Skip to main content
. Author manuscript; available in PMC: 2009 Nov 3.
Published in final edited form as: JAMA. 2008 May 28;299(20):2423–2436. doi: 10.1001/jama.299.20.2423

Table 2.

Statistically Significant Gene-variant/Cancer Associations and False Positive Report Probabilities (FPRP)

Cancer
Site		 Gene Variant Comparison MAF or
Freq at
Risk1 		OR 95%CI p-value Evid
for Pub
Bias2 		Evid
for
Het2 		Studies Cases Power3 Power3 FPRP values at Prior Probability
N OR:1.5
 OR:1.2
 OR:1.5
 OR:1.2
 Ref
0.001 0.000001 0.001 0.000001
Bladder
GSTM1 null vs. present 0.51W, 0.53S 1.5 1.3–1.6 1.9×10−14 No No 28 5072 1.0 0.017 <0.001 <0.001 <0.001 <0.001 23
GSTP1 Ile105Val GG+GA vs. AA 0.14W 1.23 1.04–1.57 0.0488 Yes No 7 1903 0.944 0.421 0.990 1.000 0.996 1.000 82
NAT2 acetylator Slow vs. rapid/intermed 0.56W 1.46 1.26–1.68 2.5×10−7 No No 36 5747 0.647 0.003 <0.001 0.163 0.039 0.976 19
NQO1 Pro187Ser CT+TT vs. CC 0.13–.0.20W 1.204 1.00–1.43 0.0457 No No 6 1066 0.994 0.500 0.977 1.000 0.988 1.000 83
XPC Ala499Val TT vs. CT+CC 0.25W, 0.31S 1.324 1.06–1.63 0.0114 No No 4 2765 0.883 0.188 0.918 1.000 0.981 1.000 84
XPD Asp312Asn GA+AA vs. GG 0.32–0.71 1.244 1.07–1.45 0.0055 No No 3 789 0.991 0.341 0.876 1.000 0.954 1.000 85
XRCC3 Thr241Met TT vs. CC 0.37 1.17 1.00–1.36 0.0409 No No 7 3112 0.999 0.629 0.976 1.000 0.985 1.000 86
Breast6
ATP1B2 −8852T>C TC vs. TT 0.23–0.33 0.88 0.77–0.99 0.0462 - Yes 2 2692 1.0 0.818 0.971 1.000 0.976 1.000 87
CASP8 Asp302His GC vs. GG 0.13 0.89 0.85–0.94 5.7×10−6 - No 14 16423 1.0 0.991 0.028 0.967 0.029 0.967 18
CHEK2 *1100delC heterozygotes vs. non-carrier 0.002–0.02W 2.4 1.8–3.2 2.5×10−9 No No 12 18329 0.001 1×10−6 0.004 0.782 0.678 1.000 21
COMT Met108/158V al GG vs. AA 0.45–0.47 1.144 1.03–1.26 0.0108 - No 11 6398 1.0 0.842 0.911 1.000 0.924 1.000 88
CYP17 rs4919687 AA vs. GG 0.26 1.17 1.03–1.34 0.0193 - No 5 5166 1.0 0.643 0.959 1.000 0.973 1.000 89
CYP17 rs4919682 TT vs. CC 0.25 1.16 1.01–1.33 0.0345 - No 5 5146 1.0 0.686 0.971 1.000 0.980 1.000 89
CYP19 TTTA10 carrier vs. non-carrier 0.01–0.02W 1.59 1.01–2.48 0.0430 - - 5 3934 0.399 0.107 0.990 1.000 0.997 1.000 90
CYP1A1 A2455G GG vs. AA 0.25S 0.72 0.53–0.99 0.0393 No No 3 2938 0.682 0.184 0.984 1.000 0.996 1.000 91
CYP1B1 Leu432Val GG +GC vs. CC 0.43W 1.5 1.1–2.1 0.0140 No No 6 2176 0.500 0.097 0.973 1.000 0.995 1.000 92
GATA3 rs570613 CT vs. TT 0.40–0.45w 0.85 0.75–0.95 0.007 - No 2 2590 1.0 0.636 0.807 1.000 0.868 1.000 93
