| Literature DB >> 29861839 |
Xiao Zhu1,2, Haibing Yu1, Qin Xiao3, Jianhao Ke4, Hongmei Li1, Zhihong Chen1, Hongrong Ding1, Shuilong Leng5, Yongmei Huang6, Jingting Zhan6, Jinli Lei6, Wenguo Fan7, Hui Luo1,6.
Abstract
CHD5 is an essential factor for neuronal differentiation and neurodegenerative diseases. Here, the targeted next generation sequencing and TaqMan genotyping technologies were carried out for CHD5 gene in a two-staged case-control study in Chinese population. The genetic statistics and gene-environment interactions were analyzed to find certain risk factors of Alzheimer's disease. We found intronic rs11121295 was associated with the risk of Alzheimer's disease at both stages including combined cohorts. This risk effect presented consistently significant associations with the alcoholic subgroups at both all stages in the stratified analysis. The gene-environment interactions further supported the above findings. Our study highlighted the potential role of CHD5 variants in conferring susceptibility to sporadic Alzheimer's disease, especially modified its risk by alcoholic intake.Entities:
Keywords: Alzheimer's disease; CHD5; Gerotarget; case-control studies; gene-environment interactions; single-nucleotide polymorphisms
Year: 2018 PMID: 29861839 PMCID: PMC5982770 DOI: 10.18632/oncotarget.23791
Source DB: PubMed Journal: Oncotarget ISSN: 1949-2553
Figure 1The association analysis of CHD5 variants with Alzheimer's disease risk and genetic mapping in the discovery study
A. Manhattan plot. The Chi square values were for the association of each variant with Alzheimer's disease risk, from two-sided Cochran-Armitage tests for trend. B. 105 permutation tests for the association analysis carried out from haploview 4.0 program (Bioinformatics 2005;21:263-5).C. and D. Q-Q plots for the test statistics of observed Chi-square values against expected Chi-square values (D, removing rs11121295). E. Linkage disequilibrium mapping. Block 1 includes SNP9~SNP10 (rs745759 and rs3888071). Block 2 includes SNP35~SNP36 (rs2273041 and rs2273040). Block 3 includes SNP115 and SNP116 (rs12564469 and rs9434711).
Association results of the selected three SNPs from next generation sequencing in discovery, replication and combined studies
| SNPs | Cases | Controls | RRHet (95% CI) | RRHom (95% CI) | |||
|---|---|---|---|---|---|---|---|
| Discovery | |||||||
| rs11121295 | 51/99/55 | 89/130/36 | 1.33 (0.86-2.05) | .197 | 2.67 (1.55-4.59) | 3.460×10-4 | 5.495×10-4 |
| rs10864393 | 55/114/36 | 49/133/73 | 0.76 (0.48-1.21) | .249 | 0.44 (0.25-0.77) | .003 | .004 |
| rs9434741 | 8/60/137 | 12/112/131 | 0.80 (0.31-2.07) | .651 | 1.57 (0.62-3.96) | .337 | .003 |
| Replication | |||||||
| rs11121295 | 105/198/94 | 174/262/74 | 1.25 (0.92-1.70) | .147 | 2.11 (1.43-3.11) | 1.603×10-4 | 2.760×10-4 |
| rs10864393 | 76/225/96 | 94/262/154 | 1.06 (0.75-1.51) | .736 | 0.77 (0.52-1.15) | .197 | .137 |
| rs9434741 | 20/173/204 | 24/236/250 | 0.88 (0.47-1.64) | .687 | 0.98 (0.53-1.82) | .947 | .605 |
| Combined | |||||||
| rs11121295 | 156/297/149 | 263/392/110 | 1.28 (1.00-1.64) | .054 | 2.28 (1.67-3.13) | 2.445×10-7 | 6.463×10-7 |
| rs10864393 | 131/339/132 | 143/395/227 | 0.94 (0.71-1.24) | .645 | 0.64 (0.46-0.87) | .005 | .003 |
| rs9434741 | 28/233/341 | 36/348/381 | 0.86 (0.51-1.45) | .573 | 1.15 (0.69-1.93) | .593 | .031 |
D,derived alleles; A, ancestral alleles; Het, heterozygous variants; Hom, homozygous variants.
