### 7.1 Meeting Minutes +- Date and attendees +- Items discussed +- Decisions made +- Action items with owners and due dates + +### 7.2 Record Retention +- Management review records retained for 5 years +- Available for regulatory inspection + +## 8. Related Documents + +- FRM-008 Management Review Agenda Template +- FRM-009 Management Review Minutes Template + +--- + +## Revision History + +| Rev | Date | Description | Author | +|-----|------|-------------|--------| +| 1.0 | [DATE] | Initial release | [AUTHOR] | diff --git a/SOPs/Histology/.gitkeep b/SOPs/Histology/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/SOPs/Molecular/.gitkeep b/SOPs/Molecular/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/SOPs/Safety/.gitkeep b/SOPs/Safety/.gitkeep new file mode 100644 index 0000000..dcf2c80 --- /dev/null +++ b/SOPs/Safety/.gitkeep @@ -0,0 +1 @@ +# Placeholder diff --git a/SOPs/Specimen-Handling/.gitkeep b/SOPs/Specimen-Handling/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/SOPs/Specimen-Handling/SOP-PATH-001-Specimen-Accessioning.md b/SOPs/Specimen-Handling/SOP-PATH-001-Specimen-Accessioning.md new file mode 100644 index 0000000..389c7e7 --- /dev/null +++ b/SOPs/Specimen-Handling/SOP-PATH-001-Specimen-Accessioning.md @@ -0,0 +1,293 @@ +# Standard Operating Procedure: Pathology Specimen Accessioning + +| Document ID | SOP-PATH-001 | +|-------------|-------------| +| Title | Pathology Specimen Accessioning and Processing | +| Revision | 1.0 | +| Effective Date | [DATE] | +| Author | [AUTHOR] | +| Approved By | [APPROVER] | +| Department | Anatomic Pathology | + +--- + +## 1. Purpose + +To establish standardized procedures for the receipt, accessioning, and initial processing of pathology specimens to ensure proper identification, optimal preservation, and regulatory compliance. + +## 2. Scope + +This procedure applies to all anatomic pathology specimens including: +- Surgical pathology specimens +- Cytology specimens +- Skin biopsies +- Bone marrow biopsies +- Autopsy specimens + +## 3. Responsibilities + +### 3.1 Accessioning Staff +- Receive and log specimens +- Verify specimen-requisition match +- Assign case numbers +- Distribute to appropriate areas + +### 3.2 Histology Technician +- Process tissue specimens +- Embed and section specimens +- Prepare slides for pathologist review + +### 3.3 Pathologist +- Perform gross examination +- Dictate gross description +- Review slides and render diagnosis + +### 3.4 Laboratory Director +- Ensure quality standards +- Review policies and procedures +- Oversee accreditation compliance + +## 4. Definitions + +| Term | Definition | +|------|------------| +| Accession | Process of receiving and logging specimens | +| Fixation | Chemical preservation of tissue | +| Grossing | Macroscopic examination and description | +| Cassette | Container for tissue during processing | +| Block | Paraffin-embedded tissue section | + +## 5. Equipment and Materials + +- Specimen containers (various sizes) +- 10% neutral buffered formalin (NBF) +- Requisition forms +- Barcoded labels +- Cassettes +- Tissue processor +- Embedding station +- Microtome +- Slides and coverslips + +## 6. Procedure + +### 6.1 Specimen Receipt + +#### 6.1.1 Verification at Receipt +Upon receiving each specimen: +- [ ] Container properly labeled with patient identifiers +- [ ] Requisition form accompanies specimen +- [ ] Container intact without leakage +- [ ] Specimen in appropriate fixative (if applicable) +- [ ] Time of collection documented + +#### 6.1.2 Label Verification + +**Minimum required on container:** +| Element | Present | +|---------|---------| +| Patient name | ☐ | +| Second identifier (MRN, DOB) | ☐ | +| Specimen type/site | ☐ | +| Date of collection | ☐ | +| Collector identification | ☐ | + +**Requisition must include:** +| Element | Present | +|---------|---------| +| Patient name and identifiers | ☐ | +| Ordering physician | ☐ | +| Specimen source/site | ☐ | +| Clinical history | ☐ | +| Date/time of collection | ☐ | +| Date/time of receipt in lab | ☐ | + +#### 6.1.3 Discrepancy Handling + +If discrepancies exist: +1. Do NOT accessioned until resolved +2. Contact ordering physician/collector +3. Document resolution in LIS +4. Complete discrepancy log + +| Discrepancy Type | Required Action | +|------------------|-----------------| +| Name mismatch | Contact collector, do not process | +| Missing information | Request completion before accessioning | +| Damaged container | Document, assess specimen integrity | +| No requisition | Hold specimen, request requisition | +| Unlabeled specimen | Do not process until properly labeled | + +### 6.2 Accessioning + +#### 6.2.1 Case Number Assignment +1. Log specimen into Laboratory Information System (LIS) +2. System assigns unique accession number +3. Format: [Year]-S[Sequential#] (e.g., 2024-S12345) +4. Generate specimen labels + +#### 6.2.2 Labeling +1. Apply barcoded labels to: + - Specimen container + - Cassettes + - All associated paperwork +2. Verify label matches requisition +3. Apply orientation labels if applicable + +#### 6.2.3 Specimen Categorization + +| Category | Description | Priority | +|----------|-------------|----------| +| Routine | Standard turnaround | 2-3 days | +| Rush | Expedited processing | 24-48 hours | +| STAT | Emergency | Same day | +| Intraoperative | Frozen section | Immediate | + +### 6.3 Fixation Assessment + +#### 6.3.1 Optimal Fixation Times + +| Specimen Type | Minimum | Optimal | Maximum | +|---------------|---------|---------|---------| +| Small biopsy (≤5mm) | 6 hours | 6-12 hours | 24 hours | +| Medium tissue (5-15mm) | 12 hours | 12-24 hours | 48 hours | +| Large specimen (>15mm) | 24 hours | 24-48 hours | 72 hours | + +#### 6.3.2 Fixative Requirements +- Standard: 10% neutral buffered formalin (10:1 ratio) +- Breast tissue for biomarkers: Cold ischemia <1 hour, fixed within 1 hour +- Special fixatives per protocol (e.g., Bouin's, B5) + +Document: +- Time of collection (if available) +- Time of receipt in fixative +- Time placed in processor + +### 6.4 Gross Examination (Grossing) + +#### 6.4.1 Pre-Grossing Preparation +1. Verify specimen identity +2. Review clinical history and prior pathology +3. Gather appropriate supplies +4. Photograph specimen (if indicated) + +#### 6.4.2 Gross Description Components + +**Standard elements:** +- [ ] Specimen type and site +- [ ] How received (container, fixative) +- [ ] Dimensions (3 measurements) +- [ ] Weight (if applicable) +- [ ] External appearance +- [ ] Cut surface appearance +- [ ] Lesion description (size, location, margins) +- [ ] Sections submitted summary + +**For resection specimens:** +- [ ] Orientation (sutures, clips, inks) +- [ ] Margin assessment +- [ ] Lymph node identification +- [ ] Relationship of lesion to margins + +#### 6.4.3 Inking Protocol + +| Color | Common Usage | +|-------|--------------| +| Black | Anterior/superficial | +| Blue | Posterior/deep | +| Green | Superior | +| Orange | Inferior | +| Red | Medial | +| Yellow | Lateral | + +Document inking scheme in gross description. + +#### 6.4.4 Section Submission + +| Specimen Type | Standard Sections | +|---------------|-------------------| +| Small biopsy | Entire specimen | +| Skin ellipse | 3mm cross-sections, all margins | +| Breast lumpectomy | Lesion, margins (6 directions), representative | +| Colon resection | Tumor (4 sections), margins, nodes, mucosa | + +### 6.5 Tissue Processing + +#### 6.5.1 Processing Steps +1. Dehydration (graded alcohols) +2. Clearing (xylene) +3. Infiltration (paraffin) +4. Total processing time: 8-14 hours + +#### 6.5.2 Processing Schedules + +| Schedule | Duration | Specimen Types | +|----------|----------|----------------| +| Routine overnight | 12-14 hours | Standard specimens | +| Extended | 16-20 hours | Fatty tissue, large specimens | +| Rapid | 2-4 hours | Urgent specimens | +| Rush microwave | 1-2 hours | STAT specimens | + +### 6.6 Embedding + +1. Orient