Genome-wide association studies (GWAS) of prostate cancer have identified more than 30 risk associated variants, which in aggregate are estimated to account for approximately 20% of the familial risk of prostate cancer1–12
. Aside from admixture, and fine-mapping studies which identified multiple independent risk variants at 8q2413,14
, and a more recent GWAS among Japanese men which identified five novel loci9
, discoveries in prostate cancer have come from studies in men of European ancestry. However, prostate cancer incidence in men of African ancestry is greater than in non-African populations15
, with the disparity presumably reflecting both differences in prevalence of environmental risk factors and susceptibility alleles that are shared among men of African descent. For example, the risk variants at 8q24, many of which are more common in men of African ancestry14
, could contribute partly to the greater incidence of prostate cancer in this population, and provide some support for the hypothesis of a genetic contribution underlying racial/ethnic disparities in disease risk.
We assembled a consortium of prostate cancer studies that included men of African ancestry and conducted a GWAS to search for additional risk loci that may be more common in men of African descent. Stage 1 included 3,621 African American prostate cancer cases and 3,502 African American controls drawn from 11 studies (Supplementary Table 1
, Online Methods). Genotyping in stage 1 was conducted using the Illumina Infinium 1M Duo. Following quality control exclusions (Online Methods
), the stage 1 analysis consisted of 1,047,986 SNPs (MAF≥0.01) examined in 3,425 cases and 3,290 controls.
In comparing, for all SNPs, the observed with the expected distribution of p-values from a 1-df trend test there was evidence of inflation in the test statistic (λ=1.11). Principal components analysis highlights the high degree of admixture in this population and the over-inflation diminished following additional adjustment for ancestry (λ=1.03; Supplementary Figure 1
, Online Methods
). The association of four SNPs achieved genome-wide significance in the stage 1 sample with p-values between 5.4×10−9
(). These SNPs were located in known prostate cancer risk regions; three at 8q24 (rs10505483, rs1456315 and rs7824364 at 128.173–128.205 Mb (NCBI36) and one at 11q13 (rs7130881 at 67.75 Mb).
A plot of the −log10 P-values by chromosome.
We selected 17 SNPs (p<2×10−5
) located outside of known prostate cancer risk regions to examine in a second stage. The associations of these 17 SNPs with prostate cancer risk were not influenced substantially by population stratification in the stage 1 sample, as evaluated by principal components analysis (Supplementary Table 2
). The stage 2 sample included 1,396 cases and 2,383 controls of African ancestry from seven independent studies: six U.S.-based studies and one study in Ghana. Of the 17 SNPs, only marker rs7210100 at 17q21 was significantly associated with risk in the stage 2 studies (OR=1.55; p=2.5×10−5
; ). None of the other SNPs selected in stage 1 were significantly associated with risk in the stage 2 sample (all p-values >0.05); SNP rs13116912 was excluded due to deviating from Hardy-Weinberg Equilibrium in the majority of stage 2 studies. The results for all 17 SNPs in stage 1 and stage 2 are presented in Supplementary Table 3
The association of variant rs7210100 at 17q21 with prostate cancer risk in men of African ancestry.
We further examined the association with rs7210100 in a third stage that included three studies among men of African descent, a study from the U.S (SCORE), a study in Senegal (PROGRÈS), and a study in Barbados (PCBP). SNP rs7210100 was found to be positively associated with risk in all three studies (stage 3: 471 cases and 904 controls; combined OR= 2.07, p=1.5×10−5; ).
