Background
Methods
Subjects
Genotyping
Single nucleotide polymorphism (SNP) selection
Sequenom assay
Statistical analysis
Error checking
Association analysis
Multiple testing correction
Results
Family-based studies
LD block/Tagb | Haplotypea | TR | NT | OR | CI | P-value |
---|---|---|---|---|---|---|
Block 2 (rs716546-rs716547-rs9971243) | CCT | 75 | 52 | 1.44 | (1.01, 2.05) | 0.0505 |
Block 2 (rs716546-rs716547-rs9971243) | CTC | 2 | 10 | 0.20 | (0.04, 0.91) | 0.0386 |
rs6480245, rs12266823
b
| GA | 44 | 84 | 0.52 | (0.36, 0.75) | 0.0005 |
rs6480245, rs12266823
b
| GC | 242 | 186 | 1.30 | (1.07, 1.58) | 0.0078 |
Gene | LD block/Tagb | Hapa | IMGSAC(Multiplex families) | IMGSAC(Singleton families) |
Northern Dutch
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
TR
|
NT
|
OR/CI
|
P
-value
|
TR
|
NT
|
OR/CI
|
P
-value
|
TR
|
NT
|
OR/CI
|
P
-value
| |||
LRRN3
| Block 2 (rs10261004-rs214884) | GC | 9 | 26 | 0.35 (0.16, 0.74) | 0.005 | ||||||||
LRRN3
| Block 2 (rs10261004-rs214884) | TT | 44 | 20 | 2.20 (1.30, 3.73) | 0.004 | ||||||||
LRRN1
| Block 3 (rs10510278-rs696489) | AC | 98 | 70 | 1.40 (1.03, 1.90) | 0.037 | ||||||||
LRRN1
| Block 3 (rs10510278-rs696489) | TT | 61 | 85 | 0.72 (0.52, 1.00) | 0.057 | ||||||||
LRRN1
| rs10780025, rs13100776
b
| AT | 18 | 37 | 0.49 (0.28, 0.85) | 0.014 | ||||||||
LRRTM3
| rs1925613, rs10762138
b
| CT | 8 | 20 | 0.40 (0.18, 0.91) | 0.036 | ||||||||
LRRTM3
| rs1925613, rs1925624
b
| AT | 139 | 102 | 1.36 (1.06, 1.76) | 0.020 | ||||||||
LRRTM3
| rs2619652, rs12785206
b
| CC | 18 | 7 | 2.57 (1.07, 6.16) | 0.043 | ||||||||
LRRTM3
| rs2619652, rs12785206
b
| TT | 9 | 22 | 0.41 (0.19, 0.89) | 0.029 | ||||||||
LRRTM3
| rs1925613, rs12785206
b
| CT | 8 | 21 | 0.38 (0.17, 0.86) | 0.024 |
Case-control study
SNP
|
Population
|
Model
|
OR
|
CI
|
P-value
|
---|---|---|---|---|---|
rs10261004 | Northern Dutch | Additive G | 0.44 | (0.26, 0.75) | 3.00E-03 |
rs10261004 | Northern Dutch | TT versus GG/GT | 2.42 | (1.33, 4.41) | 4.00E-03 |
rs1998753 | Northern Dutch | Additive G | 0.10 | (0.05, 0.20) | 5.68E-12 |
rs1998753 | Northern Dutch | AG versus GG/AA | 9.64 | (5.06, 18.38) | 5.68E-12 |
rs17279006 | Overall | Additive G | 0.62 | (0.45, 0.84) | 2.22E-03 |
rs17279006 | Overall | AA versus GG/AG | 1.65 | (1.19, 2.29) | 2.59E-03 |
rs17279006 | Multiplex (IMGSAC) | AA versus GG/AG | 2.14 | (1.28, 3.59) | 3.96E-03 |
rs17279006 | Multiplex (IMGSAC) | Additive G | 0.49 | (0.30, 0.79) | 4.00E-03 |
rs1925613 | Overall | CC versus AA/AC | 1.81 | (1.37, 2.39) | 2.97E-05 |
rs1925613 | Overall | Additive C | 1.35 | (1.16, 1.57) | 7.82E-05 |
rs1925613 | Singleton (IMGSAC) | CC versus AA/AC | 3.01 | (1.66, 5.47) | 2.81E-04 |
rs1925613 | Singleton (IMGSAC) | Additive C | 1.80 | (1.27, 2.54) | 8.97E-04 |
rs10997482 | Overall | Additive G | 1.38 | (1.20, 1.60) | 9.81E-06 |
rs10997482 | Overall | GG versus AA/AG | 1.60 | (1.27, 2.00) | 4.63E-05 |
rs10997482 | Singleton (IMGSAC) | Additive A | 0.54 | (0.38, 0.77) | 6.85E-04 |
rs10997482 | Singleton (IMGSAC) | GG versus AA/AG | 2.41 | (1.45, 4.03) | 7.45E-04 |
rs2619652 | Overall | Additive T | 0.76 | (0.67, 0.88) | 1.57E-04 |
rs2619652 | Overall | TT versus CC/CT | 0.63 | (0.49, 0.81) | 2.71E-04 |
rs2619652 | Singleton (IMGSAC) | Additive T | 0.58 | (0.41, 0.82) | 1.95E-03 |
rs2619652 | Singleton (IMGSAC) | TT versus CC/CT | 0.34 | (0.17, 0.69) | 2.56E-03 |
rs10740268 | Overall | TT versus CC/CT | 0.51 | (0.38, 0.70) | 2.16E-05 |
rs10740268 | Overall | Additive C | 1.84 | (1.38, 2.45) | 3.48E-05 |
rs12785206 | Overall | TT versus CC/CT | 1.49 | (1.20, 1.86) | 3.96E-04 |
rs12785206 | Singleton (IMGSAC) | CC/CT versus TT | 0.37 | (0.22, 0.65) | 4.20E-04 |
rs12785206 | Singleton (IMGSAC) | Additive C | 0.48 | (0.31, 0.74) | 1.00E-03 |