Genetic Variant Burden Rises with BMI: Insights from Rare and Low-Frequency Variants in Obesity

Abstract

Adult obesity, including morbid obesity, has reached epidemic proportions worldwide. Yet, the current genetic models based on BMI-associated common variants identified through genome-wide association studies (GWAS) explain only a modest fraction of BMI variability. Contribution of rare and low-frequency variants to polygenic obesity remains incompletely defined. Leveraging whole-exome sequences of 1138 adults spanning normal-weight, overweight, obese and morbidly obese (MO) categories from Kuwait and Qatar, we catalogued cohort-specific rare and low-frequency deleterious variants differentiating MO individuals from normal-weight individuals. Cross-cohort comparisons identified 147 risk variants seen in [≥]2 MO individuals from one cohort and in [≥]1 MO individual from the other; among these, 27 variants occurred in [≥]2 MO individuals from each cohort. The risk genes were enriched in obesity-related pathways and tissues, with most harbouring GWAS variants associated primarily with obesity traits followed by metabolic and brain-related traits. Duodenal tissue expression data exhibited significant dysregulation of key risk genes in MO individuals. Variants from the 147-list and 27-list occurred in 87% and 49% of MO individuals, respectively; MO-variant burden correlated positively with BMI (r=0.30 and r=0.31, respectively) across the overweight-obese-MO categories. Combinations of a finite set of low-frequency coding variants substantially shape the continuum of polygenic obesity.