| Literature DB >> 23570452 |
Xiaoping Li1, Rong Luo, Xiaoyang Mo, Rongjian Jiang, Hong Kong, Wei Hua, Xiushan Wu.
Abstract
BACKGROUND: Dilated cardiomyopathy (DCM) has been extensively investigated for many years, but its pathogenesis remains uncertain. The ACTC1 gene was the first sarcomeric gene whose mutation was shown to cause DCM; recent studies have indicated that the HSPB7 and ZBTB17 genes are also associated with DCM. To assess the potential role of these three genes in DCM, we examined 11 single nucleotide polymorphisms (SNPs) in the ZBTB17, HSPB7 and ACTC1 genes: namely, rs10927875 in ZBTB17; rs1739843, rs7523558, and rs6660685 in HSPB7; rs533021, rs589759, rs1370154, rs2070664, rs3759834, rs525720 and rs670957 in ACTC1.Entities:
Mesh:
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Year: 2013 PMID: 23570452 PMCID: PMC3626695 DOI: 10.1186/2047-783X-18-10
Source DB: PubMed Journal: Eur J Med Res ISSN: 0949-2321 Impact factor: 2.175
Sequences of PCR primers, amplicon sizes, temperatures and GC content in SNPs of , and in DCM patients and control subjects
| | | | | | |
| rs10927875 | GCCAGAGTGGATGATCACTG | TTCTGTTTCCACCACTGTAG | 91 | 54.2 | 55 |
| | | | | | |
| rs1739843 | TGTCCTCACTCTGCCATCAC | TGGGCAGAGGGAGCCTGAG | 99 | 50.8 | 50 |
| rs7523558 | GCCCAGCACCTATTTATAGC | CTCATAGGCCAGTGATGAAG | 94 | 46.6 | 35 |
| rs6660685 | TACTGTCCCACAGCCAGCAC | TCTTCTCAGCCTCCTGGTG | 98 | 50.8 | 58.8 |
| | | | | | |
| rs533021 | GGCCTTCCATTTGAATATGC | GTATGAGAGCACATTTTCTG | 96 | 45.1 | 33.3 |
| rs589759 | CTTCTCACCTCCCTAATTCC | TGTGGCCTGGAGGCTTTAAG | 96 | 49.4 | 45 |
| rs1370154 | GCAGCAACTCATTCTAGAG | TTTCATACCTGAAAAGCAG | 108 | 45.2 | 24 |
| rs2070664 | CATAACAATGACTGCTGCAC | ATAGCTTGTGGAGATAGGTC | 100 | 46.9 | 60 |
| rs3759834 | TCTCCATCAAAGTATTTGCC | GATGAGCATCTTTAAACTGG | 100 | 52 | 45 |
| rs525720 | GTTCTTGACTGGAGCTTTG | GCCAGTGCCCAGTTTTCTAT | 103 | 45.6 | 33.3 |
| rs670957 | ATGCCAAGAGTAGAACTGCC | TCTGACACCAGTCCCATTTC | 97 | 45.5 | 50 |
DNA variants identified in,, and
| | | | | | | |
| rs10927875 | Intron 16299312 C>T | Non-coding | Nor-reported non-coding SNP | 0.025 | 0.025 | 0.9417 |
| | | | | | | |
| rs1739843 | Intron 16343254 C>T | Non-coding | Reported non-coding SNP | 0.413 | 0.381 | 0.7898 |
| rs7523558 | 5′ near gene 16346732 G>A | Non-coding | Nor-reported non-coding SNP | 0.156 | 0.15 | 0.7933 |
| rs6660685 | 5′ near gene 16346988 G>A | Non-coding | Nor-reported non-coding SNP | 0.029 | 0.028 | 0.9112 |
| | | | | | | |
| rs533021 | 3′ UTR 35080931 T>C | Non-coding | Reported non-coding SNP | 0.446 | 0.453 | 1.0000 |
| rs589759 | 3′ UTR 35081574 C>T | Non-coding | Reported non-coding SNP | 0.524 | 0.497 | 0.2017 |
| rs1370154 | 3′ UTR 35082225 G>A | Non-coding | Reported non-coding SNP | 0.45 | 0.466 | 0.8150 |
| rs2070664 | Intron 35085201 A>G | Non-coding | Nor-reported non-coding SNP | 0.47 | 0.491 | 0.9324 |
| rs3759834 | 5′ near gene 35088705 T>C | Non-coding | Nor-reported non-coding SNP | 0.06 | 0.058 | 0.6522 |
| rs525720 | 5′ near gene 35089134 G>A | Non-coding | Nor-reported non-coding SNP | 0.254 | 0.248 | 0.4169 |
| rs670957 | 5′ near gene 35089432 A>G | Non-coding | Nor-reported non-coding SNP | 0.482 | 0.5 | 0.5963 |
HWE(P), P value from Hardy-Weinberg equilibrium test in the control group; ObsHET, observed heterozygosity; PretHET, present heterozygosity.
