| Literature DB >> 27464509 |
Shanshan Shao1, Yanfeng Niu2, Xiaohui Zhang1, Rui Kong1, Jia Wang1, Lingfei Liu1, Xiu Luo1, Jiajia Zhang3, Ranran Song1.
Abstract
KIAA0319 at the DYX2 locus is one of the most extensively studied candidate genes for developmental dyslexia (DD) owing to its important role in neuronal migration. Previous research on associations between KIAA0319 genetic variations and DD has yielded inconsistent results. It is important to establish a more precise estimate of the DD risk associated with these genetic variations. We carried out a meta-analysis of association studies involving KIAA0319 polymorphisms and DD risk. The results of pooled analysis indicated that none of the six investigated markers in or near the KIAA0319 gene are associated with DD. However, a stratified analysis by the study population revealed opposite associations involving KIAA0319 rs4504469 in European and Asian subgroups. The stratified analysis also showed that the KIAA0319 rs9461045 minor allele (T allele) has a protective effect in Asians. This meta-analysis has allowed us to establish the effects of specific KIAA0319 polymorphisms on DD risk with greater precision, as they vary across populations; analyzing one single nucleotide polymorphism at a time could not fully explain the genetic association for DD.Entities:
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Year: 2016 PMID: 27464509 PMCID: PMC4964335 DOI: 10.1038/srep30454
Source DB: PubMed Journal: Sci Rep ISSN: 2045-2322 Impact factor: 4.379
Figure 1Gene structure and location of six single nucleotide polymorphisms (SNPs) in or near the KIAA0319 gene in this meta-analysis; one SNP in exon 4 of KIAA0319: rs4504469; two SNPs in intron 1of KIAA0319: rs6935076 and rs761100; two SNPs located in the promoter region of KIAA0319 gene: rs9461045 and rs3212236; one SNP in intron 2 of the TTRAP gene: rs2143340.
Exons are represented by numbered grey rectangles. Black parts represent gene’s upstream, introns or downstream.
Characteristics of included studies.
| Study | Publication year | Study population | Design type | Case/control (family) | KIAA0319 marker |
|---|---|---|---|---|---|
| Harold D | 2006 | Cardiff of UK | Case/control | 350/273 | rs761100, rs4504469, rs3212236, rs6935076, rs2143340 |
| Brkanac Z | 2007 | Washington | TDT | 191 | rs4504469, rs6935076 |
| Couto JM | 2010 | Toronto | TDT | 156 | rs4504469, rs6935076, rs761100, rs2143340 |
| Newbury DF# | 2011 | UK | Case/control | 188/363 | rs9461045, rs761100, rs4504469, rs3212236, rs2143340 |
| Newbury DF* | 2011 | UK | Case/control | 331/363 | rs9461045, rs761100, rs4504469, rs3212236, rs2143340 |
| Elbert A | 2011 | Toronto | TDT | 156 | rs9461045, rs3212236 |
| Kirsten H | 2011 | German | case–control | 272/548 | rs9461045 |
| Venkatesh SK | 2013 | Indian | Case/control | 210/256 | rs9461045, rs4504469, rs3212236 |
| Becker J | 2014 | Eight European countries | Case/control | 958/1150 | rs9461045, rs761100, rs4504469, rs3212236, rs6935076, rs2143340 |
| Eicher JD$ | 2014 | Colorado | TDT | 292 | rs3212236 |
| Eicher JD& | 2014 | Italy | TDT | 304 | rs3212236 |
| Shao SS | 2015 | Chinese | Case/control | 402/401 | rs9461045, rs4504469 |
*Case group is composed of independent dyslexia cases;
#Case group is composed of dyslexia probands;
$ and & represent two independent cohorts from Colorado and Italy, respectively.
Figure 2Summary of estimated risk of developmental dyslexia associated with six markers in or near the KIAA0319 gene based on meta-analysis.
Meta-analysis for associations between KIAA0319 polymorphisms and DD.
