Abstract
Abstract Background Alzheimer disease (AD) is the fourth leading cause of death in Puerto Rico. The Puerto Rican (PR) population has a high proportion of older adults (18%, over > 65), with 12.5% of them suffering from ADThese statistics highlight the need to investigate the genetic risk factors underlying AD in the PR population, as it could lead to the development of targeted treatments and therapies. Moreover, the ancestrally admixed makeup of the PR population provides an opportunity to assess the role of the European (∼67%), African (∼20%) and Amerindian (∼13%) ancestry in AD risk. We performed genome wide association analysis (GWAS) using whole genome sequence data to identify genetic risk/protective factors associated with AD in the PR population. Method The PR dataset includes WGS and phenotype data from 640 individuals, comprising 335 AD and 305 cognitively unimpaired (CU) controls. To account for the population substructure, we calculated the global ancestry (principal components) using EIGENSTRAT. We performed GWAS analyses with a generalized linear mixed‐model using the SAIGE software. The model included genotype, sex, age, and principal components (population substructure) as fixed effects and genetic relationship matrix as a random effect. The genetic relationship matrix was calculated based on genomic data and accounted for the relatedness among the individuals in the dataset. Result We identified four suggestive significant loci (P<1×10 −6 ) associated with the risk of AD in PRs: NACC2 (pv = 4.8×10 −7 ) on chromosome 9, SCN8A (pv = 9.3×10 −7 ) on chromosome 12, FOXK2 (pv = 9.9×10 −7 ) on chromosome 17, and APOEe4 (pv = 6.8×10 −8 ) on chromosome 19. Eight additional AD loci with the same lead marker from European GWAS study (Bellenquez et al.) showed nominal significance: FERMT2 (pv = 6.2×10 −3 ), TREM2 (pv = 8.0×10 −3 ), CLU (pv = 1.8×10 −2 ), RASGEF1C (pv = 2.4×10 −2 ), ADAM17 (pv = 3.5×10 −2 ), DOC2A (pv = 4.3×10 −2 ), GRN (pv = 4.4×10 −2 ) and SORL1 (pv = 5.1×10 −2 ). Conclusion This study identified three suggestive novel significant loci (NACC2, SCN8A, and FOXK2) associated with AD risk in PRs. In addition, GWAS study on PRs with a high proportion of European ancestry was able to replicate nine AD loci previously identified in European studies. These findings provide new insights into the genetic architecture of AD in the PR population.