Figure 8.

Comparison of the power of sib-pair linkage mapping, haplotype association mapping, and admixture mapping. A, Power as a function of sample size. These charts present the number of case-control or sib-sib pairs that are expected to be required to detect a disease locus. To set thresholds for genomewide significance, we assume that 300,000 independent markers have been tested for haplotype mapping (including the real risk allele) and that there is perfect information extraction for linkage and admixture mapping, with all samples having a proportion of population A ancestry (for example, European ancestry in African Americans) of M_i=20%. These represent idealized scenarios, so that, in practice, 1.2- to 2-fold more samples would be required than are shown here (see the “Methods” section). For simplicity, we assume that the allele that is being studied is the only one at the locus that increases risk for the disease (with all other alleles conferring equal and lower risk). These results show that, for low-penetrance risk alleles (1.3-fold, 1.5-fold, and 2-fold increased risk due to the allele rather than ancestry) that differ substantially in frequency across populations, admixture mapping requires many fewer samples than linkage mapping (although usually more samples than haplotype-based association mapping). B, Power as a function of number of genotypes. These charts correspond to the same scenarios but report the number of genotypes required rather than the number of samples. The advantages of admixture mapping are most apparent in this comparison, since many fewer markers are required for a whole-genome admixture scan than a whole-genome association scan.