A block-free hidden Markov model for genotypes and its application to disease association

Gad Kimmel*, Ron Shamir

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

We present a new stochastic model for genotype generation. The model offers a compromise between rigid block structure and no structure altogether: It reflects a general blocky structure of haplotypes, but also allows for "exchange" of haplotypes at nonboundary SNP sites; it also accommodates rare haplotypes and mutations. We use a hidden Markov model and infer its parameters by an expectation-maximization algorithm. The algorithm was implemented in a software package called HINT (haplotype inference tool) and tested on 58 datasets of genotypes. To evaluate the utility of the model in association studies, we used biological human data to create a simple disease association search scenario. When comparing HINT to three other models, HINT predicted association most accurately.

Original languageEnglish
Pages (from-to)1243-1260
Number of pages18
JournalJournal of Computational Biology
Volume12
Issue number10
DOIs
StatePublished - Dec 2005

Keywords

  • Algorithm
  • Expectation maximization
  • Genotype
  • Haplotype
  • Hidden Markov model
  • Single-nucleotide polymorphism

Fingerprint

Dive into the research topics of 'A block-free hidden Markov model for genotypes and its application to disease association'. Together they form a unique fingerprint.

Cite this