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Genome-wide association studies assume a priori hypotheses about candidate genes or regions that might be associated with disease; rather, they test single-nucleotide polymorphisms (SNPs) throughout the genome for possible evidence of genetic susceptibility. Associations plotted as −log10 P values for a genome-wide association study in 1522 cases with rheumatoid arthritis and 1850 controls, showing single data points for SNPs with P 10−4 (lower horizontal red line) for 22 autosomes and the X chromosome. The predefined level of significance, at 510−8 is shown with a horizontal blue line. SNPs at PTPN22 on chromosome 1, the major histocompatibility comples (MHC) on chromosome 6, and the TRAF1-C5 locus on chromosome 9 exceed this threshold.

Reproduced with permission from Plenge et al.47