Genes and transplant outcomes: the search for "associations".

The successful completion of the human genome project and subsequent development of assays for genome-wide association studies (GWAS) has allowed for a powerful, somewhat unbiased review of the entire genome to localize common genetic variants (single-nucleotide polymorphisms or SNPs and other allelic variants). The field has virtually explodedVa recent PubMed search using the key words SNPs and associations yield more than 13,000 citations for the past decade (more than three per day) with studies ranging from genes associated with responsiveness to cancer therapy to the calving variations among cows (1). The question specific to our commentary here is whether or not there are genes closely associated with various transplant outcomes. A study by Clatworthy et al. seeks to address this question and provides an example to illustrate some of the important issues that these types of studies encounter (2). The goal of this study was to determine if a SNP associated with a non-functioning FcFRIIB (rs1050501) affected susceptibility to renal allograft rejection, graft loss, or recipient survival. They determined the FcFRIIB genotype in 2851 Caucasian and 570 Afro-Caribbean renal transplant recipients including 236 with a primary diagnosis of systemic lupus erythematosis. They found that the frequency of the SNP homozygosity (T/T) was 2.2% in Caucasians, 6.8% in Afro-Caribbeans, and 3.8% in recipients with the primary diagnosis systemic lupus erythematosis. They found no differences in the incidence of rejection, graft survival, or patient survival. Patient survival at 10 years was 87% in homozygous wild type and 72% in heterozygous and 74% in homozygous SNP allotype, but this did not reach statistical significance. There are many important issues in this fascinating and emerging field, and we encourage the readers of Transplantation to explore some excellent reviews (3, 4). However, here we confine our discussion to three areas that we believe are particularly related to transplantation and the current study under consideration. The first issue is the outcome that is studied. Complex outcomes such as patient and graft survival have many causes (5) and thus are unlikely to be associated with any one gene. Even more specific factors associated with graft loss such as the development of donor-specific alloantibody are likely multifactorial, with each modifying factor having a complex genetic ‘‘cause’’. For example, absorption of immunosuppression, drug metabolism, and variations in immune responsiveness have all been shown to be influenced by differences in DNA among individuals (6Y8). As in other conditions, the narrower the focus, the more likely that a gene association will be demonstrable. The second issue has to do with study design and sample size. Transplant studies are notoriously difficult to power sufficiently, and the possibility of declaring a factor unimportant when it actually does have an association with an outcome (a type II error) is a concern in these types of GWAS in transplantation. A significant effect is hard to demonstrate if the SNP is rare or if it has only a minor effect on outcomes, or both. For example, with a T/T SNP frequency of 2.2% as seen in Caucasians in the Clatworthy study, more than a thousand events (e.g., graft failures or deaths) are required to detect various hazard ratios between two genotype groups with 80% power and a type I error rate of 0.05 (Fig. 1; solid line). According to this analysis, a hazard ratio of 0.5 would require 800 to 1,000 events. With smaller relative risk effects (hazard ratios near 1), extremely large numbers of events are required. This can be overcome by including more study patients or increasing follow-up times to increase the number of patients reaching the event, but both options are costly. Another solution would be to study SNPs with much higher frequency in the study population. For example, if the T/T SNP frequency was 50%, the number of events necessary ANALYSIS AND COMMENTARY