Skip to main content
Article thumbnail
Location of Repository

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

By J.-F. Lefebvre and 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 (ρobs) 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 ρobs 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

Topics: Investigations
Publisher: Genetics Society of America
OAI identifier: oai:pubmedcentral.nih.gov:2323797
Provided by: PubMed Central
Download PDF:
Sorry, we are unable to provide the full text but you may find it at the following location(s):
  • http://www.pubmedcentral.nih.g... (external link)
  • Suggested articles


    To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.