HAPLOFREQ-Estimating Haplotype Frequencies Efficiently

A commonly used tool in disease association studies is the search for discrepancies between the haplotype distribution in the case and control populations. In order to find this discrepancy, the haplotypes frequency in each of the populations is estimated from the genotypes. We present a new method HAPLOFREQ to estimate haplotype frequencies over a short genomic region given the genotypes or haplotypes with missing data or sequencing errors. Our approach incorporates a maximum likelihood model based on a simple random generative model which assumes that the genotypes are independently sampled from the population. We first show that if the phased haplotypes are given, possibly with missing data, we can estimate the frequency of the haplotypes in the population by finding the global optimum of the likelihood function in polynomial time. If the haplotypes are not phased, finding the maximum value of the likelihood function is NP-hard. In this case we define an alternative likelihood func...

• Type: Journal
• Year: 2006
• Where: JCB
• Authors: Eran Halperin, Elad Hazan
• Keywords: Haplotype, JCB 2006, Likelihood Functions, Relaxed Likelihood