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Table 2 Odds ratios (ORs) for top 5 SNP-mutation associations, by mutation type

From: Gastrointestinal stromal tumors: a case-only analysis of single nucleotide polymorphisms and somatic mutations

KIT exon 11 codon 557–558 deletion Gene MMP10 MMP1 MMP10 SELP GRN
SNP rs3819099 rs17293642 rs17293348 rs6131 rs5848
MAF a 0.11/0.20 0.11/0.20 0.12/0.20 0.18/0.30 0.31/0.45
OR (95% CI) 2.29 (1.30, 4.01) 2.17 (1.25, 3.77) 2.16 (1.24, 3.77) 1.81 (1.18, 2.78) 1.78 (1.17, 2.73)
p-value 0.004 0.006 0.007 0.007 0.007
KIT exon 11 other (non-codon 557–8) deletion Gene ITGAE CDK2 FCER1G ZAP70 LIF
SNP rs1716 rs2069398 rs11421 rs2276645 rs737812
MAF a 0.25/0.45 0.07/0.19 0.15/0.27 0.40/0.22 0.35/0.20
OR (95% CI) 2.86 (1.71, 4.78) 2.62 (1.34, 5.13) 2.13 (1.24, 3.64) 0.49 (0.28, 0.83) 0.47 (0.26, 0.83)
p-value 0.00006 0.005 0.006 0.008 0.01
KIT exon 11 insertion Gene SH2B3 CLCF1 GZMB IFI16 GMIP
SNP rs3184504 rs17608 rs8192917 rs866484 rs880090
MAF a 0.43/0.23 0.32/0.48 0.24/0.41 0.26/0.44 0.32/0.48
OR (95% CI) 0.31 (0.15, 0.64) 2.55 (1.38, 4.72) 2.33 (1.28, 4.24) 2.36 (1.27, 4.40) 2.20 (1.23, 3.94)
p-value 0.002 0.003 0.006 0.007 0.008
KIT exon 11 point mutation Gene MMP7 PTGER3 PTPN12 MMP7 SLAMF1
SNP rs10502001 rs959 rs3750050 rs14983 rs2295612
MAF a 0.18/0.29 0.18/0.31 0.16/0.29 0.19/0.29 0.17/0.07
OR (95% CI) 2.20 (1.32, 3.66) 1.99 (1.25, 3.17) 2.01 (1.25, 3.25) 2.03 (1.22, 3.39) 0.33 (0.15, 0.74)
p-value 0.003 0.004 0.004 0.006 0.007
Other KIT mutation Gene LILRA4 LAG3 IL4R MMP1 ITGAE
SNP rs2241384 rs870849 rs1805015 rs4754880 rs1716
MAF a 0.17/0.36 0.36/0.42 0.18/0.36 0.18/0.36 0.27/0.50
OR (95% CI) 2.89 (1.36, 6.16) 2.76 (1.33, 5.74) 2.75 (1.32, 5.75) 2.49 (1.22, 5.09) 2.46 (1.22, 4.99)
p-value 0.006 0.007 0.007 0.01 0.01
PDGFRA mutation Gene IL10 F13A1 PLAU PECAM1 SPINK5
SNP rs3024498 rs1050783 rs4065 rs1050382 rs6892205
MAF a 0.21/0.41 0.14/0.33 0.46/0.24 0.47/0.31 0.49/0.31
OR (95% CI) 0.31 (0.16, 0.60) 0.31 (0.16, 0.61) 2.65 (1.37, 5.13) 0.43 (0.24, 0.78) 2.31 (1.26, 4.24)
p-value 0.0004 0.0007 0.004 0.006 0.007
Wild type Gene TAPBP ESR1 NCF2 STAT2 FGA
SNP rs2071888 rs6557171 rs2274064 rs2066807 rs6050
MAF a 0.48/0.29 0.38/0.46 0.43/0.38 0.06 /0.15 0.26/0.39
OR (95% CI) 0.37 (0.20, 0.67) 2.26 (1.35, 3.79) 2.35 (1.34, 4.13) 3.00 (1.32, 6.83) 2.02 (1.19, 3.44)
p-value 0.001 0.002 0.003 0.009 0.009
  1. aMinor allele frequency (MAF) among those without mutation / MAF among those with mutation.