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. 2010 Nov 23;2(1):19–29.

Supplemental Table 2.

Significant SNPs (P < 0.05) in telomere biology genes associated with osteosarcoma before correction for multiple tests

Gene SNP Minor allele MAF (%) Controls* MAF (%) Cases OR† 95% Cl P Padj Model or Test§ Gene P
ATM rsl800889 T 5.4 1.6 0.27 (0.08, 0.87) 0.028 0.833 Dominant 0.251
ATM rs228606 T 40.3 47.9 1.39 (1.03, 1.88) 0.029 0.870 Log-additive
ATM rs618499 A 43.2 36.3 0.73 (0.54, 0.99) 0.049 1.000 Log-additive
BLM rs2532105 A 15.1 19.8 1.58 (1.03, 2.42) 0.037 1.000 Dominant 0.428
BLM rs2518968 C 45.1 52.6 1.37 (1.01, 1.85) 0.042 1.000 Log-additive
DDX1 rs2890489 G 38.1 47.4 1.49 (1.11, 2.01) 0.009 0.114 Log-additive 0.071
DDX1 rslO169288 G 38.3 47.4 1.49 (1.10, 2.01) 0.010 0.125 Log-additive
DDX1 rs4668944 A 40.8 48.9 1.41 (1.05, 1.89) 0.024 0.309 Log-additive
DDX1 rs807629 G 33.4 40.6 1.38 (1.02, 1.87) 0.036 0.462 Log-additive
N0LA3 rsl7236875 C 11.2 15.6 1.62 (1.03, 2.56) 0.036 0.544 Dominant 0.321
N0LA3 rs2279686 C 48.5 56.3 1.36 (1.02, 1.83) 0.037 0.559 Log-additive
N0LA3 rs7162607 A 45.3 37.5 0.74 (0.55, 0.99) 0.043 0.647 Log-additive
PARP1 rs3219123 A 5.3 1.6 0.28 (0.09, 0.89) 0.032 0.773 Dominant 0.276
PARP2 rs3093938 G 0.00 1.04 2.4×1010 (0, inf) 0.004 0.083 Fishers Exact Test 0.034
PARP2 rs3093919 G 0.04 1.04 31.07 (2.78, 347.8) 0.011 0.238 Fishers Exact Test
PARP2 rsll622655 G 25.8 32.8 1.40 (1.02, 1.92) 0.034 0.716 Log-additive
PARP2‡ rslO147163 C 26.7 33.9 1.41 (1.03, 1.92) 0.033 0.298 Log-additive
PARP2‡ rs3093942 C 21.4 27.6 1.53 (1.01, 2.31) 0.045 0.407 Dominant
PARP2‡ rs4981998 T 24.4 30.7 1.38 (1.00, 1.90) 0.047 0.422 Log-additive
POT1 rs727505 A 29.3 22.4 0.70 (0.49, 0.99) 0.047 0.331 Log-additive 0.217
TEP1 rs2104977 A 15.2 21.4 1.56 (1.02, 2.40) 0.041 1.000 Dominant 0.674
TERF1 rs2306492 A 31.6 18.1 0.48 (0.33, 0.69) 0.0001 0.0025 Log-additive 0.0009
TERF1 rs9298211 T 31.1 18.4 0.50 (0.34, 0.72) 0.0003 0.0052 Log-additive
TERF1 rs2306494 G 31.5 18.9 0.51 (0.35, 0.74) 0.0003 0.0065 Log-additive
TERF1 rs2929585 G 30.9 18.8 0.52 (0.36, 0.75) 0.0005 0.0091 Log-additive
TERF1 rs2929586 G 30.8 18.8 0.52 (0.36, 0.75) 0.0005 0.0095 Log-additive
TERF1 rs2929593 T 31.2 19.3 0.52 (0.36, 0.75) 0.0005 0.0101 Log-additive
TERF1 rs7001277 A 31.6 19.8 0.53 (0.37, 0.76) 0.0006 0.0125 Log-additive
TERF1 rs3116136 C 23.8 30.7 1.42 (1.04, 1.94) 0.028 0.559 Log-additive
TERF1 rs6990223 T 0.95 2.6 2.72 (1.02, 7.27) 0.047 0.940 Fishers Exact Test
TERT rs4073918 C 21.9 30.2 1.51 (1.11, 2.07) 0.010 0.145 Log-additive 0.102
TINF2 rs2748516 A 5.7 9.9 2.01 (1.18, 3.41) 0.010 0.137 Dominant 0.074
TNKS rs6985140 G 7.4 13.5 2.09 (1.29, 3.38) 0.003 0.129 Dominant 0.043
TNKS rs4474027 G 6.3 10.9 1.96 (1.18, 3.26) 0.010 0.484 Dominant
TNKS rs6984737 G 6.1 10.4 1.91 (1.14, 3.21) 0.014 0.713 Dominant
TNKS rsl0090277 G 6.2 10.4 1.86 (1.11, 3.12) 0.019 0.937 Dominant
TNKS rsll249944 A 5.5 9.3 1.88 (1.08, 3.27) 0.025 1.000 Dominant
TNKS rs5002815 T 6.5 10.4 1.80 (1.07, 3.03) 0.025 1.000 Dominant
TNKS rs5002814 G 6.5 10.4 1.79 (1.07, 3.01) 0.027 1.000 Dominant
TNKS rsl0093972 C 6.6 10.4 1.76 (1.05, 2.95) 0.032 1.000 Dominant
TNKS rsll787443 T 6.9 10.5 1.72 (1.02, 2.88) 0.040 1.000 Dominant
†

Odds ratio (95% confidence intervals) using a log-additive genetic model, adjusted for gender; MAF = minor allele frequency;

*

includes orthopedic controls and controls from PLCO; Padj = Bonferroni corrected P by gene;

§

results are shown for the model or test with the best fit for the data and significant P value;

‡

these SNPs are located downstream of PARP2 and upstream of TEP1.