Table 5 Relative Efficiency of Partial Genotyping versus Fully Informative Genotyping. The table gives the percentage relative efficiency of partial (homozygous deletion versus other) genotyping with the proposed test compared to full genotyping. Numbers less than 100% indicate the proposed test with partial genotyping is less efficient than the standard test with full genotyping. LR 1 and LR 2 refer to the proposed likelihood ratio tests with 1- and 2-df, respectively. TDT refers to the transmission-disequilibrium test. Schaid LR Gen refers to Schaid's 2-df likelihood ratio test [26]. Calculations are based on Table 3.
From: Analysis of case-parent trios at a locus with a deletion allele: association of GSTM1 with autism
| Â | Â | LR 1 versus | LR 1 versus | LR 2 versus | |||
|---|---|---|---|---|---|---|---|
| Â | Â | TDT | Schaid LR Gen | ||||
q | r 0 | r1 = 1 | r1 = | r1 = 1 | r1 = | r1 = 1 | r1 = |
.25 | 1.5 | 240 | 24 | 120 | 34 | 70 | 14 |
| Â | 2.5 | 218 | 27 | 107 | 35 | 98 | 29 |
.50 | 1.5 | 148 | 44 | 119 | 62 | 90 | 48 |
| Â | 2.5 | 138 | 51 | 107 | 64 | 93 | 56 |
.75 | 1.5 | 114 | 76 | 121 | 105 | 94 | 82 |
| Â | 2.5 | 108 | 77 | 112 | 97 | 95 | 77 |