Table 2 The power of F_HapMiner and the single-locus TDT (SL-TDT) on each SNP for different penetrance models using the CF dataset (sample size = 50 pedigrees). SNP are ordered and grouped based on their minor allele frequencies (MAF).
From: A novel approach for haplotype-based association analysis using family data
| Â | Â | Â | Penetrance Set A | Penetrance Set B | Penetrance Set C | |||
|---|---|---|---|---|---|---|---|---|
Group | MAF | SNP | SL-TDT | F_HapMiner | SL-TDT | F_HapMiner | SL-TDT | F_HapMiner |
Low | 0.03572 | 16 | 0.07 | 0.07 | 0.44 | 0.56 | 0.24 | 0.38 |
| Â | 0.05358 | 2 | 0.08 | 0.02 | 0.34 | 0.39 | 0.31 | 0.23 |
| Â | 0.08925 | 13 | 0.40 | 0.55 | 0.96 | 1.00 | 0.89 | 1.00 |
| Â | 0.10711 | 11 | 0.51 | 0.55 | 0.95 | 1.00 | 0.98 | 1.00 |
| Â | 0.12502 | 8 | 0.42 | 0.60 | 0.99 | 1.00 | 0.95 | 1.00 |
Medium | 0.14283 | 9 | 0.52 | 0.74 | 0.98 | 1.00 | 0.99 | 1.00 |
| Â | 0.14283 | 15 | 0.41 | 0.55 | 0.94 | 1.00 | 0.97 | 1.00 |
| Â | 0.14287 | 14 | 0.38 | 0.42 | 0.88 | 0.95 | 0.93 | 0.98 |
| Â | 0.14288 | 10 | 0.59 | 0.80 | 0.98 | 1.00 | 1.00 | 1.00 |
| Â | 0.16074 | 7 | 0.28 | 0.31 | 0.67 | 0.85 | 0.77 | 0.95 |
| Â | 0.21425 | 4 | 0.06 | 0.02 | 0.14 | 0.08 | 0.16 | 0.17 |
| Â | 0.26789 | 12 | 0.46 | 0.64 | 0.77 | 0.94 | 0.97 | 1.00 |
High | 0.35716 | 3 | 0.42 | 0.58 | 0.64 | 0.84 | 0.95 | 1.00 |
| Â | 0.41073 | 18 | 0.74 | 0.85 | 0.65 | 0.90 | 0.99 | 1.00 |
| Â | 0.42859 | 19 | 0.69 | 0.85 | 0.73 | 0.87 | 1.00 | 1.00 |
| Â | 0.4286 | 1 | 0.38 | 0.58 | 0.52 | 0.67 | 0.86 | 1.00 |
| Â | 0.46427 | 6 | 0.64 | 0.82 | 0.68 | 0.80 | 0.98 | 1.00 |
| Â | 0.48213 | 5 | 0.57 | 0.78 | 0.55 | 0.81 | 0.99 | 1.00 |
| Â | 0.48216 | 17 | 0.43 | 0.68 | 0.54 | 0.67 | 0.89 | 1.00 |