IGFBP3 −202 C>A AA vs. CC 0.45W 0.92 0.86–0.99 0.0202 - No 10 13101 1.0 0.996 0.963 1.000 0.963 1.000 18
NBS1 657del5 carrier vs. non-carrier 0.02W 3.13 1.40–7.00 0.0055 - - 2 786 0.037 0.010 0.993 1.000 0.998 1.000 94
POR Gly5Gly GG vs. AA 0.21–0.25A 1.58 1.04–2.41 0.0329 - No 4 1038 0.405 0.101 0.988 1.000 0.997 1.000 95
PR PROGINS T2/T2 vs. T1/T1 0.14 0.32 0.16–0.65 0.0014 - - 4 1106 0.021 0.004 0.987 1.000 0.998 1.000 90
PTGS2 Ex10+837 CC vs. TT 0.35W 0.80 0.66–0.97 0.0231 - No 3 2194 0.968 0.339 0.960 1.000 0.986 1.000 96
TGFB1 Leu10Pro TT vs. CC 0.38W 1.16 1.08–1.25 6.9×10−5 - No 11 12946 1.0 0.813 0.090 0.990 0.108 0.992 18
TGFBR1 *6A *9A/*6A + *6A/*6A vs. *9A/*9A 0.12–0.15 1.38 1.14–1.67 0.0009 No - 7 1420 0.804 0.075 0.537 0.999 0.925 1.000 97
WDR79 Arg68Gly GG vs. CC 0.21–0.23W 1.60 1.04–2.47 0.0332 - No 2 2692 0.385 0.097 0.989 1.000 0.997 1.000 87
WDR79 Phe150Phe CT vs. CC 0.15–0.16W 1.15 1.00–1.32 0.0485 - No 2 2655 1.0 0.727 0.979 1.000 0.985 1.000 87
XRCC1 Arg399Gln AA vs. GG 0.30S 1.6 1.1–2.3 0.0125 No No 4 1567 0.364 0.060 0.968 1.000 0.995 1.000 98
Colorectal
CCND1 G870A GA vs. GG 0.12–0.64 1.18 1.06–1.32 0.0031 No No 12 4618 1.0 0.616 0.792 1.000 0.861 1.000 99
GSTT1 null null vs. present 0.21W, 0.44S 1.37 1.17–1.60 8.1×10−5 - - 11 1490 0.874 0.047 0.074 0.988 0.598 0.999 16
MTHFR 677 C/T TT vs. CC 0.32W0.40S 0.83 0.75–0.93 0.0007 No No 25 12261 1.0 0.472 0.570 0.999 0.737 1.000 100
MTHFR A1298C CC vs. CA+AA 0.29W, 0.22S 0.81 0.69–0.96 0.0124 No No 14 4764 0.988 0.372 0.938 1.000 0.976 1.000 101
NAT2 acetylator5 rapid vs. slow 0.32–0.77W, 0.46–0.95S 1.084 1.00–1.16 0.0421 - No 18 6741 1.0 0.998 0.972 1.000 0.972 1.000 47
NQO1 Pro187Ser CT+TT vs. CC 0.11–0.23W 1.184 1.02–1.35 0.0206 No No 5 1637 1.0 0.597 0.941 1.000 0.964 1.000 83
XPC Lys939Gln CA vs. AA 0.65S,0.61W 1.324 1.11–1.56 0.0014 No No 2 1060 0.933 0.132 0.546 0.999 0.895 1.000 102
Esophageal
ALDH2 *2*2 *2*2 vs. *1*1 0.10–0.33S 0.36 0.16–0.80 0.0128 No No 5 705 0.065 0.020 0.995 1.000 0.998 1.000 103
CYP1A1 Ile462Val GG vs. AA 0.21–0.25S 2.52 1.62–3.91 3.9×10−5 No No 9 754 0.010 0.0 0.783 1.000 0.988 1.000 104
XPD Lys751Gln AC+CC vs. AA 0.07–0.37 1.394 1.15–1.68 0.0007 No No 4 1053 0.785 0.064 0.456 0.999 0.911 1.000 85
Gastric
CDH1 -160C>A CA+AA vs. CC 0.14–0.16S 0.81 0.67–0.99 0.0343 No No 7 1174 0.971 0.391 0.976 1.000 0.990 1.000 105
GSTT1 null null vs. present 0.13–0.26W 1.27 1.03–1.56 0.0240 No No 8 835 0.944 0.294 0.960 1.000 0.987 1.000 106
