Gene Total SNPs Coding SNPs nsSNPs Total SNPs MAF>5% Novel SNPs Novel nsSNPs Novel SNPs MAF>5% BMC Cancer 2009, 9:438 Table 1: SNP Discovery Summary. SMRT NCoR SRC-3 SRC-1 Total 61 33 18 8 120 43 25 11 7 86 17 10 8 1 36 are provided in Additional File 1. Of these, 86 coding SNPs were identified resulting in 36 nonsynonymous SNPs (nsSNPs). SMRT contained the largest number of SNPs (61 total, 43 coding, and 17 nsSNPs). Despite its close relationship with SMRT, NCoR contains far fewer SNPs (33 total, 25 coding, and 10 nsSNPs). This is espe- cially evident when only common SNPs are considered (minor allele frequency [MAF]>5%; 16 in SMRT, 1 in NCoR). The position of the coding SNPs and the MAF is schematically presented in Figure 1. By conducting the sequencing in two populations, we were able to distinguish SNPs unique to a particular pop- ulation. We identified 66 SNPs unique to African Ameri- cans and 23 SNPs unique to Caucasian Americans (see Additional File 1). This distribution is similar to that reported previously in the SNP@Ethnos database for Yoruban and European populations and is hypothesized to arise from bottlenecks in non-African population his- Table 2: Summary of associations in entire population http://www.biomedcentral.com/1471-2407/9/438 16 1 5 3 25 32 30 10 2 74 6 9 3 0 18 7 0 1 0 8 tory[19] However, most of the unique SNPs found in Cau- casians were rare, possibly suggesting that these are recent alterations since only 4 out of the 23 unique SNPs (17%) were found in more than a single individual. On the other hand, 31 out of the 66 unique SNPs (47%) in African Americans were found in more than a single individual. It is important to note that some of the population unique SNPs are rare and since only 48 individuals were sequenced for each population, they could appear as unique SNPs purely by chance. From our sequencing effort we identified 74 SNPs in these four coregulators not previously represented in dbSNP or reported in the recent study by Haiman et al [16] (Table 1, columns on the right). We will refer to these SNPs as novel SNPs. Surprisingly, 8 of these novel SNPs were found at MAF>5% (7 within SMRT and 1 within SRC-3). Of the 74 novel SNPs, 18 were nonsynonymous, again with SMRT harboring many of the alterations. This illustrates that SNP SRC-1 rs1804645 P1272S SRC-3 rs6094752 C218R SRC-3 rs2230782 Q586H SRC-3 rs2076546 T960T SMRT rs2229840 A1706T Genotypes Cases Controls CC (%) CT (%) TT (%) CC (%) CT (%) TT (%) GG (%) CG (%) CC (%) AA (%) AG (%) GG (%) GG (%) AG (%) AA (%) 1147 (94.2) 1432 (94.9) 69 (5.6) 77 (5.1) 2 (0.2) 0 (0.0) [CT + TT]<-> [CC] 1089 (89.9) 1330 (89.3) 116 (9.6) 152 (10.2) 6 (0.5) 8 (0.5) [CT + TT]<-> [CC] 988 (80.8) 1207 (80.3) 226 (18.5) 272 (18.1) 9 (0.7) 24 (1.6) [CC]<-> [GG + GC] 1011 (82.7) 1240 (82.2) 202 (16.5) 249 (16.5) 9 (0.8) 20 (1.3) [AG + GG]<-> [AA] 789 (66.2) 1004 (67.6) 357 (30.0) 423 (28.5) 45 (3.8) 57 (3.9) [AG + GG]<-> [AA] Odds ratios (OR) with 95% confidence intervals (95% CI) and P-values. Please note that the results excluding samples (345 cases/1190 controls) that have been analysed in a previous study (14) are *OR = 0.37, 95%CI = 0.13-1.08, p = 0.059 and °OR = 1.13, 95%CI = 0.80-1.59, p = 0.491. OR 1 1.11 - 1.15 1 0.93 0.92 0.93 1 1.11 0.46 0.45* 1 0.99 0.55 0.96° 1 1.07 1.01 1.06 95% CI 0.80-1.56 - 0.82-1.60 0.72-1.20 0.32-2.65 0.73-1.19 0.83-1.23 0.21-0.99 0.21-0.98* 0.25-1.22 0.25-1.22 0.79-1.17° 0.91-1.27 0.67-1.50 0.91-1.25 P 0.510 - 0.405 0.587 0.871 0.575 0.881 0.042 0.041* 0.961 0.135 0.702° 0.407 0.982 0.441 Page 5 of 9 (page number not for citation purposes)