Ptrend were calculated in logistical regression models with adjustment for age, gender, smoking and drinking status.
Stratification analysis for associations between rs11121295 and AD risk in the discovery, replication and combined studies
| Variables | Discovery study | Replication study | Combined study | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Cases/controls | OR (95% CI) | Cases/controls | OR (95% CI) | Cases/controls | OR (95% CI) | |||||||
| GG | AA+AG | GG | AA+AG | GG | AA+AG | |||||||
| Age (ys) | ||||||||||||
| ≤60 | Feb-33 | 20/183 | 0.56(0.12-2.49) | 0.435 | Apr-68 | 39/366 | 0.55(0.19-1.60) | 0.266 | 6/101 | 59/549 | 0.55(0.23-1.31) | 0.174 |
| >60 | 53/3 | 130/36 | 4.89(1.44-16.58) | 0.005 | 90/6 | 264/70 | 3.98(1.67-9.47) | 8.700×10-4 | 143/9 | 394/106 | 4.28(2.11-8.67) | 1.508×10-5 |
| | 0.011 | 0.003 | 8.621×10-5 | |||||||||
| Gender | ||||||||||||
| Females | 29/11 | 85/80 | 2.48(1.16-5.30) | 0.017 | 47/18 | 161/149 | 2.42(1.34-4.35) | 0.003 | 76/29 | 246/229 | 2.44(1.53-3.88) | 1.220×10-4 |
| Males | 26/25 | 65/139 | 2.22(1.19-4.15) | 0.011 | 47/56 | 142/287 | 1.70(1.10-2.63) | 0.017 | 73/81 | 207/426 | 1.86(1.30-2.65) | 6.325×10-4 |
| | 0.647 | 0.176 | 0.193 | |||||||||
| Education | ||||||||||||
| Less | 34/18 | 108/116 | 2.03(1.08-3.80) | 0.026 | 42/26 | 145/149 | 1.66(0.97-2.85) | 0.064 | 76/44 | 253/265 | 1.81(1.20-2.72) | 4.207×10-3 |
| More | 21/18 | 47/87 | 2.16(1.05-4.45) | 0.035 | 52/43 | 140/229 | 1.98(1.25-3.12) | 0.003 | 73/61 | 187/316 | 2.02(1.38-2.97) | 2943×10-4 |
| 0.743 | 0.047 | 0.07 | ||||||||||
| Smoking | ||||||||||||
| Never | 33/27 | 115/165 | 1.97(1.13-3.41) | 0.015 | 59/77 | 208/262 | 0.97(0.66-1.42) | 0.857 | 96/104 | 323/427 | 1.22(0.89-1.67) | 0.212 |
| Ever+current | 18/9 | 35/47 | 2.69(1.08-6.69) | 0.031 | 25/29 | 92/116 | 1.09(0.60-1.98) | 0.786 | 43/38 | 127/163 | 1.45(0.89-2.38) | 0.138 |
| | 0.484 | 0.917 | 0.651 | |||||||||
| Drinking | ||||||||||||
| Never | 29/26 | 113/168 | 1.66(0.93-2.96) | 0.086 | 54/55 | 189/297 | 1.54(1.02-2.34) | 0.041 | 83/81 | 302/465 | 1.58(1.13-2.21) | 0.008 |
| Ever+current | 26/7 | 37/47 | 4.72(1.85-12.07) | 6.941×10-4 | 41/18 | 98/111 | 2.58(1.39-4.78) | 0.002 | 67/25 | 135/158 | 3.14(1.88-5.24) | 7.164×10-6 |
| | 0.008 | 0.049 | 8.755×10-4 | |||||||||
P, P value for haplotype model, which obtained in logistic regression with adjustment for age, sex, smoking status and drinking status.
P, means P or P.