IL1RN VNTR *2 carrier vs. LL 0.22–0.29W 1.30 1.09–1.54 0.0029 No No 16 2293 0.951 0.177 0.716 1.000 0.931 1.000 107
MTHFR C677T TT vs. CT+CC 0.35–0.57M 1.52 1.31–1.77 4.9×10−8 No No 16 2727 0.432 0.001 <0.001 0.140 0.057 0.984 20
P53 Arg72Pro GG vs. CC 0.41–0.49S 0.84 0.72–0.99 0.0319 No - 8 1295 0.997 0.538 0.974 1.000 0.986 1.000 108
TNF-A -308G>A AA vs. GG 0.04–0.16M 1.49 1.11–1.99 0.0074 No No 19 3660 0.518 0.071 0.930 1.000 0.990 1.000 109
Glioma
ATR rs11920625 AG vs. GG 0.08W 1.40 1.11–1.77 0.0047 - No 5 1010 0.718 0.099 0.873 1.000 0.980 1.000 110
CHAF1A rs243356 CT vs. CC 0.21W 1.33 1.10–1.60 0.0028 - No 5 1010 0.899 0.138 0.735 1.000 0.948 1.000 110
CHAF1A rs243341 CT vs. TT 0.26W 1.25 1.04–1.50 0.0169 - No 5 1010 0.975 0.330 0.944 1.000 0.980 1.000 110
CHAF1A rs105038 CT vs. CC 0.26W 1.25 1.04–1.50 0.0169 - No 5 1010 0.975 0.330 0.944 1.000 0.980 1.000 110
CHAF1A rs2992 GG vs. AA 0.26W 1.47 1.05–2.04 0.023 - No 5 1010 0.548 0.112 0.975 1.000 0.995 1.000 110
DCLRE1B rs3761936 CC vs. TT 0.19W 0.36 0.20–0.65 0.0007 - No 5 1010 0.020 0.003 0.972 1.000 0.996 1.000 110
DCLRE1B rs12022378 TT vs. CC 0.19W 0.36 0.20–0.65 0.0007 - No 5 1010 0.020 0.003 0.972 1.000 0.996 1.000 110
ERCC1 rs3212986 GT vs. GG 0.27W 0.76 0.63–0.92 0.0045 - No 5 1010 0.911 0.172 0.842 1.000 0.966 1.000 110
ERCC1 rs3212955 AG vs. AA 0.26W 0.79 0.66–0.96 0.0137 - No 5 1010 0.956 0.296 0.949 1.000 0.984 1.000 110
IL4 rs2243248 TG vs. TT 0.05W 1.44 1.05–1.97 0.0231 - No 2 654 0.601 0.127 0.974 1.000 0.994 1.000 111
IL6 rs1800795 GG vs. CC 0.45W 0.70 0.51–0.96 0.0271 - No 2 654 0.619 0.140 0.977 1.000 0.995 1.000 111
NEIL3 rs12645561 CT vs. CC 0.13W 1.29 1.05–1.59 0.0161 - No 5 1010 0.921 0.249 0.949 1.000 0.986 1.000 110
MSH5 rs707938 CC vs. TT 0.36W 0.67 0.50–0.89 0.0065 - No 5 1010 0.514 0.066 0.917 1.000 0.989 1.000 110
POLD1 rs1673041 AA vs. CC 0.26W 0.53 0.35–0.79 0.0022 - No 5 1010 0.130 0.013 0.933 1.000 0.993 1.000 110
RPA3 rs4140805 GG vs. TT 0.40W 1.43 1.11–1.85 0.0061 - No 5 1010 0.642 0.091 0.910 1.000 0.986 1.000 110
RPA3 rs2160138 CC vs. TT 0.44W 1.46 1.14–1.88 0.003 - No 5 1010 0.583 0.064 0.852 1.000 0.981 1.000 110
RPA3 rs6947203 TT vs. CC 0.33W 1.47 1.11–1.94 0.0068 - No 5 1010 0.557 0.076 0.921 1.000 0.988 1.000 110
TP53 rs8079544 CT vs. CC 0.06W 1.34 1.04–1.72 0.0226 - No 5 1010 0.812 0.193 0.964 1.000 0.991 1.000 110
Head/neck
GSTM1 null null vs. present 0.47–0.54W 1.16 1.01–1.33 0.0345 Yes No 11 3754 1.0 0.686 0.971 1.000 0.980 1.000 112
