|
SNPa
|
Risk Alleleb
|
Locus
|
hetc
|
hom
|
AA
|
BB
|
NC
|
N
|
CHI sq
|
Direction
|
% LOHd
|
N LOH
|
Affy SNP
|
Rsquared
|
|---|
|
rs1243180
|
NA
|
10p12
| | | | | | | | | | | | |
|
rs1243188
|
minor/A
|
10p12
|
112
|
183
|
22
|
6
|
41
|
364
|
0.0025
|
yes
|
0.20
|
28
|
SNP_A-2024177
|
0.881
|
|
rs7098100
|
minor/B
|
10p12
|
132
|
181
|
1
|
9
|
41
|
364
|
0.0114
|
yes
|
0.07
|
10
|
SNP_A-8636193
|
0.781
|
|
rs757210
|
NA
|
17q12
| | | | | | | | | | | | |
|
rs11658063
|
minor/B
|
17q12
|
23
|
148
|
44
|
44
|
105
|
364
|
1.0000
|
.
|
0.79
|
88
|
SNP_A-8714923
|
0.704
|
|
rs9303542
|
NA
|
17q21
| | | | | | | | | | | | |
|
rs4451990
|
minor/B
|
17q21
|
20
|
197
|
49
|
61
|
37
|
364
|
0.2526
|
.
|
0.85
|
110
|
SNP_A-2282117
|
1
|
|
rs12944592
|
minor/B
|
17q21
|
24
|
198
|
54
|
60
|
28
|
364
|
0.5741
|
.
|
0.83
|
114
|
SNP_A-1836563
|
1
|
|
rs12452212
|
minor/A
|
17q21
|
19
|
196
|
74
|
53
|
22
|
364
|
0.0624
|
yes
|
0.87
|
127
|
SNP_A-2128564
|
1
|
|
rs9894812
|
minor/A
|
17q21
|
20
|
198
|
70
|
48
|
28
|
364
|
0.0428
|
yes
|
0.86
|
118
|
SNP_A-2209606
|
1
|
|
rs8170
|
NA
|
19p13
| | | | | | | | | | | | |
|
rs34084277
|
minor/B
|
19p13
|
80
|
260
|
9
|
8
|
7
|
364
|
0.8084
|
.
|
0.18
|
17
|
SNP_A-1788674
|
1
|
|
rs2072590
|
NA
|
2q31
| | | | | | | | | | | | |
|
rs711830
|
minor/B
|
2q31
|
77
|
160
|
8
|
14
|
105
|
364
|
0.2008
|
.
|
0.22
|
22
|
SNP_A-8652216
|
0.965
|
|
rs7651446
|
NA
|
3q25
| | | | | | | | | | | | |
|
rs344008
|
minor/A
|
3q25
|
58
|
297
|
2
|
3
|
4
|
364
|
0.6547
|
.
|
0.08
|
5
|
SNP_A-8543714
|
0.85
|
|
rs2292336
|
minor/B
|
3q25
|
48
|
299
|
2
|
5
|
10
|
364
|
0.2568
|
.
|
0.13
|
7
|
SNP_A-8587822
|
0.85
|
|
rs17380639
|
minor/A
|
3q25
|
28
|
320
|
11
|
3
|
2
|
364
|
0.0325
|
yes
|
0.33
|
14
|
SNP_A-2078455
|
0.85
|
|
rs11782652
|
minor/B
|
8q21
|
38
|
291
|
8
|
7
|
20
|
364
|
0.7963
|
.
|
0.28
|
15
|
SNP_A-8702651
|
.
|
|
rs10088218
|
major/A
|
8q24
|
47
|
280
|
11
|
11
|
15
|
364
|
1.0000
|
.
|
0.32
|
22
|
SNP_A-1801410
|
.
|
|
rs1516974
|
major/A
|
8q24
|
45
|
291
|
4
|
15
|
9
|
364
|
0.0116
|
no
|
0.30
|
19
|
SNP_A-2088878
|
1
|
|
rs3814113
|
NA
|
9p22
| | | | | | | | | | | | |
|
rs7032221
|
major/B
|
9p22
|
123
|
201
|
6
|
11
|
23
|
364
|
0.2253
|
yes
|
0.12
|
17
|
SNP_A-8603886
|
1
|
|
rs10738467
|
major/B
|
9p22
|
111
|
206
|
5
|
11
|
31
|
364
|
0.1336
|
yes
|
0.13
|
16
|
SNP_A-8328297
|
0.892
|
|
rs10962668
|
major/B
|
9p22
|
103
|
177
|
7
|
22
|
55
|
364
|
0.0053
|
yes
|
0.22
|
29
|
SNP_A-4198891
|
0.794
|
- a SNPs in bold are those named in the GWAS iCOG publication [29] All others are linked as indicated by the R-squared value of >0.7. If the minor allele is the risk allele named, it is assumed that this will also be the case for the linked SNP
- b Minor = risk allele is the less frequent allele in the population. A, B = risk allele corresponds to the “A” or “B” allele respectively in the Affymetrix array nomenclature. NA = not on Affymetrix SNP6 array
- c Het = Number of cases where germline and tumour are heterozygous, hom = cases where germline is heterozygous, AA, BB = germline is heterozygous, tumour is homozygous for A or B respectively, NC = no call in either tumour or germline. N = total number
- d % LOH is the number of individuals with loss of one allele divided by the total number of heterozygous individuals as measured at that SNP, i.e. not the overall % of LOH that could be determined from all cases using a wider genetic window. This may therefore include regions of extreme allelic imbalance (e.g. likely for 8q24)