FPRP values for associations between AD risk and rs11121295 frequencies (GG vs. AA+AG)
| Variables | Statistical | Prior probability | |||
|---|---|---|---|---|---|
| powera | .1 | .01 | .001 | .0001 | |
| AD risk in >60 years old group | |||||
| Discovery study | .327 | .008 | .029 | .443 | .742 |
| Replication study | .552 | .005 | .010 | .288 | .539 |
| Combined study | .815 | .002 | .009 | .081 | .205 |
| AD risk in drinking group | |||||
| Discovery study | .434 | .254 | .418 | .585 | .737 |
| Replication study | .276 | .011 | .366 | .649 | .813 |
| Combined study | .691 | .004 | .010 | .203 | .516 |
MDR analysis for the prediction of AD risk with and without rs11121295
| Best interaction models | Cross-validation | Average prediction error | |
|---|---|---|---|
| Distcovery study | |||
| 1 | 94/100 | 0.392 | <.0001 |
| 1,2 | 93/100 | 0.323 | <.0001 |
| 1,2,3 | 97/100 | 0.354 | <.0001 |
| 1,2,3,4 | 98/100 | 0.225 | <.0001 |
| 1,2,3,4,5 | 90/100 | 0.329 | <.0001 |
| 1,2,3,4,5,6b | 100/100 | 0.261 | <.0001 |
| Replication study | |||
| 1 | 93/100 | 0.383 | <.0001 |
| 1,2 | 96/100 | 0.372 | <.0001 |
| 1,2,3 | 92/100 | 0.394 | <.0001 |
| 1,2,3,4 | 97/100 | 0.373 | <.0001 |
| 1,2,3,4,5 | 89/100 | 0.256 | <.0001 |
| 1,2,3,4,5,6b | 99/100 | 0.211 | <.0001 |
| Combined study | |||
| 1 | 97/100 | 0.336 | <.0001 |
| 1,2 | 97/100 | 0.312 | <.0001 |
| 1,2,3 | 90/100 | 0.375 | <.0001 |
| 1,2,3,4 | 96/100 | 0.213 | <.0001 |
| 1,2,3,4,5 | 97/100 | 0.168 | <.0001 |
| 1,2,3,4,5,6b | 100/100 | 0.134 | <.0001 |
Labels: 1, age; 2, rs11121295; 3, drinking status; 4, education; 5, gender; 6, smoking status.
a, P value for 1000-fold permutation test. b, the best model with maximum cross-validation consistency and minimum prediction error rate.
Demographics of patients with Alzheimer’s disease and controls in three study cohorts
| Characteristics | Discovery cohort | Replicative cohort | Combined cohort | ||||||
|---|---|---|---|---|---|---|---|---|---|
| Cases | Controls | Cases | Controls | Cases | Controls | ||||
| No.of subjects | 205 | 255 | 397 | 510 | 602 | 765 | |||
| Origin | NC | NC | SC | SC | NC+SC | NC+SC | |||
| Females, n (%) | 114 (55.61) | 91 (35.69) | <.001a | 208 (52.39) | 167 (32.75) | <.001a | 322 (53.49) | 258 (33.73) | <.001a |
| Age (mean ± SD) | 73.5±10.2 | 41.5±9.1 | <.001b | 73.0±10.2 | 47.2±10.7 | <.001b | 73.2±10.3 | 44.8±10.3 | <.001b |
| Less education, n (%) | 137 (66.83) | 134 (52.55) | .002a | 187 (47.10) | 175 (34.31) | .003a | 324 (53.82) | 309 (40.39) | <.001a |
| missing | 0 | 16 | 18 | 63 | 18 | 79 | |||
| Cigarette smoking, n (%) | 53 (25.85) | 56 (21.96) | .417a | 117 (29.47) | 145 (28.43) | .871a | 170 (28.24) | 201 (26.27) | .573a |
| missing | 0 | 7 | 13 | 26 | 13 | 33 | |||
| Alcohol drinking, n (%) | 63 (30.73) | 54 (21.18) | .030a | 139 (35.01) | 129 (25.29) | .003a | 202 (33.55) | 183 (23.92) | <.001a |
| missing | 0 | 7 | 15 | 29 | 15 | 36 | |||
| Hypertention, n (%) | 26 (12.68) | 0 | 43 (10.83) | 0 | 69 (11.46) | 0 | |||
| Stroke, n (%) | 4 (1.95) | 0 | 7 (1.76) | 0 | 11 (1.83) | 0 | |||
| Diabetes, n (%) | 30 (14.63) | 0 | 51 (12.85) | 0 | 81 (13.46) | 0 | |||
NC, North China; SC, South China; SD, standard deviation.
aPearson Chi-square test. bMann-Whitney U-test.