| KIAA0319 markers | No.* | Study population | MAF in controls# | Sample sizecases/controls (families) | OR (95% CI) | Heterogeneity | Model for meta-analysis | Egger’s test | |||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Q statistic ( | I2 (%) | z | |||||||||
| rs4504469 | 8 | Total | 0.13~0.43 | 2439/2443 and 347 | 1.04 (0.85–1.27) | 0.706 | 32.375 (<0.001) | 82.27 | 1.034 | 0.301 | |
| 4 | European | 0.40~0.43 | 1827/1786 | 5.427 (0.143) | 45.11 | −1.552 | 0.121 | ||||
| 2 | Asian | 0.13, 0.26 | 612/657 | 0.210 (0.647) | 0.00 | – | – | ||||
| 2 | North American | – | 347 | 1.03 (0.71–1.48) | 0.889 | 2.535 (0.111) | 60.55 | – | – | ||
| rs761100 | 5 | Total | 0.39~0.46 | 1827/1786 and 156 | 0.95 (0.75–1.21) | 0.689 | 20.002 (<0.001) | 83.28 | Random | −0.472 | 0.637 |
| 4 | European | 0.39~0.46 | 1827/1786 | 0.99 (0.75–1.31) | 0.951 | 18.207 (<0.001) | 87.18 | Random | 0.089 | 0.929 | |
| 1 | North American | – | 156 | 0.78 (0.55–1.10) | 0.155 | – | – | – | – | – | |
| rs6935076 | 4 | Total | 0.35, 0.36 | 1308/1423 and 347 | 1.01 (0.75–1.37) | 0.930 | 13.957 (0.003) | 83.65 | Random | −0.794 | 0.427 |
| 2 | European | 0.35, 0.36 | 1308/1423 | 1.17 (0.83–1.63) | 0.371 | 6.273 (0.012) | 84.06 | Random | – | – | |
| 2 | North American | – | 347 | 0.85 (0.49–1.45) | 0.540 | 5.135 (0.023) | 80.53 | Random | – | – | |
| rs3212236 | 8 | Total | 0.17~0.35 | 2037/2042 and 752 | 0.94 (0.85–1.04) | 0.233 | 7.812 (0.349) | 17.94 | Fix | −0.433 | 0.665 |
| 5 | European | 0.17~0.19 | 1827/1786 and 304 | 0.95 (0.84–1.06) | 0.327 | 3.675 (0.452) | 15.81 | Fix | −1.324 | 0.185 | |
| 1 | Asian | 0.35 | 210/256 | 0.75 (0.55–1.01) | 0.056 | – | – | – | – | – | |
| 2 | North American | – | 448 | 1.14 (0.85–1.53) | 0.375 | 0.150 (0.698) | 0.00 | Fix | – | – | |
| rs9461045 | 7 | Total | 0.18~0.42 | 2361/2718 and 156 | 0.93 (0.84–1.02) | 0.114 | 4.727 (0.579) | 0.00 | Fix | −0.094 | 0.925 |
| 4 | European | 0.18~0.19 | 1749/2061 | 0.98 (0.87–1.10) | 0.678 | 1.841 (0.606) | 0.00 | Fix | 0.368 | 0.713 | |
| 2 | Asian | 0.39, 0.42 | 612/657 | 0.154 (0.695) | 0.00 | Fix | – | – | |||
| 1 | North American | – | 156 | 0.94 (0.64–1.39) | 0.770 | – | – | – | – | – | |
| rs2143340 | 5 | Total | 0.15~0.16 | 1827/1786 and 156 | 1.03 (0.91–1.16) | 0.653 | 3.898 (0.420) | 0.01 | Fix | 0.489 | 0.625 |
| 4 | European | 0.15~0.16 | 1827/1786 | 1.01 (0.89–1.14) | 0.903 | 2.243 (0.523) | 0.00 | Fix | −0.479 | 0.632 | |
| 1 | North American | – | 156 | 1.41 (0.86–2.31) | 0.175 | – | – | – | – | – | |
*The number of studies.
#The range of minor allele frequency (MAF) in the control group of the included studies.
Figure 3Regional linkage disequilibrium plot for SNP rs4504469 in CEU and JPT + CHB population panels.
CEU: Utah residents with Northern and Western European ancestry from the CEPH collection; JPT + CHB: Combined panel of Japanese in Tokyo, Japan and Han Chinese in Beijing, China.
Sensitivity analysis of pooled ORs for KIAA0319 polymorphisms and DD.
| Study omitted | OR(95% CI) | I2 | ||
|---|---|---|---|---|
| For rs4504469 | ||||
| Harold D, 2006 | 1.10 (0.91–1.33) | 0.347 | 0.001 | 77.85 |
| Brkanac Z, 2007 | 1.07 (0.86–1.33) | 0.570 | 0.000 | 84.56 |
| Couto JM, 2010 | 1.02 (0.82–1.26) | 0.882 | 0.000 | 84.73 |
| Newbury DF*, 2011 | 1.07 (0.85–1.34) | 0.576 | 0.000 | 83.63 |
| Newbury DF#, 2011 | 1.06 (0.84–1.33) | 0.624 | 0.000 | 84.75 |
| Venkatesh SK, 2013 | 0.97 (0.82–1.16) | 0.754 | 0.004 | 74.21 |
| Becker J, 2014 | 1.05 (0.83–1.33) | 0.664 | 0.000 | 81.25 |
| Shao SS, 2015 | 0.99 (0.81–1.20) | 0.897 | 0.001 | 79.73 |
| For rs761100 | ||||
| Harold D, 2006 | 1.05 (0.89–1.24) | 0.531 | 0.082 | 55.63 |
| Couto JM, 2010 | 0.99 (0.75–1.31) | 0.951 | 0.000 | 87.18 |
| Newbury DF*, 2011 | 0.92 (0.68–1.24) | 0.583 | 0.000 | 86.18 |
| Newbury DF#, 2011 | 0.88 (0.70–1.11) | 0.286 | 0.004 | 78.69 |
| Becker J, 2014 | 0.93 (0.68–1.28) | 0.668 | 0.000 | 83.87 |
| For rs6935076 | ||||
| Harold D, 2006 | 0.91 (0.68–1.22) | 0.524 | 0.051 | 72.22 |
| Brkanac Z, 2007 | 0.98 (0.64–1.50) | 0.922 | 0.001 | 90.26 |
| Couto JM, 2010 | 1.14 (0.92–1.42) | 0.232 | 0.043 | 65.97 |
| Becker J, 2014 | 1.01 (0.64–1.59) | 0.962 | 0.002 | 85.56 |
*Case group is composed of independent dyslexia cases.
#Case group is composed of dyslexia probands.