| Literature DB >> 26474478 |
Yuping Xu1, Zhiqiang Li2, Fenglian Ai1, Jianhua Chen2, Qiong Xing1, Ping Zhou1, Zhaolian Wei1, Yongyong Shi2, Xiao-Jin He1, Yunxia Cao1.
Abstract
To date, eleven genome-wide significant (GWS) loci (P < 5×10-8) for polycystic ovary syndrome (PCOS) have been identified through genome-wide association studies (GWAS). Some of the risk loci have been selected for replications and validated in multiple ethnicities, however, few previous studies investigated all loci. Scanning all the GWAS variants would demonstrate a more informative profile of variance they explained. Thus, we analyzed all the 17 single nucleotide polymorphisms (SNPs) mapping to the 11 GWAS loci in an independent sample set of 800 Chinese subjects with PCOS and 1110 healthy controls systematically. Variants of rs3802457 in C9orf3 locus (P = 5.99×10-4) and rs13405728 in LHCGR locus (P = 3.73×10-4) were significantly associated with PCOS after the strict Bonferroni correction in our data set. The further haplotype analysis indicated that in the block of C9orf3 gene (rs4385527 and rs3802457), GA haplotype played a protective role in PCOS (8.7 vs 5.0, P = 9.85×10-6, OR = 0.548, 95%CI = 0.418-0.717), while GG haplotype was found suffering from an extraordinarily increased risk of PCOS (73.6% vs79.2%, P = 3.41×10-5, OR = 1.394, 95%CI = 1.191-1.632). Moreover, the directions of effects for all SNPs were consistent with previous GWAS reports (P = 1.53×10-5). Polygenic score analysis demonstrated that these 17 SNPs have a significant capacity on predicting case-control status in our samples (P = 7.17×10-9), meanwhile all these gathered 17 SNPs explained about 2.40% of variance. Our findings supported that C9orf3 and LHCGR loci variants were vital susceptibility of PCOS.Entities:
Mesh:
Year: 2015 PMID: 26474478 PMCID: PMC4608705 DOI: 10.1371/journal.pone.0140695
Source DB: PubMed Journal: PLoS One ISSN: 1932-6203 Impact factor: 3.240
Characteristics of the case and the control subjects.
| Characteristic | Cases(n = 800) | Controls(n = 1110) | P value |
|---|---|---|---|
| Age (ys) | 26.5 ± 3.6 | 26.8 ± 3.8 | 0.082 |
| BMI | 23.5 ± 4.3 | 20.4 ± 2.2 | <0.001 |
| T (ng/dl) | 58.2 ± 43.8 | - | - |
| FSH (IU/L) | 6.1 ± 2.2 | - | - |
| LH (IU/L) | 11.8 ± 7.1 | - | - |
| PRL (ng/ml) | 16.5 ± 8.6 | - | - |
| Fasting Glucose (mmol/l) | 5.5 ± 0.9 | - | - |
| 2h-Glucose (mmol/l) | 6.8 ± 2.7 | - | - |
| Fasting Insulin (μIU/mL) | 14.0 ± 18.1 | - | - |
| 2h-Insulin (μIU/mL) | 83.4 ± 69.3 | - | - |
| HOMA-IR | 3.6 ± 4.6 | - | - |
Data are presented as the mean ± standard deviation. BMI: body mass index; T: total testosterone; FSH: follicular-stimulating hormone; LH: luteinizing hormone; PRL: prolactin; 2h-Glucose and 2h-Insulin: glucose and insulin levels at 2 hours after OGTT; HOMA-IR: homeostasis model assessment-insulin resistance.
Information of the 17 SNPs detected.
| Gene | SNP ref. | Loci | Allele | Location |
|
|---|---|---|---|---|---|
|
| rs12468394 | 2p21 | C>A | Intron | 0.190 |
|
| rs13429458 | 2p21 | A>C | Intron | 0.456 |
|
| rs12478601 | 2p21 | C>T | Intron | 0.199 |
|
| rs13405728 | 2p16.3 | A>G | Intron | 0.310 |
|
| rs2268361 | 2p16.3 | C>T | Intron | 0.191 |
|
| rs2349415 | 2p16.3 | C>T | Intron | 0.153 |
|
| rs4385527 | 9q22.32 | G>A | Intron | 0.751 |
|
| rs3802457 | 9q22.32 | G>A | Intron | 0.882 |
|
| rs10818854 | 9q33.3 | G>A | Intron | 0.344 |
|
| rs2479106 | 9q33.3 | A>G | Intron | 0.706 |
|
| rs10986105 | 9q33.3 | T>C | Intron | 0.247 |
|
| rs1894116 | 11q22.1 | A>G | Intron | 0.655 |
|
| rs705702 | 12q13.2 | A>G | Upstream | 0.916 |
|
| rs2272046 | 12q14.3 | A>C | Intron | 0.250 |
|
| rs4784165 | 16q12.1 | T>G | Intron | 0.775 |
|
| rs2059807 | 19p13.3 | A>G | Intron | 0.825 |
|
| rs6022786 | 20q13.2 | G>A | intergenic region | 0.825 |
SNP ref.: single necleaue polymorphism reference; Allel: major > minor HWE: Hardy–Weinberg equilibrium, P HWE more than 0.05 indicated that the cases and the controls obeyed Hardy–Weinberg equilibrium.
