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Comparison of Methods to Account for Relatedness in Genome-Wide Association Studies with Family-Based Data

Figure 4

Manhattan plots for the real phenotype using FaST-LMM exact and alternative software packages.

The points marked in red denote the confirmed significant region from Fakiola et al. (2013). FLMM_E = FaST-LMM using exact calculation, MQLS1972 = MQLS using 1972 genotyped individuals, RT1972 = ROADTRIPS using 1972 genotyped individuals, FBATaff = FBAT using transmissions to affecteds only, FBATboth = FBAT using transmissions to both affecteds and unaffecteds. Results from all other LMM methods were indistinguishable from FLMM_E and so are not shown.

Figure 4