A novel method with improved power to detect recombination hotspots from polymorphism data reveals multiple hotspots in human genes

Am J Hum Genet. 2005 Nov;77(5):781-94. doi: 10.1086/497579. Epub 2005 Sep 16.


We introduce a new method for detection of recombination hotspots from population genetic data. This method is based on (a) defining an (approximate) penalized likelihood for how recombination rate varies with physical position and (b) maximizing this penalized likelihood over possible sets of recombination hotspots. Simulation results suggest that this is a more powerful method for detection of hotspots than are existing methods. We apply the method to data from 89 genes sequenced in African American and European American populations. We find many genes with multiple hotspots, and some hotspots show evidence of being population-specific. Our results suggest that hotspots are randomly positioned within genes and could be as frequent as one per 30 kb.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • African Continental Ancestry Group
  • Computer Simulation
  • European Continental Ancestry Group
  • Genetic Variation*
  • Genetics, Population
  • Genome, Human*
  • Humans
  • Likelihood Functions
  • Models, Genetic
  • Polymorphism, Genetic
  • Recombination, Genetic
  • Sequence Analysis, DNA / methods