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Chunk #6 — Materials and methods — SNP genotyping

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Association between polymorphisms in catechol-O-methyltransferase (COMT) and cocaine-induced paranoia in European-American and African-American populations.
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Most of the family DNA samples were obtained from immortalized cell lines, but some samples were directly extracted from blood or saliva. A total of 17 SNPs across the COMT gene were genotyped in all samples in the family-based study (Table 2). Locations of all SNPs are presented in Figure 1. Fifteen of these SNPs (all except rs737865 and rs165599) were genotyped in the set of unrelated individuals. In the samples obtained from families, we genotyped 3 SNPs, rs737865, rs4680 and rs165599, by TaqMan 5′ nuclease assay available through Applied-Biosystem's Assay-On-Demand service (Applied Biosystems, Foster City, CA). PCR amplifications were conducted using 2 ng of DNA, 1× TaqMan universal PCR master mix (Applied Biosystems, Foster city, CA), and 0.5× SNP genotyping assay mix (Applied Biosystems, Foster city, CA). PCR conditions were as follows: denaturation step of 95°C for 10 min, followed by 65 cycles of at 95°C for 15 sec and 60°C for 1 min. Amplification was performed on PTC-200 cyclers (MJ Research, Hercules, CA) and data were analyzed using the ABI Prism 7900HT Sequence Detector System and software version