title: Identifying haplotype block structure using an ancestor-derived model.
abstract: Recently, haplotype-based association studies have become popular for detecting disease-related or drug-response-associated genes. In these studies, it has been gradually recognized that a haplotype block structure is important. A rational and automatic method for identifying the haplotype block structure from SNP data has been desired. We have developed a new method using an ancestor-derived model and the minimum description length principle. The proposed method was applied to real data on the TAP2 gene in which a recombination hotspot was previously reported in human sperm data. The proposed method could identify an appropriate haplotype block structure, while existing methods failed. The performance of the proposed method was also investigated in a simulation study. The proposed method presented a better performance in real data analysis and the simulation study than existing methods. The proposed method was powerful from the viewpoint of hotspot sensitivity and was robust to mutation except at the edge of a sequence.
authors.affiliation: The Institute of Statistical Mathematics, Tokyo, 106-8569, Japan. fujisawa@ism.ac.jp.
authors.forename: Hironori
authors.initials: H
authors.lastname: Fujisawa
authors.affiliation: Genome Center, Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan.
authors.forename: Minoru
authors.initials: M
authors.lastname: Isomura
authors.affiliation: The Institute of Statistical Mathematics, Tokyo, 106-8569, Japan.
authors.forename: Shinto
authors.initials: S
authors.lastname: Eguchi
authors.affiliation: Genome Center, Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan.
authors.forename: Masaru
authors.initials: M
authors.lastname: Ushijima
authors.affiliation: Genome Center, Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Miyata
authors.affiliation: Genome Center, Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan.
authors.forename: Yoshio
authors.initials: Y
authors.lastname: Miki
authors.affiliation: Genome Center, Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan.
authors.forename: Masaaki
authors.initials: M
authors.lastname: Matsuura
mesh_terms: D000071450:ATP Binding Cassette Transporter, Subfamily B, Member 3; D018528:ATP-Binding Cassette Transporters / Q000235:genetics; D003198:Computer Simulation; D005838:Genotype; D006239:Haplotypes; D006801:Humans; D015810:Linkage Disequilibrium; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic
chemical_list: D000071450:ATP Binding Cassette Transporter, Subfamily B, Member 3; D018528:ATP-Binding Cassette Transporters; C071692:TAP2 protein, human