Table 1:
LAI true positive rate estimates per ancestry per comparison
| Test | Mean TPR (SD) per ancestry | |||||
|---|---|---|---|---|---|---|
| Aim of comparison | Simulation model name | Analysis parameters* | AMR | EUR | AFR | |
| Impact of Demography | Proportions | Average 3-way | 15%/60%/25%, 9gen, chr1 | 0.884 (0.224) | 0.986 (0.018) | 0.986 (0.026) |
| Even 3-way | 33%/33%/34%, 9gen, chr1 | 0.933 (0.082) | 0.966 (0.130) | 0.991 (0.008) | ||
| Even 2-way | 50%/50%/0, 9gen, chr1 | 0.918 (0.120) | 0.992 (0.008) | N/A | ||
| Average 2-way | 70%/30%/0, 9gen, chr1 | 0.935 (0.058) | 0.987 (0.014) | N/A | ||
| Extreme proportions, high AMR | 95%/5%/0, 9gen, chr1 | 0.937 (0.054) | 0.961 (0.134) | N/A | ||
| Extreme proportions, high EUR | 5%/95%/0, 9gen, chr1 | 0.845 (0.280) | 0.998 (0.003) | N/A | ||
| Generations since admixture | Average 3-way | 15%/60%/25%, 9gen, chr1 | 0.884 (0.224) | 0.986 (0.018) | 0.986 (0.026) | |
| Average 3-way | 15%/60%/25%, 12gen, chr 1 | 0.906 (0.117) | 0.982 (0.016) | 0.989 (0.013) | ||
| Average 3-way | 15%/60%/25%, 17gen, chr1 | 0.896 (0.162) | 0.977 (0.017) | 0.984 (0.011) | ||
| Features of data/analysis | Reference Panel | Average 3-way, low N - well matched AMR reference | 15%/60%/25%, 9gen chr1. HGDP AMR reference | 0.884 (0.224) | 0.986 (0.018) | 0.986 (0.026) |
| Average 3-way, medium N - admixed AMR reference | 15%/60%/25%, 9gen chr1. 1KG PEL as AMR reference | 0.878 (0.224) | 0.986 (0.018) | 0.989 (0.013) | ||
| Average 3-way, high N - admixed + unmatched AMR reference | 15%/60%/25%, 9gen chr1. 1KG PEL + EAS as AMR reference | 0.875 (0.223) | 0.983 (0.019) | 0.991 (0.009) | ||
| Data type | Average 3-way | 15%/60%/25%, 12gen, all autosomes. WGS density | 0.935 (0.025) | 0.983 (0.005) | 0.989 (0.004) | |
| Average 3-way | 15%/60%/25%, 12 gen, all autosomes. SNP array density | 0.938 (0.029) | 0.977 (0.008) | 0.982 (0.004) | ||
| Average 3-way | 15%/60%/25%, 12 gen, all autosomes. Imputed SNP array density | 0.927 (0.026) | 0.982 (0.004) | 0.987 (0.003) | ||
| Window size | Average 3-way | 15%/60%/25%, 12gen, all autosomes, 0.1 cM | 0.939 (0.023) | 0.979 (0.005) | 0.991 (0.003) | |
| Average 3-way | 15%/60%/25%, 12gen, all autosomes, 0.2 cM (default) | 0.935 (0.025) | 0.983 (0.005) | 0.989 (0.004) | ||
| Average 3-way | 15%/60%/25%, 12gen, all autosomes, 0.4 cM | 0.923 (0.026) | 0.984 (0.005) | 0.980 (0.005) | ||
*
Analysis parameters: Admixture proportions of simulated cohort (AMR/EUR/AFR), number of generations since admixture, simulated chromosome, other parameters.