HER2 in Gastric / GEJ Carcinoma
HER2 testing performance, heterogeneity, and reproducibility in gastric and gastroesophageal cancers
What this project is
HER2 scoring in gastric and gastroesophageal carcinoma is known to be harder than in breast — there is more intratumoral heterogeneity, more variation in fixation, and the scoring rubric is different. This project characterizes HER2 interpretation at Memorial across these dimensions.
Objectives
- Quantify inter-observer agreement on HER2 IHC scoring among department pathologists.
- Map the intratumoral heterogeneity of HER2 expression using WSI-level annotations.
- Describe the correlation (and discordance) between IHC and ISH.
- Identify the subset of cases where biopsy-vs-resection scoring diverges.
Status
| Stream | Status |
|---|---|
| Cohort identification | Complete |
| IHC / ISH database | Curated |
| Agreement study | Pilot scoring round complete |
| Heterogeneity annotation (QuPath) | Active |
| Manuscript | Outline drafted |
Data
- Gastric / GEJ resections and biopsies with HER2 IHC and reflex ISH.
- De-identified scanned slides on the Memorial share.
- Annotations in QuPath, exported as GeoJSON per the group SOP.
Tools and repositories
HER2-intratumoral-heterogeneity— primary repo.- Annotation SOP: see Home → Protocols and SOPs.
- Agreement statistics:
meddecide(kappa, weighted kappa, ICC).
How to contribute
- Attend an annotation calibration session.
- Score the pilot batch and compare to the reference scorer.
- Contribute GeoJSON annotations following the naming convention in the repo README.
Pitfalls
- HER2 scoring differs between biopsy (focal positivity accepted) and resection rules — never aggregate them without the specimen-type column.
- Slide-level tumor percentage matters for downstream heterogeneity metrics. Don’t skip the tumor-area annotation even when the HER2 score alone is the question.