Abstract: The disclosure provides methods for identifying genomic loci that are differentially methylated in neoplastic cancers, e.g., esophageal cancers. Identification of methylated genomic loci, and optionally in combination with the identification of somatic mutations in TP53, has numerous uses, including for example, to characterize disease risk, to predict responsiveness to therapy, to non-invasively diagnose subjects and to treat subjects determined to have gastrointestinal neoplasias.

Abstract: Embodiments discussed herein facilitate determination of cancer stages based at least in part on shape, size, and/or texture features of cancer nuclei. One example embodiment is a method, comprising: accessing at least a portion of a digital whole slide image (WSI) comprising a tumor; segmenting (e.g., via a first deep learning model) the tumor on the at least the portion of the digital WSI; segmenting (e.g., via a second deep learning model) cancer nuclei in the segmented tumor; extracting one or more features from the segmented cancer nuclei; providing the one or more features extracted from the segmented cancer nuclei to a trained machine learning model; and receiving, from the machine learning model, an indication of a cancer stage of the tumor.

Abstract: The disclosure provides methods for identifying genomic loci that are differentially/methylated in neoplastic cancers, e.g., esophageal cancers. Identification of methylated genomic loci, and optionally in combination with the identification of somatic mutations in TP53, has numerous uses, including for example, to characterize disease risk, to predict responsiveness to therapy, to non-invasively diagnose subjects and to treat subjects determined to have gastrointestinal neoplasias.

Abstract: The disclosure provides methods for identifying genomic loci that are differentially methylated in colorectal neoplasias. Identification of methylated genomic loci has numerous uses, including for example, to characterize disease risk, to predict responsiveness to therapy, to non-invasively diagnose subjects and to treat subjects determined to have colorectal neoplasias.