Table 4. .
Power in Nuclear Families with Four Offspring when MAF at Associated SNP Is 0.05 or 0.5[Note]
| Power (α=10-7) for Genotypes |
ELOD for Genotypes |
ELOD per Genotype (×1,000) for Genotypes |
||||||||||
| Observed |
Imputed |
Observed |
Imputed |
Observed |
Imputed |
|||||||
| MAF at Trait-Associated SNP, Family Structure, and No. of Genotyped Children |
SCORE | LRT | SCORE | LRT | SCORE | LRT | SCORE | LRT | SCORE | LRT | SCORE | LRT |
| MAF = .05: | ||||||||||||
| Both parents genotyped at candidate SNP; phenotype and flanking-marker data available for both parents and 4 siblings: | ||||||||||||
| 4 | 97.8 | 98.0 | 97.8 | 98.0 | 13.19 | 13.41 | 13.19 | 13.41 | 8.79 | 8.94 | 8.79 | 8.94 |
| 3 | 97.4 | 97.4 | 97.9 | 98.0 | 11.42 | 11.70 | 13.15 | 13.37 | 9.14 | 9.36 | 10.52 | 10.70 |
| 2 | 87.4 | 88.7 | 97.8 | 97.9 | 9.54 | 9.82 | 13.09 | 13.31 | 9.54 | 9.82 | 13.09 | 13.31 |
| 1 | 68.3 | 70.3 | 97.6 | 97.7 | 7.52 | 7.79 | 12.92 | 13.14 | 10.02 | 10.38 | 17.22 | 17.52 |
| 0 | 36.2 | 40.2 | 62.3 | 65.4 | 5.66 | 5.84 | 7.07 | 7.35 | 11.31 | 11.69 | 14.14 | 14.70 |
| One parent genotyped at candidate SNP; phenotype and flanking-marker data available for both parents and 4 siblings: | ||||||||||||
| 4 | 96.5 | 96.7 | 97.3 | 97.5 | 11.53 | 11.71 | 12.99 | 13.21 | 9.22 | 9.37 | 10.39 | 10.56 |
| 3 | 88.1 | 88.9 | 97.0 | 97.1 | 9.56 | 9.77 | 12.61 | 12.81 | 9.56 | 9.77 | 12.61 | 12.81 |
| 2 | 66.4 | 68.2 | 95.9 | 95.9 | 7.46 | 7.67 | 11.77 | 11.94 | 9.94 | 10.22 | 15.69 | 15.92 |
| 1 | 32.1 | 34.8 | 88.2 | 88.4 | 5.26 | 5.47 | 9.83 | 9.93 | 10.53 | 10.93 | 19.65 | 19.85 |
| 0 | 3.4 | 4.4 | 8.3 | 9.7 | 2.91 | 3.03 | 3.60 | 3.68 | 11.63 | 12.11 | 14.39 | 14.73 |
| No parents genotyped at candidate SNP; phenotype and flanking-marker data available for both parents and 4 siblings: | ||||||||||||
| 4 | 85.8 | 85.9 | 96.7 | 96.8 | 9.39 | 9.52 | 12.19 | 12.37 | 9.39 | 9.52 | 12.19 | 12.37 |
| 3 | 66.8 | 67.5 | 94.0 | 94.2 | 7.35 | 7.49 | 11.10 | 11.23 | 9.79 | 9.98 | 14.80 | 14.98 |
| 2 | 29.3 | 32.3 | 81.9 | 82.2 | 5.23 | 5.37 | 8.86 | 8.93 | 10.46 | 10.75 | 17.72 | 17.86 |
| 1 | 4.3 | 5.9 | 24.0 | 24.2 | 2.89 | 3.01 | 4.83 | 4.82 | 11.56 | 12.04 | 19.31 | 19.28 |
| No parents genotyped; phenotype and flanking-marker data available for offspring only: | ||||||||||||
| 4 | 85.8 | 85.9 | 85.8 | 85.9 | 9.39 | 9.52 | 9.39 | 9.52 | 9.39 | 9.52 | 9.39 | 9.52 |
| 3 | 66.8 | 67.4 | 82.6 | 82.7 | 7.35 | 7.48 | 8.88 | 8.99 | 9.79 | 9.98 | 11.84 | 11.98 |
| 2 | 29.3 | 32.3 | 66.6 | 67.3 | 5.23 | 5.37 | 7.47 | 7.54 | 10.46 | 10.75 | 14.95 | 15.08 |
| 1 | 4.3 | 5.9 | 19.7 | 20.9 | 2.89 | 3.01 | 4.52 | 4.54 | 11.56 | 12.04 | 18.10 | 18.16 |
| MAF = .50: | ||||||||||||