Genotypic and allelic frequencies of SNPs from, and genes in DCM patients and controls
| | | | | ||||
| rs10927875 | C/C | C/T | TT | C | T | 0.05 | 5.19(1.00, 27.03) |
| Patients | 88(0.946) | 5(0.054) | 0 | 181(0.973) | 5(0.054) | | |
| Controls | 187(0.989) | 2(0.011) | 0 | 376(0.995) | 2(0.011) | | |
| | | | | | | | |
| rs1739843 | C/C | C/T | T/T | C | T | 0.81 | 0.95(0.64, 1.42) |
| Patients | 49(0.521) | 43(0.457) | 2(0.021) | 141(0.75) | 47(0.250) | | |
| Controls | 103(0.545) | 74(0.392) | 12(0.063) | 280(0.741) | 98(0.259) | | |
| rs7523558 | A/A | A/G | G/G | A | G | 0.96 | 0.98(0.52, 1.87 ) |
| Patients | 0(0) | 15(0.161) | 78(0.839) | 15(0.081) | 171(0.919) | | |
| Controls | 1(0.005) | 29(0.153) | 159(0.841) | 31(0.082) | 347(0.918) | | |
| rs6660685 | A/A | A/G | G/G | A | G | 0.11 | 3.29(0.78, 13.91) |
| Patients | 0 | 5(0.053) | 90(0.947) | 5(0.026) | 185(0.974) | | |
| Controls | 0 | 3(0.016) | 181(0.984) | 3(0.008) | 365(0.992) | | |
| | | | | | | | |
| rs533021 | C/C | C/T | T/T | C | T | 0.36 | 1.19(0.82, 1.73) |
| Patients | 13(0.149) | 39(0.448) | 35(0.402) | 65(0.374) | 109(0.626) | | |
| Controls | 21(0.111) | 84(0.444) | 84(0.444) | 126(0.333) | 252(0.667) | | |
| rs589759 | C/C | C/T | T/T | C | T | 0.25 | 1.22(0.87, 1.73) |
| Patients | 25(0.258) | 48(0.495) | 24(0.247) | 98(0.505) | 96(0.495) | | |
| Controls | 54(0.286) | 102(0.540) | 33(0.175) | 210(0.556) | 168(0.444) | | |
| rs1370154 | A/A | A/G | G/G | A | G | 0.77 | 0.93(0.58, 1.50) |
| Patients | 7(0.156) | 18(0.4) | 20(0.444) | 32(0.356) | 58(0.644) | | |
| Controls | 26(0.141) | 85(0.462) | 73(0.397) | 137(0.372) | 231(0.628) | | |
| rs2070664 | A/A | A/G | G/G | A | G | 0.84 | 1.04(0.73, 1.47) |
| Patients | 33(0.344) | 42(0.438) | 21(0.219) | 108(0.562) | 84(0.438) | | |
| Controls | 62(0.328) | 92(0.487) | 35(0.185) | 216(0.571) | 162(0.429) | | |
| rs3759834 | C/C | C/T | T/T | C | T | 0.72 | 0.82(0.29, 2.37) |
| Patients | 0 | 5(0.053) | 90(0.947) | 5(0.026) | 185(0.974) | | |
| Controls | 0 | 12(0.063) | 177(0.937) | 12(0.032) | 366(0.968) | | |
| rs525720 | A/A | A/G | G/G | A | G | 0.42 | 0.81(0.48, 1.36) |
| Patients | 2(0.022) | 19(0.211) | 69(0.767) | 23(0.128) | 157(0.872) | | |
| Controls | 3(0.016) | 52(0.275) | 134(0.709) | 58(0.153) | 320(0.847) | | |
| rs670957 | A/A | A/G | G/G | A | G | 0.09 | 1.36(0.95, 1.94) |
| Patients | 19(0.211) | 44(0.489) | 27(0.3) | 82(0.456) | 98(0.544) | | |
| Controls | 55(0.293) | 90(0.479) | 43(0.229) | 200(0.532) | 176(0.468) | ||
CI, confidence interval; OR, odds ratio in which the minor allele was viewed as an exposure factor in the case-controlled study.
Figure 1Pairwise linkage disequilibrium (LD) values calculated between tagging SNPs in , and The value within each diamond represents the pairwise correlation between tagging SNPs (measured as D), defined by the upper left and the upper right sides of the diamond. The diamond without a number corresponds to D= 1. Shading represents the magnitude and significance of the pairwise LD, with darker red reflecting higher LD values and white indicating lower LD values.
Haplotype analysis of SNPs between DCM patients and control subjects
| GG | 0.426 | 0.418 | 0.028 | 0.8681 | |
| | AA | 0.371 | 0.363 | 0.038 | 0.8456 |
| | GA | 0.192 | 0.209 | 0.211 | 0.6460 |
| | AG | 0.011 | 0.010 | 0.008 | 0.9293 |
| GG | 0.544 | 0.464 | 3.166 | 0.0752 | |
| | GA | 0.328 | 0.383 | 1.589 | 0.2075 |
| AA | 0.127 | 0.150 | 0.524 | 0.4691 |