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Table 2 Significant SNPs after Bonferroni correction by gene (P adj)

From: A comprehensive candidate gene approach identifies genetic variation associated with osteosarcoma

Pathway Gene SNP Genomic position   Minor Allele MAF (%) Controls MAF (%) Cases OR 95% CI P P adj Model or Test§ Gene P
DNA repair FANCM rs1367580 Chr14: 44714339 Ex14+316 (V878L) T 10.4 16.7 1.97 (1.26-3.08) 0.0031 0.034 Dominant 0.019
   rs11845507 Chr14: 44721715 IVS16-1012 A 10.5 16.7 1.96 (1.25-3.06) 0.0033 0.037 Dominant  
   rs4900664 Chr14: 44732264 IVS20-2861 T 9.3 15.3 2.00 (1.25-3.17) 0.0035 0.038 Dominant  
   rs7141145 Chr14: 44733578 IVS20-1547 A 10.3 16.5 1.95 (1.24-3.07) 0.0039 0.043 Dominant  
  MDM2 rs1690916 Chr12: 67521673 downstream, no gene A 42.5 31.3 0.62 (0.45-0.85) 0.0029 0.026 Additive 0.016
  MPG rs216614 Chr16: 60334 upstream, in RHBDF1 A 0.7 3.1 4.80 -- 0.0036 0.047 Fisher's 0.027
Growth and hormone FGF2 rs11737764 Chr4: 124046230 downstream, in NUDT6 T 8.1 14.1 2.12 (1.33-3.39) 0.0016 0.036 Dominant 0.020
  FGFR3 rs6599400 Chr4: 1754823 upstream, no gene A 33.0 42.6 1.51 (1.12-2.03) 0.0069 0.021 Additive 0.017
  GH1 rs11079515 Chr17: 59359377 downstream, no gene G 37.9 49.5 1.61 (1.20-2.16) 0.0016 0.005 Additive 0.002
   rs7921 Chr17: 59359991 downstream, in CD79B A 27.2 16.1 0.52 (0.35-0.76) 0.0009 0.003 Additive  
  GNRH2 rs3761243 Chr20: 2971022 upstream, no gene C 29.7 40.5 1.60 (1.19-2.16) 0.0020 0.031 Additive 0.021
  IGF1 rs7956547 Chr12: 101382946 IVS2+10605 C 26.3 15.8 0.53 (0.36-0.79) 0.0019 0.040 Additive 0.021
  1. MAF = minor allele frequency;
  2. Odds ratios were estimated using logistic regression models with the most common allele or genotype as the referent, adjusted for gender;
  3. § Results are shown for the model or test chosen to deal with rare variants in the sequence of logistic regression on the additive trend model, logistic regression on the dominant model, or the Fisher's Exact Test.