TABLE 1.
Comparison of VDR haplotype frequencies estimated from different methods
| Haplotypes | EM-Parent | EM-Sib | EM-Single | GH-Sib | GH-Family | FAMHAP-Sib |
|---|---|---|---|---|---|---|
| GTAT | 0.0024 | 0.0010 | — | 0.0738 | 0.0046 | — |
| GTAC | 0.1257 | 0.1208 | 0.1337 | 0.0705 | 0.1147 | 0.1197 |
| GTGT | 0.1453 | 0.1421 | 0.1143 | 0.1066 | 0.1479 | 0.1498 |
| GTGC | — | — | 0.0028 | 0.0246 | 0.0149 | — |
| GCAT | 0.0104 | 0.0068 | 0.0073 | 0.0721 | 0.0321 | 0.0062 |
| GCAC | 0.2180 | 0.2089 | 0.1839 | 0.1197 | 0.1686 | 0.2135 |
| GCGT | 0.2298 | 0.2355 | 0.2865 | 0.1754 | 0.2167 | 0.2436 |
| GCGC | 0.0025 | — | — | 0.0754 | 0.0149 | — |
| ATAT | 0.0021 | 0.002 | 0.0023 | 0.0066 | 0.0046 | — |
| ATAC | 0.0173 | 0.0278 | 0.0001 | 0.0131 | 0.0103 | 0.0204 |
| ATGT | 0.0885 | 0.0826 | 0.0799 | 0.0393 | 0.0768 | 0.0830 |
| ATGC | 0.0021 | 0.0027 | 0.0041 | 0.0213 | 0.0057 | — |
| ACAT | 0.0010 | 0.006 | 0.0018 | 0.0033 | 0.0092 | — |
| ACAC | 0.0404 | 0.0472 | 0.0759 | 0.0443 | 0.0585 | 0.0480 |
| ACGT | 0.1144 | 0.1053 | 0.1075 | 0.0885 | 0.1147 | 0.1061 |
| ACGC | — | — | — | 0.0656 | 0.0057 | — |
| Discrepancy | — | 0.0342 | 0.1059 | 0.3260 | 0.0922 | 0.0338 |
In Tables 1–3, haplotype frequencies that are estimated from parental samples using the conventional EM algorithm (i.e., EM-Parent) are treated as “true” haplotype frequencies in the population. The discrepancy of haplotype frequencies was calculated using Equation 7. Values in italics are those haplotypes whose frequencies deviated >5% from those estimated from the EM-Parent. FAMHAP-Sib and FAMHAP-Sib-R yielded identical results for haplotypes with small numbers of loci.