Rare-variant association analysis: study designs and statistical tests.

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PERCH: a unified framework for disease gene prioritization (2017, background): “Alternatively, aggregate analysis of multiple variants within a genomic region or gene, the rare-variant association test, is more powerful and has less multiple testing penalties [Li and Leal, 2008; Morris and Zeggini, 2010; Lee et al., 2014].”
GENETICS AND PATHOGENESIS OF INFLAMMATORY BOWEL DISEASE (2016, background): “Common human genetic polymorphisms, as the term implies, occur in a given population with a minimum frequency of 5% (13).”
Accurate proteome-wide missense variant effect prediction with AlphaMissense (2023, background): “This resource could also inform studies of complex trait genetics ( 50 , 51 ).”
Dissecting the genetics of complex traits using summary association statistics (2016, methodology): “…done either using burden tests , which assume that all rare variants in a candidate gene have the same direction of effect, or using overdispersion tests , which assume that rare variants in a candidate gene can impact a complex trait in either direction; hybrid omnibus tests are also possible 35 .”