tissue in cassette per protocol +2. Embed in paraffin at 60°C +3. Cool on cold plate +4. Verify block identity + +### 6.7 Microtomy + +1. Face block until full tissue visible +2. Cut at specified thickness (typically 4-5 µm) +3. Float sections on warm water bath +4. Pick up on labeled slide +5. Dry slides before staining + +### 6.8 Slide Preparation + +1. H&E staining (routine) +2. Special stains per request/protocol +3. Immunohistochemistry as ordered +4. Coverslip slides +5. Verify slide-block-patient match + +## 7. Quality Control + +### 7.1 Daily QC +- [ ] Reagent checks +- [ ] Processor function verification +- [ ] Temperature monitoring +- [ ] Staining controls + +### 7.2 Specimen Quality Metrics + +| Metric | Target | +|--------|--------| +| Specimen rejection rate | <2% | +| Accessioning errors | <0.5% | +| Lost specimens | 0 | +| Turnaround time (routine) | ≤48 hours | +| Block/slide discrepancies | <0.1% | + +## 8. Documentation + +- FRM-PATH-001 Specimen Receipt Log +- FRM-PATH-002 Gross Description Template +- FRM-PATH-003 Processing Log +- Discrepancy reports +- QC logs + +## 9. References + +- CAP Laboratory Accreditation Checklist +- ASCO/CAP Guidelines for Biomarker Testing +- CLIA regulations +- Institutional policies + +--- + +## Revision History + +| Rev | Date | Description | Author | +|-----|------|-------------|--------| +| 1.0 | [DATE] | Initial release | [AUTHOR] | diff --git a/Templates/SOP-Template.md b/Templates/SOP-Template.md new file mode 100644 index 0000000..2e9f35e --- /dev/null +++ b/Templates/SOP-Template.md @@ -0,0 +1,62 @@ +# Standard Operating Procedure: [Title] + +| Document ID | SOP-XXX | +|-------------|---------| +| Title | [Title] | +| Revision | 1.0 | +| Effective Date | [DATE] | +| Author | [AUTHOR] | +| Approved By | [APPROVER] | +| Department | [DEPARTMENT] | + +--- + +## 1. Purpose + +[State the purpose of this procedure] + +## 2. Scope + +[Define the scope and applicability] + +## 3. Responsibilities + +### 3.1 [Role 1] +- [Responsibility] +- [Responsibility] + +### 3.2 [Role 2] +- [Responsibility] +- [Responsibility] + +## 4. Definitions + +| Term | Definition | +|------|------------| +| | | + +## 5. Procedure + +### 5.1 [Section Title] + +[Procedure steps] + +### 5.2 [Section Title] + +[Procedure steps] + +## 6. Related Documents + +- [List related procedures, forms, etc.] + +## 7. References + +- [External standards, regulations, etc.] + +--- + +## Revision History + +| Rev | Date | Description | Author | +|-----|------|-------------|--------| +| 1.0 | [DATE] | Initial release | [AUTHOR] | diff --git a/Work Instructions/WI-001-Template.md b/Work Instructions/WI-001-Template.md new file mode 100644 index 0000000..68167f1 --- /dev/null +++ b/Work Instructions/WI-001-Template.md @@ -0,0 +1,68 @@ +# Work Instruction: [Title] + +| Document ID | WI-001 | +|-------------|--------| +| Title | [Title] | +| Revision | 1.0 | +| Effective Date | [DATE] | +| Author | [AUTHOR] | +| Approved By | [APPROVER] | +| Department | [DEPARTMENT] | + +--- + +## 1. Purpose + +[Describe the purpose of this work instruction] + +## 2. Scope + +[Define what activities this instruction covers] + +## 3. Safety Precautions + +- [List any safety requirements] +- [Personal protective equipment needed] +- [Hazards to be aware of] + +## 4. Equipment/Materials Required + +| Item | Specification | +|------|---------------| +| | | +| | | + +## 5. Procedure + +### Step 1: [Title] +[Detailed instructions] + +### Step 2: [Title] +[Detailed instructions] + +### Step 3: [Title] +[Detailed instructions] + +## 6. Acceptance Criteria + +[Define what constitutes successful completion] + +## 7. Records + +| Record | Location | Retention | +|--------|----------|-----------| +| | | | + +## 8. References + +- [Related SOPs] +- [Specifications] +- [Standards] + +--- + +## Revision History + +| Rev | Date | Description | Author | +|-----|------|-------------|--------| +| 1.0 | [DATE] | Initial release | [AUTHOR] |