Background
Methods
Subjects
Pooled DNA sequencing
Genotyping in Trio Families
SNaPshot
Estimated minor allele frequency | Estimated relative risk (for minor allele frequency >0.15) | ||||
---|---|---|---|---|---|
Locus | rsID | Control pool | HLA-DRB1*1501 positive pool | HLA-DRB1*1501 negative pool | Familial pool |
CCL2
| |||||
-2581A>G
|
1024611
|
0.5
|
0.9
|
0.8
|
0.7
|
-2138A>T
|
1024610
|
0.3
|
1.2
|
1.5
|
1.5
|
CCL11
| |||||
-488C>A
|
17735961
|
0.2
|
1.2
|
1.2
|
1.3
|
67G>A (A>T)
+
|
3744508
|
0.1
|
-
|
-
|
-
|
CCL8
| |||||
-572C>T
|
3138035
|
0.3
|
1.1
|
1.0
|
1.2
|
† 205A>C (K>Q)+
| 3138038 | 0.2 | 0.8 | 0.8 | 0.7 |
CCL5 (-)
| |||||
-471C>T
|
2107538
|
0.2
|
1.2
|
1.3
|
1.1
|
CCL16 (-)
| |||||
-595C>A
|
854680
|
0.1
|
-
|
-
|
-
|
CCL14 (-)
| |||||
-649T>A
|
854682
|
0.2*
|
1.1*
|
1.0*
|
1.4*
|
CCL15 (-)
| |||||
-1284A>C
|
854628
|
<0.1
|
-
|
Undetectable
|
-
|
136+88C>T
|
Novel
|
0.3
|
0.8
|
0.6
|
0.5
|
CCL23 (-)
| |||||
-289A>C
|
854655
|
0.2*
|
0.7*
|
0.5*
|
1.0*
|
316T>C (M>V)+
|
1003645
|
0.2*
|
1.0*
|
0.7*
|
1.0*
|
SNPlex™
Additional genotyping of validation cohort
Analyses & statistics
Results
Identification and analysis of SNPs in CC chemokine genes by DNA pool sequencing
Population genetics of individually genotyped markers
(a) 5' block | ||||
---|---|---|---|---|
CCL2 -2581A>G |
CCL2 -2138A>T |
CCL11 -488C>A |
CCL11 67G>A | Haplotype Frequency |
Haplotypes | ||||
A | A | C | G | 0.33 |
G | A | C | G | 0.29 |
A | A | A | A | 0.19 |
A | T | C | G | 0.18 |
Minor allele frequency | ||||
G | T | A | A | |
0.29 | 0.19 | 0.19 | 0.20 | |
(b) 3' block | ||||
CCL14 -649T>A |
CCL15 -1284A>C |
CCL23 316T>C |
CCL23 -289A>C | Haplotype Frequency |
Haplotypes | ||||
T | A | T | A | 0.76 |
A | A | C | C | 0.12 |
A | C | C | C | 0.07 |
Minor allele frequency | ||||
A | C | C | C | |
0.23 | 0.08 | 0.20 | 0.20 | |
(c) Minor allele frequencies of remaining SNPs | ||||
SNP | Minor allele frequency | |||
CCL8 -572C>T | T 0.37 | |||
CCL5 -471C>T | T 0.19 | |||
CCL16 -595C>A | A 0.22 | |||
CCL15 136+88C>T | T 0.05 |
Linkage disequilibrium and haplotypes
Analysis for transmission distortion across single markers and haplotypes
Single-locus transmission disequilibrium
Locus | All families | HLA-DRB1*1501 positive | HLA-DRB1*1501 negative | RR-MS | SP-MS | Male | Female | |||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
T:N | P | T:N | P | T:N | P | T:N | P | T:N | P | T:N | P | T:N | P | |
*CCL2 -2581A>G | 79:89 | 0.4 | 48:57 | 0.4 | 31:32 | 0.9 | 51:68 | 0.1 | 21:16 | 0.4 | 16:13 | 0.60 | 63:76 | 0.3 |
