Pan-cancer computational histopathology reveals mutations, tumor composition and prognosis

We use deep transfer learning to quantify histopathological patterns across 17,355 hematoxylin and eosin-stained histopathology slide images from 28 cancer types and correlate these with matched genomic, transcriptomic and survival data. This approach accurately classifies cancer types and provides spatially resolved tumor and normal tissue distinction. Automatically learned computational histopathological features correlate with a large range of recurrent genetic aberrations across cancer types. This includes whole-genome duplications, which display universal features across cancer types, individual chromosomal aneuploidies, focal amplifications and deletions, as well as driver gene mutations. There are widespread associations between bulk gene expression levels and histopathology, which reflect tumor composition and enable the localization of transcriptomically defined tumor-infiltrating lymphocytes. Computational histopathology augments prognosis based on histopathological subtyping and grading, and highlights prognostically relevant areas such as necrosis or lymphocytic aggregates. These findings show the remarkable potential of computer vision in characterizing the molecular basis of tumor histopathology.