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This article is part of the supplement: Proceedings of the 12th European workshop on QTL mapping and marker assisted selection

Open Access Proceedings

Haplotyping via minimum recombinant paradigm

Jules Hernández-Sánchez* and Sara Knott

Author Affiliations

Institute of Evolutionary Biology, University of Edinburgh, King's Buildings (Ashworth Laboratories), West Main Roads, EH9 3JT, Edinburgh, UK

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BMC Proceedings 2009, 3(Suppl 1):S7  doi:10.1186/1753-6561-3-S1-S7

Published: 23 February 2009

Abstract

Background

Haplotypes can increase the power of gene detection over genotypes and are essential to estimate linkage disequilibrium.

Methods

Haplotyping was based on the minimum recombinant paradigm, whereby a phase is obtained only if it uniquely minimises the number of recombinants within a full sib family. Performance of this method was tested across three different data sets, consisting of genotypes and pedigree.

Results

The percentage of phased alleles ranged from ~80% to ~95%, and the percentage of correct phases reached ~99% in all cases. A measure of uncertainty was obtained via simulations. A partial haplotyping algorithm consisting of four deterministic rules was almost as effective as a full one consisting of six deterministic rules, and took up to 5 times less time to compute.

Conclusion

Haplotyping via the minimum recombinant paradigm is consistently reliable and computationally efficient. A single simulation is enough to produce a population-wide uncertainty estimate associated with a set of all reconstructed haplotypes.