*CCL2 -2138A>T | 56:75 | 0.1 | 35:41 | 0.5 | 21:34 | 0.08 | 41:56 | 0.1 | 12:15 | 0.6 | 13:13 | 1 | 43:62 | 0.06 |
CCL11 -488C>A | 88:96 | 0.6 | 45:59 | 0.2 | 43:37 | 0.5 | 68:69 | 0.9 | 15:17 | 0.7 | 20:22 | 0.8 | 68:74 | 0.6 |
*CCL11 67G>A | 71:65 | 0.6 | 39:37 | 0.8 | 32:28 | 0.6 | 54:46 | 0.4 | 14:13 | 0.8 | 15:15 | 1 | 56:50 | 0.6 |
CCL8 -572C>T | 143:127 | 0.3 | 84:78 | 0.6 | 59:49 | 0.3 | 107:96 | 0.4 | 23:22 | 0.9 | 28:32 | 0.6 | 115:95 | 0.2 |
*CCL5 -471C>T | 64:70 | 0.6 | 45:35 | 0.3 |
19:35
|
0.03
| 47:50 | 0.8 | 14:13 | 0.9 | 14:18 | 0.5 | 50:52 | 0.8 |
CCL16 -595C>A | 103:91 | 0.4 | 58:53 | 0.6 | 45:38 | 0.4 | 76:66 | 0.4 | 14:19 | 0.4 | 19:19 | 1 | 84:72 | 0.3 |
CCL14 -649T>A | 100:88 | 0.4 | 64:49 | 0.2 | 36:39 | 0.7 |
81:56
|
0.03
|
9:22
|
0.02
| 17:21 | 0.5 | 83:67 | 0.2 |
*CCL15 136+88C>T | 18:10 | 0.1 | 11:6 | 0.2 | 7:4 | 0.4 | 15:6 | 0.05 | 2:3 | 0.7 | 2:3 | 0.7 | 16:7 | 0.06 |
*CCL15 -1284A>C | 29:27 | 0.8 | 21:20 | 0.9 | 8:7 | 0.8 | 25:17 | 0.2 | 2:5 | 0.3 | 3:6 | 0.3 | 26:21 | 0.5 |
CCL23 316T>C | 85:90 | 0.7 | 54:57 | 0.8 | 31:33 | 0.8 | 70:58 | 0.3 |
8:21
|
0.02
| 13:22 | 0.1 | 72:68 | 0.7 |
*CCL23 -289A>C | 62:71 | 0.4 | 42:42 | 1 | 20:29 | 0.2 | 51:46 | 0.6 | 9:17 | 0.1 |
8:19
|
0.03
| 54:52 | 0.9 |
Haplotype TDT
Haplotype | Frequency | Transmitted | Non-transmitted | χ2(1df) | P (uncorrected) |
---|---|---|---|---|---|
(a) Local cohort | |||||
5' haplotype block | |||||
4-marker haplotypes | |||||
CCL2 -2581.CCL2 -2138.CCL11 -488.CCL11 67 (n = 162 trio families) | |||||
A.A.C.G | 0.33 | 57.0 | 85.0 | 5.50 | 0.02 |
A.T.C.G | 0.18 | 61.0 | 40.0 | 4.36 | 0.04 |
3-marker haplotypes | |||||
CCL2 -2581.CCL2 -2138.CCL11 -488 (n = 162 trio families) | |||||
A.A.C | 0.33 | 56.0 | 86.0 | 6.33 | 0.01 |
A.T.C | 0.18 | 61.0 | 40.0 | 4.36 | 0.04 |
CCL2 -2138.CCL11 -488.CCL11 67 (n = 162 trio families) | |||||
A.C.G | 0.63 | 70.1 | 92.0 | 2.96 | 0.09 |
T.C.G | 0.18 | 60.9 | 40.0 | 4.34 | 0.04 |
2-marker haplotypes | |||||
CCL2 -2581.CCL2 -2138 (n = 204 trio families) | |||||
A.A | 0.52 | 89.1 | 117.1 | 3.80 | 0.05 |
CCL2 -2138.CCL11 -488 (n = 162 trio families) | |||||
A.C | 0.62 | 69.2 | 93.1 | 3.50 | 0.06 |
T.C | 0.18 | 60.8 | 39.9 | 4.32 | 0.04 |
(b) Independent cohort (n = 169 trio families)CCL2 -2138.CCL11 -488 | |||||
A.C | 0.63 | 75.1 | 86.0 | 0.74 | 0.4 |
T.C | 0.20 | 59.9 | 52.0 | 0.56 | 0.5 |
(c) Combined dataset (n = 331 trio families) CCL2 -2138.CCL11 -488 | |||||
A.C | 0.62 | 144.4 | 179.1 | 3.73 | 0.05 |
T.C | 0.19 | 120.6 | 91.9 | 3.89 | 0.05 |