Skip to main content

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.
Back to article page

Clinical Sarcoma Research

ISSN: 2045-3329