Fraction of informative recombinations: a heuristic approach to analyze recombination rates.

Genetics
J-F Lefebvre, D Labuda

Abstract

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 approximately 80% of recombinations in one-third and approximately 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 ...Continue Reading

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Citations

Jan 30, 2010·BMC Bioinformatics·Julie HussinDamian Labuda
Jan 30, 2013·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Marcos Pérez-LosadaKeith A Crandall
Mar 2, 2010·American Journal of Human Genetics·Damian LabudaMarie-Hélène Roy-Gagnon

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