In addition to strong justification for the selection of the gene under study, a second area that should be justified is the genotyping strategy: if only a select number of polymorphisms in a gene are being genotyped, how and why were those selected? There are several methods for selecting polymorphisms – one can utilize SNP content from a preexisting GWAS array or genotype custom content individually or en masse (e.g., as offered by the Illumina Golden Gate technology; Hodgkinson et al., 2008). Prices for GWAS arrays, especially those designed to include custom content, have dropped considerably, and often it is far more expensive and less cost-efficient to genotype a small number of polymorphisms than to genotype in large scale. In some cases, the technology required to genotype a particular variant, especially one that is not a SNP (e.g., a variable number of tandem repeats) is specialized and may entail unique requirements as most commercial arrays and custom genotyping platforms may not include this. Nonetheless, if only a few SNPs can be genotyped, tagging a gene may be preferable to simply
