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. 2020 Aug 27;113(5):616–625. doi: 10.1093/jnci/djaa132

Table 2.

Association results for top 15 DNA repair genes and 24 candidate PCa genes

Gene Rank/81a Chr No. of var Carrier frequencies
 Aggressive vs nonaggressive
 Metastatic vs nonaggressive
Non-agg Agg M1 OR (95% CI) P b P adj OR (95% CI) P b P adj
Top 15 genes
 BRCA2c 1 13 59 0.00829 0.02491 0.01927 3.19 (1.94 to 5.25) 8.58 x 10-7 d 6.95 x 10-5 2.88 (1.22 to 6.83) .02 .25
 PALB2c 2 16 16 0.00108 0.00650 0.01071 6.31 (1.83 to 21.68) 4.79 x 10-4 d .02 7.71 (1.62 to 36.72) .009 .19
 TP53BP1 3 15 2 0.00360 0.00072 0 0.18 (0.04 to 0.86) .01 .36 — .07 .51
 ATMc 4 11 47 0.00757 0.01552 0.02141 1.88 (1.10 to 3.22) .02 .38 2.71 (1.19 to 6.2) .02 .25
 GEN1c 5 2 8 0.00396 0.00072 0 0.22 (0.05 to 1.02) .03 .42 — .23 .64
 ALKBH3 6 11 5 0.00865 0.00469 0 0.50 (0.25 to 1.01) .049 .53 — .01 .21
 APLF 7 2 5 0.00216 0.00036 0 0.17 (0.02 to 1.44) .05 .53 — .06 .51
 RECQL 8 12 10 0.00757 0.00433 0 0.52 (0.25 to 1.07) .07 .53 — .005 .19
 FANCG 9 9 3 0.00180 0.00036 0 0.17 (0.02 to 1.55) .07 .53 NA NA NA
 MLH1c 10 3 11 0.00865 0.01227 0.01285 1.62 (0.94 to 2.82) .08 .53 2.15 (0.8 to 5.75) .15 .63
 FANCM 11 14 11 0.00829 0.01300 0.01071 1.61 (0.93 to 2.79) .08 .53 1.1 (0.39 to 3.13) .85 .94
 DCLRE1C 12 10 4 0.00180 0.00036 0 0.20 (0.02 to 1.72) .09 .53 NA NA NA
 MDC1 13 6 2 0.00180 0.00036 0 0.20 (0.02 to 1.78) .10 .53 — .31 .72
 EXO1 14 1 6 0.00577 0.00975 0.00857 1.70 (0.90 to 3.23) .10 .53 1.43 (0.46 to 4.47) .56 .87
 FANCD2 15 3 4 0.00216 0.00072 0 0.28 (0.06 to 1.42) .10 .53 — .12 .61
Remaining candidate PCa DNA repair genes
  BRIP1c 16 17 7 0.00252 0.00072 0.00214 0.32 (0.06 to 1.59) .13 .67 0.93 (0.1 to 8.66) .95 .97
  CHEK2c 17 22 16 0.01405 0.01913 0.02141 1.38 (0.89 to 2.14) .14 .68 1.63 (0.76 to 3.51) .23 .64
  MUTYHc 28 1 10 0.01333 0.01661 0.01713 1.27 (0.81 to 1.99) .30 .81 1.51 (0.67 to 3.4) .34 .73
  MSH2c 31 2 9 0.00108 0.00217 0.00214 2.06 (0.46 to 9.28) .33 .81 NA NA NA
  BRCA1c 37 17 15 0.00252 0.00361 0.00428 1.55 (0.56 to 4.29) .39 .85 2.11 (0.37 to 12.21) .42 .80
  MSH6c 39 2 8 0.00396 0.00578 0.00428 1.36 (0.62 to 2.98) .44 .89 1.19 (0.24 to 5.86) .84 .94
  MRE11Ac 41 11 8 0.00216 0.00144 0 0.61 (0.17 to 2.25) .45 .89 — .19 .64
  ATRc 48 3 9 0.01766 0.01552 0.01285 0.87 (0.57 to 1.34) .53 .90 0.81 (0.33 to 1.99) .64 .90
  NBNc 50 8 6 0.00180 0.00144 0.00642 0.69 (0.18 to 2.60) .58 .93 4.11 (0.83 to 20.3) .10 .59
  WRNc 52 8 7 0.00396 0.00542 0.00214 1.22 (0.55 to 2.74) .62 .96 0.48 (0.06 to 3.95) .45 .80
  PMS2c 62 7 7 0.00144 0.00108 0.00214 0.82 (0.17 to 3.96) .81 .98 NA NA NA
  FANCLc 67 2 7 0.00973 0.00903 0.01071 1.05 (0.60 to 1.85) .87 .98 1.21 (0.44 to 3.35) .72 .92
  XPCc 70 3 3 0.00108 0.00108 0.00214 1.14 (0.22 to 5.85) .88 .98 NA NA NA
  FAM175Ac 79 4 8 0.00180 0.00181 0 0.97 (0.26 to 3.60) .97 .98 NA NA NA
  ERCC2c 80 19 13 0.00324 0.00361 0.00642 0.98 (0.39 to 2.46) .97 .98 2.48 (0.59 to 10.46) .24 .64
  RAD51Cc — 17 4 0.00036 0.00144 0 NA NA NA NA NA NA
  RAD51Dc — 17 2 0.00036 0.00072 0.00214 NA NA NA NA NA NA
  SLX4c — 16 5 0.00108 0.00072 0 NA NA NA NA NA NA
  XRCC2c — 7 4 0.00036 0.00108 0 NA NA NA NA NA NA
a

Ranking is based on the P values for aggressive vs nonaggressive PCa. Em dash (—) = effect could not be calculated because no alleles were present in metastatic cases; Agg = aggressive cases; CI = confidence interval; M1 = metastatic cases; NA = test not performed because the minor allele count was 5 or less between nonaggressive and metastatic cases; Non-agg = nonaggressive cases; OR = odds ratio; P adj = Benjamini-Hochberg adjusted P values, calculated using an alpha 0.05; PCa = prostate cancer; Chr = chromosome; Var = number of pathogenic, likely pathogenic, and deleterious variants identified.

b

P values are calculated using the likelihood-ratio test. All tests of statistical significance are 2-sided.

c

Subset of 24 literature-curated candidate PCa genes.

d

Statistically significant.