pathology-report-checker

Pathology Report Compliance Checker

Analyze surgical pathology cancer reports against CAP (College of American Pathologists), ICCR (International Collaboration on Cancer Reporting), and AAPA (American Association of Pathology Assistants) guidelines.

Performance Notes

CRITICAL: Always read the relevant reference file BEFORE producing analysis or templates. The skill's value comes from grounded clinical guidelines, not memorized knowledge.

• Take time to load the correct diagnosis + macroscopy reference files
• Quality of structured output matters more than speed
• Do not skip cross-validation (pT vs size, pN vs nodes, margins vs R)
• Match the report's language (English/Turkish) in the output

Trigger Phrases

Action	English	Turkish
Compliance Check	"Check this report for CAP compliance"	"Bu raporu CAP uyumluluğu için kontrol et"
Synoptic Template	"Generate breast synoptic template"	"Meme sinoptik şablonu oluştur"
Tumor Board Summary	"Generate tumor board summary"	"Tümör kurulu özeti oluştur"
Free-text → Synoptic	"Convert to synoptic format"	"Sinoptik formata dönüştür"
Auto-fill	"Suggest pTNM staging"	"pTNM evrelemesi öner"
Amendment	"Generate amendment for this"	"Düzeltme oluştur"
SNOMED Coding	"What's the SNOMED code for..."	"... için SNOMED kodu nedir?"
TNM Calculator	"Calculate stage for pT2 N1 M0"	"pT2 N1 M0 için evreyi hesapla"

Mode Selection

Determine the task before reading any references:

• Compliance checking → follow Compliance Check Workflow below
• Template generation → follow Template Generation Workflow below
• Tumor board summary → follow Summary Generation Workflow below
• Staging calculation only → read references/staging/tnm_stage_calculator.md
• SNOMED/ICD-O-3 codes → read references/coding/snomed_ct_codes.md
• Free-text conversion → read references/converters/freetext_to_synoptic.md
• Auto-fill suggestions → read references/autofill/autofill_suggestions.md
• Amendment drafting → read references/amendments/amendment_generator.md

Supported Report Types

Type	CAP Protocol	ICCR Dataset
Breast invasive carcinoma	Breast.Invasive	Invasive Carcinoma of the Breast
Colorectal primary resection	ColoRectal	Colorectal Cancer
Exocrine pancreas carcinoma	Panc.Exo	Carcinoma of the Exocrine Pancreas
Gastric carcinoma	Stomach	Gastric Carcinoma

Reference Files

Diagnosis (CAP/ICCR required elements)

Tumor	File
Breast	references/diagnosis/breast_invasive_carcinoma.md
Colorectal	references/diagnosis/colorectal_resection.md
Pancreas	references/diagnosis/exocrine_pancreas.md
Gastric	references/diagnosis/gastric_carcinoma.md

Macroscopy (AAPA-integrated)

Tumor	File
Common	references/macroscopy/MACROSCOPY_COMMON.md
Breast	references/macroscopy/breast_macroscopy.md
Colorectal	references/macroscopy/colorectal_macroscopy.md
Pancreas	references/macroscopy/pancreas_macroscopy.md
Gastric	references/macroscopy/gastric_macroscopy.md

Other references

Feature	File
TNM Staging	references/staging/tnm_stage_calculator.md
Synoptic Templates (EN)	references/templates/synoptic_templates.md
Synoptic Templates (TR)	references/templates/synoptic_templates_tr.md
SNOMED CT / ICD-O-3	references/coding/snomed_ct_codes.md
Tumor Board Summary	references/summaries/tumor_board_summary.md
Free-text Converter	references/converters/freetext_to_synoptic.md
Auto-fill Suggestions	references/autofill/autofill_suggestions.md
Amendment Generator	references/amendments/amendment_generator.md
Biomarker Index	references/biomarkers/BIOMARKERS_INDEX.md

Quick Search Patterns

For large reference files, use grep to find specific content quickly instead of loading the entire file.

Find tumor-type template (saves ~3,300 tokens vs full file):

grep -A 80 "## Breast Invasive" references/templates/synoptic_templates.md
grep -A 80 "## Colorectal" references/templates/synoptic_templates.md
grep -A 80 "## Pancreas" references/templates/synoptic_templates.md
grep -A 80 "## Gastric" references/templates/synoptic_templates.md

Find specific staging table:

grep -A 20 "Breast Cancer Stage" references/staging/tnm_stage_calculator.md
grep -A 20 "Colorectal Stage" references/staging/tnm_stage_calculator.md
grep -A 20 "Pancreas Stage" references/staging/tnm_stage_calculator.md
grep -A 20 "Gastric Stage" references/staging/tnm_stage_calculator.md

Find SNOMED / ICD-O-3 code:

grep -i "ductal carcinoma" references/coding/snomed_ct_codes.md
grep -i "adenocarcinoma" references/coding/snomed_ct_codes.md

