SNPweights software17 was used to assign ancestry, applied to uncleaned data because the use of Hardy–Weinberg equilibrium filters can remove ancestry informative SNPs in samples with mixed ancestry background, and is therefore not compatible with this protocol. Ancestry assignment is separate from controlling for ancestry analytically, described below. Briefly, SNPweights uses external genomic reference panels to derive ancestry informative weights for individual SNPs. We used the four-group, continental ancestry panel to quantify individual participants’ proportions of: African (YRI), European (CEU), Asian (ASI) and Native American (NAT)17 ancestry. The specific cutoffs implemented in this report for assigning ancestry—which were selected after inspection of principal components (PC) plots — and adjusting cutoffs—were as follows: European American (EA) was defined as having ⩾90% European ancestry. African American (AA) was defined as ⩾90% for the combination of African and European ancestry, and also <3% Asian and Native American ancestry. Individuals who self-identify as Latino or Hispanic (LA) in the United States may have predominately European ancestry and may have relatively recent admixture with Native American ancestry or both Native American and African ancestry. In
