Genomics/NGS¶
UC-ONC-040: Parse NGS Reports¶
Purpose: Extract data from NGS PDF or JSON.
| Property | Value |
|---|---|
| Actor | NGS Parser Service |
| Trigger | NGS report received |
| Priority | P1 |
Main Success Scenario:
1. Parse PDF/JSON NGS report
2. Extract sample ID, test type, lab
3. Prepare variant list for extraction
Acceptance Criteria: 1. [ ] Supports major NGS vendors 2. [ ] Handles PDF and JSON formats 3. [ ] Validates report integrity
UC-ONC-041: Extract Variants¶
Purpose: Extract genetic variants (VAF, mutation type).
| Property | Value |
|---|---|
| Actor | Variant Extraction Service |
| Trigger | NGS report parsed |
| Priority | P1 |
Main Success Scenario:
1. Extract variant list (gene, mutation, VAF)
2. Classify as SNV, Indel, CNV, Fusion
3. Store in genomics table
Acceptance Criteria: 1. [ ] VAF % captured 2. [ ] Mutation type classified 3. [ ] HGVS nomenclature supported
UC-ONC-042: Map to Actionable Therapies¶
Purpose: Link variants to FDA-approved or investigational treatments.
| Property | Value |
|---|---|
| Actor | Variant-Therapy Mapper |
| Trigger | Variants extracted |
| Priority | P2 |
Main Success Scenario:
1. Query variant-therapy database (e.g., OncoKB)
2. Identify actionable mutations
3. Suggest targeted therapies
4. Display in molecular tumor board summary
Acceptance Criteria: 1. [ ] FDA-approved therapies prioritized 2. [ ] Clinical trial matches suggested 3. [ ] Evidence levels annotated
UC-ONC-043: Generate Genomics Summary¶
Purpose: Create concise summary for tumor board.
| Property | Value |
|---|---|
| Actor | Genomics Summarizer |
| Trigger | NGS data complete |
| Priority | P1 |
Main Success Scenario:
1. Compile key mutations
2. Highlight actionable findings
3. Generate 1-page summary PDF
4. Attach to tumor board packet
Acceptance Criteria: 1. [ ] Summary < 1 page 2. [ ] Highlights actionable mutations 3. [ ] Exportable format
UC-ONC-044: Detect Germline vs Somatic¶
Purpose: Classify variants as germline or somatic.
| Property | Value |
|---|---|
| Actor | Germline Classification Service |
| Trigger | Variant identified |
| Priority | P2 |
Main Success Scenario:
1. Check VAF (germline typically ~50% or 100%)
2. Cross-reference with germline databases
3. Flag for genetic counseling if germline
Acceptance Criteria: 1. [ ] Germline vs somatic classification 2. [ ] Flags hereditary cancer syndromes 3. [ ] Genetic counseling referral triggered