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Annotation of digital slides was performed, circling areas of invasive carcinoma (Region of Interests, ROIs). The manual annotation of ROIs significantly enhances the prediction accuracy and reduces the need for extensively large datasets. Regions of necrosis, in situ carcinoma or benign stroma and epithelium were excluded. The images were annotated with ROIs associated to HER2+/- tumor area (TA) by a senior breast pathologist. The annotations were marked tumor boundaries and annotated by Aperio ImageScope software. The annotations were exported from the Aperio software in The Extensible Markup Language (XML) format, including X and Y coordinates corresponding to the annotated regions. We used these coordinates for each slide image to tile these regions separately from the rest of the image, labeled as HER2+ or HER2- class.
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Data set descriptions
Yale HER2 cohort:
This dataset presents 192 cases of HER2 positive and negative invasive breast carcinomas H&E slides from the Yale Pathology electronic database. All tissues and data were retrieved under permission from the Yale Human Investigation Committee protocol #9505008219 to DLR. HER2 positive cases defined as those with 3+ score by immunohistochemistry (IHC) or an equivocal (2+) IHC score with subsequent amplification by fluorescence in situ hybridization (FISH) as defined by American Society of Clinical Oncology/College of American Pathologists (ASCO/CAP) clinical practice guidelines. H&E slides generated at Yale School of Medicine include 93 HER2+ and 99 HER2- slides. The slides were scanned at Yale Pathology Tissue Services and underwent a slide quality check before they went into the scanner. The tissue samples were scanned using Vectra Polaris by Perkin-Elmer scanner using bright field whole slides scanning at 20× magnification at Brady Memorial Laboratory Rimm’s lab.
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