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. 2022 Jul 4;12:912208. doi: 10.3389/fonc.2022.912208

Table 1.

Genetic variants showing significant associations with OS risk in main meta-analyses.

Gene Variant Allelic a Ethnicity Number evaluation Genetic models MAF Effect model Risk of meta-analysis Venice Criteria c FPRP values d Credibility of evidence
Studies Cases/controls OR b (95%CI) I2 P Q P value
APE1 rs1760944 T>G Asian 2 378/616 Allelic 0.442 Fixed 0.692 (0.574–0.834) 0 0.701 <0.001 BAA 0.003 Strong
Dominant Fixed 0.610 (0.468–0.796) 0 0.748 <0.001 BAA 0.020 Strong
Recessive Fixed 0.642 (0.451–0.914) 0 0.867 0.014 BAA 0.388 Weak
BCAS1 rs3787547 G>A Asian 2 1300/1300 Allelic 0.300 Fixed 1.222 (1.088–1.373) 0 0.703 0.001 AAA 0.014 Strong
Dominant Fixed 1.295 (1.110–1.511) 0 0.694 0.001 AAA 0.020 Strong
CTLA-4 rs231775 A>G Overall 4 660/754 Allelic 0.623 Fixed 0.725 (0.620–0.846) 0 0.96 <0.001 AAA 0.001 Strong
Dominant Fixed 0.491 (0.360–0.668) 0 0.981 <0.001 AAA 0.004 Strong
Recessive Fixed 0.748 (0.596–0.938) 29.9% 0.233 0.012 BBC 0.212 Weak
Asian 3 594/629 Allelic 0.672 Fixed 0.723 (0.613–0.853) 0 0.862 <0.001 AAA 0.003 Strong
Dominant Fixed 0.506 (0.354–0.722) 0 0.97 <0.001 AAA 0.049 Strong
Recessive Fixed 0.717 (0.569–0.903) 0 0.711 0.005 BAA 0.109 Moderate
rs5742909 C>T Asian 3 486/533 Recessive Fixed 2.046 (1.028–4.073) 0.0% 0.591 0.042 CAC 0.807 Weak
ERCC3 rs4150441 T>C Asian 2 522/1047 Dominant Fixed 0.519 (0.357–0.755) 60.1% 0.113 0.001 ACA 0.108 Moderate
rs4150506 G>A Asian 2 522/1047 Allelic 0.230 Fixed 1.331 (1.123–1.576) 0 0.581 0.001 BAA 0.019 Strong
Dominant Fixed 1.348 (1.089–1.667) 0 0.775 0.006 BAA 0.117 Moderate
Recessive Fixed 1.622 (1.110–2.370) 0 0.498 0.012 BAA 0.408 Weak
HOTAIR rs7958904 C>G Asian 2 900/900 Allelic 0.710 Fixed 1.294 (1.115–1.501) 0 0.736 0.001 AAA 0.013 Strong
Dominant Fixed 1.636 (1.154–2.321) 0 0.961 0.006 AAA 0.260 Moderate
Recessive Fixed 1.298 (1.078–1.564) 0 0.768 0.006 BAA 0.110 Moderate
rs874945 C>T Asian 2 900/900 Allelic 0.189 Fixed 1.183 (1.006–1.393) 17.4% 0.271 0.042 BAA 0.455 Weak
IL-10 rs1800896 T>C Overall 2 340/420 Allelic 0.391 Fixed 1.326 (1.060–1.657) 0 0.557 0.013 BAA 0.224 Weak
Dominant Fixed 1.398 (1.009–1.936) 33.9% 0.219 0.044 BBA 0.556 Weak
IL-6 rs1800795 C>G Asian 2 322/322 Allelic 0.750 Random 0.563 (0.445–0.712) 0 0.805 <0.001 BAA 0.000 Strong
Recessive Random 0.420 (0.268–0.659) 47.6% 0.167 <0.001 BBA 0.121 Moderate
IL-8 rs4073 A>T Asian 2 299/299 Allelic 0.776 Fixed 0.625 (0.483–0.809) 0 0.793 <0.001 BAA 0.021 Strong
Dominant Fixed 0.598 (0.366–0.975) 0 0.949 0.039 BAA 0.692 Weak
Recessive Fixed 0.590 (0.424–0.819) 0 0.823 0.002 BAA 0.116 Moderate
MTAP rs7023329 A>G Asian 2 392/1578 Allelic 0.512 Fixed 0.712 (0.615–0.844) 0 0.540 <0.001 AAA 0.002 Strong
Dominant Fixed 0.650 (0.510–0.828) 0 0.439 <0.001 AAA 0.022 Strong
Recessive Fixed 0.641 (0.484–0.848) 0 0.855 0.002 BAA 0.082 Moderate
rs7027989 A>G Asian 2 392/1578 Allelic 0.824 Fixed 0.761 (0.627–0.923) 0 0.905 0.006 AAA 0.104 Strong
Recessive Fixed 0.757 (0.601–0.954) 0 0.760 0.018 AAA 0.288 Moderate
Dominant Fixed 0.557 (0.328–0.945) 0 0.751 0.030 AAA 0.693 Moderate
PRKCG rs454006 T>C Asian 2 998/998 Allelic 0.293 Fixed 1.347 (1.178–1.539) 0 0.826 <0.001 AAA 0.000 Strong
Dominant Fixed 1.204 (1.010–1.437) 15.4% 0.277 0.039 AAA 0.432 Moderate
Recessive Fixed 1.989 (1.536–2.575) 0 0.596 <0.001 BAA 0.000 Strong
RECQL5 rs820196 T>C Asian 2 397/441 Allelic 0.340 Fixed 1.445 (1.186–1.762) 0 0.742 <0.001 BAA 0.008 Strong
Dominant Fixed 1.487 (1.118–1.976) 0 0.844 0.006 BAA 0.184 Moderate
Recessive Fixed 2.153 (1.409–3.289) 0 0.700 <0.001 BAA 0.135 Moderate
TNF-α rs1800629 G>A Overall 2 160/259 Allelic 0.183 Fixed 1.743 (1.245–2.440) 0 0.582 0.001 BAA 0.107 Moderate
Dominant Fixed 1.640 (1.065–2.524) 0 0.427 0.025 BAA 0.576 Weak
Recessive Fixed 3.306 (1.541–7.093) 0 0.588 0.002 CAA 0.657 Weak
TP53 rs1042522 G>C Overall 3 515/744 Allelic 0.499 Fixed 0.738 (0.618–0.881) 0.0% 0.754 0.001 AAA 0.017 Strong
Dominant Fixed 0.591 (0.445–0.784) 14.5% 0.310 <0.001 BAA 0.024 Strong
G>C Caucasian 2 305/324 Allelic 0.342 Fixed 0.764 (0.584–0.999) 0.0% 0.503 0.049 BAA 0.526 Weak
Dominant Fixed 0.534 (0.364–0.783) 47.4% 0.168 0.001 BBA 0.163 Moderate
VEGF rs1570360 A>G Asian 3 527/692 Allelic 0.254 Fixed 1.229 (1.025–1.475) 0 0.774 0.026 BAC 0.341 Weak
rs2010963 C>G Asian 7 1489/1867 Allelic 0.338 Random 1.249 (1.089–1.432) 46.4% 0.083 0.001 ABA 0.027 Strong
Dominant Fixed 1.393 (1.190–1.630) 0 0.504 <0.001 AAA 0.001 Strong
Recessive Fixed 1.294 (1.098–1.524) 34.8% 0.163 0.002 BBA 0.038 Strong
rs3025039 C>T Asian 8 1671/2049 Allelic 0.230 Fixed 1.248 (1.120–1.391) 0 0.941 <0.001 AAA 0.001 Strong
Dominant Fixed 1.222 (1.066–1.399) 0 0.997 0.004 AAC 0.065 Weak
Recessive Fixed 1.596 (1.253–2.032) 0 0.702 <0.001 BAA 0.009 Strong
rs699947 A>C Asian 4 709/874 Allelic 0.679 Fixed 0.713 (0.615–0.827) 0 0.593 <0.001 AAA 0.000 Strong
Dominant Fixed 0.611 (0.462–0.810) 0 0.776 0.001 AAA 0.041 Strong
Recessive Fixed 0.685 (0.559–0.840) 0 0.687 <0.001 BAA 0.009 Strong
rs833061 C>T Asian 2 358/358 Allelic 0.624 Fixed 0.788 (0.638–0.974) 34.6% 0.216 0.027 BBA 0.358 Weak
VMP1 rs1295925 T>C Asian 2 1300/1300 Allelic 0.450 Fixed 0.847 (0.759–0.945) 0 0.597 0.003 AAA 0.053 Strong
Dominant Fixed 0.767 (0.651–0.902) 0 0.646 0.001 AAA 0.026 Strong
XRCC1 rs25487 T>C Asian 2 318/523 Allelic 0.481 Fixed 1.405 (1.132–1.745) 0 0.433 0.002 BAA 0.052 Moderate
Dominant Fixed 1.488 (1.055–2.099) 0 0.902 0.024 BAA 0.463 Weak
Recessive Fixed 1.564 (1.114–2.195) 50.1% 0.157 0.010 BCA 0.313 Weak
XRCC3 rs861539 G>A Asian 2 288/440 Allelic 0.272 Fixed 1.572 (1.252–1.975) 0 0.882 <0.001 BAA 0.006 Strong
Dominant Fixed 1.573 (1.161–2.133) 0 0.902 0.003 BAA 0.151 Moderate
Recessive Fixed 2.230 (1.395–3.566) 0 0.896 0.001 CAA 0.240 Weak

