Variants in the 3’ untranslated regions (3’UTR) may act as cis-regulators to modulate transcript levels. A very sensitive way to detect the effects of a variant in the 3’UTR is to examine differential expression of each allele of a single nucleotide polymorphism (SNP) inserted into a reporter gene (allele-biased expression). We recently developed a high-throughput assay, PASSPORT-seq (parallel assessment of polymorphisms in miRNA target-sites by sequencing) (Ipe et al., 2018, Rao et al., 2019), that can simultaneously and efficiently detect whether hundreds of SNPs are cis-regulators. This assay combines pooled synthesis of oligonucleotides, bulk cloning into a reporter vector, transfection of the pool into mammalian cells, and next generation sequencing (NGS) to measure differential expression. In this study, we use this assay to test the potential effect of SNPs in loci associated with AD and related phenotypes (with meta-analysis p values ≤ 0.001; (Lai et al., 2019a, Lai et al., 2019b)).
