We genotyped 31 tagging SNPs in a ~110 kb region of interest at 11q13 in the CAPS study population. The genotype distributions for all 31 SNPs were consistent with Hardy-Weinberg expectations in control subjects (P
> 0.05). We also imputed 53 SNPs (call rate > 90%) in the region based on the genotyped SNPs using the computer program IMPUTE (20
). Allele frequency differences between cases and controls in CAPS were tested for these 84 SNPs using a chi-square test (Supplementary Table 3
). Multiple SNPs in this 110 kb region were significantly associated with prostate cancer risk in allelic tests (, blue diamond). Specifically, many SNPs within a 37 kb region (68,731,000-68,768,000) flanking rs10896449 (68,751,243) and rs7931342 (68,751,073) were highly significant, and had P
-values similar to that of these two SNPs. However, none of these SNPs was significant after adjusting for rs10896449, suggesting they are dependent (, pink diamond). These SNPs can be grouped into locus 1 and were in two consecutive haplotype blocks ().
A schematic view of genetic association between SNPs at 11q13 and prostate cancer risk in CAPS
Several SNPs (68,722,000-68,731) that were immediately centromeric to the haplotypes block were not significantly associated with prostate cancer risk. Nevertheless, multiple SNPs further centromeric were found to be associated with prostate cancer risk. More importantly, most of these SNPs remained significant after adjusting for rs10896449 (, pink diamond), suggesting they are independent from rs10896449 at locus 1. They spanned four consecutive haplotype blocks and can be grouped into locus 2. We estimated the recombination rate across the region among control subjects using SequenceLDhot software (19
) and found strong evidence for a recombination hotspot between the two loci at 68,720,000-68,730,000 (P
= 1.24 × 10−15
) (). The recombination hotspot is also reported in the HapMap data (68,720,001–68,728,001, Release 21, Phase I & II). This recombination hotspot separates these two prostate cancer loci at 11q13. Across the entire 110 kb region of interest at 11q13, rs12418451 (68,691,995) at locus 2 was the most significant SNP (P
= 8.57 × 10−5
, not adjusted for rs10896449). Unlike locus 1 where no known gene is located, there are two known mRNAs in locus 2; AL137479 and BC043531) ().
As a confirmation effort, we examined these two candidate prostate cancer loci at 11q13 in three additional study populations, including Johns Hopkins Hospital (JHH) study, American Cancer Society Cancer Prevention Study-II (CPS-II) Nutrition Cohort, and the Prostate, Lung, Colon and Ovarian (PLCO) Cancer Screening Trial. One representative SNP in each locus (rs10896449 at locus 1 and rs12418451 at locus 2) was evaluated. Consistent with previous publications (1
), a significant association was found for SNP rs10896449 at locus 1 in each population (). The overall P
of the allelic test in these four populations was 1.57 × 10−11
. Similarly, allele ‘A’ of rs12418451 at locus 2 was also consistently more common in cases than in controls in each population, and was statistically significant in these three independent populations (P
= 0.002, not adjusted for rs10896449). Together with CAPS, the overall P
of the allelic test in these four populations was 1.2 × 10−6
(not adjusted for rs10896449). For both SNPs, there was no evidence for heterogeneity in allelic associations among these study populations using a Breslow-Day test for homogeneity and I2
Association of prostate cancer risk with SNPs rs10896449 at locus 1 and rs12418451 at locus 2
These two SNPs were in moderate LD in each study population (P < 0.05), with a pair-wise r2 = 0.10, 0.16, 0.12, and 0.13, respectively in CAPS, JHH, CPS-II, and PLCO. However, when the independence of these two SNPs with prostate cancer risk was tested in all four populations by including both SNPs in a logistic regression model adjusted for study population and age, both SNPs remained significant; P = 0.0001 for rs10896449 at locus 1 and P = 0.01 for rs12418451 at locus 2. No significantly multiplicative interaction between the two SNPs was found, P = 0.9.
The frequencies of risk alleles at these two SNPs were not significantly different between aggressive cases and non-aggressive cases in CAPS, JHH, CPS-II, or PLCO (Supplementary Table 4
). These two SNPs were not significantly associated with plasma PSA levels among control subjects; using an additive model, P
= 0.11 and 0.46, respectively in CAPS and JHH for rs10896449 at locus 1 and P
= 0.24 and 0.34, respectively in CAPS and JHH for rs12418451 at locus 2. PSA levels in controls subjects were not available to us for CPS-II and PLCO.