June 2013
Volume 54, Issue 15
Free
ARVO Annual Meeting Abstract  |   June 2013
Heritability Estimation of Axial Length and Refractive Error Explained by Genome-Wide Single Nucleotide Polymorphisms
Author Affiliations & Notes
  • Masahiro Miyake
    Department of Ophthalmology, Kyoto Univ Grad Sch of Medicine, Sakyoku, Kyoto City, Japan
    Center for Genomic Medicine, Kyoto Univ Grad Sch of Medicine, Sakyoku, Kyoto City, Japan
  • Kenji Yamashiro
    Department of Ophthalmology, Kyoto Univ Grad Sch of Medicine, Sakyoku, Kyoto City, Japan
  • Hideo Nakanishi
    Department of Ophthalmology, Kyoto Univ Grad Sch of Medicine, Sakyoku, Kyoto City, Japan
    Center for Genomic Medicine, Kyoto Univ Grad Sch of Medicine, Sakyoku, Kyoto City, Japan
  • Isao Nakata
    Department of Ophthalmology, Kyoto Univ Grad Sch of Medicine, Sakyoku, Kyoto City, Japan
    Center for Genomic Medicine, Kyoto Univ Grad Sch of Medicine, Sakyoku, Kyoto City, Japan
  • Yumiko Akagi-Kurashige
    Department of Ophthalmology, Kyoto Univ Grad Sch of Medicine, Sakyoku, Kyoto City, Japan
    Center for Genomic Medicine, Kyoto Univ Grad Sch of Medicine, Sakyoku, Kyoto City, Japan
  • Kyoko Kumagai
    Department of Ophthalmology, Kyoto Univ Grad Sch of Medicine, Sakyoku, Kyoto City, Japan
  • Akitaka Tsujikawa
    Department of Ophthalmology, Kyoto Univ Grad Sch of Medicine, Sakyoku, Kyoto City, Japan
  • Ryo Yamada
    Center for Genomic Medicine, Kyoto Univ Grad Sch of Medicine, Sakyoku, Kyoto City, Japan
  • Fumihiko Matsuda
    Center for Genomic Medicine, Kyoto Univ Grad Sch of Medicine, Sakyoku, Kyoto City, Japan
  • Nagahisa Yoshimura
    Department of Ophthalmology, Kyoto Univ Grad Sch of Medicine, Sakyoku, Kyoto City, Japan
  • Footnotes
    Commercial Relationships Masahiro Miyake, None; Kenji Yamashiro, None; Hideo Nakanishi, None; Isao Nakata, None; Yumiko Akagi-Kurashige, None; Kyoko Kumagai, None; Akitaka Tsujikawa, Pfizer (F); Ryo Yamada, None; Fumihiko Matsuda, None; Nagahisa Yoshimura, Canon (C), Canon (F), Nidek (C), Topcon (F), PCT/JP2011/073160 (P)
  • Footnotes
    Support None
Investigative Ophthalmology & Visual Science June 2013, Vol.54, 1734. doi:
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      Masahiro Miyake, Kenji Yamashiro, Hideo Nakanishi, Isao Nakata, Yumiko Akagi-Kurashige, Kyoko Kumagai, Akitaka Tsujikawa, Ryo Yamada, Fumihiko Matsuda, Nagahisa Yoshimura, ; Heritability Estimation of Axial Length and Refractive Error Explained by Genome-Wide Single Nucleotide Polymorphisms. Invest. Ophthalmol. Vis. Sci. 2013;54(15):1734.

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      © ARVO (1962-2015); The Authors (2016-present)

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Abstract

Purpose: Genome-wide association study (GWAS) is a powerful strategy which has identified numerous loci associated with diseases. However, although many GWASs have been conducted on high myopia, single nucleotide polymorphisms (SNPs) identified in them can explain only a small fraction of narrow-meaning heritability estimated by family studies or twin studies. Thus, we examined if SNPs typed in the GWAS can explain narrow-meaning heritability of AL and SE.

Methods: The Nagahama cohort study is an ongoing community-based cohort study, which consists of 9,804 individuals from Nagahama city, Japan. We used 3,748 individuals who are genotyped and imputed for 1,751,558 SNPs. After pruning potential relatives, 2171 individuals were finally included. Heritability is defined as a fraction of variance explained by all SNPs to that of the target phenotype, i.e. AL and SE. We estimated both variance explained by all SNPs and variance explained by SNPs in each chromosome by a linear mixed model proposed by Yang J. et al. (Nature Genetics, 2010). Age, sex, and height were included in the model as covariates.

Results: For AL and SE, heritability (± standard error) explained by all SNPs were 40.0% (± 21.2) and 61.1% (± 24.8), respectively. While the top contributor for AL was chromosome 1 explaining 11.0%, no contribution was observed in chromosome 3, 7, and 11. Though five chromosomes contributed to heritability of SE explaining more than 5.0% respectively, ten chromosomes exhibited less than 0.5% of contribution.

Conclusions: Since the estimated heritability in this study is larger than the heritability explained by previously reported SNPs, GWAS still has a potential to identify more causative loci. The difference from the heritability estimated by family or twin study would be due to the rare variants or structural variations. SE is more common-SNP-driven than AL, and responsible chromosome of SE heritability is deviated.

Keywords: 539 genetics • 605 myopia  
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