There are several limitations in this study. First, to reduce cost, we used a candidate gene approach and subjectively selected 25 SNPs from 7 IGF axis genes for study. The coverage and information of our SNP list highly depended on the data from the HapMap project. Furthermore, other types of genetic polymorphisms, such as copy number variants,
90 may be responsible for the underlying association with AMD risk. Therefore, false-negative findings are possible. On the other hand, because of the small sample size for geographic atrophy (
Table 5), false-positive findings are also possible. In addition, we used Bonferroni's correction for our hypothesis testing on the 25 SNPs. Furthermore, multiple tests were performed for each SNP. This may also increase the likelihood of false-positive findings. Although rs2872060 is implicated in AMD risk, no study has related it to major systemic diseases or mortality. However, polymorphisms in IGF axis genes are related to risk for some diseases and aging, and this may create bias. If the relationship with the other diseases is stronger and subjects with these diseases had excluded from this study, it may have create false associations with AMD or attenuated existing ones. This survival bias could be assessed by comparing disease risk or survival time between different IGF axis gene genotypes. Because the primary interest of the AREDS is eye diseases and data regarding mortality are not available, it is difficult to assess the potential survival bias. Furthermore, it was found that survival bias results in no more than a 20% effect size erosion in cohorts with a mean age of <75 years,
91 similar to our study sample. Finally, we included only white subjects in this study of the association between the 25 SNPs and advanced AMD. While previous genome-wide association studies (GWAS) in subsets of white participants from the AREDS showed inconsistencies in population stratification,
92,93 we did not find obvious population stratification in our study sample. Unlike in GWAS, which must consider the confounding effects of population stratification on the associations between diseases and SNPs from across the whole genome, in this study of the 25 candidate SNPs we are not interested in the overall population stratification. Instead, we are interested in systematic ancestry differences in allele frequencies in the 25 SNPs between cases and controls. Although PCA can be applied to assess population stratification in GWAS and candidate gene association studies as well, its power depends on both the number of SNPS and the sample size.
94 Based on the data from our advanced AMD case and controls (
n = 485), we may have had inadequate power for detecting the underlying population stratification.