Model-based inference of haplotype block variation

ABSTRACT

The uneven recombination structure of human DNA has been highlighted by several recent studies. Knowledge of the haplotype blocks generated by this phenomenon can be applied to dramatically increase the statistical power of genetic mapping. Several criteria have already been proposed for identifying these blocks, all of which require haplotypes as input. We propose a comprehensive statistical model of haplotype block variation and show how the parameters of this model can be learned from haplotypes and/or unphased genotype data. Using real-world SNP data, we demonstrate that our approach can be used to resolve genotypes into their constituent haplotypes with greater accuracy than previously known methods.

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INDEX TERMS

Primary Classification:
  J. Computer Applications
  J.3 LIFE AND MEDICAL SCIENCES
      Subjects: Biology and genetics

General Terms:
Algorithms, Experimentation, Performance

Keywords:
Bayesian Network, haplotype, haplotype block, haplotype resolution, linkage disequilibrium mapping, recombination hotspot