TABLE I.
Information of the HapMap chromosomal regions studied and hypothetical disease-causing SNP used for simulations.
| Chr. | Spanning (base pair) | No. of SNPs |
LD of adjacent loci mean (range) |
LD of all pairs of loci mean (range) |
Average prevalencea (%) |
Causal allele frequency |
||
|---|---|---|---|---|---|---|---|---|
| D′ | r2 | D′ | r2 | |||||
| 1 | 85.0 kb (75,996,416–76,081,443) | 8 | 0.99 (0.90–1.00) | 0.25 (0.04–0.76) | 0.91 (0.11–1.00) | 0.27 (0.002–0.86) | 6.30 (3.68–8.17) | 0.28 (0.08–0.38) |
| 2 | 74.7 kb (165,005,914–165,080,660) | 4 | 1.00 (1.00–1.00) | 0.31 (0.02–0.88) | 0.77 (0.31–1.00) | 0.19 (0.02–0.88) | 4.31 (4.00–4.62) | 0.14 (0.12–0.17) |
| 3 | 70.0 kb (48,181,106–48,251,081) | 4 | 1.00 (1.00–1.00) | 0.08 (0.02–0.19) | 1.00 (1.00–1.00) | 0.22 (0.02–0.86) | 5.67 (3.45–7.02) | 0.25 (0.06–0.34) |
| 4 | 97.8 kb (95,656,914–95,754,677) | 4 | 0.82 (0.45–1.00) | 0.39 (0.09–0.95) | 0.82 (0.45–1.00) | 0.29 (0.07–0.95) | 6.12 (4.85–7.79) | 0.26 (0.18–0.38) |
| 5 | 67.8 kb (86,285,103–86,352,855) | 8 | 0.99 (0.91–1.00) | 0.23 (0.02–0.65) | 0.97 (0.49–1.00) | 0.25 (0.02–0.94) | 5.37 (3.91–8.79) | 0.21 (0.09–0.43) |
| 6 | 24.5 kb (85,437,983–85,462,480) | 4 | 1.00 (1.00–1.00) | 0.32 (0.02–0.90) | 1.00 (1.00–1.00) | 0.17 (0.01–0.90) | 4.17 (3.68–5.23) | 0.11 (0.08–0.18) |
| 7 | 75.9 kb (79,276,107–79,352,038) | 4 | 1.00 (1.00–1.00) | 0.67 (0.48–0.90) | 0.93 (0.68–1.00) | 0.55 (0.31–0.90) | 4.09 (3.68–4.70) | 0.12 (0.08–0.18) |
| 8 | 24.2 kb (73,087,988–73,112,209) | 4 | 1.00 (1.00–1.00) | 0.04 (0.02–0.09) | 0.99 (0.92–1.00) | 0.13 (0.02–0.54) | 4.70 (3.99–5.79) | 0.17 (0.10–0.28) |
| 9 | 42.1 kb (69,172,556–69,214,705) | 4 | 0.98 (0.94–1.00) | 0.40 (0.01–0.69) | 0.99 (0.94–1.00) | 0.28 (0.01–0.69) | 4.65 (3.53–5.85) | 0.15 (0.07–0.23) |
| 10 | 32.9 kb (67,662,628–67,695,506) | 4 | 0.97 (0.90–1.00) | 0.10 (0.04–0.21) | 0.93 (0.73–1.00) | 0.28 (0.04–0.88) | 5.81 (4.54–8.55) | 0.23 (0.14–0.39) |
| 17 | 68.2 kb (40,248,321–40,316,535) | 25, 8 | 0.97 (0.23–1.00) | 0.22 (0.003–1.00) | 0.94 (0.17–1.00) | 0.20 (0.002–1.00) | 5.35 (3.84–7.87) | 0.22 (0.10–0.39) |
| 22 | 70.5 kb (33,606,466–33,676,951) | 8 | 1.00 (1.00–1.00) | 0.04 (0.004–0.15) | 0.84 (0.12–1.00) | 0.08 (0.001–0.67) | 4.86 (3.37–9.10) | 0.17 (0.05–0.45) |
| The total number of simulation scenarios | 89 | |||||||
a
The prevalence was calculated under a disease model representing Alzheimer's disease. In the parentheses, we list the minimum and the maximum prevalence when each SNP in turn was considered the causal locus. In real data (population of Kuopio, eastern Finland, 980 people aged 69–78), the prevalence of Alzheimer's disease was 4.7% [Kuusisto et al., 1994]. SNP, single-nucleotide polymorphism, LD, linkage disequilibrium.