Haplotype phasing: existing methods and new developments

Nat Rev Genet. 2011 Sep 16;12(10):703-14. doi: 10.1038/nrg3054.


Determination of haplotype phase is becoming increasingly important as we enter the era of large-scale sequencing because many of its applications, such as imputing low-frequency variants and characterizing the relationship between genetic variation and disease susceptibility, are particularly relevant to sequence data. Haplotype phase can be generated through laboratory-based experimental methods, or it can be estimated using computational approaches. We assess the haplotype phasing methods that are available, focusing in particular on statistical methods, and we discuss the practical aspects of their application. We also describe recent developments that may transform this field, particularly the use of identity-by-descent for computational phasing.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Base Sequence
  • Computational Biology / methods
  • Computational Biology / trends
  • Data Collection / methods
  • Data Collection / trends*
  • Databases, Genetic / trends
  • Genome-Wide Association Study / methods
  • Genome-Wide Association Study / trends
  • Haplotypes / genetics*
  • Haplotypes / physiology
  • High-Throughput Nucleotide Sequencing / methods
  • High-Throughput Nucleotide Sequencing / trends
  • Humans
  • Molecular Sequence Annotation / methods
  • Molecular Sequence Annotation / trends
  • Polymorphism, Single Nucleotide / physiology