136 lines
3.5 KiB
Markdown
136 lines
3.5 KiB
Markdown
|
# 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] |
|