APE1, apurinic/apyrimidinic endodeoxyribonuclease 1; BCAS1, brain enriched myelin associated protein 1; CTLA4, cytotoxic T-lymphocyte associated protein 4; ERCC3, excision repair cross-complementation 3; HOTAIR, HOX transcript antisense RNA; IL-10, interleukin-10; IL-6, interleukin-6; IL-8, interleukin-8; MTAP, methylthioadenosine phosphorylase; PRKCG, protein kinase C gamma; RECQL5, RecQ like helicase 5; TNF-α, tumor necrosis factor α; TP53, tumor protein p53; VEGF, vascular endothelial growth factor A; VMP1, vacuole membrane protein 1; XRCC1, X-ray repair cross complementing 1; XRCC3, X-ray repair cross complementing 3; A, adenine; C, cytosine; G, guanine; T, thymine; OR, odds ratio; CI, confidence interval; MAF, minor allelic frequency in control; NA, not applicable; FPRP, false positive report probability.

a

Allelic: Minor allelic (bold) versus major allelic (reference).

b

OR: OR < 1, decrease the susceptibility of OS (protective factor); OR > 1, increase the susceptibility of OS (susceptive factor).

c

Venice Criteria grades are for the amount of evidence, replication of the association, and protection from bias.

d

The prior probability of FPRP is 0.05 and the FPRP level of noteworthiness is 0.20.