Background
Methods
Data sets
Experiments
Results
Subsets | Components (dbSNP_rs on chromosome) | CV HMSS (Bootstrap mean and 95% CI) | Total CV accuracy (Bootstrap mean and 95% CI) | Test HMSS (Bootstrap mean and 95% CI) | Total test accuracy (Bootstrap mean and 95% CI) |
---|---|---|---|---|---|
LDA
| |||||
1 SNP* | rs10905106 on 10 | 0.498(0.498, 0.475-0.518) | 0.495(0.496, 0.474-0.516) | 0.544(0.494, 0.469-0.519) | 0.553(0.508, 0.486-0.532) |
2 SNPs* | rs10958357 on 8 rs7973936 on 12 | 0.486(0.499, 0.480-0.520) | 0.495(0.500, 0.481-0.521) | 0.556(0.498, 0.471-0.525) | 0.565(0.512, 0.491-0.535) |
1 SNP∆
| rs4375421 on 11 | 0.540(0.497, 0.474-0.519) | 0.540(0.498, 0.476-0.518) | 0.492(0.500, 0.476-0.529) | 0.491(0.499, 0.474-0.529) |
2 SNPs∆
| rs950753 on 3 rs7058025 on X | 0.570(0.493, 0.468-0.514) | 0.575(0.508, 0.486-0.530) | 0.463(0.476, 0.451-0.502) | 0.459(0.473, 0.450-0.498) |
FS | 38 SNPs | 0.604(0.500, 0.478-0.520) | 0.622(0.503, 0.482-0.523) |
0.520(0.496, 0.472-0.524)
|
0.514(0.491, 0.466-0.518)
|
SFFS | 32 SNPs | 0.622(0.497, 0.475-0.520) | 0.622(0.502, 0.479-0.525) | 0.512(0.498, 0.472-0.523) | 0.509(0.498, 0.473-0.522) |
sIB
| |||||
1 SNP* | rs12191877 on 6 | 0.611(0.605, 0.563-0.630) | 0.611(0.608, 0.580-0.631) | 0.668(0.668, 0.641-0.694) | 0.699(0.698, 0.676-0.720) |
2 SNPs* | rs12191877 on 6 rs4953658 on 2 | 0.557(0.444, 0.014-0.633) | 0.574(0.550, 0.426-0.633) |
0.674(0.674, 0.650-0.698)
|
0.685(0.684, 0.662-0.707)
|
FS | rs12191877 on 6 | 0.611(0.605, 0.563-0.630) | 0.611(0.608, 0.580-0.631) | 0.668(0.668, 0.641-0.694) | 0.699(0.698, 0.676-0.720) |
SFFS | rs2844627 on 6 rs7773175 on 6 | 0.619(0.617, 0.576-0.641) | 0.616(0.615, 0.585-0.638) | 0.659(0.658, 0.633-0.683) | 0.677(0.676, 0.655-0.699) |
Subsets | Components | Test accuracy among controls with ≥0.4 among cases(Bootstrap mean and 95% CI) | Components | Test accuracy among cases with ≥0.4 among controls(Bootstrap mean and 95% CI) |
---|---|---|---|---|
LDA
| ||||
1 SNP | rs7507133 on 19 |
0.582(0.586, 0.555-0.613)
| rs231390 on 2 |
0.607(0.591, 0.558-0.628)
|
2 SNPs,based on all combinations | ___* | ___* | ____ Δ
| ____ Δ
|
sIB
| ||||
1 SNP | rs12191877 on 6 | 0.761(0.760, 0.735-0.785) | rs7773175 on 6 | 0.731(0.731, 0.694-0.764) |
2 SNPs-based on all combinations | rs12191877 on 6 rs3823418 on 6 |
0.850(0.850, 0.826-0.870)
| rs1265078 on 6 rs1466215 on 4 |
0.749(0.748, 0.718-0.779)
|
Chr | LDA | sIB | |||||
---|---|---|---|---|---|---|---|
SNP_RS
|
Training HMSS
|
Test HMSS
|
Training HMSS
|
Test HMSS
|
P
-value(GRU) *
|
P
-value(ADO) *
| |
rs12191877 | 6 | 0.611 | 0.315 | 0.611 | 0.668 |
0
|
0
|
rs2894207 | 6 | 0.603 | 0.387 | 0.603 | 0.657 |
0
|
1.11 × 10
-16
|
rs3130517 | 6 | 0.600 | 0.414 | 0.600 | 0.608 |
0
|
4.33 × 10
-15
|
rs2394895 | 6 | 0.598 | 0.425 | 0.598 | 0.620 |
0
|
1.13 × 10
-14
|
rs2844627 | 6 | 0.598 | 0.413 | 0.598 | 0.627 |
0
|
0
|
rs3130713 | 6 | 0.597 | 0.400 | 0.597 | 0.599 |
5.55 × 10
-16
|
1.52 × 10
-14
|
rs3130467 | 6 | 0.596 | 0.415 | 0.596 | 0.605 |
1.11 × 10
-16
|
2.73 × 10
-14
|
rs9468933 | 6 | 0.595 | 0.321 | 0.595 | 0.656 |
0
|
0
|
rs7773175 | 6 | 0.585 | 0.416 | 0.585 | 0.604 |
0
|
1.33 × 10
-15
|
rs6861600 | 5 | 0.569 | 0.456 | 0.569 | 0.544 | 7.48 × 10-4
|
2.32 × 10
-8
|
rs9380237 | 6 | 0.569 | 0.405 | 0.569 | 0.628 |
0
|
1.38 × 10
-10
|
rs6887695 | 5 | 0.568 | 0.454 | 0.568 | 0.546 | 7.46 × 10-4
|
3.96 × 10
-8
|
rs3823418 | 6 | 0.568 | 0.342 | 0.120 | 0.142 |
0
|
1.11 × 10
-16
|
rs1265078 | 6 | 0.565 | 0.434 | 0.565 | 0.561 |
5.29 × 10
-11
|
3.44 × 10
-12
|
rs2647087 | 6 | 0.564 | 0.443 | 0.564 | 0.573 |
1.25 × 10
-8
|
1.21 × 10
-8
|
rs2858333 | 6 | 0.564 | 0.444 | 0.564 | 0.572 |
5.65 × 10
-8
|
1.23 × 10
-8
|
rs3132965 | 6 | 0.564 | 0.434 | 0.564 | 0.574 |
2.57 × 10
-9
|
6.62 × 10
-9
|
rs10947208 | 6 | 0.563 | 0.442 | 0.563 | 0.554 | 2.77 × 10-5
|
3.71 × 10
-8
|
rs9266846 | 6 | 0.562 | 0.458 | 0.562 | 0.548 | 1.31 × 10-5
| 3.03 × 10-7
|
rs497150 | 22 | 0.562 | 0.486 | 0.562 | 0.490 | 0.22062 | 1.67 × 10-5
|