We also performed gene-level association tests using collapsing analyses. In this approach, the proportion of cases with a qualifying variant was compared with the proportion of controls with a qualifying variant in each gene16–22. We used 12 different sets of qualifying variant filters (models) to test the association between 18,762 genes and 18,780 phenotypes (Methods; Extended Data Table 1), equating to 4.2 billion tests. The models included ten dominant models, one recessive model and one synonymous variant model that served as an empirical negative control (Methods).