GSTT1 null null vs. present 0.11–0.53S, 0.14–0.52W 1.08 1.02–1.14 0.0067 No No 23 3974 1.0 1.0 0.840 1.000 0.840 1.000 113
MGMT Leu84Phe CT+ TT vs. CC 0.16M 0.74 0.55–1.00 0.0483 - No 3 514 0.752 0.220 0.985 1.000 0.996 1.000 114
MGMT Ile143Val AG + GG vs. AA 0.13M 0.73 0.53–1.00 0.0520 - No 3 536 0.714 0.205 0.986 1.000 0.996 1.000 114
XPC PAT+/− + vs − 0.67S,0.59W 1.294 1.04–1.59 0.0187 No No 2 720 0.921 0.249 0.949 1.000 0.986 1.000 102
Leukemia (acute)
GSTM1 null null vs. present 0.28–0.57W 1.20 1.14–1.25 8.6×10−15 No No 19 3532 1.0 0.841 <0.001 <0.001 <0.001 <0.001 22
GSTP1 Ile105Val GA + GG vs. AA 0.25–0.35W 1.09 1.01–1.16 0.0147 No No 8 1571 1.0 0.999 0.869 1.000 0.869 1.000 22
GSTT1 null null vs. present 0.08–0.32W 1.19 1.14–1.29 3.5×10−8 No No 17 3484 1.0 0.581 0.023 0.960 0.039 0.976 22
MTHFR C677T TT vs. CT+CC 0.27–0.43W 0.84 0.71–0.99 0.0398 No No 13 2191 0.997 0.538 0.974 1.000 0.986 1.000 115
Lung6
CYP1A1 MspI (T3801C) MspI/MspI vs. not present 0.22W 2.36 1.16–4.81 0.0180 No No 17 1759 0.106 0.031 0.994 1.000 0.998 1.000 116
CYP1A1 exon7 poor AG+ GG vs. AA 0.26S 1.61 1.24–2.08 0.0003 No Yes 11 1176 0.294 0.012 0.477 0.999 0.956 1.000 117
CYP2D6 poor vs. extensive 0.08W 0.69 0.52–0.90 0.0080 - No 17 7504 0.600 0.082 0.912 1.000 0.987 1.000 118
GSTT1 metabolizer5 null null vs. present 0.54S 1.28 1.10–1.49 0.0014 No No 8 1364 0.980 0.203 0.596 0.999 0.877 1.000 119
MDM2 SNP309 GG vs. TT 0.37W, 0.48S 1.274 1.12–1.44 0.0002 - Yes 7 4276 0.995 0.188 0.162 0.995 0.505 0.999 13
mEH His113Tyr CC vs. TT 0.36W, 0.43S 0.70 0.51–0.96 0.0271 No Yes 8 986 0.619 0.140 0.977 1.000 0.995 1.000 120
MPO G463A AA vs. GG 0.23M 0.71 0.57–0.88 0.0020 No No 10 3688 0.717 0.072 0.711 1.000 0.961 1.000 121
XPA G23A GA vs. AA 0.37M 0.73 0.61–0.89 0.0011 No No 7 1913 0.815 0.095 0.694 1.000 0.951 1.000 14
XPC Lys939Gln CC vs. CA+AA 0.38W,0.36S, 0.28A 1.304 1.11–1.53 0.0014 No No 6 2580 0.957 0.168 0.625 0.999 0.905 1.000 84
XPD Lys751Gln CC vs. AA 0.30M 1.30 1.13–1.49 0.0002 No No 15 5004 0.980 0.125 0.143 0.994 0.566 0.999 14
XRCC1 Arg399Gln AA vs. GG 0.27–0.46S 1.34 1.16–1.54 5.2×10−5 No No 6 1702 0.944 0.060 0.038 0.975 0.383 0.998 17
Non-melanoma skin
XRCC3 Thr241Met TT vs. CC +CT 0.30–0.41W 0.76 0.62–0.93 0.0080 No No 4 1599 0.898 0.186 0.896 1.000 0.976 1.000 122
Meningioma
BRIP1 rs4968451 AC vs. AA 0.15W 1.61 1.26–2.06 0.0001 - No 5 631 0.287 0.010 0.347 0.998 0.940 1.000 123
