Pathway polygenic risk scores (pPRS) for the analysis of gene-environment interaction.

A polygenic risk score (PRS) is used to quantify the combined disease risk of many genetic variants. For complex human traits there is interest in determining whether the PRS modifies, i.e.

A prediction model for metachronous colorectal cancer: development and validation.

Background: Being able to estimate a colorectal cancer case's risk of metachronous colorectal cancer could enable risk-appropriate surveillance. The aim was to develop a risk prediction model to estimate individual 10-year risk of metachronous colorectal cancer following a colorectal cancer diagnosis.

Methods: A cohort of population-based colorectal cancer cases were recruited soon after their diagnosis between 1997 and 2012 from America, Canada, and Australia.

Gastric Polyposis and Cancer in Western Patients With Familial Adenomatous Polyposis: Epidemiology, Detection, and Management.

Patients with familial adenomatous polyposis (FAP) are at increased risk of developing cancer, with the most common sites being colorectal, duodenal/ampullary and thyroid. In the last decade, an alarming increase in gastric cancer has been reported in the Western FAP population. These cancers are often diagnosed at an advanced stage with poor prognosis, even in patients undergoing regular upper endoscopic surveillance.

Deep Gaussian process with uncertainty estimation for microsatellite instability and immunotherapy response prediction from histology.

Determining tumor microsatellite status has significant clinical value because tumors that are microsatellite instability-high (MSI-H) or mismatch repair deficient (dMMR) respond well to immune checkpoint inhibitors (ICIs) and oftentimes not to chemotherapeutics. We propose MSI-SEER, a deep Gaussian process-based Bayesian model that analyzes H&E whole-slide images in weakly-supervised-learning to predict microsatellite status in gastric and colorectal cancers. We performed extensive validation using multiple large datasets comprised of patients from diverse racial backgrounds.