genetics-genomics/Work-Instructions/WI-001-Template.md

Work Instruction: [Title]

Document ID	WI-001
Title	[Title]
Revision	1.0
Effective Date	[DATE]
Author	[AUTHOR]
Approved By	[APPROVER]
Department	Genetics & Genomics Laboratory

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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]

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Revision History

Rev	Date	Description	Author
1.0	[DATE]	Initial release	[AUTHOR]