The use of inferred haplotypes in downstream analyses.

To the Editor: In the March 2006 issue of the Journal, Marchini et al.1 provided a comprehensive description of phasing algorithms for inference of individual haplotypes from unphased genotype data. They stated that an unresolved question is “whether and, if so, how best to use inferred haplotypes in downstream analyses.”1(p.448) The question is important because knowledge of individual haplotypes is rarely an end in itself. We offer our perspective on this issue, particularly in the context of (case-control) association studies.

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