| Both parents genotyped at candidate SNP; phenotype and flanking-marker data available for both parents and 4 siblings: | ||||||||||||
| 4 | 99.2 | 99.2 | 99.2 | 99.2 | 13.09 | 13.30 | 13.09 | 13.30 | 8.73 | 8.87 | 8.73 | 8.87 |
| 3 | 96.9 | 97.3 | 99.2 | 99.3 | 11.48 | 11.75 | 12.98 | 13.19 | 9.19 | 9.40 | 10.39 | 10.55 |
| 2 | 90.7 | 91.3 | 99.2 | 99.2 | 9.55 | 9.83 | 12.69 | 12.90 | 9.55 | 9.83 | 12.69 | 12.90 |
| 1 | 70.2 | 72.2 | 98.9 | 99.0 | 7.53 | 7.80 | 11.89 | 12.09 | 10.05 | 10.40 | 15.86 | 16.11 |
| 0 | 35.0 | 38.1 | 60.9 | 63.3 | 5.50 | 5.68 | 6.94 | 7.21 | 11.01 | 11.36 | 13.89 | 14.43 |
| One parent genotyped at candidate SNP; phenotype and flanking-marker data available for both parents and 4 siblings | ||||||||||||
| 4 | 97.1 | 97.0 | 99.1 | 99.1 | 11.55 | 11.72 | 12.82 | 13.02 | 9.24 | 9.37 | 10.25 | 10.42 |
| 3 | 88.8 | 89.6 | 99.0 | 99.0 | 9.58 | 9.79 | 12.23 | 12.41 | 9.58 | 9.79 | 12.23 | 12.41 |
| 2 | 70.8 | 72.7 | 96.8 | 97.0 | 7.48 | 7.69 | 10.95 | 11.08 | 9.97 | 10.25 | 14.60 | 14.78 |
| 1 | 29.5 | 33.7 | 80.3 | 80.6 | 5.16 | 5.36 | 8.32 | 8.39 | 10.32 | 10.71 | 16.63 | 16.78 |
| 0 | 3.1 | 4.3 | 5.7 | 7.2 | 2.87 | 2.98 | 3.58 | 3.66 | 11.48 | 11.93 | 14.32 | 14.65 |
| No parents genotyped at candidate SNP; phenotype and flanking-marker data available for both parents and 4 siblings: | ||||||||||||
| 4 | 89.8 | 90.0 | 96.9 | 97.2 | 9.41 | 9.52 | 11.15 | 11.27 | 9.41 | 9.52 | 11.15 | 11.27 |
| 3 | 70.9 | 72.5 | 94.0 | 93.8 | 7.55 | 7.69 | 10.11 | 10.20 | 10.06 | 10.26 | 13.48 | 13.59 |
| 2 | 27.3 | 30.3 | 76.3 | 75.4 | 5.13 | 5.26 | 8.04 | 8.07 | 10.26 | 10.53 | 16.08 | 16.14 |
| 1 | 2.6 | 2.9 | 23.2 | 23.3 | 2.88 | 2.99 | 4.83 | 4.82 | 11.50 | 11.95 | 19.32 | 19.30 |
| No parents genotyped; phenotype and flanking-marker data available for offspring only: | ||||||||||||
| 4 | 89.8 | 90.0 | 89.8 | 90.0 | 9.41 | 9.52 | 9.41 | 9.52 | 9.41 | 9.52 | 9.41 | 9.52 |
| 3 | 70.9 | 72.4 | 85.0 | 85.8 | 7.55 | 7.69 | 8.81 | 8.90 | 10.06 | 10.26 | 11.74 | 11.86 |
| 2 | 27.3 | 30.4 | 66.4 | 66.3 | 5.13 | 5.26 | 7.34 | 7.38 | 10.26 | 10.53 | 14.68 | 14.77 |
| 1 | 2.6 | 2.9 | 18.4 | 17.9 | 2.88 | 2.99 | 4.53 | 4.53 | 11.50 | 11.95 | 18.12 | 18.11 |
Note.— Power, the ELOD, and the ELOD per genotype were evaluated by executing 1,000 simulations for each cell. A total of 250 families, each with four offspring, were simulated. The associated SNP had MAF of 0.05 or 0.50 and explained 5% of the trait variability. The associated SNP was flanked by 50 SNPs (with 0.3-cM spacing), which were used to help infer missing genotypes. Background polygenic effects accounted for 35% of the trait variability. Simulated data sets were analyzed first using only the observed genotypes and then, again, using our expected genotype score approach.