| Literature DB >> 19668483 |
Sayaka Sasaki1, Masao Ota, Akira Meguro, Ritsuko Nishizaki, Eiichi Okada, Jeewon Mok, Tetusya Kimura, Akira Oka, Yoshihiko Katsuyama, Shigeaki Ohno, Hidetoshi Inoko, Nobuhisa Mizuki.
Abstract
Although a myopia susceptibility gene has not yet been elucidated, ten candidate regions (MYP1-MYP10) have been associated with myopia by linkage analysis employing large pedigrees. We report herein on the results of our analysis pertaining to polymorphisms of LAMA1 (alpha subunit of laminin), a promising candidate gene for high myopia present in the MYP2 region of Japanese subjects with high myopia. Three hundred and thirty Japanese subjects with high myopia at a level of greater than -9.25 D and ethnically and sex matched 330 normal controls without high myopia was enrolled in this study. The thirteen SNPs located on the LAMA1 gene were analyzed using PCR and SNP-specific fluorogenic probes. Two of the SNPs were monomorphic and none of the 11 SNPs showed statistically significant association with high myopia in the Japanese population. There is no convincing evidence to prove a connection between nucleotide sequence variations in LAMA1 and high myopia. The pairwise linkage disequilibrium (LD) mapping disclosed a strong value (D' > 0.8) and narrow ranged block within these SNPs.Entities:
Year: 2007 PMID: 19668483 PMCID: PMC2701124
Source DB: PubMed Journal: Clin Ophthalmol ISSN: 1177-5467
Figure 113 SNPs analyzed in the LAMA1 gene. Vertical arrows show the 13 SNPs analyzed in this study with the #rs numbers. Left of the figure is 5′ UTR. Black boxes show the translated regions (exons) of this gene with the exon numbers below them.
Allele frequencies for the 13 SNPs in the LAMA1 gene among the Japanese patients with high myopia
| #rs334384 | C/T | 5′upstream | 120(18.5) | 528(81.5) | 112(17.2) | 540(82.8) | 0.5279 | |
| #rs334420 | C/T | 5′upstream | 387(59.7) | 261(40.3) | 398(61.4) | 250(38.6) | 0.5348 | |
| #rs334407 | A/G | Intron1 | 263(40.5) | 387(59.5) | 257(39.7) | 391(60.3) | 0.7684 | |
| #rs12454984 | C/T | Intron1 | 54(8.2) | 602(91.8) | 64(9.8) | 590(90.2) | 0.3259 | |
| #rs684634 | A/G | Exon19 | Cys⇒Cys | 548(83.8) | 106(16.2) | 547(83.4) | 109(16.6) | 0.8420 |
| #rs12961939 | A/C | Exon33 | Ser⇒Ala | 604(92.4) | 50(7.6) | 611(93.7) | 41(6.3) | 0.3355 |
| #rs12607841 | A/G | Exon37 | Ala⇒Val | 48(7.3) | 608(92.7) | 45(6.9) | 609(93.1) | 0.7585 |
| #rs11664063 | C/T | Exon39 | Ala⇒Thr | 564(86.2) | 90(13.8) | 562(85.9) | 92(14.1) | 0.8731 |
| #rs671871 | A/G | Exon44 | Ile⇒Thr | 577(88.2) | 77(11.2) | 584(89.8) | 66(10.2) | 0.3493 |
| #rs543355 | C/T | Exon55 | Thr⇒Ala | 0(0.0) | 645(100) | 0(0.0) | 658(100) | - |
| #rs683733 | A/C | Exon56 | Gly⇒Val | 0(0.0) | 652(100) | 0(0.0) | 652(100) | - |
| #rs16950868 | A/C | Intron56 | 95(14.6) | 555(85.4) | 105(16.2) | 545(83.8) | 0.4421 | |
| #rs2013077 | A/G | Intron57 | 435(66.7) | 217(33.3) | 422(64.9) | 228(35.1) | 0.4948 | |
Genotype frequencies for the 13 SNPs in the LAMA1 gene among the Japanese patients with high myopia
| #rs334384 | C/T | 11(3.4) | 98(30.3) | 215(66.4) | 13(4.0) | 86(26.4) | 227(69.6) | 0.530 | 109(33.6) | 215(66.4) | 99(30.4) | 227(69.6) | 0.371 | 11(3.4) | 313(96.6) | 13(4.0) | 313(96.0) | 0.689 |
| #rs334420 | C/T | 123(38.0) | 141(43.5) | 60(18.5) | 124(38.3) | 150(46.3) | 50(15.4) | 0.551 | 264(81.5) | 60(18.5) | 274(84.6) | 50(15.4) | 0.295 | 123(38.0) | 201(62.0) | 124(38.3) | 200(61.7) | 0.936 |
| #rs334407 | A/G | 62(19.1) | 139(42.8) | 124(38.1) | 51(15.7) | 155(47.8) | 118(36.5) | 0.352 | 201(61.8) | 124(38.2) | 206(63.6) | 118(36.4) | 0.648 | 62(19.1) | 263(80.9) | 51(15.7) | 273(84.3) | 0.262 |
