Haplotype Phylogeny of a 200kb Region in the Human Chromosome X Terminal Band (q28).

Kim,  Sangsoo

doi:2008.6.3.130

Genomics Inform > Volume 6(3); 2008 > Article

Original Article

Genomics & Informatics 2008;6(3): 130-135.

DOI: https://doi.org/10.5808/gi.2008.6.3.130

Haplotype Phylogeny of a 200kb Region in the Human Chromosome X Terminal Band (q28).

Sangsoo Kim

Department of Bioinformatics and Life Science, Soongsil University, Seoul 156-743, Korea. sskimb@ssu.ac.kr

Abstract

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.

Keywords: haplotype; SNP; phylogeny; haploview; HapMap