Ultrafast genome-wide scan for SNP–SNP interactions in common complex disease

(Downloading may take up to 30 seconds. If the slide opens in your browser, select File -> Save As to save it.)

Click on image to view larger version.

Figure 1.
Figure 1.

Group sampling. A cohort of Graphic cases is shown on the left, where the cases outlined in red—Graphic, Graphic, Graphic, and Graphic—harbor an interacting pair of recessive variables. In other words, more cases carry the recessive–recessive combination than would be expected by chance, given the marginal frequencies of each recessive allele. By repeatedly drawing random groups of Graphic cases (here Graphic), we are guaranteed to have drawn at least one group of individuals that carries both the variables in Graphic attempts with probability Graphic. These variables (and others) are quickly determined by a bitwise-AND operation between the group of cases. Then, all pairs of cocarried variables are enumerated and tested against the stage 1 null hypothesis (case-only analysis). Rejected combinations are shortlisted and followed up in stage 2 (case vs. control analysis), where an interaction is identified.

This Article

  1. Genome Res. 22: 2230-2240

Preprint Server