Identifying haplotype block structure by using 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 desirable. We have developed a new method by using an ancestor-derived model and the minimum-description-length principle. The proposed method was applied to real data in TAP2 gene in which a recombination hotspot was previously reported in human sperm data. The proposed method could identify an appropriate haplotype block structure, although existing methods failed. The performance of the proposed method was also investigated in simulation study. The proposed method presented a better performance in real data analysis and simulation study than existing methods. The proposed method was powerful from the viewpoint of hotspot sensitivity and robust to mutation except the edge of a sequence.