GWAS have no a priori hypothesis but ask whether a phenotype might be associated with any of a very large number of common SNPs distributed across the genome. The earliest GWAS chips included several hundreds of thousands of SNPs but more recent chips include up to 5 million. However, use of such large numbers of SNPs requires stringent corrections for false positive results with the current level set at around p values < 5×10−8. This has been a real challenge for GWAS of complex traits since few SNPs reach that degree of significance as can be seen from a catalogue prepared by the National Human Genome Research Institute (NHGRI). The results of all SNP-trait associations with p values < 1.0 × 10−5 in all published GWA studies (currently at 1659 publications, 10986 SNPs) have been catalogued by NHGRI and are freely available [67].
