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Genome-wide association studies (GWAS) have identified thousands of genetic variants associated with complex human traits, but only a fraction of variants identified in discovery studies achieve significance in replication studies. Replication in genome-wide association studies has been well-studied in the context of Winner’s Curse, which is the inflation of effect size estimates for significant variants due to statistical chance. However, Winner’s Curse is often not sufficient to explain lack of replication. Another reason why studies fail to replicate is that there are fundamental differences between the discovery and replication studies. A confounding factor can create the appearance of a significant finding while actually being an artifact that will not replicate in future studies. We propose a statistical framework that utilizes genome-wide association studies and replication studies to jointly model Winner’s Curse and study-specific heterogeneity due to confounding factors. We apply this framework to 100 genome-wide association studies from the Human Genome-Wide Association Studies Catalog and observe that there is a large range in the level of estimated confounding. We demonstrate how this framework can be used to distinguish when studies fail to replicate due to statistical noise and when they fail due to confounding.

 

Sustainable provision of food, energy and clean water requires understanding of the interdependencies among systems as well as the motivations and incentives of farmers and rural policy makers. Agriculture lies at the heart of interactions among food, energy and water systems. It is an increasingly energy intensive enterprise, but is also a growing source of energy. Agriculture places large demands on water supplies while poor practices can degrade water quality. Each of these interactions creates opportunities for modeling driven by sensor-based and qualitative data collection to improve the effectiveness of system operation and control in the short term as well as investments and planning for the long term. The large volume and complexity of the data collected creates challenges for decision support and stakeholder communication. The DataFEWSion National Research Traineeship program aims to build a community of researchers that explores, develops and implements effective data-driven decision-making to efficiently produce food, transform primary energy sources into energy carriers, and enhance water quality. The initial cohort includes PhD students in agricultural and biosystems, chemical, and industrial engineering as well as statistics and crop production and physiology. The project aims to prepare trainees for multiple career paths such as research scientist, bioeconomy entrepreneur, agribusiness leader, policy maker, agriculture analytics specialist, and professor. The traineeship has four key components. First, trainees will complete a new graduate certificate to build competencies in fundamental understanding of interactions among food production, water quality and bioenergy; data acquisition, visualization, and analytics; complex systems modeling for decision support; and the economics, policy and sociology of the FEW nexus. Second, they will conduct interdisciplinary research on (a) technologies and practices to increase agriculture’s contributions to energy supply while reducing its negative impacts on water quality and human health; (b) data science to increase crop productivity within the constraints of sustainable intensification; or (c) decision sciences to manage tradeoffs and promote best practices among diverse stakeholders. Third, they will participate in a new graduate learning community to consist of a two-year series of workshops that focus in alternate years on the context of the Midwest agricultural FEW nexus and professional development; and fourth, they will have small-group experiences to promote collaboration and peer review. Each trainee will create and curate a portfolio that combines artifacts from coursework and research with reflections on the broader impacts of their work. Trainee recruitment emphasizes women and underrepresented groups.