Breast Pathology

What it does

Breast Pathology reads a breast case the way it arrives at sign-out: the H&E slides of a core biopsy or excision, the ER, PR, HER2 and Ki-67 immunostains, and the sentinel or axillary lymph-node slides. Each slide is routed by its stain and marker, so one upload gives one case-level result.

On H&E the run classifies the lesion (benign, usual ductal hyperplasia, flat epithelial atypia, atypical ductal hyperplasia, DCIS, invasive carcinoma of no special type or invasive lobular carcinoma), scores the three Nottingham components and measures stromal TILs. On IHC it returns the HER2 score with membrane-staining percentages, ER and PR positivity with Allred and H-score, and the Ki-67 index. Node slides are screened for metastases, and the largest deposit sets the isolated-tumour-cell, micrometastasis or macrometastasis category.

Intended use

Decision support for the biomarker panel and the node screen, where agreement between readers is weakest: HER2 null versus ultralow versus 1+, ER-low results, and small deposits in a long series of node slides. Each score is reported with its antibody clone, and the cell overlay shows what was counted.

Who it is for

Breast and general surgical pathologists, residents, and labs that score biomarkers manually. Developers use the run to add structured biomarker and nodal results to a LIS or a tumour-board workflow.

Accepted input

• Diagnostic slides: H&E whole-slide images of a core biopsy or excision.
• Biomarker slides: ER, PR, HER2 and Ki-67 IHC slides of the same tumour; any subset can be sent.
• Nodes: H&E slides of sentinel or axillary lymph nodes, one or more per node.
• Formats: DICOM VL Whole Slide Microscopy Image or vendor files (SVS, NDPI, MRXS, iSyntax, SCN, BIF, CZI, OME-TIFF).

Requirements

Requirement	Why
Stain and marker per slide (and antibody clone for IHC)	Routes each slide to the right scoring and is reported with the score
Pixel spacing in µm/px	Deposit size in mm and mitotic counts per area need calibration
Part labels for node slides	Nodal results are reported per node

Optional context

Clinical history and prior treatment can be passed in clinical_context. Specimens after neoadjuvant therapy are not graded for residual cancer burden.

The result

One JSON result per case, with per-slide values and a case summary.

Section	Content
Histologic type	Lesion category from benign through atypia and DCIS to invasive NST or lobular carcinoma
Nottingham grade	Tubule formation, nuclear pleomorphism and mitotic count, combined into grade 1–3
ER and PR	% positive tumour nuclei, intensity distribution, Allred score, H-score and ER-low flag
HER2 score	0 (null or ultralow), 1+, 2+ or 3+ with % complete and incomplete membrane staining and a HER2-low flag
Ki-67 index	Global and hot-spot index with a positive and negative cell overlay
Stromal TILs	Stromal TILs percentage with the tumour and stroma map it was measured on
Lymph node metastases	Per node: metastasis detected, largest deposit size and ITC, micrometastasis or macrometastasis
Draft report	Opt-in (options.report): an English narrative that interprets the result for the reader (findings, impression, limitations); every number is checked against the findings

Standards

• Biomarkers: ASCO/CAP HER2 2023 including HER2-low reporting; ASCO/CAP ER/PR 2020 (ER-low 1–10 %); IKWG 2021 Ki-67 recommendations; International TILs Working Group 2014 method.
• Diagnosis and grade: WHO Classification of Breast Tumours, 5th edition; Nottingham (Elston–Ellis) grade.
• Nodes: AJCC 8th edition pN categories: isolated tumour cells ≤0.2 mm, micrometastasis >0.2–2 mm, macrometastasis >2 mm.
• Reporting and DICOM: CAP breast invasive carcinoma and DCIS protocols; scores in SR TID 1500, node masks as Segmentation, positive and negative cells as Microscopy Bulk Simple Annotations; FHIR R4 with one Observation per biomarker.