| #rs12454984 | C/T | 4(1.2) | 46(14.0) | 278(84.8) | 2(0.6) | 60(18.4) | 265(81.0) | 0.244 | 50(15.2) | 278(84.8) | 62(19.0) | 265(81.0) | 0.207 | 4(1.2) | 324(98.8) | 2(0.6) | 325(99.4) | 0.414 |
| #rs684634 | A/G | 229(70.0) | 90(27.5) | 8(2.5) | 230(70.1) | 87(26.5) | 11(3.4) | 0.769 | 319(97.6) | 8(2.4) | 317(96.7) | 11(3.3) | 0.489 | 229(70.0) | 98(30.0) | 230(70.1) | 98(29.9) | 0.980 |
| #rs12961939 | A/C | 278(85.0) | 48(14.7) | 1(0.3) | 287(88.0) | 37(11.4) | 2(0.6) | 0.387 | 326(99.7) | 1(0.3) | 324(99.4) | 2(0.6) | 0.561 | 278(85.0) | 49(15.0) | 287(88.0) | 39(12.0) | 0.258 |
| #rs12607841 | A/G | 3(0.9) | 42(12.8) | 283(86.3) | 2(0.6) | 41(12.5) | 284(89.9) | 0.212 | 45(13.7) | 283(86.3) | 43(13.1) | 284(86.9) | 0.831 | 3(0.9) | 325(99.1) | 2(0.6) | 325(99.4) | 0.656 |
| #rs11664063 | C/T | 243(74.3) | 78(23.9) | 6(1.8) | 245(74.9) | 72(22.0) | 10(3.1) | 0.536 | 321(98.2) | 6(1.8) | 317(96.9) | 10(3.1) | 0.311 | 243(74.3) | 84(25.7) | 245(74.9) | 82(25.1) | 0.857 |
| #rs671871 | A/G | 256(78.3) | 65(19.9) | 6(1.8) | 262(80.6) | 60(18.5) | 3(0.9) | 0.532 | 321(98.2) | 6(1.8) | 322(99.1) | 3(0.9) | 0.318 | 256(78.3) | 71(21.7) | 262(80.6) | 63(19.4) | 0.462 |
| #rs543355 | C/T | 0(0.0) | 0(0.0) | 329(100) | 0(0.0) | 0(0.0) | 329(100) | - | 0(0.0) | 327(100) | 0(0.0) | 329(100) | - | 0(0.0) | 327(100) | 0(0.0) | 329(100) | - |
| #rs683733 | A/C | 0(0.0) | 0(0.0) | 326(100) | 0(0.0) | 0(0.0) | 326(100) | - | 0(0.0) | 326(100) | 0(0.0) | 326(100) | - | 0(0.0) | 326(100) | 0(0.0) | 326(100) | - |
| #rs16950868 | A/C | 10(3.1) | 75(23.1) | 240(73.8) | 12(3.7) | 81(24.9) | 232(71.4) | 0.548 | 85(26.2) | 240(73.8) | 93(28.6) | 232(71.4) | 0.482 | 10(3.1) | 315(96.9) | 12(3.7) | 313(96.3) | 0.664 |
| #rs2013077 | A/G | 153(46.9) | 129(39.6) | 44(13.5) | 138(42.5) | 146(44.9) | 41(12.6) | 0.381 | 282(86.5) | 44(13.5) | 284(87.4) | 41(12.6) | 0.081 | 153(46.9) | 173(53.1) | 138(42.5) | 187(57.5) | 0.251 |
Figure 2LD patterns of the LAMA1 locus. Pairwise LD between SNPs within LAMA1 locus are evaluated by D′ Structures of low to high LD in the LAMA1 locus are shown in colored region. The case is above and the control is below the diagonal line.
Frequency analysis of the estimated haplotype for the SNPs within the LAMA1 gene in Japanese myopia patients and control subjects
| 01 | T | C | G | T | A | A | G | C | A | C | A | 0.157 | 0.174 | 0.88(0.58–1.34) | 0.293 |
| 02 | T | T | A | T | A | A | G | C | A | C | A | 0.141 | 0.105 | 1.40(0.87–2.24) | 0.096 |
| 03 | T | C | G | T | A | A | G | C | A | C | G | 0.070 | 0.068 | 1.04(0.57–1.91) | 0.495 |
| 04 | T | C | G | T | G | A | G | C | A | C | A | 0.052 | 0.022 | 2.46(1.01–5.97) | 0.010 |
| 05 | T | T | A | T | A | A | G | C | A | C | G | 0.044 | 0.028 | 1.60(0.68–3.73) | 0.102 |
| 06 | C | C | G | T | A | A | G | C | A | C | A | 0.028 | 0.026 | 1.05(0.41–2.71) | 0.408 |
| 07 | C | T | A | T | A | A | G | C | A | C | G | 0.023 | 0.021 | 1.14(0.40–3.25) | 0.396 |
| 08 | T | C | G | T | A | A | G | C | A | A | G | 0.021 | 0.014 | 1.44(0.44–4.72) | 0.274 |
| 09 | T | C | G | T | A | A | G | T | A | C | A | 0.020 | 0.026 | 0.75(0.26–2.12) | 0.299 |
| 10 | T | C | G | T | A | A | A | C | A | C | A | 0.018 | 0.012 | 1.47(0.40–5.35) | 0.377 |
Odds ratio (OR) of estimated haplotypes are indicated. OR is calculated by Woolf’s formular using estimated frequncies. p value (P < 0.05) is significant by a χ2 test.
This value is not significant after Bonferroni correction.