Find amendment template:

grep -A 15 "Addendum Template" references/amendments/amendment_generator.md
grep -A 15 "Correction Template" references/amendments/amendment_generator.md

Workflows

Compliance Check Workflow

1. Determine report type: From report content identify organ, specimen type, tumor type, and language (English/Turkish).
2. Load reference files: Read the matching diagnosis and macroscopy files from references/.
3. Extract elements: Parse the report using the EN/TR terminology equivalents listed inside each reference file.
4. Analyze:
   • 4a. Check missing/empty elements by severity (CRITICAL / MAJOR / MINOR).
   • 4b. Cross-validate: pT vs tumor size, pN vs positive node count, margins vs R classification, node count vs adequacy threshold (12 colorectal, 15 breast, etc.).
   • 4c. Compute quality metrics: Completeness (40%) + Clarity (20%) + Consistency (40%).
   • 4d. Check macroscopy/gross description for completeness and gross-vs-microscopic concordance.
5. Generate output: Produce a QA report with compliance score, status, listed gaps grouped by severity, and recommendations.
6. Verify staging: Cross-check pTNM categories against the AJCC 8th edition stage group using references/staging/tnm_stage_calculator.md.

Template Generation Workflow

1. Identify tumor type and specimen type from the request.
2. Use grep to load only the relevant section of references/templates/synoptic_templates.md (or synoptic_templates_tr.md for Turkish).
3. Optionally pre-fill with user-provided values (e.g., "2.3 cm Grade 2 IDC", "pT2 N1a").
4. Return a formatted template containing every required CAP element with placeholders for the rest.

Summary Generation Workflow

1. Extract key findings: patient age/sex, diagnosis, procedure, pT/pN/pM, stage group, margins, node ratio, biomarkers.
2. Read format examples from references/summaries/tumor_board_summary.md.
3. Produce a 3-5 line MDT-ready summary in the report's language.

Severity Levels

Level	Elements	Score Impact
CRITICAL	pT, pN, margins, grade, receptors	-15 each
MAJOR	LVI, PNI, tumor size, node counts	-5 each
MINOR	Focality, gross details	-2 each

Score formula: 100 - (Critical × 15) - (Major × 5) - (Minor × 2)

Score	Status
90-100	COMPLIANT
70-89	INCOMPLETE - MINOR
50-69	INCOMPLETE - MAJOR
<50	INCOMPLETE - CRITICAL

Supported Input Formats

Format	Extensions	Use Case
Plain Text	.txt, .md	Interactive CLI, direct paste
PDF	.pdf	Scanned or digital reports
Word	.docx	Office documents
Excel/CSV	.xlsx, .xls, .csv	Batch processing, LIS exports
Images	.jpg, .png, .tiff	Scanned paper reports (Claude Vision)

Excel batch format

Expected columns:

• report_text (required): Full pathology report text
• patient_id (optional): Case identifier
• tumor_type (optional): breast, colorectal, gastric, or pancreas (auto-detected if absent)

Example Outputs

Compliance check (breast, English)

COMPLIANCE ANALYSIS
Tumor: Breast invasive carcinoma
Protocol: CAP Breast.Invasive

COMPLIANCE SCORE: 82/100
STATUS: INCOMPLETE - MINOR

MISSING ELEMENTS (3):
CRITICAL (1):
  - ER/PR/HER2 receptor studies (-15)
MAJOR (2):
  - Lymphovascular invasion status (-5)
  - Perineural invasion status (-5)

CROSS-VALIDATION:
- pT2 consistent with 2.3 cm tumor size (AJCC 8th)
- pN1a consistent with 2 positive nodes
- Margins negative (5 mm) -> R0 correct

RECOMMENDATIONS:
1. Add IHC results for ER, PR, HER2
2. Document LVI presence/absence
3. Document PNI presence/absence

Tumor board summary

58F with invasive ductal carcinoma of the left breast.
Lumpectomy: 2.3 cm IDC, Grade 2, pT2 N1a M0 (Stage IIB).
Margins negative. LVI present. Nodes 2/15 positive.
ER 95% / PR 80% / HER2 negative / Ki-67 25%.

Important Notes

1. Always read the matching reference file before analyzing — do not rely on memory.
2. Cross-validate pT/pN/stage against size, nodes, and margins for every report.
3. Check macroscopy for gross-vs-microscopic discordance (>20% size mismatch is a flag).
4. Match the report language: English in → English out; Turkish in → Turkish out.
5. Severity matters: prioritize CRITICAL gaps in the summary; MINOR gaps go at the end.
6. This skill assists with QA only. Do not replace clinical judgment; pathologist sign-out is final.

When Not To Use

• Non-cancer pathology (inflammatory, infectious, autoimmune)
• Cytology specimens (FNA, brushings, fluids)
• Tumor types other than breast invasive, colorectal, exocrine pancreas, or gastric
• Hematopathology, dermatopathology, neuropathology
• Frozen-section/intra-operative consultations