Table 2. .
Power for Nuclear Families with Two Offspring and Different Sets of Individuals Genotyped at the Candidate SNP[Note]
| Power (α=10-7) for Genotypes |
ELOD for Genotypes |
ELOD per Genotype (×1,000) for Genotypes |
||||||||||
| Observed |
Imputed |
Observed |
Imputed |
Observed |
Imputed |
|||||||
| Family Structure and No. of Children Genotyped at the Candidate SNP | SCORE | LRT | SCORE | LRT | SCORE | LRT | SCORE | LRT | SCORE | LRT | SCORE | LRT |
| Both parents genotyped at candidate SNP; phenotype and flanking-marker data available for both parents and both siblings: | ||||||||||||
| 2 children | 99.4 | 99.4 | 99.4 | 99.4 | 13.31 | 13.68 | 13.31 | 13.68 | 9.51 | 9.77 | 9.51 | 9.77 |
| 1 child | 95.3 | 96.2 | 99.0 | 99.1 | 10.72 | 11.09 | 12.80 | 13.15 | 10.21 | 10.56 | 12.19 | 12.52 |
| 0 children | 75.2 | 76.4 | 87.8 | 88.9 | 7.81 | 8.05 | 9.11 | 9.41 | 11.16 | 11.50 | 13.01 | 13.44 |
| One parent genotyped at candidate SNP; phenotype and flanking-marker data available for both parents and both siblings: | ||||||||||||
| 2 children | 95.1 | 95.6 | 98.4 | 98.4 | 10.46 | 10.73 | 12.08 | 12.39 | 9.96 | 10.22 | 11.50 | 11.80 |
| 1 child | 68.8 | 70.7 | 91.4 | 91.9 | 7.40 | 7.66 | 9.64 | 9.84 | 10.57 | 10.94 | 13.77 | 14.06 |
| 0 children | 9.7 | 12.5 | 19.9 | 21.2 | 3.93 | 4.06 | 4.66 | 4.75 | 11.23 | 11.60 | 13.31 | 13.57 |
| No parents genotyped at candidate SNP; phenotype and flanking-marker data available for both parents and both siblings: | ||||||||||||
| 2 children | 68.2 | 70.2 | 86.2 | 86.2 | 7.39 | 7.57 | 8.87 | 9.05 | 10.56 | 10.81 | 12.67 | 12.93 |
| 1 child | 10.8 | 13.8 | 34.4 | 36.9 | 4.00 | 4.14 | 5.50 | 5.58 | 11.43 | 11.83 | 15.71 | 15.94 |
| No parents genotyped; phenotype and flanking-marker data available for offspring only: | ||||||||||||
| 2 children | 68.2 | 70.1 | 68.2 | 70.1 | 7.39 | 7.57 | 7.39 | 7.57 | 10.56 | 10.81 | 10.56 | 10.81 |
| 1 child | 10.8 | 13.8 | 25.0 | 26.6 | 4.00 | 4.14 | 4.88 | 4.96 | 11.43 | 11.83 | 13.94 | 14.17 |
Note.— Power, the ELOD, and the ELOD per genotype were evaluated by executing 1,000 simulations for each cell. A total of 350 families, each with two offspring, were simulated. The associated SNP had MAF of 0.30 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 with use of only the observed genotypes and then, again, with use of our expected genotype score approach.