The NCS-1 gene is located on chromosome 9 spanning 65,114 bp (UCSC Genome Browser on Human Feb. 2009 (GRCh37/hg19) Assembly) and 8 exons (Fig. 1A). Seven intronic SNPs (rs4837479, rs7849345, rs3824544, rs10819611, rs947513, rs2277200, rs7873936) and one SNP located in the alternative promoter (rs1342043) were genotyped. These SNPs were selected using the Tagger algorithm as part of the Haploview software based upon HapMap data with a minor allele frequency (MAF) cut-off set at 20% [2]. These SNPs captured 42% of AA (ASW) alleles (Fig. 1B) and only 12% of EA (CEU) alleles (3 SNPs) with r2 of 0.8 (Fig. 1C). Genotyping of the populations in the current study was divided into two phases. In the first phase of genotyping, all 8 SNPs were genotyped in our AA discovery sample collected from TRC. The second phase of genotyping included genotyping our replication sample of AA and EA populations using only the 3 SNPs (rs7849345, rs10819611, rs1342043) which had shown a trend toward significance in the first phase. SNP genotyping was performed using Applied Biosystems Taqman® SNP Genotyping Assays. For quality control purposes, 10% of samples were genotyped in duplicates.
