BMC Cancer 2009, 9:438 http://www.biomedcentral.com/1471-2407/9/438 SRC-1 P1272S: forward 5'-CCCTCCTCCTCAGAGT- TCTCT-3', reverse 5'-CCTTCATGTCTGGTGACTGATACC- 3'; TaqMan probes: forward 5'-CAGGTGGAGTTTGC-3'- VIC, reverse 5'-CAGGTGAAGTTTGC-3'-FAM. 2.1.31 http://www.mc.vanderbilt.edu/prevmed/ps/. With the total sample size, we had 80% power to detect OR of 0.79/1.26 and 0.57/1.56 for carrier frequencies of 30% and 5%, respectively. SMRT A1706T: forward 5'-ACCTCGCAGCAGATGCA-3', reverse 5'-GAGGCCCCTCAGCATATCAG-3'; TaqMan probes: forward 5'-CCACAACACGGCCAC-3'-VIC, reverse 5'-CACAACGCGGCCAC-3'-FAM. Genotyping call rates for all studies were >97%. The SNP assays were validated by re-genotyping 5% of all samples. The concordance rate for all SNPs varied from 99 to 100%. Statistical Analysis Hardy-Weinberg equilibrium test was undertaken using the chi-square "goodness-of-fit" test. Crude odds ratios (ORs), 95% confidence intervals (95% CIs) and P values were computed by unconditional logistic regression using a tool offered by the Institute of Human Genetics, Techni- cal University Munich, Germany http://ihg.gsf.de/cgi-bin/ hw/hwa1.pl. Power calculations were determined using power and sample size calculator software PS version Haplotype Analysis Haplotypes of variants located in the same gene were determined using the PHASE 2 software created by Stephens et al. [18], or SNPHAP 1.3 software created by David Clayton http://www-gene.cimr.cam.ac.uk/clayton/ software/snphap.txt. Each individual was assumed to carry the most likely pair of haplotypes and the haplotype distributions were estimated based on the controls. Results/Discussion SNP Discovery Complete coding regions and 25 bp of the flanking intronic regions of SRC-1, SRC-3, NCoR, and SMRT were fully sequenced in both directions using Sanger sequenc- ing in 96 apparently normal individuals (48 Caucasian American, 48 African American) generating a total of ~5.8 MB of sequence. From this effort we identified 120 SNPs (61 in SMRT, 33 in NCoR, 18 in SRC-3, and 8 in SRC-1). A summary of the results is shown in Table 1 and details SFNigPurdeisc1overy in (A) SRC-1, (B) SRC-3, (C) NCoR, and (D) SMRT SNP discovery in (A) SRC-1, (B) SRC-3, (C) NCoR, and (D) SMRT. Vertical lines delineate the position of SNPs iden- tified by our resequencing effort. The height of the vertical lines represents the frequency at which the SNP was found. Black lines represent novel SNPs, grey lines represent SNPs found in dbSNP. Solid lines represent nonsynonymous SNPs, dashed lines represent synonymous SNPs. Positions of SNPs genotyped for risk associations are pointed out by arrows. Page 4 of 9 (page number not for citation purposes)