Identifying haplotype block structure using an ancestor-derived model

Hironori Fujisawa, Minoru Isomura, Shinto Eguchi, Masaru Ushijima, Satoshi Miyata, Yoshio Miki, Masaaki Matsuura

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Pages (from-to)738-746
Number of pages9
JournalJournal of Human Genetics
Issue number9
Publication statusPublished - 2007 Sep


  • Ancestral haplotype
  • Haplotype block
  • Linkage disequilibrium
  • Minimum description length principle
  • Recombination hotspot

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)


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