Table 1.
Application of PL-EM on the LPL Data[Note]
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Results from |
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| Haplotype | ID | Jackson, MS(N=24; k=28) | North Karelia, Finland (N=24; k=20) | Rochester, MN(N=23; k=22) |
| 01000001000000000100000 | H1 | .063 (.035) | .219 (.059) | .348 (.069) |
| 01000001100000000100000 | H2 | … | .073 (.039) | .045 (.031) |
| 00100110100000000000000 | H3 | .146 (.051) | … | .043 (.030) |
| 00100110100000010001100 | H4 | .104 (.044) | … | … |
| 00100110000000010000000 | H5 | .063 (.035) | … | … |
| 10101000011111110011101 | H6 | .063 (.035) | … | … |
| 00100001000000000100000 | H7 | … | .146 (.051) | .023 (.023) |
| 01000110000000000000000 | H8 | .021 (.021) | .125 (.048) | … |
| 00100000111111100011100 | H9 | … | .083 (.040) | … |
| 10111100111111111011111 | H10 | … | … | .087 (.042) |
Note.— The LPL data are based on a study by Nickerson et al. (1998). A total of 88 sites in the 7.9-kb region have been reported among the 71 individuals. Of these 88 biallelic markers, 23 met the following two criteria: (1) minor-allele frequency >20% and (2) marker missing data <2%. Both PL-EM and HAPLOTYPER were applied, to phase the entire 71 subjects by using only these 23 markers. N and k represent the sample size and the number of distinct haplotypes, respectively. Numbers shown in parentheses represent SEs of the frequency estimates. PL-EM appears to output almost the same number of haplotypes as does HAPLOTYPER (k=28, k=20, and k=22 vs. k=28, k=19, and k=22, for the Jackson, North Karelia, and Rochester samples, respectively). The number of distinct haplotypes is greatest in the Jackson sample (African Americans) and is smallest in the North Karelia sample (white Europeans). The Rochester sample shares H1 and H3 with the Jackson sample and shares H1, H2, and H7 with the North Karelia sample, indicating that this American-white population may be the result of admixture between black and European-white populations.