Histology-informed tiling of whole tissue sections improves the interpretability and predictability of cancer relapse and genetic alterations
Willem Bonnaffé, Yang Hu, Andrea Chatrian, Mengran Fan, Stefano Malacrino, Sandy Figiel, CRUK ICGC Prostate Group, Srinivasa R. Rao, Richard Colling, Richard J. Bryant, Freddie C. Hamdy, Dan J. Woodcock, Ian G. Mills, Clare Verrill, Jens Rittscher
组织病理学家通过评估组织学结构(如前列腺癌中的腺体)来建立癌症等级。 然而,数字病理学管道通常依赖于基于网格的平铺,而忽略了组织结构。 这引入了不相关的信息并限制了可解释性。 我们引入了组织学知识平铺(HIT),它使用语义分割从整个幻灯片图像(WSI)中提取腺体,作为多实例学习(MIL)和表型的生物有意义的输入补丁。 在ProMPT队列的137个样本中,HIT获得了0.83 + / - 0.17的腺体级骰子评分。 通过在ICGC-C和TCGA-PRAD队列中从760个WSI中提取380,000个腺体,HIT将MIL模型AUC提高了10%,用于检测与上皮-间充质过渡(EMT)和MYC相关的基因的拷贝数变异(CNV),并揭示了15个腺体簇,其中几个与癌症复发,致癌突变和高Gleason有关。 因此,HIT提高了MIL预测的准确性和可解释性,同时通过在特征提取过程中专注于具有生物学意义的结构来简化计算。
Histopathologists establish cancer grade by assessing histological structures, such as glands in prostate cancer. Yet, digital pathology pipelines often rely on grid-based tiling that ignores tissue architecture. This introduces irrelevant information and limits interpretability. We introduce histology-informed tiling (HIT), which uses semantic segmentation to extract glands from whole slide images (WSIs) as biologically meaningful input patches for multiple-instance learning (MIL) and phenotypi...