Learning to predict RNA sequence expressions from whole slide images with applications for search and classification

TCGA kidney dataset

The data used in this study was obtained from TCGA (https://portal.gdc.cancer.gov/). Only cases that have WSI as well as RNAseq profile were considered. We selected H&E-stained formalin-fixed, paraffin-embedded (FFPE) diagnostic slides. The retrieved cases included three subtypes, clear cell carcinoma, ICD-O 8310/3, (ccRCC), chromophobe type – renal cell carcinoma, ICD-O 8317/3, (crRCC), and papillary carcinoma, ICD-O 8260/3, (pRCC). For transcriptomic data, we utilized Fragments Per Kilobase of transcript per Million mapped reads upper quartile (FPKM-UQ) files. The…