The main difference between currently available GWA panels involves the number of SNPs for which probes are included and the resulting genomic coverage obtained by this selection. Some of the latest panels also contain probes for analysing copy number variations (CNVs), although there are also methods for identifying these in-silico from genotyping intensities. Current commercially available genotyping panels typically range in capacity from 300K up to 1M SNPs but there are also focused panels that only capture a few hundred SNPs. The design of the panels mainly falls into three categories, containing SNPs 1) more or less randomly selected, 2) chosen because they are tagSNPs and 3) chosen as part of a focused selection based on previously implicated functional importance or for lying within or nearby genes that could have a role for different diseases such as cancer. TagSNP panels have been shown to provide better coverage of common variation 17. An important note is that the calculated coverage by the selection of tagSNPs is currently based on coverage of all common SNPs genotyped in HapMap, not of the remaining
