Genetics, Vol. 178, 2069-2079, April 2008, Copyright © 2008
doi:10.1534/genetics.107.082255

Fraction of Informative Recombinations: A Heuristic Approach to Analyze Recombination Rates

J.-F. Lefebvre* and D. Labuda*,{dagger},1

* Centre de Recherche, CHU Sainte-Justine, {dagger} Département de Pédiatrie, Université de Montréal, Montreal, Quebec H3T 1C5, Canada

1 Corresponding author: Centre de Recherche, CHU Sainte-Justine, 3175 Côte Sainte-Catherine, Montreal, Quebec H3T 1C5, Canada.
E-mail: damian.labuda{at}umontreal.ca

In this article we present a new heuristic approach (informative recombinations, InfRec) to analyze recombination density at the sequence level. InfRec is intuitive and easy and combines previously developed methods that (i) resolve genotypes into haplotypes, (ii) estimate the minimum number of recombinations, and (iii) evaluate the fraction of informative recombinations. We tested this approach in its sliding-window version on 117 genes from the SeattleSNPs program, resequenced in 24 African-Americans (AAs) and 23 European-Americans (EAs). We obtained population recombination rate estimates ({rho}obs) of 0.85 and 0.37 kb–1 in AAs and EAs, respectively. Coalescence simulations indicated that these values account for both the recombinations and the gene conversions in the history of the sample. The intensity of {rho}obs varied considerably along the sequence, revealing the presence of recombination hotspots. Overall, we observed ~80% of recombinations in one-third and ~50% in only 10% of the sequence. InfRec performance, tested on published simulated and additional experimental data sets, was similar to that of other hotspot detection methods. Fast, intuitive, and visual, InfRec is not constrained by sample size limitations. It facilitates understanding data and provides a simple and flexible tool to analyze recombination intensity along the sequence.