A haplotype inference method based on sparsely connected multi-body ising model

Masashi Kato, Qian Ji Gao, Hiroshi Chigira, Hiroyuki Shindo, Masato Inoue

研究成果: Article査読

1 被引用数 (Scopus)

抄録

Statistical haplotype inference is an indispensable technique in the field of medical science. The method usually has two steps: inference of haplotype frequencies and inference of diplotype for each subject. The first step can be done by using the expectation-maximization (EM) algorithm, but it incurs an unreasonably large calculation cost when the number of single-nucleotide polymorphism (SNP) loci of concern is large. In this article, we describe an approximate probabilistic model of haplotype frequencies. The model is constructed by using several distributions of nearby local SNPs. This approximation seems good because SNPs are generally more strongly correlated when they are close to one another on a chromosome. To implement this approach, we use a log linear model, the Walsh-Hadamard transform, and a combinatorial optimization method. Artificial data suggested that the overall haplotype inference of our method is good if there are nine or more local consecutive SNPs. Some minor problems should be dealt with before this method can be applied to real data.

本文言語English
論文番号012022
ジャーナルJournal of Physics: Conference Series
233
DOI
出版ステータスPublished - 2010

ASJC Scopus subject areas

  • 物理学および天文学(全般)

フィンガープリント

「A haplotype inference method based on sparsely connected multi-body ising model」の研究トピックを掘り下げます。これらがまとまってユニークなフィンガープリントを構成します。

引用スタイル