Identifying haplotype block structure using an ancestor-derived model.
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.
Fujisawa
Hironori
H
The Institute of Statistical Mathematics, Tokyo, 106-8569, Japan. fujisawa@ism.ac.jp.
Isomura
Minoru
M
Genome Center, Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan.
Eguchi
Shinto
S
The Institute of Statistical Mathematics, Tokyo, 106-8569, Japan.
Ushijima
Masaru
M
Genome Center, Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan.
Miyata
Satoshi
S
Genome Center, Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan.
Miki
Yoshio
Y
Genome Center, Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan.
Matsuura
Masaaki
M
Genome Center, Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan.
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
D000071450:ATP Binding Cassette Transporter, Subfamily B, Member 3; D018528:ATP-Binding Cassette Transporters; C071692:TAP2 protein, human