Subsequent studies following the initial Uhl et al. (2001) study increased the SNP marker density to 10 thousand (Q. R. Liu, et al., 2005), 100 thousand (Johnson, et al., 2006), 500 thousand (Q. R. Liu, et al., 2006) and 1 million (Drgon, et al., 2011; Drgon, et al., 2010; G. R. Uhl, et al., 2007). Subsequent studies have also conducted genome-wide association with copy number variants (Drgon, Montoya, et al., 2009). Beginning with the 2005 study, the marker density was sufficient to begin to discuss individual “candidate” genes. Even at this stage many more positive markers than expected by chance were associated with the initial Uhl et al. (2001) study or with previous whole-genome linkage studies, a pattern which continued to develop throughout the series of studies. As these studies progressed, it was necessary to consider more carefully, and much more explicitly than the field was often ready to accept, the tradeoff between false positive and false negative rates in the criteria used to identify genes as being “positive” in any particular analysis (for a detailed consideration of this issue
