Bioscience massarray system

In the pilot screening, 84 variants were genotyped using Luminex MagPlex^®-TAG^™ bead array (Luminex, Austin, TX) and/or the Agena Bioscience^™ MassARRAY system (Agena Bioscience^™, San Diego, CA) (Tables S3–S5). One variant, MAK p.K433fs, was genotyped by PCR followed by gel electrophoresis. A minimum of 1494 DNA samples were genotyped.
Subsequently, an expanded AJ carrier screening clinical test was developed based on Agena Bioscience^™ technology and included assessment of 67 variants causative of 18 conditions (Table S6). A minimum of 1390 individuals and 6813 individuals from a general population sample that excluded individuals with 100% self-reported AJ ancestry were tested (Table 1).

We reviewed a list of 13 single nucleotide polymorphisms within 8 genes that were previously associated with measures of PPI and/or related neurophysiological or neurocognitive measures in mixed samples of SZ patients and HS (Greenwood et al. 2011 (link), 2013 (link)); of these, 4 SNPs within 4 genes yielded sufficient minor allele frequencies to permit meaningful analyses in the present sample: rs158337 (GRID2), rs40184 (SLC6A3), rs1394785 (ERBB4), and rs1337697 (GRIN3A). Genotyping of SNPs was performed using iPLEX Gold chemistry on Agena Bioscience MassARRAY^® System (Agena Bioscience, San Diego, CA) at the Roswell Park Cancer Institute Genomics Shared Resource facility. Two multiplex assays were designed using Assay Design Suite v2.0 (Agena) software and genotyping was performed as per manufacturer protocol. Briefly, a locus-specific PCR reaction was carried out, followed by an allele-specific primer extension reaction (iPLEX assay primers in Supplemental Methods). The genotypes for each SNP were obtained after visual inspection and corrections of the spectra using MassARRAY Typer Analyzer v4 (Agena).