Adjustment for global ancestry or local ancestry (African versus European) in the stage 1 studies did not influence the results for rs7210100 (OR= 1.41 without adjustment for ancestry; OR=1.40 adjusted for global ancestry; OR=1.43 adjusted for global and local ancestry. The effect estimate for rs7210100 was also similar in men with <15% global European ancestry (1,251 cases and 1,325 controls; OR=1.41) as well as in cases and controls estimated to have 2 chromosomes of African ancestry at this location (2,214 cases and 2,080 controls; OR=1.47). We observed no evidence of heterogeneity of the association by study for this variant in the stage 1 (phet
=0.89), stage 2 (phet
=0.25), or stage 3 studies (phet
=0.51), or among all studies (phet
=0.58). Results for all SNPs examined in the replication stages were also unaffected when adjusting for European ancestry in studies in which information on global ancestry was available (Supplementary Tables 4 and 5
In combining the results across all three stages (5,262 cases and 6,554 controls), rs7210100 was strongly and significantly associated with risk (OR = 1.51; 95% CI, 1.35–1.69; p=3.4×10−13
). The risk for heterozygote and homozygote carriers was 1.49 (95 % CI, 1.32–1.68) and 2.73 (95% CI, 1.50–4.96), respectively. We did not find any stronger signal with imputed SNPs to the Phase 2 HapMap populations in the surrounding region at chromosome 17q21 (, Supplementary Figure 2
Figure 2 A regional plot of the −log10 P-values for genotyped (squares) and imputed (circles) SNPs at the chromosome 17q21 risk locus in the stage 1 African American sample. The shading depicts the strength of the correlation (r2) between SNP rs7210100 (more ...)
The association with rs7210100 was similar when stratifying on age (p=0.72) and first-degree family history of prostate cancer (p=0.36). We also observed no significant difference in the association of rs7210100 with prostate cancer stage (p=0.94) or tumor grade (p=0.11) at diagnosis. However, the association with rs7210100 was greater for non-advanced disease when classified based on stage and grade (Gleason Score <8 and localized stage, 2,433 cases and 6,554 controls: OR=1.67, p=8.6×10−12) than for advanced disease (Gleason Score ≥8 or non-localized disease, 1,719 cases and 6,554 controls: OR=1.27, P=5.0×10−3: phet = 6.0×10−3).
Among controls with PSA levels measured and ≤4 ng/ml (n=2,383) we found no significant association between PSA levels and rs7210100 genotype (p=0.58). Limiting the analysis to controls with PSA levels (<4 ng/ml) and cases from these studies did not change the association between rs7210100 and prostate cancer risk (n=3,157 cases and 2,383 controls; OR=1.62, p=4.5×10−8).
The variant rs7210100 is located in intron 1 of the ZNF652
gene on chromosome 17q21.32. ZNF652
encodes a zinc-finger protein transcription factor that has been shown to interact with the Eight-Twenty-One (ETO) protein, CBFA2T3, which acts as a transcriptional repressor by forming complexes with corepressor proteins and HDACs16
. Co-expression of ZNF652 and the androgen receptor in prostate tumors has been associated with a decrease in relapse-free survival17
. A common variant just upstream of the ZNF652
gene has also been associated with blood pressure in a GWAS of men and women of European ancestry18
. Sequencing of the 5 coding exons of ZNF652
in 48 subjects (with over-sampling of risk allele carriers; Online Methods
) did not reveal a coding variant strongly correlated with rs7210100. Further work is needed to map this locus in order to nominate optimal candidate markers, in addition to rs7210100, for functional studies in pursuit of regulatory effects of one or more variants in the region.
The risk allele of rs7210100 is relatively uncommon in men of African ancestry (4–7%), and is extremely rare (<1%) in non-African populations as reported by the 1000 Genomes Project. The frequency of the risk allele in men of West African ancestry (Ghana and Senegal) is very similar to that observed in African Americans as well as men from East Africa (Uganda, n=111; RAF=0.04). GWAS in populations of European ancestry have not pointed to this region of 17q21 as a risk locus for prostate cancer (Supplemental Figure 3
). Together these observations suggest that the underlying biologically relevant allele may be limited to populations of African descent. As reported by the National Cancer Institute’s, Surveillance, Epidemiology and End Results (SEER) Program, prostate cancer incidence in African American men is 1.56-times higher than the incidence of non-Hispanic Whites. Since approximately 10% of African American men carry this variant that increases their risk 1.50-fold over non-carriers, we estimate that this locus may be responsible for as much as 9% (95% CI, 6–12%) of the greater incidence of prostate cancer to African American men (Online Methods
In summary, we detected a marker of risk for prostate cancer that appears specific to men of African descent, who have an increased incidence and mortality of this disease. These findings provide strong support for conducting GWAS in diverse populations to identify markers of risk that may be population-specific and which could contribute to racial and ethnic disparities in disease incidence. Further work is needed to characterize the 17q21 region and conduct the functional studies required to understand the role of this germ-line variation in prostate cancer susceptibility.