Association analysis of previous GWAS risk variants with PCOS, adjusted for BMI.
| Gene | SNP | Minor allele | Controls N (%) | Cases N (%) | OR [95% CI] |
| OR ( |
|---|---|---|---|---|---|---|---|
|
| rs12468394 | A | 541(24.4) | 343(21.4) | 0.79 [0.66–0.94] | 9.10 × 10−3 |
|
|
| rs13429458 | C | 348(16.4) | 211(13.8) | 0.78 [0.63–0.96] | 0.020 |
|
|
| rs12478601 | T | 574(25.9) | 369(23.1) | 0.80 [0.67–0.94] | 8.92 × 10−3 |
|
|
| rs13405728 | G | 546(24.6) | 307(19.2) | 0.72 [0.60–0.86] |
|
|
|
| rs2268361 | T | 1121(50.7) | 734(46.3) | 0.87 [0.75–1.00] | 0.055 | 0.87 (9.89 × 10−13) |
|
| rs2349415 | T | 391(18.4) | 304(20.6) | 1.15 [0.95–1.39] | 0.147 | 1.19 (2.35 × 10−12) |
|
| rs4385527 | A | 251(15.8) | 392(17.7) | 0.86 [0.71–1.05] | 0.140 | 0.84 (5.87 × 10−9) |
|
| rs3802457 | A | 102(6.4) | 224(10.1) | 0.62 [0.48–0.82] |
|
|
|
| rs10818854 | A | 182(8.2) | 153(9.6) | 1.29 [1.00–1.67] | 0.055 | 1.51 (9.40 × 10−18) |
|
| rs2479106 | G | 488(22.0) | 354(22.1) | 1.02 [0.86–1.21] | 0.835 | 1.34 (8.12 × 10−19) |
|
| rs10986105 | C | 153(7.0) | 145(9.3) | 1.48 [1.13–1.94] | 4.41 × 10−3 |
|
|
| rs1894116 | G | 453(20.5) | 366(23.1) | 1.30 [1.09–1.55] | 3.79 × 10−3 |
|
|
| rs705702 | G | 530(23.9) | 433(27.1) | 1.18 [0.99–1.39] | 0.059 | 1.27 (8.64 × 10−26) |
|
| rs2272046 | C | 80(4.0) | 50(3.5) | 0.87 [0.59–1.29] | 0.499 | 0.70 (1.95 × 10−21) |
|
| rs4784165 | G | 726(35.1) | 534(36.6) | 1.05 [0.90–1.23] | 0.540 | 1.15 (3.64 × 10−11) |
|
| rs2059807 | G | 641(29.5) | 508(32.8) | 1.15 [0.98–1.35] | 0.082 | 1.14 (1.09 × 10−8) |
|
| rs6022786 | A | 737(34.1) | 541(35.3) | 1.05 [0.90–1.22] | 0.541 | 1.13 (1.83 × 10−9) |
OR, odds ratio; 95% CI, 95% confidence interval; SNPs with P value less than 2.9 × 10−3 are marked in bold.
Haplotype analysis of THADA gene, FSHR gene, C9orf3 gene and DENND1A gene between the controls and the cases.
| Haplotype | Controls N (%) | Cases N (%) | OR[95%CI] |
|
|---|---|---|---|---|
|
| ||||
| A A T | 144.17(6.8) | 104.97(6.9) | 0.996 [0.767–1.293] | 0.977 |
| A C T | 311.57(14.7) | 190.78(12.5) | 0.814[0.670–0.988] | 0.038# |
| C A C | 1571.86(73.9) | 1185.74(77.5) | 1.162[0.986–1.370] | 0.073 |
|
| ||||
| C C | 752.99(35.7) | 534.04(36.4) | 1.034 [0.900–1.188] | 0.635 |
| C T | 296.01(14.0) | 248.96(17.0) | 1.255 [1.045–1.508] | 0.015# |
| T C | 972.01(46.0) | 628.96(42.9) | 0.881 [0.771–1.008] | 0.065 |
| T T | 90.99(4.3) | 54.04(3.7) | 0.850 [0.603–1.198] | 0.353 |
|
| ||||
| A G | 362.06(16.4) | 229.14(14.4) | 0.860 [0.719–1.030] | 0.101 |
| G A | 193.07(8.7) | 79.15(5.0) | 0.548 [0.418–0.717] |
|
| G G | 1626.93(73.6) | 1259.86(79.2) | 1.394 [1.191–1.632] |
|
|
| ||||
| A G C | 143.85(6.5) | 135.93(8.7) | 1.351 [1.059–1.725] | 0.015# |
| G A A | 1683.77(76.5) | 1213.31(77.6) | 1.032 [0.880–1.210] | 0.698 |
| G G A | 328.08(14.9) | 193.61(12.4) | 0.799 [0.660–0.968] | 0.021# |
The SNP sites for the block of THADA gene is: rs12468394, rs13429458 and rs12478601. The SNP sites for the block of FSHR gene is: rs2268361 and rs2349415. The SNP sites for the block of C9orf3 gene is: rs4385527 and rs3802457. The SNP sites for the block of DENND1A gene is: rs10818854, rs2479106 and rs10986105. P value less than 0.0125 are marked in bold. P value less than 0.05 but more than 0.0125 are marked with#