The first replication dataset was from the San Diego Sibling Pair investigation and genotyped on the Illumina HumanCNV370-duo array (Illumina, San Diego, CA, USA). This study was approved by the Human Subjects Protection Committee of the University of California, San Diego. The same quality review and imputation used in COGA were performed. This dataset included both unrelated and related individuals. Empirical kinships were estimated from genomewide genotype data using the vcf2kinship tool as implemented in RVTESTS and adjusted in mixed models using RVTESTS (Zhan et al., 2016). The majority of the dataset had European ancestry; therefore, only EA samples was used (SD-EA, N=206, 68 AD cases and 138 controls). Only sex was available and included as a covariate.
