Do Genes Associated with Dyslexia of Chinese Characters Evolve Neutrally?
Abstract
:1. Introduction
2. Materials and Methods
2.1. Examined SNPs
2.2. Study Populations
2.2.1. Study Populations for nSL
2.2.2. Study Populations for 2D SFS-Based Statistics
2.3. nSL
2.4. 2D SFS-Based Statistics
2.4.1. Overview of 2D SFS-Based Statistics
2.4.2. Simulations
2.4.3. Screening of the Candidate Core Regions under Selective Sweep
2.4.4. Searching for the Target Site of Natural Selection (“Target Site”)
3. Results
3.1. nSL
3.2. 2D SFS-Based Statistics
3.2.1. Screening of the Candidate Core Regions under Selective Sweep
3.2.2. Searching for the Target Site of Natural Selection
rs17031962 on GNPTAB
rs3789228 on DCDC2, as the Younger SNP of rs1091047
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Gene | Core SNP | Chr. | Position | Risk Allele | Derived Allele Frequency | References | |
---|---|---|---|---|---|---|---|
(GRCh37/hg19) | EAS | (EAS and KPGP) | |||||
KIAA0319L | rs28366021 | 1 | 36,022,859 | Ancestral | 0.234 | (0.227) | [15] |
ROBO1 | rs4535189 | 3 | 79,489,971 | Derived | 0.366 | (0.373) | [14] |
DCDC2 | rs807724 | 6 | 24,278,869 | Ancestral | 0.957 | (0.956) | [20] |
DCDC2 | rs1091047 | 6 | 24,295,256 | Ancestral | 0.817 | (0.823) | [12] |
KIAA0319 | rs2760157 | 6 | 24,578,272 | Ancestral | 0.456 | (0.470) | [21] |
KIAA0319 | rs807507 | 6 | 24,579,867 | Derived | 0.188 | (0.187) | [21] |
KIAA0319 | rs4504469 | 6 | 24,588,884 | Derived | 0.112 | (0.122) | [15] |
DOCK4 | rs2074130 | 7 | 111,487,098 | Derived | 0.101 | (0.115) | [15] |
DRD2 | rs1079727 | 11 | 113,289,182 | Derived | 0.416 | (0.420) | [22] |
GNPTAB | rs17031962 | 12 | 102,146,558 | Ancestral | 0.294 | (0.297) | [23] |
DYX1C1 | rs11629841 | 15 | 55,777,638 | Derived | 0.058 | (0.056) | [24] |
DYX1C1 | rs3743205 | 15 | 55,790,530 | Derived | 0.035 | (0.037) | [25] |
intergenic region | rs8049367 | 16 | 3,980,445 | Derived | 0.339 | (0.340) | [26] |
NAGPA | rs882294 | 16 | 5,092,118 | Derived | 0.189 | (0.188) | [23] |
DIP2A | rs2255526 | 21 | 47,971,539 | Derived | 0.264 | (0.262) | [27] |
Gene | Core SNP | Normalized nSL | p-Value |
---|---|---|---|
KIAA0319L | rs28366021 a | 0.0771 | 0.469 |
ROBO1 | rs4535189 | −0.1882 | 0.575 |
DCDC2 | rs807724 | 1.1328 | 0.129 |
DCDC2 | rs1091047 | −0.5967 | 0.725 |
KIAA0319 | rs2760157 | −2.1853 | 0.986 |
KIAA0319 | rs807507 | 0.7329 | 0.232 |
KIAA0319 | rs4504469 | 0.7098 | 0.239 |
DOCK4 | rs2074130 | 0.3068 | 0.379 |
DRD2 | rs1079727 | −0.1744 | 0.569 |
GNPTAB | rs17031962 | 1.2369 | 0.108 |
DYX1C1 | rs11629841 | −0.0922 | 0.537 |
DYX1C1 | rs3743205 | −0.1939 | 0.577 |
intergenic region | rs8049367 | −0.4421 | 0.671 |
NAGPA | rs882294 | 0.2399 | 0.405 |
DIP2A | rs2255526 | - | - |
Gene | Core SNP | Number of Derived Alleles = 1008 | Length of the Core Region | Number of Segregating Sites | p-Value | |
---|---|---|---|---|---|---|
KIAA0319L | rs28366021 | 236 | 330,223 | 2204 | 0.1476 | 0.718 |
ROBO1 | rs4535189 | 369 | 124,626 | 866 | 0.1287 | 0.316 |
ROBO1 | rs73129039 a | 363 | 124,626 | 866 | 0.1232 | 0.303 |
DCDC2 | rs807724 | 965 | 5910 | 53 | 0.6742 | 0.159 |
DCDC2 | rs1091047 | 824 | 41,134 | 334 | 0.3044 | 0.111 |
DCDC2 | rs3789228 b | 782 | 41,134 | 334 | 0.2020 | 0.068 * |
KIAA0319 | rs2760157 | 460 | 7387 | 53 | 0.7765 | 0.939 |
KIAA0319 | rs807507 | 189 | 11,475 | 81 | 0.0220 | 0.111 |
KIAA03219 | rs4504469 | 113 | 32,025 | 241 | 0.0736 | 0.529 |
DOCK4 | rs2074130 | 102 | - | - | - | - |
DRD2 | rs1079727 | 419 | 38,525 | 372 | 0.1370 | 0.260 |
GNPTAB | rs17031962 | 296 | 136,804 | 868 | 0.0400 | 0.038 * |
DYX1C1 | rs11629841 | 58 | 130,280 | 1113 | 0.0589 | 0.769 |
DYX1C1 | rs3743205 | 35 | 242,254 | 2024 | 0.0680 | 0.963 |
DYX1C1 | rs79024225 c | 31 | 242,254 | 2024 | 0.0308 | 0.758 |
intergenic region | rs8049367 | 342 | 14,513 | 177 | 0.1486 | 0.428 |
NAGPA | rs882294 | 191 | 34,706 | 339 | 0.2875 | 0.905 |
DIP2A | rs2255526 | 266 | 67,101 | 661 | 0.0899 | 0.361 |
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Nishiyama, K.V.; Satta, Y.; Gojobori, J. Do Genes Associated with Dyslexia of Chinese Characters Evolve Neutrally? Genes 2020, 11, 658. https://doi.org/10.3390/genes11060658
Nishiyama KV, Satta Y, Gojobori J. Do Genes Associated with Dyslexia of Chinese Characters Evolve Neutrally? Genes. 2020; 11(6):658. https://doi.org/10.3390/genes11060658
Chicago/Turabian StyleNishiyama, Kumiko V., Yoko Satta, and Jun Gojobori. 2020. "Do Genes Associated with Dyslexia of Chinese Characters Evolve Neutrally?" Genes 11, no. 6: 658. https://doi.org/10.3390/genes11060658
APA StyleNishiyama, K. V., Satta, Y., & Gojobori, J. (2020). Do Genes Associated with Dyslexia of Chinese Characters Evolve Neutrally? Genes, 11(6), 658. https://doi.org/10.3390/genes11060658