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Four genome-wide association studies, all in populations of European descent, have identified 20 independent single nucleotide polymorphisms (SNPs) in 20 regions that are associated with prostate cancer risk. We evaluated these 20 SNPs in a combined African American (AA) study, with 868 prostate cancer patients and 878 control subjects. For 17 of these 20 SNPs, implicated risk-associated alleles were found to be more common in these AA cases than controls, significantly more than expected under the null hypothesis (P = 0.03). Two of these 17 SNPs, located at 3p12, and Region 2 at 8q24, were significantly associated with prostate cancer risk (P < 0.05), and only SNP rs16901979 at Region 2 of 8q24 remained significant after accounting for 20 tests. A multivariate analysis of additional SNPs across the broader 8q24 region revealed three independent prostate cancer risk-associated SNPs, including rs16901979, rs13254738, and rs10086908. The first two SNPs were ~20 kb apart and the last SNP, a novel finding from this study, was ~100 kb centromeric to the first two SNPs. These results suggest that a systematic evaluation of regions harboring known prostate cancer risk SNPs implicated in other races is an efficient approach to identify risk alleles for AA. However, studies with larger numbers of AA subjects are needed, and this will likely require a major collaborative effort to combine multiple AA study populations.
Recent genome-wide association studies (GWAS) in four study populations of European descent have revealed more than a dozen prostate cancer risk-associated loci (1-8). Additional independent prostate cancer risk-associated loci were identified in fine mapping studies of these initially discovered loci (9-15). Confirmation of these risk loci among populations of European descent has been reported, but studies examining AA are limited. No GWAS of prostate cancer in AA has been published to date, and confirmation studies in AA were primarily limited to SNPs at 8q24 (9,11,16). The goal of this study was to systematically evaluate, in an AA population, all reported prostate cancer risk associated loci identified in men of European descent.
Four independent study populations of AA were included in this combined analysis of 868 cases and 878 controls, including a hospital-based case-control study from Johns Hopkins Hospital (JHH) (2), a population-based case-control study in the western part of North Carolina (NC), a hospital-based case-control study from Wake Forest University School of Medicine (Wake) (17), and a hospital-based case-control study from Washington University School of Medicine (WashU) (Supplementary methods and Table 1).
We selected 20 SNPs that were significantly associated with prostate cancer risk in four previous GWASs (1-8) and follow-up confirmation and fine mapping studies of European descent (9-15). We also selected 14 additional SNPs in the broader 8q24 region that were implicated in several AA populations (9,11,16). In addition, a subset (N = 58) of ancestry informative markers (AIMs) that have large differences in allele frequencies between the two parental populations of AA (Europeans and Africans) were also included (18). These SNPs were genotyped using a MassARRAY iPLEX system (Sequenom, Inc. San Diego, CA). The range of genotyping call rate is from 0.989 to 0.999, with an average of 0.996. The concordance rate was 99.5% among the duplicated samples. Each of the autosomal SNPs was in Hardy-Weinberg equilibrium (P ≥ 0.05) among control subjects using Fisher's exact test. The proportion of European ancestry was estimated for each subject based on the 58 AIMs using the computer program, STRUCTURE (19). Subjects with a proportion of European ancestry greater than 0.8 or with a high proportion of missing genotype data (> 50%) were excluded. A logistic regression model was employed to test for association under an additive model and adjusting for age, ancestry proportion, and study (Supplementary methods).
Association tests were first performed for each of the 20 SNPs that were implicated in populations of European descent in this combined AA study (Table 2, upper panel). For 17 of these 20 SNPs, the implicated risk-associated alleles were found to be more common in these AA cases than controls, and the differences were statistically significant for two of these SNPs (P < 0.05). The number of SNPs that have the same direction of association as in European populations significantly exceeded the expected number of 10 under the null hypothesis that none of these SNPs are associated with prostate cancer risk in AA (P = 0.03, goodness-of-fit test, following a chi-squared distribution with 1 degree of freedom), suggesting that some of these SNPs may also be associated with prostate cancer risk in AA. It is estimated that the study has 80% power to detect SNPs with allelic OR ≥ 1.3 and minor allele frequency ≥ 20% at a significance level of 0.05. The limited number of SNPs reaching statistical significance level in this study may reflect the limited statistical power to detect association of moderate effect. We have also compared the association results for the 20 SNPs between this study in African Americans and previous published studies in Caucasians (Supplementary Table 1). The strength of associations is similar amongst African Americans and Caucasians, although these SNPs have very different allele frequencies in African Americans and Caucasians.
