Nature Reviews Genetics 12, 703-714 (October 2011) | doi:10.1038/nrg3054

Article series: Study designs

Haplotype phasing: existing methods and new developments

Sharon R. Browning1 & Brian L. Browning2  About the authors


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.

Author affiliations

  1. Department of Biostatistics, University of Washington, Seattle, Washington 98195, USA.
  2. Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington 98195, USA.

Correspondence to: Sharon R. Browning1 Email:

Correspondence to: Brian L. Browning2 Email:

Published online 16 September 2011