Non-Hodgkin Lymphoma
IL10 −3575T>A TA+AA vs. TT 0.36W 1.11 1.01–1.23 0.0379 - No 8 3030 1.0 0.932 0.979 1.000 0.980 1.000 124
IL1RN 9589A>T AT +TT vs. AA 0.27W 1.08 1.00–1.17 0.0547 - No 8 3020 1.0 0.995 0.983 1.000 0.984 1.000 124
MTHFR 677C>T TT vs. CC 0.29–0.45W 1.17 1.02–1.34 0.0241 No No 11 4121 1.0 0.643 0.959 1.000 0.973 1.000 125
TNF −308G>A GA+AA vs. GG 0.14W 1.19 1.05–1.33 0.0039 - No 8 2718 1.0 0.559 0.685 1.000 0.795 1.000 124
Ovarian
CDK6 IVS2–4184C>T CT vs. CC 0.21W 1.09 1.00–1.19 0.0521 - No 11 3597 1.0 0.984 0.982 1.000 0.982 1.000 126
CDKN1B Val109Gly GG vs. TT 0.25W 0.79 0.65–0.95 0.0149 - Yes 11 3618 0.964 0.285 0.927 1.000 0.977 1.000 126
CDKN2A/2 B *4780C>T CT vs. CC 0.27W 0.89 0.81–0.97 0.0113 - Yes 11 3601 1.0 0.933 0.888 1.000 0.895 1.000 126
Prostate
AR CAG21 >CAG21vs. ≤CAG21 0.50M 1.19 1.07–1.31 0.0008 No No 22 4274 1.0 0.568 0.279 0.997 0.405 0.999 127
AR GGN16 ≤GGN16 vs. >GGN16 0.50W 1.31 1.06–1.61 0.0113 No No 8 1918 0.901 0.202 0.919 1.000 0.981 1.000 127
CDH1 −160C>A AA+CA vs. CC 0.14–0.61M 1.31 1.08–1.60 0.0071 No Yes 8 2633 0.908 0.195 0.899 1.000 0.977 1.000 105
CYP17 rs2486758 TC vs. TT 0.21M 1.07 1.00–1.14 0.043 - No 7 7914 1.0 1.0 0.973 1.000 0.973 1.000 89
CYP17 rs6892 AG vs. AA 0.18M 1.08 1.00–1.15 0.0309 - No 7 8013 1.0 0.999 0.942 1.000 0.942 1.000 89
RNASEL Asp541Glu GT +GG vs. TT 0.42–0.57W 1.27 1.13–1.44 0.0001 - No 6 3038 0.995 0.188 0.162 0.995 0.505 0.999 15
Upper digestive tract
XRCC1 Arg399Gln AG+GG vs. AA 0.28–0.47M 0.85 0.75–0.98 0.0172 No No 7 1672 1.0 0.607 0.962 1.000 0.976 1.000 128
Urothelial
CDH1 −160C>A AA vs. CC 0.23–0.43W, 0.14–0.61S 2.57 1.55–4.24 0.0002 No No 3 558 0.018 0.001 0.926 1.000 0.994 1.000 105
1

Minor allelic frequency for WWhites, SAsians, MMixedor AAfricans or frequency at risk for variants that are not SNPs.

2

Evidence for publication bias and heterogeneity represent whether quality assessment of studies was performed and the corresponding results from those tests as reported by each published meta- or pooled analysis. “−” Dash indicates unclear whether test was performed.

3

Statistical power to detect an OR of 1.5 (0.67=1/1.5) or an OR of 1.2 (0.83=1/1.2)

4

Fixed effect estimate

5

Phenotype and genotype methods of detection.

6

Although HRAS1 alleles were significantly associated with breast cancer this finding is the consequence of an error in genotyping - see text.

*

Shading indicates noteworthiness of association at 0.2 level