Two of these 17 SNPs, located at 3p12, and Region 2 at 8q24, were significantly associated with prostate cancer risk (P < 0.05) in this AA study. Of these, SNP rs16901979 at Region 2 of 8q24 (nominal P = 1.9 × 10-5) is the only SNP that reached a study-wide significance level of 0.05 after adjustment for 20 independent tests. In addition, considerable but not statistically significant differences in allele frequencies between cases and controls were also found for SNPs at 7p15, 8q24 (region 3), 17q12 (Region 1), and Xp11 (P < 0.1). Notably, SNP rs2735839 at 19q13 (KLK3) showed a reversed direction of association compared to that observed in Caucasians (P = 0.056).
We have also estimated the ORs for each study population separately and tested homogeneity of the OR among four study populations using a Breslow-Day homogeneity test (Supplementary Table 2). Significant heterogeneity (nominal P < 0.05) was found for two SNPs, rs11649743 and rs6981122. However, they were not statistically significant after taking multiple testing into account.
When 14 additional SNPs at 8q24 that were previously implicated in several AA study populations were examined in this combined study, 7 were significantly associated with prostate cancer risk at nominal P < 0.05 (Table 2, lower panel). A multivariate analysis of all nominally significant 8q24 SNPs using a step-wise procedure and adjusted for ancestry proportion, age, and study populations revealed three independent prostate cancer risk-associated SNPs; they were rs13254738 (P = 0.007), rs16901979 (P = 0.013), and rs10086908 (P = 0.001). The first two SNPs have been previously implicated in populations of European descent (2,3,6,8-11) and AA (2,9,11,16). They were ~20 kb apart and were in weak LD in the AA control subjects (r2 = 0.23) (Fig 1). The last SNP (rs10086908), ~100 kb centromeric to the first two SNPs (r2 = 0 with each of the two SNPs), was a novel finding. This SNP was evaluated in this study because it was initially implicated in a subset of the JHH AA study (372 cases and 350 controls, P = 0.003, unpublished data). The association was replicated in the remaining 481 cases and 524 controls of this study (P = 0.03). We did not observe any significant pair-wise interaction among the three independent 8q24 risk SNPs, with P values ranging from 0.34 to 0.65.
Several other 8q24 SNPs, although not statistically significant in the multivariate analysis (P > 0.05), had results that were consistent with previous reports and warrant further evaluations in larger studies. Specifically, SNPs rs6983267 (Region 3), rs7000448 (Region 1), rs7008482, and rs780321 were reported to be associated with prostate cancer risk in at least one previous AA study (9,11,16). On the other hand, consistent with the results from two previous AA studies (11,16), we did not find evidence for prostate cancer association with SNP rs1447295.
We have also tested the association between SNPs and disease aggressiveness. Although the association with prostate cancer was generally stronger among aggressive PCa patients, no statistically significant difference in allele frequencies of these SNPs were found between aggressive and non-aggressive prostate cancer patients (Supplementary Table 3).
Although AAs have the highest incidence and mortality rate of prostate cancer, this group is severely under studied. GWAS of prostate cancer in AA can be a powerful approach to identify genetic risk variants; however, this is difficult to implement at this time because large sample sizes are needed for both the initial discovery and subsequent confirmation stages. A systematic evaluation of risk variants implicated in populations of European descent among AA is a feasible and effective alternative that has been empirically demonstrated in this study. The discovery of three prostate cancer risk variants in AA, if confirmed, may be substantial, especially when considering that only three factors (age, family history, and race) have been documented in the past. In the future, these risk factors may be used to identify men at increased risk to prostate cancer for early screening, prevention, and diagnosis.
Several additional implications are worth noting. Novel prostate cancer risk variants at 8q24 in AA suggest that additional prostate cancer risk variants in AA may exist in the regions flanking other prostate cancer risk-associated SNPs that have been previously implicated by genome-wide studies of populations of European descent. In addition, the generally smaller LD blocks in AA may provide better positional information on causal, functional variants. Fine mapping association studies of each region harboring known prostate cancer risk-associated SNP among AA study populations are warranted. In addition, the substantially different genetic background and environmental exposures between populations of European and African descent may provide a unique opportunity to study gene-gene and gene-environmental interactions in disease risk (20). Finally, our results suggest that studies with larger numbers of AA subjects are needed to detect risk variants with moderate effect, and this will likely require a major collaborative effort to combine multiple AA study populations.
The authors thank all the study subjects who participated the study. We acknowledge the contribution of multiple physicians and researchers in designing and recruiting study subjects, including Drs. Bruce J. Trock and Alan W. Partin. The support of the St. Louis Men's Group Against Cancer to A.S. K, William T Gerrard, Mario A Duhon, John and Jennifer Chalsty, and P Kevin Jaffe to W.B.I is gratefully acknowledged.
Funding: National Cancer Institute [CA129684, CA105055, CA106523, CA95052 to J.X., CA112517, CA58236 to W.B.I., CA86323 to AWP, CA112028 to A.S.K.]; Department of Defense [W81XWH-06-1-0245 to B.C., PC051264 to J.X, PCw81XWH-07-1-0122 to W.B.I.]; and the American Cancer Society [CNE-101119 to J.J.H].