Table 1.

Comparison of LD at prostate cancer risk loci detected in European ancestry populations that were replicated versus not replicated in other ancestral populations

Mean r2
Test populationReplicated SNPsNot replicatedP
African Americans
 Number of SNPs4160
 AFR0.13 ± 0.060.12 ± 0.050.37
 EUR0.21 ± 0.100.18 ± 0.090.19
 Number of SNPs4232
 ASN0.24 ± 0.120.18 ± 0.090.01
 EUR0.21 ± 0.090.23 ± 0.090.60
 Number of SNPs2249
 LAT0.21 ± 0.090.18 ± 0.080.05
 EUR0.22 ± 0.100.19 ± 0.090.15

NOTE: LD is measured by the correlation coefficient (r2) between the index SNP reported as associated with prostate cancer in a European ancestry population and all other SNPs within a 500-kb window (250 kb on either side of the index SNP). For each index SNP in the different comparisons, a pair of mean r2 (one for each population) is calculated using all the r2 corresponding to the same pair's SNP/index SNP in both populations. For each pair SNP/index SNP, when both r2 were under 0.05 in both populations, the pair was excluded from the analysis. LD is based on data from the 1000 Genomes Project; further details are given in Supplementary Table S2.

Data for each mean of each index SNP are reported in Supplementary Table S2.

Mean r2 is the mean of the mean for each locus.

For the AFR/EUR comparison, the subgroup of index SNPs associated with prostate cancer includes SNPs that are directly associated with prostate cancer (N = 27) and SNPs in high LD with another SNP associated with prostate cancer (N = 14).

Abbreviations: AFR, African American; EUR, European; ASN, Asian; LAT, Latino.