Introduction

216 Y.J. Li and Q. Fan

detect genes with small to moderate genetic effects on disease risk as expected in complex diseases. The caveat to their conclusion is that a sufficient density of markers must be screened to ensure that the actual disease locus, or one in strong linkage disequilibrium (LD) with the disease locus, will be tested. With the availability of genome wide high-density single-nucleotide polymorphism (SNP) arrays (or SNP chips), genome wide association (GWA) studies have become feasible to achieve “large-scale” association testing. In the past few years, GWA studies have proven to be a powerful approach to uncover new disease genes or genetic loci for several different diseases.2

The genetic basis of myopia is supported by data from familial aggregation, segregation, and twin studies. The review of genetic studies of myopia to date can be found in Chapters 3.1–3.5 [Note: refer to Chapters by Drs. Young, Baird, and Khor]. Almost all studies were based on the framework of genome wide linkage scans, association study for selected candidate genes, or sequencing of the promoter and exons of candidate genes to identify functional variants. Although the number of GWA publications is growing in the past few years, no GWA reports for myopia or its related phenotypes have been published until recently by Nakanishi et al.,3 for which they identified a chromosome 11q24.1 locus for the pathological myopia (high myopia with axial length > 28.0 mm in both eyes), a selected subgroup of high myopia. To our knowledge, several myopia-related GWA studies are underway, particularly using existing epidemiologic cohorts of myopia, at the time of writing this chapter. It is expected that more GWA papers will be published within a year or two.

Unlike association studies of candidate genes that are limited to specific biological function or chromosome regions of interest, GWA studies utilize hundreds of thousands of markers across the genome to evaluate the association between markers and disease-related phenotypes on the genomewide scale. The GWA study is considered an unbiased approach to survey most of the genome for susceptible or causal variants since no assumptions are made for any pre-selected regions or genes for association tests. While this approach is more comprehensive than conventional candidate gene association studies, several layers of challenges have arisen due to the significantly increased data and tests that we face for the GWA study. In the following sections, we will provide a general review of conducting a GWA study and relate it to myopia. Through this chapter, examples illustrated were obtained from the GWA data of 929 Chinese samples from Singapore Cohort Study of the Risk factors for Myopia (SCORM), for which

217 Statistical Analysis of Genome-wide Association Studies for Myopia

genotyping was conducted using Illumina HumanHap 550 (http://www. illumina.com/).

Phenotypes for Myopia Genetic Studies

The diagnosis of myopia is determined by refractive errors, sphere (SPH), or spherical equivalent (SE = sphere + 1/2(cylinder)). The most frequently studied phenotypes in myopia genetic studies are various dichotomous disease states of myopia (e.g. common myopia, moderate myopia, high myopia) defined by different thresholds of SPH or SE. Among them, high myopia was probably investigated the most, resulting in 10 out of 16 MYP loci reported to link to high myopia.4–13 In contrast, the uses of quantitative refractive errors for myopia genetic studies are much fewer.14 Furthermore, although other ocular biometrics, such as axial length, anterior chamber depth, and corneal curvature, are highly correlated to refraction error, contribute to the determination of refraction, and show high heritability in families,15 they have not been widely investigated for genetic association. Clearly, these ocular biometrics are valuable endophenotypes for searching genes that may affect myopia development.

In Table 1, we listed several quantitative ocular biometrics and dichotomous disease states of myopia that can be considered for genetic association studies. Even with the most frequently studied dichotomous phenotypes such as myopia and high myopia, the definition of various myopic states was not standardized in the myopia genetic research community. SPH and SE have been used alternatively in the literature for defining the disease state of myopia. In addition, different thresholds of refraction error (in diopters (D)) have been used for declaring the severity of myopia. For instance, −6.00 D or −5.00 D have been alternatively used as the threshold for defining high myopia.

Considering the needs of replication evidence for GWA studies, investigators should be mindful of the consistency in phenotypes across studies. With the lack of a gold standard on defining various degrees of myopia diseases status, one will need to make sure that the same thresholds or definition of myopia cases and controls are consistent across all datasets to be investigated.

An additional caveat of myopia related phenotypes is that each biometric measure can be obtained from right and left eyes. An affected status of myopia is mostly defined when at least one eye reaches the given threshold