Standardized Pipeline for Metabolism and Cognition in GO-DS21 Mouse Model: Investigating Down Syndrome Comorbidities

Down syndrome (DS) is the most prevalent form of intellectual disability (ID) globally, with an incidence rate of approximately 1 in 1000 births, affecting over 5 million individuals worldwide. DS is characterized by a genetic profile that predisposes individuals to a range of medical and cognitive conditions, including ID and obesity, which place considerable demands on healthcare systems and families alike. Mouse models carrying DS-related genetic mutations offer valuable tools for investigating the pathophysiological mechanisms underlying DS-associated behavioral and metabolic alterations. These models also allow for an evaluation of the impact of both intrinsic and extrinsic environmental factors, aiding in the development of biomarkers and personalized therapies for individuals with DS. In this article, we establish a detailed and comprehensive phenotyping pipeline designed to incorporate high-resolution assessments of cognitive, metabolic, and behavioral variables. Using advanced phenotyping techniques alongside standardized protocols in DS mouse models, this approach systematically captures the variability of DS-associated traits. Our phenotyping pipeline aims to cover the pathways leading to cognitive dysfunction and metabolic imbalances in DS, paving the way for targeted intervention strategies. © 2026 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Diet challenge (chow diet vs. high-fat diet) Basic Protocol 2: Fecal or saliva microbiota analysis Basic Protocol 3: Body composition assessment by quantitative nuclear magnetic resonance Basic Protocol 4: Indirect calorimetry Basic Protocol 5: Blood collection and processing Basic Protocol 6: Oral glucose tolerance test Basic Protocol 7: Long-term monitoring of social groups Alternate Protocol 1: Analysis of short-term dyadic interactions between unfamiliar mice of the same genotype Alternate Protocol 2: Analysis of short-term dyadic interactions of mice from the tested strain with an unfamiliar C57BL/6J mouse Basic Protocol 8: Intraperitoneal insulin sensitivity test Basic Protocol 9: Y-maze spontaneous alternation test Alternate Protocol 3: Y-maze spontaneous alternation test version 2 Basic Protocol 10: Marble-burying analysis Alternate Protocol 4: Marble-burying analysis version 2 Basic Protocol 11: Object location memory/novel object recognition Alternate Protocol 5: Novel object recognition in the Y-maze apparatus Basic Protocol 12: Nest-building test Basic Protocol 13: Sucrose preference analysis Basic Protocol 14: Histopathology © 2026 by John Wiley & Sons, Inc.