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KMID : 1132720080060030130
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Genomics & Informatics
2008 Volume.6 No. 3 p.130 ~ p.135
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Haplotype Phylogeny of a 200kb Region in the Human Chromosome X Terminal Band (q28)
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Kim Sang-Soo
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Abstract
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The haplotypes of a 200 kb region in the human chromosome X terminal band (q28) were analyzed using the
International HapMap Project PhaseII data, which had been collected for three analysis panels (YRI, CEU, and CHB＋JPT). When multiple linkage disequilibrium blocks were encountered for a panel, the neighboring haplotypes that had crossover rate of 5% or more in the panel were combined to generate ’haploid’ configurations. This resulted in 8, 7, and 5 ’haploid’ configurations for the panels of YRI, CEU, and CHB＋JPT, respectively. The multiple sequence alignment of these
’haploids’ was used for the calculation of allele-sharing distances and the subsequent principal coordinate analysis. Two ’haploids’ in CEU and CHB＋JPT were hypothesized as ’parental’ in light of the observations that the successive recombinants of these haploids can model two other haploids in CEU and CHB＋JPT, and that their configurations were consistent with those in YRI. This study demonstrates the utility of haplotype phylogeny in understanding population evolution.
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KEYWORD
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haplotype, SNP, phylogeny, haploview, HapMap
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