Variability of haplotype phase and its effect on genetic analysis

One of the challenging problems toward understanding characteristics of the human genome is phasing haplotype information from genotype data. Among many proposed approaches towards solving the genotype phasing problem, PHASE and expectation-maximization (EM) algorithms are the most commonly used methods to obtain haplotype phase. This study has applied both methods to two important genetic regions - Interleukin-1 (IL-1) and cystic fibrosis (CF) - with 166 (spans 51 kb) and 238 (spans 188 kb) single nucleotide polymorphisms (SNPs) respectively, genotyped from 90 unrelated individuals. For analysis, the phased haplotypes from the PHASE and EM algorithms were used to observe the level of difference. The analyses found a significant difference in allele frequency (p Lt 0.001 for IL-1 and p Lt 0.05 for CF). In contrast to other comparison studies, the analysis was extended to find variability in common haplotype blocks. In comparison between the two algorithms, the performance of the PHASE algorithm is more robust than the EM-algorithm.