The basic idea behind the PASSPORT assay is to determine whether the alternate alleles at a SNP are differentially expressed as RNA. This is done by transfecting a pool of expression vectors containing both alleles at all chosen SNPs, and examining biases in allelic expression by comparing at each SNP the ratio of alleles in the RNA to their ratio in the expression vectors transfected into the cell. The PASSPORT-seq assay was conducted as previously described in detail (Rao 2019). Briefly, the assay involves (a) synthesis of a pool of oligonucleotides that includes both alleles of 296 SNPs, each flanked by 25 nt of their genomic sequence (Oligomix®, LC Sciences, Houston, TX) (Supplementary Table S2), (b) cloning them in bulk into reporter plasmid pIS-0 (12178, Addgene, Cambridge, MA) and preparing DNA, (c) transient transfection of the pooled DNA into cells, (d) extraction and purification of DNA and RNA from the cells, and (e) quantitation of the relative amounts of RNA and DNA for each oligonucleotide by next-generation sequencing. We tested expression in two neuroblastoma cell lines, SH-SY5Y (CRl-2266, ATCC, Manassas,
